Success in Academic Surgery: Basic Science [2nd ed.] 978-3-030-14643-6;978-3-030-14644-3

Table of contents :
Front Matter ....Pages i-viii
How to Set Up, Staff, and Fund Your Basic Science or Translational Research Laboratory (Jashodeep Datta, J. Joshua Smith)....Pages 1-12
Choosing a Good Scientific Mentor and Being a Good Mentee (Mark L. Kovler, David J. Hackam)....Pages 13-20
Effective Time Management Strategies for Conducting Laboratory Research (Evie Carchman)....Pages 21-30
Maintaining an Effective Lab Notebook and Data Integrity (Andrew J. Murphy)....Pages 31-41
Statistics for Bench Research (Timothy W. King)....Pages 43-52
Ethics in Laboratory Research (Sidd Dalal, Luke Brewster)....Pages 53-63
Modern Techniques for DNA, RNA, and Protein Assessment (Jurgis Alvikas, Matthew D. Neal)....Pages 65-104
Considerations for Immunohistochemistry (Swathi Balaji, Hui Li, Emily Steen, Sundeep G. Keswani)....Pages 105-144
Utilizing Flow Cytometry Effectively (Yue Guan, Jonathan B. Mitchem)....Pages 145-155
Effective Cell Culture (Patrick B. Schwartz, Sean M. Ronnekleiv-Kelly)....Pages 157-169
Gene-Editing Techniques (Kevin W. Freeman)....Pages 171-179
Stem Cells and Tissue Engineering (Troy A. Markel)....Pages 181-201
Animal Models in Surgical Research (Morgan L. Hennessy, Allan M. Goldstein)....Pages 203-212
Microbiome: Current Status and Future Applications (Rafael G. Ramos-Jimenez, Michael J. Morowitz)....Pages 213-232
Systems Biology: Generating and Understanding Big Data (Stephanie S. Kim, Timothy R. Donahue)....Pages 233-243
Back Matter ....Pages 245-252

Citation preview

Success in Academic Surgery Series Editors: Lillian Kao · Herbert Chen

Gregory Kennedy Ankush Gosain Melina Kibbe Scott A. LeMaire Editors

Success in Academic Surgery: Basic Science Second Edition

Success in Academic Surgery Series Editors: Lillian Kao The University of Texas Health Science Centre Houston, TX  USA Herbert Chen Department of Surgery University of Alabama at Birmingham Birmingham, AL  USA

All of the intended volume editors are highly successful academic surgeons with expertise in the respective fields of basic science, clinical trials, health services research, and surgical education research. They are all also leaders within the Association for Academic Surgery (AAS). The previous AAS book, Success in Academic Surgery: Part I provided an overview with regards to the different types of surgical research, beginning one’s academic career, and balancing work and life commitments. The aims and scopes of this series of books will be to provide specifics with regards to becoming successful academic surgeons with focuses on the different types of research and academic careers (basic science, clinical trials, health services research, and surgical education). These books will provide information beyond that in the introductory book and even beyond that provided in the Fall and International Courses. The target audience would be medical students, surgical residents, and young surgical faculty. We would promote bulk sales at the Association for Academic Surgery (AAS) Fall Courses (www.aasurg.org) which take place prior to the American College of Surgeons meeting in October, as well as the AAS International Courses which take place year-round in Australasia, Colombia, West Africa, and France. Courses are also planned for India, Italy, and Germany and potentially in the United Kingdom and Saudi Arabia. As the AAS expands the course into other parts of the world, there is a greater need for an accompanying series of textbooks. The AAS has already received requests for translation of the book into Italian. These books would be closely linked with the course content and be sold as part of the registration. In 2011, there were 270 participants in the Fall Courses. In addition, we would anticipate several hundred participants combined per year at all of the international courses. More information about this series at http://www.springer.com/series/11216

Gregory Kennedy Ankush Gosain  •  Melina Kibbe Scott A. LeMaire Editors

Success in Academic Surgery: Basic Science Second Edition

Editors Gregory Kennedy Division of Gastrointestinal Surgery University of Alabama Birmingham, AL USA Melina Kibbe UNC School of Medicine University of North Carolina Chapel Hill, NC USA

Ankush Gosain Le Bonheur Children’s Hospital University of Tennessee Health Science Centre Memphis, TN USA Scott A. LeMaire Baylor College of Medicine Houston, TX USA

ISSN 2194-7481     ISSN 2194-749X (electronic) Success in Academic Surgery ISBN 978-3-030-14643-6    ISBN 978-3-030-14644-3 (eBook) https://doi.org/10.1007/978-3-030-14644-3 © Springer Nature Switzerland AG 2019 Chapter 5 and 9 was created within the capacity of an US governmental employment. US copyright protection does not apply. This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

Welcome to the second edition of Success in Academic Surgery: Basic Science. This updated volume is meant to provide a foundation for starting a basic science research career as an academic surgeon-scientist. A number of the topics we cover in this text were presented in the first edition and are fundamental to any basic science enterprise [1]. However, we have invited new authors to provide fresh perspectives on these topics. Taking a practical approach, the authors cover a suggested timeline for the initial academic appointment, including how to set up and fund the laboratory, identifying appropriate scientific mentors, time management techniques, and fundamentals of data integrity. Fundamental considerations, including statistical analysis, laboratory ethics, modern techniques for DNA, RNA and protein assessment, animal models, and flow cytometry are covered. We have also added several new topics that reflect the rapidly changing pace of basic science written by experts in the field. These include chapters on stem cells, tissue engineering, gene editing techniques, microbiome analysis, and systems biology. Surgical science has a long history, dating back to the 1700s with John Hunter, who established academic surgery as being firmly rooted in an understanding of anatomy, physiology, and pathology [2]. Seminal advances in the care of medical and surgical patients have been brought about by the work of surgeon-scientists too numerous to list, but including such giants in our field as Harvey Cushing, Alfred Blalock, Lester Dragstedt, Joseph Murray, Basil Pruitt, and Frances Moore. Dr. Moore, in his presidential address to the Society of University Surgeons 50 years ago, championed the surgeon-scientist as being uniquely qualified to bring “knowledge from the biological sciences to the patient’s bedside and back again.” [3]. Since the publication of the first edition of this text 6 years ago, there is a rapidly increasing awareness of the challenges faced by today’s surgeons in establishing their basic science research programs [4]. These include declining federal funding, declining success rates in obtaining funding, increasing clinical demands (often driven by productivity and compensation models that disincentivize research), rapid evolution of technology, and a significant lack of mentorship [2, 5]. Recent studies of successful surgeon-scientists have identified factors associated with success; mentorship, time management, and persistence were identified as keys to success [5–7]. We have structured this volume to enable you, the reader, to develop these skills and to provide you with a peer and mentor group that can help you overcome obstacles on your path to scientific success. v

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We are extremely grateful to all of the authors for sharing their time, knowledge, and expertise in contributing chapters to this book. We are indebted to the series editors, Drs. Kao and Chen, for entrusting us with this second edition of the book, and to the editors of the first edition, Drs. Kibbe and LeMaire, for paving the way in the first edition. We appreciate the guidance of Prakash Marudhu, the project coordinator at Springer Nature who was extremely responsive through the publication process and without whom we could not have delivered this final product. Finally, we would like to thank the current and past members of our laboratories, as well as colleagues and friends in the field of Surgical Basic/Translational Science for continually making science stimulating and fun.

References 1 . Success in academic surgery: basic science. New York: Springer; 2013. 2. Evers BM.  The evolving role of the surgeon scientist. J Am Coll Surg. 2015;220(4):387–95. https://doi.org/10.1016/j.jamcollsurg.2014.12.044. Epub 2015/03/01. 3. Moore FD. The university in American surgery. Surgery. 1958;44(1):1–10. Epub 1958/07/01. 4. Kibbe MR, Velazquez OC.  The extinction of the surgeon scientist. Ann Surg. 2017;265(6):1060–1. https://doi.org/10.1097/SLA.0000000000002192. Epub 2017/05/10. 5. Keswani SG, Moles CM, Morowitz M, Zeh H, Kuo JS, Levine MH, Cheng LS, Hackam DJ, Ahuja N, Goldstein AM, Basic Science Committee of the Society of University S. The future of basic science in academic surgery: identifying barriers to success for surgeon-scientists. Ann Surg. 2017;265(6):1053–9. https://doi. org/10.1097/SLA.0000000000002009. Epub 2016/09/20. 6. Kodadek LM, Kapadia MR, Changoor NR, Dunn KB, Are C, Greenberg JA, Minter RM, Pawlik TM, Haider AH. Educating the surgeon-scientist: a qualitative study evaluating challenges and barriers toward becoming an academically successful surgeon. Surgery. 2016;160(6):1456–65. https://doi.org/10.1016/j. surg.2016.07.003. Epub 2016/08/16. 7. Goldstein AM, Blair AB, Keswani SG, Gosain A, Morowitz M, Kuo JS, Levine M, Ahuja N, Hackam DJ, Basic Science Committee of the Society of University S. A roadmap for aspiring surgeon-scientists in today’s healthcare environment. Ann Surg. 2019;269(1):66–72. https://doi.org/10.1097/SLA.0000000000002840. Epub 2018/06/30. Birmingham, AL Memphis, TN 

Gregory Kennedy Ankush Gosain

Contents

1 How to Set Up, Staff, and Fund Your Basic Science or Translational Research Laboratory ��������������������������������������������������������������������������������   1 Jashodeep Datta and J. Joshua Smith 2 Choosing a Good Scientific Mentor and Being a Good Mentee������������  13 Mark L. Kovler and David J. Hackam 3 Effective Time Management Strategies for Conducting Laboratory Research������������������������������������������������������������������������������������������������������  21 Evie Carchman 4 Maintaining an Effective Lab Notebook and Data Integrity ����������������  31 Andrew J. Murphy 5 Statistics for Bench Research��������������������������������������������������������������������  43 Timothy W. King 6 Ethics in Laboratory Research ����������������������������������������������������������������  53 Sidd Dalal and Luke Brewster 7 Modern Techniques for DNA, RNA, and Protein Assessment ��������������  65 Jurgis Alvikas and Matthew D. Neal 8 Considerations for Immunohistochemistry �������������������������������������������� 105 Swathi Balaji, Hui Li, Emily Steen, and Sundeep G. Keswani 9 Utilizing Flow Cytometry Effectively������������������������������������������������������ 145 Yue Guan and Jonathan B. Mitchem 10 Effective Cell Culture�������������������������������������������������������������������������������� 157 Patrick B. Schwartz and Sean M. Ronnekleiv-Kelly 11 Gene-Editing Techniques�������������������������������������������������������������������������� 171 Kevin W. Freeman 12 Stem Cells and Tissue Engineering���������������������������������������������������������� 181 Troy A. Markel

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13 Animal Models in Surgical Research ������������������������������������������������������ 203 Morgan L. Hennessy and Allan M. Goldstein 14 Microbiome: Current Status and Future Applications�������������������������� 213 Rafael G. Ramos-Jimenez and Michael J. Morowitz 15 Systems Biology: Generating and Understanding Big Data������������������ 233 Stephanie S. Kim and Timothy R. Donahue Index�������������������������������������������������������������������������������������������������������������������� 245

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How to Set Up, Staff, and Fund Your Basic Science or Translational Research Laboratory Jashodeep Datta and J. Joshua Smith

Abstract

Establishing a basic or translational research laboratory is a significant undertaking that requires rigorous commitment, supportive mentorship, and meticulous planning. This chapter will review the resources that are typically required, including space, time, personnel, equipment, and mentorship. It will then discuss various options in fulfilling such needs as well as avenues to acquire funding, including intramural and extramural sources. Finally, we will briefly consider how to maintain the laboratory once it has been established and how to respond to unexpected setbacks. Keywords

Basic science research · Translational research · Laboratory · Set up · Staff Funding · Space · Equipment · Regulations

Introduction Appropriate resources, well-established protected time, commitment from senior clinical and laboratory mentors, and a supportive and collaborative environment are essential for even the most dedicated surgical investigator interested in developing a basic/translational science initiative. Defined broadly, resources include not only protected time but also research space, funding resources, equipment and J. Datta Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA J. J. Smith (*) Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA e-mail: [email protected] © Springer Nature Switzerland AG 2019 G. Kennedy et al. (eds.), Success in Academic Surgery: Basic Science, Success in Academic Surgery, https://doi.org/10.1007/978-3-030-14644-3_1

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supplies, and key technical personnel, along with enthusiastic and supportive collaborators and senior mentors. The strategies and resources required vary based on the research agenda to be pursued. As such, one size does not fit all. Moreover, the current ­funding climate and competing demands for revenue generation at the hospital level may limit resources and require the surgical investigator to make challenging decisions on how to achieve his/her goals. Therefore, before embarking on this career choice, it is critical to outline as best as possible what your objectives are, why you want to pursue them, and how committed you are to this pathway. Assuming you have previously engaged in such introspection and are now ready to engage your future as a serious surgeon-scientist, this chapter will discuss considerations necessary for a successful and fulfilling career in surgical investigation.

Protected Time The initial “package” that you will seek should contain the relevant tangible resources needed to accomplish your research aspirations. Traditionally, this will include a combination of space, equipment, supplies, personnel, and start-up funds. We will consider each of these elements separately in the following sections. However, the most critical aspect of your package is protected time. The best technician or postdoctoral fellow in the world will not be as committed to your success as you are. If you plan well (and are fortunate), you will end up with talented research personnel who are experienced in techniques beyond your own and who will bring their skills to your laboratory effort. However, you need to physically spend time in your own laboratory on a regular basis, creating the vision and driving the science. From this concept emanates the holy grail of “protected time.” This is time when you will be able to go to your laboratory/office and work, whether on experiments or manuscripts or grants, without clinical responsibilities and a minimal possibility of being disturbed. In reality, this is easier said than done, since referring physicians and patients may not understand why you are unavailable for these “protected” periods of time during the week. Moreover, surgeons are conditioned to take complete responsibility for their own patients’ welfare, regardless of time of day or day of week. Critical to this notion is the backing of the Department Chairperson and your Service Chief; without their support, this “protection” will fail. The most common model is to carve out a certain number of days (or “half-­days”) per week without assigned clinical responsibilities, recognizing that emergencies may occur during those times. The often spoken about goal of “50% protected time” is difficult to achieve in many environments, particularly without extramural funding or dedicated intramural funding to support a salary that affords 50% protection. An alternative option to the “days-per-week” model is to seek longer (e.g., 2–3 weeks long) blocks devoid of clinical responsibility; admittedly, this is feasible in few surgical specialties or practice settings. However, proponents of this approach indicate that they can make most progress on grant proposals and manuscripts when they devote consecutive days and weeks to planning and writing. Ultimately, these decisions are also based on whether your experiments require hours, days, or weeks to complete. A model for success may be to limit your practice to a narrowly defined

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niche, particularly one that does not generate many emergencies. Furthermore, your mission will be greatly facilitated by cooperative partners who are willing to cover for you when you need to be in the lab for that all-important last experiment or simply have to close your door and write a grant or a manuscript.

Schedule and Time Management Protected time is great in principle, but not always practical especially in the context of a busy call week. Patients will need your attention and may have complications at a time when you are most needed in the lab. Furthermore, it is unlikely that your grant support will compensate you (or your department) adequately for the clinical revenue you forego while in the laboratory. Some compromises may be required, but in these authors’ opinions, the surgeon-scientist should still be paid on par with the full-time clinical surgeon. Since a salary reduction cannot be the solution, what is? This is where creative and flexible schedule/time management is essential. First, acknowledge that your “workweek” may be many hours longer than your clinical colleagues at times. Moreover, research activities can spill over into nights, weekends, and holidays. An efficient way to manage this dilemma is to consolidate your research time. One suggestion is to try to front-load clinical work at the beginning of the week and schedule research time at the end of the week. This strategy allows you to not only be attentive to patient-related issues that arise in the first few postoperative days but also continue any additional research-related duties into the late week and early weekend. Of course, your clinical colleagues may also prefer to schedule cases early in the week, so this may not always be possible. Second, communication with and buy-in from your clinical partners and scientific collaborators will be key, particularly since you will often be leaning on them for assistance. Having a supportive clinical Service Chief and partners who understand your mission cannot be overstated. Third, the constant competing tensions of the clinical and research realms can be difficult to juggle because they are such distinct environs: one fastpaced and exhilarating and the other measured and tranquil. In the authors’ opinion, one approach that has allowed effective time management in this regard is physically separating oneself from the clinical space—for example, having a dedicated research/lab office or having your clinical office in the same building in which your lab is housed. Finally, a supportive leadership team that understands the constraints on your time, is dedicated to your success, and resists the temptation to burden you with increasing clinical activities or distracting committee assignments may be the most important component of time/schedule management.

Research Space Space requirements will vary depending on your scientific endeavors. Researchers working in cancer genomics and those in fundamental vascular biology will need different amounts and types of space. The most critical decision here is whether to

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seek your own dedicated laboratory space or to share space (as is often the case in the “embedded” research model). Either model requires institutional commitment and significant personal investment. If it is your own lab space, the onus is on you to set it up, equip it, and to secure funds to pay for those resources. This is a very challenging way to start and requires much more planning, calculating, and multiple resource allocation strategy sessions before you start. This approach can be very rewarding but should not be initiated without significant discussions with senior leaders in the Department and the Medical Center. Shared space may not be as exciting but can be very practical and efficient at least in the beginning stages of your career. This model is increasingly seen across the country, particularly for young surgeon-scientists, and has many advantages. You may even share space with other junior investigators—who can be an important like-minded peer group—and allows the advantage of having the ready and sage advice of the senior primary investigator (PI). This person can also give added weight to early grants and provide seed money forays as your scientific mentor. Equipment and administrative costs will also be sharply reduced, which may allow you to negotiate other key resources. Often overlooked in this decision are the advantages of shared space for your research technician or research fellow; he/she also has an instant peer group that can provide both technical and moral support. Of course, you should make sure that you have some territory to call your own within the shared space and can successfully (and collegially) cohabitate with your labmates.

Equipment and Supplies: Things You Will Need to Purchase Once you have identified space in which to work, you need to equip it. As for laboratory space, you will need to first decide whether equipment should be yours or shared. Your own equipment will never have a waiting line, but you will also have to pay for it, and your financial resources will likely be finite. Conversely, shared equipment may be less available to you, but it will be less expensive. Moreover, it will often be better equipment with more technical capabilities than you can afford. A good rule of thumb is that if you think you will be using a piece of equipment for more than an hour a day, you should consider buying it. Very large and expensive equipment will almost certainly need to be shared; on the other hand, such equipment can often be found in dedicated core facilities. Since your needs may change and your budget will be limited to start, it may be a good idea to share equipment whenever possible and purchase only what you need. Note that there is etiquette to sharing equipment, which includes a formal request to the senior PI and an offer to pay partly for the cost of maintenance if you anticipate being a heavy user. For equipment that you will dedicate to your own work, options will vary inversely in convenience and cost. Except for the most unique equipment, you should not pay retail catalog prices. Ideally, you should assemble a list of all of the basic lab equipment you plan to purchase and put this out to bid to select major equipment companies. Most feature “new lab” discounts and some flexibility in pricing for

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large orders. Be alert also to institutional discounts for new equipment, as well as used equipment. In general, it is advisable to avoid used equipment when needed for “mission-critical” applications. On the other hand, one might contemplate buying used equipment for more generic applications, i.e., water baths, incubators, shakers, etc. When purchasing these items used, ask about at least a short-term warrantee, and be prepared to thoroughly inspect and test each piece of used equipment when it arrives. It is also important to see if the institution you are joining has “lightly used” or “never used” equipment that is underutilized or that has never been touched in an abandoned laboratory space or from a retired investigator. Supplies are the least discretionary issue. You require the necessary reagents to execute your experiments, and you cannot purchase these reagents used. If you have sufficient funds, you may be able to negotiate a discount on your initial supplies purchase as part of your “new lab” discount or for 1–2 years from the same vendor. If you are purchasing antibodies or other reagents of which you only need a small aliquot, you may be able to share them with a colleague doing similar work and hence share the cost.

Laboratory Personnel and Technical Assistance It is unlikely that you will succeed as a surgeon-scientist without a motivated and reliable lab technician. Here you get what you pay for, and there are few shortcuts. An experienced and productive research fellow may be worth his/her weight in gold but is hard to find. Research technicians are easier to recruit but are of variable experience, quality, and work ethic. Moreover, research fellows are more expensive to recruit and retain than entry-level technicians. Research fellows and technicians vary in other ways beyond cost. A fellow will stay with you for approximately 2–3 years depending on their situations (surgery resident/fellow, Ph.D. postdoctoral scientist), whereas a technician may be available for longer periods. This mandates the competing tensions of productivity and continuity. A productive research fellow is typically motivated to publish and set up their own career for the future, while a technician may not always be as motivated. In this regard, a research fellow has more to gain if the lab succeeds because his/ her career depends on evidence of productivity; a technician can always get another job if funding dries up. A fellow may be more likely than a technician to stay late to meet with you when you are out of the OR or come in early or on the weekends to keep the experiments moving. Conversely, a well-trained technician may stay with you forever and provides a great degree of continuity that is sacrificed when the fellow moves on to their next position. You will also encounter opportunities to incorporate untrained volunteers (e.g., high school or medical students) into your laboratory efforts. This is an enthusiastic (and free) workforce but will require more of your time for more dedicated teaching and supervision. Treat them like you would want to be treated the first time you walked into a laboratory. If paired with a research fellow or a dedicated technician, these individuals can be valuable assets to your research mission. Start them on

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smaller tasks (e.g., abstracting medical records or obtaining and processing clinical samples), and if they excel, move them on to more challenging or technically demanding tasks. Of course, their quality and level of motivation will vary, but you have to creatively find ways to maximize their potential and your productivity. Set clear expectations and provide constructive feedback; this is a good opportunity to assume a mentorship role early in your scientific career. Beyond this, inspire them to love what you are passionate about, and your goals will automatically align. Many medical centers have programs for high school and medical students. These programs will pay them for their time in the laboratory, and this is a useful endeavor for both you and them if expectations are managed wisely.

Mentorship Early mentorship from a clinical and scientific standpoint as a surgeon-scientist is essential. It is unrealistic to think that you will instantly be an expert in your field either clinically or scientifically, and even after excellent training, the first 3–5 years will be full of challenges and learning opportunities. A solid clinical mentor will guide you, help protect you, and introduce you as an expert to referring physicians and new colleagues. In addition, this person can help with difficult clinic cases or operative challenges. A stellar laboratory mentor will likewise help you launch the science portion of your career with minimal stumbling. They should provide smooth transition to the correct collaborators and help in forming and writing your first grants and papers, in addition to assistance with hiring your first set of technicians or graduate students. Learning to run a lab takes time, and learning this from a more senior and seasoned research scientist is important. The details of budgeting, personnel management, and grantsmanship take months and sometimes years to master—a solid mentor in this regard is invaluable. Few surgeons emerge from their residency or fellowship with sufficient knowledge, laboratory acumen, and organizational skills to embark as solo scientists successfully. A research mentor can ensure your forward progress and help you minimize delays, mistakes, and “blind alleys.” Identification of a mentor is something you must do early; think about who this person is at each place along the way during a job hunt. It is completely unnecessary for this person to have similar skill sets or a similar background as yours—sometimes a unique skill set and background are the perfect complement to your developing scientific career. You will need a mentor who compliments you, has a genuine interest in your development, and who will be overjoyed and proud when you succeed. Excellent mentors are special people because they are willing to give more than they will get and do so freely and without expectation of repayment or excess credit. Finding your mentor is an active process and one you must take very seriously. Certainly, this person could be recommended to you by your Chairperson, Service Chief, or a colleague in your specialty knowledgeable about your work. Sometimes it requires interviewing a select few candidates that could serve as your mentor to determine if they have a true desire to help you succeed and grow as a developing scientist. This process is up to you, and you should contact the potential mentor, be

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active in seeking them out, and make sure you have researched them well before sitting down with them for an interview. Of course, if someone who knows you well can introduce you via email, at a conference, or even at a meeting face-to-face, that is an excellent start. There are multiple ways to introduce yourself to a potential mentor. Face-toface meetings are always best so you can show your prior work and what you plan on doing in the future and thus gauge their interest and insight into your science. However, this is not always feasible, so a basic introduction via phone or email could be a reasonable start. Always have an agenda for the meeting, be prompt, and honor their time and space. Your first impression of them and theirs of you will be critical going forward so it is important to be organized, think about how you might fit into their scientific goals/purposes, and be willing to discuss limitations and challenges. Once you have been introduced or have interviewed someone whom you think will be a suitable mentor, then you will need to follow up with them to ensure they are willing to proceed in mentoring you. Things to remember when selecting a mentor are the following: (1) Does this person have the necessary skills and/or resources that I do not have and that I need? (2) Is there chemistry relative to our personalities and work ethics? (3) Is this person collaborative and inclusive? (4) Are there prior mentees that are available for me to speak with who can vouch for this person? (and will the prospective mentor happily give me a list of people to call/email?) (5) What does the mentor have to offer that will give my research program unique impact and scientific rigor? (6) What is the mentor’s history of funding and their mentees’ success rate in funding? (7) Have they mentored anyone like me before? (8) Do they have time to devote to my early development, eventual challenges, and difficulties? Once you have satisfactory answers to these questions and the potential mentor seems interested in moving forward, then you should move quickly to formalize the relationship and let your Chairperson and Chief of Service know of your plans. This team of senior people working on your behalf and with you will be essential to your development and success.

Collaborators Collaborators are key components in the modern success of the surgeon-scientist. These people are different than your primary mentor but still play an important role in helping your science succeed by giving you access to specialized technology, equipment, or personnel that you or your mentor do not have access to or have the time to employ directly in your laboratory footprint. Science today is indeed a team sport, and you will be required to assemble a group of specialized teammates with unique and focused skills. The collaborator should be an expert in the related field and should be able to accelerate your work with intellectual energy and also with time and money if needed. They can give credibility to papers and funding mechanisms, provide critical insight and input to your science, and should still have your development and interest in mind. You must remember they will also need credit for their work, and you should treat them graciously.

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Grant Funding Obtaining grant funding for surgeon-scientists has become increasingly difficult and competitive. In a survey-based article recently published in the Annals of Surgery, the authors show that over an 8-year period (2006–2014), total NIH funding to surgical departments dropped from $185M to $157M; at the same time, total NIH funding increased from $6.2B to $6.9B [1]. It is unclear whether this is the cause of, or the result of, the decline in the number of surgeons pursuing careers in basic and translational research. In fact, one of the critical obstacles identified by junior faculty, among whom the questionnaire from this study was circulated, was a “challenging funding environment.” Despite these challenges, it is the authors’ opinion that early-career funding success can be possible, particularly with some thought and advanced planning. This section will outline some strategies to help you navigate these challenges. The key to obtaining early-career awards, whether it is society- or institution-­ based, is advanced and meticulous planning. It is important to start developing your thought processes and goals for your work early; what better way to do this than to get to the business of writing a grant? The amounts from these awards typically range from $25,000 to $75,000, and the duration of support can range from 1 to 2 years. Of course, persistence pays off when it comes to grant applications. In the manuscript referenced above, a clear correlation was observed between the number of applications submitted by faculty and the likelihood of being funded. In fact, 85% of faculty who submitted more than eight grant applications over a 3-year period obtained competitive funding [1]. However, while the goal is to apply frequently to as many grants as possible, the greatest payoff from this process is the crystallization of ideas, focusing of aims, and fine-tuning of research strategy. The important exercise is to solidify the science and improve your grant-writing skills. This process will also give you multiple opportunities to get active feedback from your mentorship team as they read your specific aims and critique your work. These authors recommend an early foray into the funding landscape by application to society-based grants and career development awards. Fortunately, there are a number of such grants available to young surgeon-scientists from flagship societies including the Association for Academic Surgery (AAS), the American College of Surgeons (ACS), the American Surgical Association (ASA), the Society of Surgical Oncology (SSO), the American Society of Colon and Rectal Surgeons (ASCRS), the American Pediatric Surgical Association (APSA), the Society for Surgery of the Alimentary Tract (SSAT), and the Society for Vascular Surgery (SVS), among others. Table 1.1 represents a list that the senior author made identifying these sources, the funding lines, and deadlines for submission. The funding from these sources can supplement your existing startup funds or in some cases may be used to supplement your laboratory mentor’s funds for use when a “high-risk, potentially high-reward” experiment comes along. Obviously you can also contribute to a general laboratory pool to help pay for basic supplies, but the funds have to be designated for your use and specific research activities. In the spirit of the adage—“funding begets funding”—these monies are also a way to establish a track record and prepare you for bigger items like K-08 or R-01

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Table 1.1  Early-career grant opportunities Granting society AAS Roslyn Award NIH Loan Repayment Program ASCRS Limited Project Grant ASCRS Career Development Grant American Surgical Association American College of Surgeons-Clowes Award MSKCC Society Award ASCO Career Development Award ACS Faculty Research Fellowships MSKCC Faculty Research Award SSO Clinical Investigator Awards SSAT Career Development Award SSAT/ASCRS Joint Research Award

Deadline August November November March June August April September November December January January February

Amount $50,000 $35,000 $50,000 $75,000 $75,000 $45,000 $65,000 $66,000 $40,000 $75,000 $50,000 $50,000 $50,000

Duration 1 year 2 years 1 year 2 years 2 years 5 years 1 year 3 years 2 years 2 years 2 years 2 years 2 years

awards or more lucrative, multi-year society grants (e.g., American Heart Association, American Association for Cancer Research, American Cancer Society, etc.). Another important resource for early-career funding is your local institution. For example, there are institution-specific, young investigator or junior faculty awards in place, and it is highly recommended that you avail yourself to these early in your tenure. These funds are generally flexible and can be utilized when you need them for specific projects and ideas or could be added to your embedded laboratory working funds. Many of these are also renewable. It is important to have discussions about how to allocate monies earned in this manner and with other grant sources with your research mentor. It is also important to keep your clinical mentor up to date, and they are often key letter writers for many of these grant mechanisms to vouch for your protected time and expertise. Since all early-career grants and career development awards are directed toward the junior investigator, their stipulations typically require a mentor or a mentor team. Typically one-third of the review is focused on the science; one-third on the candidate’s promise for future development, as exemplified by previous accomplishments, letters of recommendation, and personal statements; and one-third on mentorship and the institutional environment. Junior faculty members sometimes conclude from this that the scientific proposal itself is therefore relatively less important, but this is untrue. A poorly written or poorly supported proposal casts doubt on the candidate’s ability and the ability of the mentor(s) to help the candidate, as well as on the feasibility of the proposal itself. Although there may be less emphasis in a career development review on the overall novelty and scientific significance of the proposal, the science and rationale must still be solid and compelling. It is not realistic to expect a junior faculty member to do Nobel Prizewinning work in his or her first efforts, and reviewers will recognize this in a career development review. A primary focus for these types of career development awards is the rigorous acquisition of skills and preliminary data that will make the applicant competitive for future independent funding and a career in science.

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While the nuances of writing a successful grant are beyond the scope of this chapter, a few points merit mention. First, give yourself enough time. This way you will cover all the bases and think it through carefully. Remember, if the proposal is hurried, it will read that way. We all think our grants are impenetrable, but often we are wrong. Therefore, show the grant to your (funded) colleagues who will read it critically. Of note, they need to see the grant 1–2 months before you plan to submit. Let them know that you have a thick skin for constructive criticism. The point is for them to shoot holes in it; your success will depend on you being able to plug all the holes before submission. Write, rewrite, and rewrite again. Second, preliminary data are important. The data must support the hypothesis and/or the feasibility of the techniques to be used to address the hypothesis. You may need to use published data to support your ability to be productive in the environment in which you are working. Be able to rationalize your ideas. Be focused and precise and ask one to two important questions, not five. Style counts. How you present your team, your institution, and your data will all reflect on how you are expected to perform in your laboratory. You, the environment in which you work, and your mentorship team should be highlighted in the best manner possible so you can catch the reviewers’ eye. Finally, submit only when you and your mentors think the grant proposal is the best it can possibly be.

Putting It All Together in “The Package” Your laboratory package may consist of a total sum of money allocated to you at inception, an equal amount to be allocated annually, or a front-loaded amount for the first year to buy equipment and get started and then lower amounts for succeeding years when it will be assumed you need only more supplies and help but not more equipment. Depending on how your finances are structured, you may be able to buy all your equipment up front, or you may need to apportion out equipment expenses over your period of financial support, purchasing the most urgently required or heavily used pieces of equipment first and borrowing or sharing others until more funds are available. Careful discussions during negotiation of your start-­up package and overall package with your Chairperson, Service Chief, and scientific mentor are critical as you estimate realistic numbers and set expectations. Another key question is: How many years of financial support do you want? Realistically, you will want to seek intramural financial support until you can obtain extramural funding. Depending on your previous level of experience, it will likely take you at least 3–5 years to achieve this. It is unlikely, however, that your Chairperson will offer you a blank check in this regard, and you may wish to negotiate for a 3-year commitment with the possibility of obtaining further intramural funding if you can demonstrate appropriate progress (as defined by mutually agreed-­upon benchmarks, such as application for extramural funding by year 3 or end of year 4). Ideally, you should establish your vision and negotiate for support before taking a position, having considered carefully not only what you want but also what your Chairperson or Chief or mentor wants you to achieve. In your negotiations, we suggest that you focus on setting shared, realistic goals with the leadership rather than on dollars or square feet. Moreover, finding the combination of a committed

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Chairperson, Service Chief, and scientific mentor should be your first priority. Next, having established goals with this group, try to set a mutually agreeable timetable for milestones toward achieving the long-term goal. Then, and only then, in the authors’ opinion, should you broach the subject of how the leadership will help you to pay for these efforts. Careful planning and a realistic goal-setting will give the leadership confidence in your strategy, and they may be more willing to commit resources if they are tied to realistic milestones. Of course, this strategy does have some risks; if the timetable is not met, you must be prepared to either give up your support and your laboratory efforts or convince the chair that this timetable was not realistic.

Responding to Failure Finally, we would like to address the reality and response to failure. If you are skillful and fortunate, your grants will be funded. However, most grants do not get funded. So, what then? You have to determine why. Approach reviews with humility. Reviewers do not know your plans and may not be familiar with your unique ideas. The authors have often found that when the reviewers try to fill in the blanks left unclear in proposals, they usually infer something different from what was intended. Show the summary statement to your mentors, collaborators, and funded colleagues to get their opinions. Then, you have five options: (1) revise and resubmit, (2) redirect to another agency, (3) refocus to another project, (4) abandon the current idea set and start afresh, or (5) give up. We strongly endorse critical revision and resubmission. Keep trying, keep fighting—persistence is key. It is important to prepare your resubmission with the frame of mind that you must satisfy the reviewers. First, answer all queries in the summary statement. Be clear, concise, and complete. It is a privilege to have a review with queries and weaknesses that subject the grant to a favorable resubmission. You must link the responses to the reviewers’ queries and weaknesses to the areas in the grant body where the modifications were made. Always thank the reviewers for their thoughtful critiques. As stated regarding the original application, give yourself time to complete a good resubmission. Second, if more data is necessary, make progress and resubmit—this may mean skipping a submission cycle. Third, you may also have to diversify your funding search. When you are close to funding, consider a return to the intramural source for bridge funding. This will allow you to continue your work while awaiting a funding decision. Your institution may require that you repay this bridge support if the grant is funded. Finally, it is important to realize that there will come times in even the most determined surgeon-scientist’s career when things just do not seem to be working. Experiments fail. Papers and grants get rejected. This is reality for all of us and is expected. Again, persistence pays off, and sometimes these are opportunities to reinvent yourself, re-imagine your science, or move in a new direction based on critical feedback and input from external sources and your internal advisory team. You should be prepared to consider several issues to redirect your efforts when all the pieces do not come together. Recalibrate your priorities, refocus your energies, and try to address why you are doing this in the first place. The way you respond to failure will define your successes.

12 Protected Time • Model of days/week OR weeks/months • Limit practice to narrow clinical niche • Frontload clinical activities weekly • Separate academics physically from clinical workspace • Supportive partners and leadership

J. Datta and J. J. Smith Research Space & Equipment • Own lab space or “embedded” in mentor’s lab • Each option has pros & cons • OWN: You set it up, equip and staff it • EMBEDDED: Share resources, personnel, intellectual capital • Equipment can be own or shared • Supplies relatively non-negotiable

Personnel • Fundamental differences between tech and research fellow beyond cost

Mentorship & Collaborators • Both clinical and scientific mentors are necessary

• Vary in quality and work ethic

• Decide on mentor early, usually during negotiation process

• Need help from mentor to recruit the right help

• CLINICAL: Support, protect, advise in tough clinical cases

• Untrained volunteers (residents & medical students) can be valuable assets

• SCIENTIFIC: Navigate early stumbling blocks, recruit right help, assist with grants • Find mentors & collaborators with complementary strengths

Funding

• Early funding sources are societal and intramural • Plan early, apply often—goal is to refine research strategy • “Funding begets funding” – small grants set the stage for K or R awards • Early-career awards focus as much on the research as mentorship and career plan

Fig. 1.1  Graphical representation of key points related to protected time, research space/equipment, personnel, mentorship/collaborators, and funding

Summary Establishing a basic or translational research laboratory is a significant undertaking that requires rigorous personal commitment and initiative, meticulous planning, passionate and supportive mentorship, and committed institutional leadership. Assuming these elements are fulfilled, there are other disparate pieces that need to come together for a successful scientific mission. These include protected space, time, personnel, equipment, and mentorship. Figure 1.1 gives a graphical representation of the key points we have reviewed relative to what it takes to set up, staff, and fund your laboratory efforts. Once the foundation for success has been established, obtaining intramural and extramural funding is the lifeblood of a laboratory effort. The authors believe that, even in the currently unfavorable funding climate, it is extremely important to champion the cause of surgeon-scientists focusing on basic and translational research. Acknowledgments  The authors gratefully acknowledge the previous authors Marc Basson and Harvey Bumpers.

Reference 1. Keswani SG, et al. The future of basic science in academic surgery. Ann Surg. 2017;265:1053–9.

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Choosing a Good Scientific Mentor and Being a Good Mentee Mark L. Kovler and David J. Hackam

Abstract

Being a good mentor is complicated requiring time and effort. The benefits gained from serving as a mentor should not be understated as many times, the mentor is credited for the success of mentees. However, this should not discount the role of the mentee. Being a good mentee also requires time, effort, and thought. Here we will describe the critical elements of being a mentor and mentee. Keywords

Surgeon-scientist · Mentorship · Mentor · Mentee · Generosity · Academic surgery

Introduction The “surgeon-scientist” is a surgeon engaged in bench research who is dedicated to studying the fundamentals of surgical disease. The surgeon-scientist is in a unique position to contribute to the advancement of our understanding and treatment of surgical diseases and have led the evolution of the field of surgery since its very beginnings. However, the current academic environment presents several challenges to surgeons involved in basic science research. Decreased grant funding, increased competition from non-surgeons for limited grant funding, everincreasing requirements for clinical productivity, and increasing administrative burdens are all barriers to the success of the surgeon-scientist. Not only do these M. L. Kovler · D. J. Hackam (*) Division of Pediatric Surgery, Department of Surgery, Johns Hopkins Children’s Center, Johns Hopkins University, Baltimore, MD, USA e-mail: [email protected]; [email protected] © Springer Nature Switzerland AG 2019 G. Kennedy et al. (eds.), Success in Academic Surgery: Basic Science, Success in Academic Surgery, https://doi.org/10.1007/978-3-030-14644-3_2

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challenges make it more difficult for junior faculty members to succeed in balancing a clinical practice and scientific research; they also decrease the abundance of mentors as the mentor role necessitates a wealth and security of these ever-limited resources. Preserving the surgeon-scientist as an entity requires a concerted effort and several forces, and one of the essential foundations of such a career is effective mentorship. Yet, the building an effective mentorship relationship itself can be challenging for both the mentor and the mentee, in part because of an absence of structured guidelines as to how the relationship should be established. We now seek to define the essential attributes of mentorship and present a framework for selecting a good scientific mentor and, as importantly, being a good mentee.

Defining Mentorship A mentor is an experienced and trusted advisor. Mentors can play several roles including counselor, role model, sponsor, coach, and also, in many cases, friend. The overriding principle of mentorship in surgical-science is that of a more practiced and veteran individual or team of individuals who guides a mentee in the development and establishment of a successful clinical practice, creation of a scientific center, and academic advancement. A mentee, in contrast, is a person who is directed and advocated for by a mentor or team of mentors. While much has been written on mentorship, less has been discussed regarding “menteeship.” The mentee plays an active role in guiding the mentor-­mentee relationship because at the root of the product of this relationship is the mentee’s career.

Mentorship by Career Stage While this chapter is largely dedicated to a framework for junior faculty members aspiring for success in academic surgery, mentorship is critical at all career stages. For medical students, mentors play a critical role in helping the student to decide on a specialty and residency. Mentors are central to medical student success in the residency match process as they advise students on programs to apply to and to write letters of recommendation. A well-written letter from a dedicated mentor is often cited as a top selection criterion by residency program directors. Many students participate in research with their mentors. While this is frequently clinical research, those medical students particularly interested in a scientific career may be part of a dual-degree MD-PhD program and attain scientific training through a dedicated scientific mentor during medical school. In other circumstances, medical students find mentorship from junior and senior surgical residents who recently went through the match process themselves. One of the most important values of performing

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research with a mentor is not only the scholarly activity and the publications that ensue but also the opportunity to expand on this personal research journey during the interview. Surgical residency is another career stage when mentorship plays a critical role as evidenced by the literature that up to 70% of residents go into the specialty of their mentor. Again, surgical residents seek mentors that are both senior residents and faculty. Most junior residents will describe a senior resident or two who have taken a special interest in them or have been “taken under their wing.” Senior resident mentors provide guidance in technical skill acquisition and in the acquisition of basic clinical knowledge. Further, they are a very important resource for identifying faculty mentors and opportunities for academic development. It is also important for surgical residents to develop mentor-mentee relationships with faculty. Guidance during residency includes post-training career plans and ideas for academic development. Similar to the medical student residency match, dedicated mentors play a significant role in fellowship matching. Perhaps at no stage in the career of a surgeon-scientist is mentorship more critical than for the junior faculty member. Junior faculty in academic surgical departments face daunting challenges with regard to limited funding and resources. At the same time, they are working to launch a robust clinical practice and establish a reputation. Additionally, they are frequently faced with the challenge of navigating a new institution with its own norms. The mentor team assists in guiding the junior faculty member through the “politics” of the department and institution, helps with obtaining independent funding, and assists with scientific efforts. The effective mentor will be described further below. Finally, while senior faculty provide mentorship, they also gain insight as mentees themselves. Senior faculty may seek out mentors especially when they branch out from their role as surgeon-scientist to include more administrative responsibilities. Promotions may lead to a change in institutions, when mentorship is critical to navigate their new environment. In summary, throughout the career of a surgeon-scientist, mentorship has an influence on career choice, promotion, and productivity.

Choosing a Good Scientific Mentor Defining an Effective Mentor It is certainly easier to define an ineffective or absent mentor than the elements that make up an effective one. Yet, most established surgeon-scientists will describe mentors who meant a great deal to their career. However, pinpointing what made them effective can be elusive, and thus a junior faculty member in search of a mentor may find themselves at a loss. We believe there are certain prerequisites for effective mentors that should be sought after when pursuing a mentor-mentee relationship.

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Experience By definition, an effective mentor has a depth of experience. For aspiring academic surgeon-scientists, it is important to seek out mentors with experience in academic surgical departments and science. Because no single mentor may fit the exact career aspirations of a mentee, they can look for a team of mentors with different experiences, as discussed below. Experience and gained wisdom are an important entity that the mentor possesses that the mentee lacks, and in essence much of mentorship involves the transfer of that gained knowledge from mentor to mentee. Additionally, a differential level of experience is one of the factors that distinguishes friendship from mentorship. So, in choosing a good scientific mentor, one should look for those with more depth of experience. Moreover, trainees tend to gravitate toward research mentors that have spent the most clinical time with them, while potentially overlooking outstanding research mentors on other clinical rotations, or with less clinical exposure. Mentees should focus on those mentors with the passion, commitment, and experience to serve as excellent mentors, above and beyond that which they experience on their clinical rotations.

Personal Dedication The mentor-mentee relationship is built on personal dedication, investment, and trust. While both parties certainly benefit from the relationship, on the surface, the mentee benefits more than the mentor. Therefore, an effective mentor must show a high level of commitment and an element of altruism. The motivation for mentorship comes in many forms. Shared personal experiences, an interest in giving back to their profession, and a gratitude for mentors in their own career are some of the reasons why effective mentors devote time and resources to their mentee. In truth however, an effective mentor-mentee relationship should be as beneficial to the mentor as it is to the mentee.

Generosity Generosity in mentorship comes in many forms. As stated, transfer of experience and expertise is one of the defining characteristics of a mentor-mentee relationship. For this transfer to occur effectively, a mentor must be generous with sharing their knowledge. For example, a scientific mentor who is independently funded can share previous grant applications with a junior faculty member, giving them insight into the process and what a fundable grant looks like. Similarly, a clinical mentor may assist in developing the mentees practice by asking them to participate in interesting cases or deferring referrals to their junior partner. Both of these instances require generosity of experience—on both occasions, the mentor is sharing a resource that took years or decades to develop with an unseasoned mentee.

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Generosity also comes in the form of generosity of recognition. The effective mentor defers credit to their mentee in order to elevate the mentee’s status. As discussed, this requires that the effective mentor no longer requires full credit for an accomplishment. They have to reach a status in their career that allows them to be generous with recognition in order for this to occur. But simply reaching that status does not insure shared recognition. A mentor who appears greedy or selfish with credit should be avoided, but a mentor who is known for recognizing their mentees accomplishments publicly and through authorship should be sought after. Similarly, generosity of financial support can be especially important for junior faculty members. The goal of the junior faculty member interested in a career as a surgeon-scientist is early independent funding. In order to accomplish this, they will need preliminary data and evidence of independence. An effective mentor can foster this through “start-up funding” in the form of financial backing and allocation of lab space and resources. Finally, time is a scarce resource for all surgeon-scientists. By description, an effective mentor is a busy surgeon-scientist themselves and often have burdensome administrative responsibilities as their career has progressed. Generosity of time is an important consideration when identifying a good scientific mentor and can come in several forms: regularity, accessibility, extent, and value of time spent mentoring. Experience, recognition, financial support, and time are scarce resources in academic surgery. The effective mentor must not only have an abundance of these means in order to generously share with a mentee, they must also have a level of altruism as the distribution may come at some level of personal or professional sacrifice.

Roles of an Effective Mentor The effective mentor plays several roles. As discussed, transference of experience and knowledge is the overriding principle in mentorship. But not every decision a mentor made in their life or career is appropriate for every mentee. It is therefore important for the mentor to provide career guidance but not necessarily dictate a mentee’s career. The effective mentor helps their mentee create a plan (5-year, 10-year, career) and outlines interval attainable achievements in order to meet that plan. For the aspiring surgeon-scientist, these include concrete actions such as grant preparation and achievement of independent funding, peer-reviewed publication, and presentation at institutional and national meetings. The effective mentor also provides sponsorship and advocacy. This occurs on an institutional level in the form of promotional support and nationally in the form of backing for positions within societies. The effective mentor also assists with planning work-life balance and providing opportunities for networking.

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Establishing a Team of Mentors Given the complexities and demands of a career as surgeon-scientist, it is unlikely in the current environment that a single individual can satisfy all of the mentoring needs of a junior faculty member. It is challenging that a single mentor can effectively mentor a large number of mentees in a department. For the sake of efficiency, it is important to establish a team of mentors and mentoring networks. For example, the junior faculty member beginning their career oftentimes requires a clinical and a scientific mentor. A clinical mentor is one who will guide them in establishing a practice, help with obtaining referrals, and assist with difficult clinical decisions and operations and a scientific mentor, who will guide them in establishing a lab, a focused line of research, obtaining grant funding, and providing introductions to cross-disciplinary collaborators.

Being a Good Mentee Discussions of mentorship are often dominated by the description of a meaningful mentor, and while prioritizing mentorship is currently at the forefront of our profession, the role of the mentee is less appreciated. However, we believe that the success and productivity of a mentor-mentee relationship is actually reliant on being a good mentee. For the mentee, “the more you give, the more you get.” The good mentee is dedicated, is reliable, and shows a high level of work ethic. She arrives at the mentorship meetings on time, prepared, and open to guidance. Further, the mentee guides and facilitates the mentor’s efforts. The good mentee enables the working relationship by planning meetings, asking important questions, and inviting constructive feedback. While this may appear self-explanatory on the surface, and sometimes is, for those struggling to find a good mentor, a focus on the process of being a good mentee can make for a more satisfactory mentor-mentee relationship.

Beginning the Mentor-Mentee Relationship Initiation of the mentor-mentee partnership can occur by either the party and by a variety of fashions. Recently, a number of innovative strategies have been put in place by surgical departments around the nation to encourage initiation of mentor-­ mentee partnerships. Whichever way this occurs, the mentee will always play a significant role in seeking out mentors. Mentees should be proactive and set up meetings with potential mentors that have similar interest to discuss their goals. The mentee should come to these meetings prepared to discuss their aims including 5-year, 10-year, and career goals and a potential timeline for achievement. Meetings should include direct discussion of the mentor’s past mentoring experience. Etiquette for these meetings may seem obvious for some, but it is important to note that a good mentee will prepare an updated curriculum vitae before the meeting, familiarize themselves with the clinical and research interest of the mentor, express appreciation for opportunity to meet, prepare questions, and accept feedback.

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Additionally, mentees should seek mentors with like-minded interests and work styles. A good mentee will be honest about professional chemistry and appropriateness of a personal match and not simply seek out any successful surgeon-scientist in their department. A good mentee should also be mindful of initiating and continuing mentorship relationships that are not compatible. A failed mentor-mentee relationship can be a significant setback for both parties involved—the mentee feels disheartened and defeated, and the mentor is left with a negative impression of the mentee and may be less willing to mentor in the future. Initiation of mentor-mentee relationships should occur early. A good mentee seeks mentorship at all levels of their career from medical student to senior faculty. As discussed, the need for mentorship is fluid and changing as a career develops. Additionally, as mentioned, a team of mentors is frequently necessary. Further, in academic surgery, mentors may leave an institution for promotion and opportunity elsewhere. For all these reasons, it is important for a good mentee to stay active in seeking mentors. The stagnant mentee will find themselves failing at inopportune times.

Maintenance of the Mentor-Mentee Relationship The responsibility for maintaining the mentor-mentee partnership falls on the mentee more so than the mentor. The principles of good communication, respect, and responsibility can guide a good mentee in protecting the relationship. Communication between mentors and mentees occurs though a variety of mechanisms. Phone calls, text messages, emails, and informal “drop-in” chats all occur regularly. A good mentee will discover the mechanisms by which their mentor likes to communicate. Good communication also implicates keeping a mentor “up to date.” The good mentee will correspond regarding career progress, project status, grants, and papers. Further, the good mentee responds at the earliest time possible to a communication from their mentor. The good mentee shows respect to an effective mentor in a number of ways. The mentee respects the mentor’s time as a precious and scarce resource. The good mentee recognizes that time spent with them is time spent away from the mentor’s family and personal career. Therefore, meetings and discussions should be focused. The good mentee prepares for these opportunities by proposing a focused agenda and brings directed questions. It is also important to point out that the mentor’s opinion should be respected. This includes response to criticism. The bad mentee responds defensively and becomes argumentative when criticized by their mentor. In contrast, the good mentee tries to see their mentor’s point of view and perspective and politely asks clarify questions. Most importantly, the good mentee is a responsible individual worthy of an effective mentor. The good mentee meets deadlines. Therefore, time management is a skill that the good mentee attains. In being accountable, it is also the good mentee’s responsibility to decline a mentor’s request if they cannot meet expectations. While the good mentee often feels the need to say “yes” to every opportunity to contribute, repeated failure to meet deadlines and responsibilities puts the mentor-­ mentee partnership at risk.

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Summary and Conclusions Mentorship has always been a critical aspect of the surgical-science career. However, with the current challenges in academic surgery, there may be no more important time for mentorship in academic surgery than the present. It is incumbent on our profession to meet the mentoring needs of aspiring surgeon-scientist if we are to maintain our role in the advancement of academic surgery, and it is compulsory for the young surgeons of today to be active mentees.

Suggested Reading Goldstein AM, Blair AB, Keswani SG, et  al. A roadmap for aspiring surgeon-scientists in todayʼs healthcare environment. Ann Surg. 2019;269(1):66–72. https://doi.org/10.1097/ SLA.0000000000002840. Kibbe MR, Pellegrini CA, Townsend CM, Helenowski IB, Patti MG. Characterization of mentorship programs in departments of surgery in the United States. JAMA Surg. 2016;151(10):900– 6. https://doi.org/10.1001/jamasurg.2016.1670. Souba WW.  Mentoring young academic surgeons, our most precious asset. J Surg Res. 1999;82(2):113–20. https://doi.org/10.1006/jsre.1999.5596. Thakur A, Fedorka P, Ko C, Buchmiller-Crair TL, Atkinson JB, Fonkalsrud EW. Impact of mentor guidance in surgical career selection. J Pediatr Surg. 2001;36(12):1802–4. https://doi. org/10.1053/jpsu.2001.28842. Zerzan JT, Hess R, Schur E, Phillips RS, Rigotti N. Making the most of mentors: a guide for mentees. Acad Med. 2009;84(1):140–4. https://doi.org/10.1097/ACM.0b013e3181906e8f.

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Effective Time Management Strategies for Conducting Laboratory Research Evie Carchman

Abstract

Time is a precious commodity for those conducting basic science research. For surgeon-scientists, effective time management is an important skill to master. This includes detailed, advanced planning of experiments for the day, week, month, and beyond. Efficient collection of data will not only provide preliminary data for grant proposals, but will allow for timely publication of results, proper utilization of personnel and funds, fulfillment of commitments, and the establishment of balance—to the extent possible—between work and life outside the laboratory. Ineffective time management can delay your academic advancement, increase personal stress, and decrease personal satisfaction. Instead of trying to create more time in a day, or more days in a week, effective time management allows us to use our time wisely. Keywords

Time management · Organization · Prioritization · Productivity · Efficiency

Definition Time management is the process of organizing and planning how to divide time between specific activities, which enables us to work smarter, not harder [1]. While new technologies allow us to stay connected to our work at all times and virtually anywhere, this convenience can also take a toll. Time management is an increasingly relevant subject due to the dissolving boundary between work and personal time and our desire to maintain a semblance of a work-life balance. As we seek to E. Carchman (*) University of Wisconsin, Madison, WI, USA e-mail: [email protected] © Springer Nature Switzerland AG 2019 G. Kennedy et al. (eds.), Success in Academic Surgery: Basic Science, Success in Academic Surgery, https://doi.org/10.1007/978-3-030-14644-3_3

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accomplish more in the same (or less) time, we can utilize effective time management skills to accomplish both day-to-day and long-term goals.

Benefits The clear benefits of effective time management include: • Greater productivity and efficiency. –– When time is not wasted, you can get more work done in a day. –– By accomplishing more in the same period of time, there is more time for other activities that will increase your productivity or work-life balance. • Enhanced professional reputation. –– When others recognize that you do not waste time, especially theirs, you build a reputation as a person who gets things done. This reputation is important for the academic surgeon. Other researchers seek collaborators with individuals who contribute to a project by maximizing time and efforts. • Less stress. –– Along with greater productivity and efficiency, you will experience less stress regarding deadlines and the balance between work and personal life. Decreased stress improves work satisfaction, prevents procrastination, and reinforces effective time management strategies. • Greater opportunities to achieve important life and career goals. –– With evidence of your productivity, due to effective time management, more opportunities for advancement in both work and your personal life are more likely to follow.

Failing to Manage Your Time Effectively Drawbacks to ineffective time management include: • Missed deadlines. –– When you do not prioritize and schedule your work time appropriately, it is likely that you will be working up to deadlines or even missing them—an investment of work and time without any reward. This time and effort could have been utilized to complete another project successfully. • Inefficient work flow. –– False starts impede an efficient work flow. You need to plan your activities for the day, estimate the time required to complete them, create a backup plan for when things come up unexpectedly, and avoid context switching between research, clinical obligations, administrative duties, and teaching during the same day. • Poor work quality.

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–– Without effective time management, you are likely to be working on proposals and projects right up to the deadline. Rushed work is bound to be incomplete or contain multiple mistakes (spelling, formatting, etc.). Finishing your work ahead of a deadline allows time for fact checking, ensuring that formatting is correct, having the work reviewed by editors/experts, getting feedback, and making revisions. Work completed according to schedule is more likely to represent your ideas accurately and to be a version that you are proud to present to others. Similarly, with regard to rushed work in the laboratory, mistakes can occur with experimental design (forgetting appropriate controls) and experimental execution (calculating incorrect dilutions and dosing). Substandard work is obvious to others and can delay acceptance of publications, prevent awarding of grants, and require the repetition of experiments. All of which are a waste of resources, including the valuable time of the people who work in your lab. • A tarnished professional reputation and a stalled career. –– Professional colleagues will take notice of low-quality work and an inability to complete projects. Signs of ineffective time management contribute to a poor reputation that is extremely difficult to overcome. A tarnished reputation can significantly stall your professional advancement, making colleagues less likely to consider you for committees, collaborations, book chapters, invited lectures, tenure, etc. • Higher stress levels. –– Ineffective prioritization of projects, missed deadlines, and a skewed work-­ life balance create unnecessary stresses that can significantly impede work, perpetuating the issues above.

How to Your best chance for successful time management is to begin with an introspective survey of your current skills. By understanding where you are now, you will be more likely to make improvements and succeed. The following are some suggested time management strategies (Fig. 3.1).

Set Clear Goals First, determine your short-term and long-term career and life goals. These goals should be specific, attainable, and measurable. A fair amount of time should be spent on this activity, as it determines the direction of the steps that follow. Clear goals will allow you to more easily identify the tasks needed to attain them. Larger goals can then be broken down into the discrete actions. For example, your overarching goal may be to attain tenure at your institution. Underlying this goal are the components of research, teaching and service outlined by your institution’s tenure review process.

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Say no

Be flexible

Time management strategies

Have a contingency plan

Set clear goals

Utilize people/resources

Prioritize Avoid distractions/interruptions

Conquer procrastination Organize and plan Block time Review progress

Fig. 3.1  Time management strategies. This figure demonstrates strategies for time management

The research goal may be comprised of NIH funding, publications, and abstracts. Your stated abstracts goal may consist of submitting four abstracts this year. Under publications goal, you may plan to submit two basic science and three clinical papers this year. Under the basic science papers goals, you might place two of your current research projects. Under these research project goals are the experiments needed to complete the paper and so on. You will need to use your limited time in a manner to meet the goals that have been set above. You should ask yourself frequently: How does each of my actions bring me closer to my goals? Additionally, these overarching goals should be reassessed periodically (at least annually).

Prioritize Next, prioritize the goals and the steps that are required to attain them. This action will allow you to focus your time on those goals that need to be completed in the near future or on those that will require a significant amount of time to complete. Prioritization is not focusing on getting more stuff done, but eliminating tasks that are not useful to attaining your goals while determining which of the useful tasks should be tackled first. Then you can direct your time toward completing the most valuable tasks with the time you have. Prioritization is especially important when you have too many good ideas—without prioritization you may end up jumping around from idea to idea. The only way that you can carry good ideas to fruition is by prioritizing your goals.

Spend Time Organizing and Planning Once you have organized and set your goals, spend time planning how to reach them. Take the time to arrange your emails, documents, and office in a way that makes sense for you. For example, I organize my drafted papers and grants in folders in Box, a content management and file-sharing service provided by my workplace. I make these

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folders accessible to our department’s editors, grant managers, and graphic designers to review, make edits, and monitor the progress of projects. I also have a 3′ × 4′ whiteboard in my office with sections delineated for grants, papers, abstracts, teaching, clinical trials, mentoring, and lectures. Underneath each section I write my goals, along with applicable deadlines. When a goal has been reached, I write the date of completion next to it. This allows me to update my CV appropriately and ensure that I am on track for tenure. During the planning/organization process, identify a convenient mechanism for listing and tracking your goals and tasks. In addition to a well-made plan, a to-do list will save you time. It is important to note that to be most effective, the to-do list should be easily accessible in various environments (office, laboratory, operating room, home, etc.) to allow you to refer to it at any time. This could take the form of a calendar on your phone, an application that syncs across all of your devices, or a physical notebook that you always carry with you. To make things clearer, you can also create separate to-do lists for clinical, research, or home activities. Each of the tasks on a list should be discrete and attainable. Beside each task, note your estimation of the time that will be required to complete the task, bearing in mind that we often underestimate the amount of time it takes to complete a task. This way you can organize your time wisely. • To-do lists can be very effective, allowing you to focus your mind on important objectives. As prioritization and organization may change based on the progress of projects, these lists should be updated or reviewed at least weekly. • To-do lists also make you less likely to forget tasks, which is easy to do with a very busy academic career where you wear multiple hats (surgeon, teacher, clinician, scientist, parent, etc.). • The act of writing the list can help you organize your thoughts and prioritize things further. • Creating a list allows you to see the bigger picture while also making sure the details are not forgotten. • Creating lists can also save you time, as you can refer to the lists when updating your CV or academic accomplishments. • You are less likely to be sidetracked when referring to a list. • The act of crossing things off of your list is also rewarding. In the organization of your time, it is important to understand and accept that there will be instances when one task cannot be finalized without completing another task first. This needs to be considered during the organization phase to prevent wasting time and effort. Thus, you need to be able to envision all of the steps that are required to complete the task, and tasks should be listed in order of priority.

Block Time Next, you should schedule time to achieve the goals you have prioritized. This means that your calendar should have actual time blocked out for drafting papers, writing grants, reviewing data, meeting with your lab members, going to dinner

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with your partner, etc. Your clinical staff should know that this time is protected: NO, you cannot add a patient in clinic during that time; NO, you cannot add one more case during that time. You should always block a little more time than you think you need, to allow yourself to get in right frame of mind and prevent the feeling of being rushed. Administrative tasks such as emails, phone calls, and signing charts can fill up your day quickly and cut into your allotted research time. You should schedule separate times during the week to complete these tasks. In addition, try to group similar tasks on the same day. It is hard for anyone to write a grant when they are worried about the notes for the 17 patients they saw in clinic that morning. Therefore, try not to block your research time on the same day as you have clinical responsibilities [2]. I avoid context switching by scheduling my protected research time on Monday and Tuesday, followed by operating room and clinic on Wednesday and Thursday. This leaves Friday for catch-up and administrative tasks. By putting my research days at the beginning of the week, I can review last week’s progress and results in our scheduled lab meeting on Monday and then prioritize the experiments, data analysis, etc. that I and my staff need to do in the lab throughout week.

Be Flexible Even with blocked or protected time, in some cases you will need to be flexible. There will be instances when you are on call and an emergency case comes in on your research day. Even if you are not on call, one of your postoperative patients may need your attention during the time you have blocked out to write a grant. Unavoidable personal life events will also occur. To prevent anger and frustration, and to address these acute and important surprises, you will need to cultivate flexibility, an important coping skill for when things go wrong. Instead of being paralyzed by disruptions and complications, you need to determine the next course of action and move forward. It may be helpful to block in a buffer time in anticipation of unforeseen events and also because most of us underestimate the amount of time that it takes to complete a task. Finally, it is important to note that time management is not only a technique; it is a frame of mind. Your ability to deal mentally with disruptions and setbacks reduces the amount of time wasted when they occur.

Have a Contingency Plan When we juggle multiple roles (surgeon, researcher, teacher, parent, etc.), there are likely to be interruptions that require immediate attention. Therefore, you should always have a contingency plan in place. For example, parents should establish backup help for when a caregiver gets sick and find babysitters who are able to work on short notice. Since my spouse and I are both surgeons, we have a nanny who is available to take “call” on the days that we are both on call. We pay our nanny a little

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extra during that time to take “call” and more if she called in. Remember that to be maximally effective, one needs to be flexible.

Review Your Progress You should routinely (weekly or at least bimonthly) review your progress on various projects to ensure that you are meeting your goals in the desired timeframe. In other words, take a moment to examine your goals for the year (abstracts, manuscripts, lectures, grants) that are listed on the white board (or on whatever form of list you have chosen). To remind yourself to do this, add these periodic progress reviews to your organizing system of choice (calendar, list, etc.). At these reviews, you may need to adjust your calendar to allot more time to projects that are lagging; such recalibration is appropriate and allows for maximization of your time.

Utilize Resources/People You cannot and should not do everything yourself. Therefore, you should be intimately aware of all of the resources and people available to help you at your institution (grant support staff, editors, statisticians, graphic designers, administrative assistants, etc.) and in your region (food delivery services, nannies, babysitters, landscapers, electricians, plumbers, housecleaning services, etc.). All available resources should be used to maximize your efficiency and productivity. For example, your mentor or institution may be able to aid with biosafety or animal protocols, and there may even be boilerplate documents already available to adapt for grant applications. By delegating tasks that would normally require your time, you can free up time for other activities. Delegation is especially important when there are others available who are better suited for that task than you are (e.g., graphic designers). If possible, have an administrative assistant add activities to your calendar (send emails with deadlines to put on your calendar), and schedule your professional meetings, travel, and lodging. Decide which tasks can also be delegated at home (someone to clean the house, mow the lawn, prepare meals, grocery shop, etc.). Organizing your daily, monthly, and annual priorities in a list form will allow you determine the things that you will need to delegate. When delegating tasks to others, it is very important to communicate the necessary components of the work that you want them to complete, so that you are not wasting their time or yours. You not only want them to carry out the task, but to do it correctly. The quality of your communication regarding the delegated task is usually directly related to the quality of work that you receive. Furthermore, you should check in with these individuals often to follow up on the progress of the work. If check-ins do not occur, is likely that you will be frustrated to find out later—often right before a deadline—that one of the delegated tasks was not done or needs to be

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redone in a rush because it was not done correctly. Choose the right person for the task, provide clear instructions, and follow up on their progress often. You should also share what you are working on or problems you are experiencing with your colleagues, family, friends, and mentor, as they can potentially provide time-saving advice for completing these tasks or addressing specific problems.

Avoid Distractions or Interruptions Surgeon-scientists often have competing responsibilities (clinical, teaching, administrative, and familial). To use your allotted time efficiently, make an effort to avoid interruptions when working. One strategy is to try to block time early in the morning to complete activities—as the day progresses, there are more opportunities for unexpected distractions. Other tricks include putting a “Do not disturb unless it is an emergency” sign on your door, turning off email pop-ups and alerts, and closing the electronic medical administration record (EMAR) when working. It is tempting to check your email or the EMAR. You should block off time for this and stick to the activity that is scheduled during the current blocked time. Regardless of the number of things you need to complete, if you cannot focus on the task at hand, it will not get done or it will get done haphazardly. Rather than trying to accomplish many things at once, you have to identify what is the most important at the time and focus on that. Try to finish one task before jumping into the next. This requires using the prioritization techniques you performed previously and blocking out the other tasks. Some rare individuals have the capacity to multitask and produce quality work, but for most of us, this is not the case. Multitasking is possible with select activities to maximize efficiency; you might evaluate your progress on these tasks to determine if this is improving efficiency or not. For example, I am a fan of responding to my emails while on the elliptical machine at the gym.

Conquer Procrastination This step requires self-awareness about when you are the most effective. Are you an early bird or a night owl? You should block your time accordingly. It is also important to review your progress to make sure that your self-assessment is actually correct. When you are on a streak, try to identify the factors in your surroundings that may have enhanced your productivity. This way, you can recreate the conditions in the future. For example, I’ve discovered that ambient noises are very distracting to me; a white noise machine helps me focus. Learning to recognize and avoid potential distractions is also helpful. You are likely to encounter days when you are tired from being on call, depressed about a recent grant or paper rejection, or just don’t feel like working. On these days self-motivation is key. You need to realize that the tasks at hand are the building blocks for what you are trying to achieve in your life. It could be that the task seems daunting and you don’t even know where to start. This is especially common in

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large tasks, such as writing an NIH grant. To accomplish the goal, divide it into discrete parts (specific aims page, animal section, human subjects, etc.), and then allocate time for each of these parts.

Say No When others recognize your productivity, you will be invited to join committees, write papers, mentor students or residents, contribute book chapters, and assist your own mentors with their projects. It is important to determine if these activities will contribute to your short-term and long-term career goals. If these requests do not help meet your goals, then you should turn them down. Sometimes this can be very hard, especially if it involves your mentor, chair, or a senior faculty member. But in order to have time to meet the goals you have set, you will need to abstain. In the end, there is just not enough time to do everything that is offered to you. Knowing your daily, monthly, and annual priorities in a list form will allow you determine the things that you will need to turn down. Remember, quality of work is more important in most situations that quantity of work.

How Time Management Relates to Laboratory Research All of the above strategies are relevant for time management in any situation, especially when conducting laboratory research. You should set clear short- and long-­ term goals regarding your research program. These goals should then be prioritized, as it is not uncommon to have many good ideas with limited time, resources, and personnel. Once prioritized, organize your approach to achieving these goals. This includes good communication with research staff regarding experiments: confirm that the experiments will be conducted in the correct fashion, follow up on the execution, and discuss ways to solve problems that arise. You should block time on your calendar to meet with your personnel to discuss the above; to read and review new literature regarding your area of research; to write abstracts, grants, and papers; to meet with individuals managing your research funds (I recommend quarterly); to go over research presentations with your staff; and to meet with collaborators. This blocked time should be kept separate from clinical, teaching, and administrative duties. Given the unpredictability and frequent frustrations of laboratory research, you have to be flexible and adapt your research plan based on unexpected results, difficulties with assays or models, and problems with research personnel, funding, etc. One should also have a contingency plan for any set of experiments, anticipating potential limitations and pitfalls (a requirement of many grant submissions) prevents wasted time when challenges occur. You should frequently review the progress of experiments and your research program to address areas that may be falling behind schedule or unexpected results.

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As much as possible, you should utilize the resources and people that are available to you at your institution. This is especially true with laboratory research. For example, use core facilities with expertise in assays/experiments that are technically challenging (e.g., electron microscopy) or that require a large amount of time (e.g., histology core facilities for sample processing and cryosectioning). Delegation is an important tool in successful laboratory research. You do not have the time to write grants, papers, and abstracts and to review data in addition to conducting the day-to-day activities of the lab. Therefore, weekly lab meetings should be scheduled to review the progress of the experiments and plan out the experiments and tasks for the next week, month, or year. When it comes to writing grants and papers, it is important to avoid distractions and interruptions, to use your time efficiently, and structure your day to avoid procrastination. Finally, it is not uncommon to be asked to be involved in other research projects. If these projects will require your time and attention and are not directly in line with your research goals—a polite “NO” is advised.

References 1. Pugh CM.  Time management. In: Chen H, Kao LS, editors. Success in academic surgery. London: Springer; 2012. p. 235–50. 2. Gosain A, Chen H. Effective time management strategies for conducting laboratory research. In: Kibbe MR, LeMaire SA, editors. Effective time management strategies for conducting laboratory research. London: Springer; 2014. p. 29–39.

4

Maintaining an Effective Lab Notebook and Data Integrity Andrew J. Murphy

Abstract

Efficient, organized, and detailed data maintenance are the cornerstones of a successful laboratory. Furthermore, institutional and federal requirements mandate proper maintenance, documentation, and dissemination of experimental data in a way that is rigorous and reproducible. The complexity of data generated in the modern laboratory setting presents a significant challenge to these principles of proper record keeping and data integrity. This chapter will focus on the elements of the scientific method, data maintenance, and paper and electronic record keeping that can be used to facilitate successful laboratory operations for the surgeon-­ scientist conducting basic research. In addition, there is recent increased emphasis on measures to ensure experimental rigor and reproducibility supported by the scientific community and National Institutes of Health. This chapter will introduce the surgeon-scientist to the critical aspects of these requirements to ensure compliance with grant submission guidelines and common author instructions for manuscript submission. Keywords

Notebook · Laboratory · Electronic · Data integrity · Rigor · Reproducibility Data archiving

A. J. Murphy (*) Department of Surgery, St. Jude Children’s Research Hospital, Memphis, TN, USA Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA e-mail: [email protected] © Springer Nature Switzerland AG 2019 G. Kennedy et al. (eds.), Success in Academic Surgery: Basic Science, Success in Academic Surgery, https://doi.org/10.1007/978-3-030-14644-3_4

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Introduction The academic surgeon is intimately familiar with the importance of a detailed operative note. A properly dictated operative note allows the surgeon to revisit the indication, decision-making, technique, and potential shortcomings of an operation even years after the procedure was performed. The same attention to detail must also be utilized in the keeping of an effective laboratory notebook and maintaining data integrity in the academic surgical laboratory. Efficient, organized, and detailed data maintenance are the cornerstones of a successful laboratory. Furthermore, institutional and federal requirements mandate proper maintenance, documentation, and dissemination of experimental data in a way that is rigorous and reproducible. The complexity of data generated in the modern laboratory setting presents a significant challenge to these principles of proper record keeping and data integrity. This chapter will focus on the elements of the scientific method, data maintenance, and paper and electronic record keeping that can be used to facilitate successful laboratory operations for the surgeon-scientist conducting basic research.

The Challenges of Record Keeping Data in the modern scientific laboratory may come in the form of handwritten notes, computer printouts, gel images, blots, spreadsheets, photographs, slides, computer files, and even massive electronic datasets related to genomic or proteomic investigations. These data can be tangible or electronic. Electronic data can be accessed using a wide variety of computer software. Furthermore, these electronic data can be stored on local hard drives, USB drives, or on cloud storage. The obvious challenge is to integrate these data into a decipherable system that can be shared among laboratory members and collaborators [1]. Lapsing into slack record-keeping practices can make manuscript preparation and internal or external review of scientific data problematic and can therefore directly impact the success of a laboratory. All team members must participate in rigorous record-keeping practices to optimize the reporting of confident, accurate, and transparent scientific data. For these reasons, the record-keeping practices and organizational skills of a candidate lab member should be strongly considered prior to their recruitment.

Legal Aspects The laboratory notebook guidelines discussed in this chapter are also designed to facilitate legal determination of the exact timing of a scientific discovery in the event of a patent dispute. For much of recent history, US patent law favored a first-­ to-­invent rather than a first-to-file approach. However, the America Invents Act, passed in 2011, aligned the USA with the rest of the world by converting to a first-­ to-­file approach for patents filed after March 16, 2013. This law has rendered the legal utility of laboratory notebooks in patent disputes more limited [2]. However,

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investigators are now encouraged to be much more proactive in filing for patents related to their research, and appropriate record-keeping practices can greatly facilitate gathering the appropriate information for the application process. Investigators should consult their institutional offices of technology licensing regarding recommendations for this process upon initiating their research program or when preparing for publication of a significant manuscript.

Paper Laboratory Notebooks Although it is essentially impossible for a traditional paper laboratory notebook to contain the entirety of data related to an experiment in the contemporary laboratory, the notebook can still contain essential details about the scientific method and can also serve as the index of record keeping for results that are not amenable to a paper format. In fact, a paper notebook is often the easiest way to record routine research results during the actual conduct of an experiment. Each lab member should maintain their own laboratory notebook. The notebook should have bound, serially numbered pages to alleviate concerns about data omission. Loose leaf notebooks without serial numbering of pages, while convenient, can raise concerns about possible tampering of data or proper maintenance of data integrity. Pages should not be skipped or left blank. Prior entries should be referenced by page number and date when continued. Notes should be recorded in permanent ink. All entries in the notebook must be legible and in the primary language selected by the primary investigator so that they can be reviewed by all current and future lab members when necessary. The notebook should be kept in the laboratory and should never leave the institution, even temporarily. Loss or theft of data can result in catastrophic loss of productivity and progress for the scientific laboratory, and thus this point must be stressed to each new laboratory member during their orientation period. Laboratory notebooks should be backed up by photocopying or scanning when possible. Laboratory notebooks should not depart with trainees when they have completed their involvement in the laboratory. Rather, departing trainees can make copies of their laboratory notebooks when appropriate. Laboratory notebooks are the property of the laboratory and institution. Completed notebooks should be kept in a designated, secure location within the laboratory for a specified number of years. The bound notebook should contain a table of contents at the beginning, and each experiment should be dated and entered in chronological order. The title, primary investigator and co-investigator names, purpose, hypothesis, and methods should be explicitly written in the notebook at the beginning of an experiment. Specific reagents should be listed in the description of methods along with the manufacturer and catalog numbers for future reference. Reagents from collaborators or other investigators should be noted for proper acknowledgment on publication. Recipes for buffers or other reagents should be explicitly written into the notebook at least once. The best practice is to write out the experimental methods in granular detail once they have been established and may be generalized to a laboratory protocol [1]. A collection of laboratory protocols should also be kept separately within the

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laboratory for the benefit of all members. Future experiments can simply reference the detailed entries of methods when appropriate. Experimental results and impressions should be catalogued in the laboratory notebook on an ongoing basis [1]. Keeping results in the notebook often involves taping or gluing images of gels or other data into the notebook. In addition to the cataloguing of raw data in this manner, orienting comments and information should be written into the notebook to ease data review after time lapses or when revisiting a project. Make sure to label all gel images in the notebook at the time they are placed onto a page. An effective way of maintaining proper research results is to summarize the day’s work and results into a paragraph in the lab notebook at the end of each day, accompanied by a written brief experimental plan for the next day. Paper laboratory notebooks cannot possibly contain the entire spectrum of research results, particularly those from instrument-generated computer files and other large electronic datasets. However, the pages of the laboratory notebook can be used to refer to file locations and computer programs which can be used to review the referenced data. In the contemporary laboratory, most every notebook page should explicitly refer to an electronic file location in which related results are stored. These references should be confirmed by the primary investigator or laboratory manager. The ideal file location is on a password-protected, shared drive accessible to all appropriate individuals in the lab rather than on personal or single hard-drive storage. Automatic and regular backing up of files should be utilized at regular intervals (daily and automatic if possible). For industry and federally regulated laboratories, recorded experiments require signatures by the researcher and a witness. The witness is typically someone who is not directly related to the project but can understand the work that is presented. The witness can attest to the authenticity of the research performed, which is extremely important should legal defense of research integrity become necessary. While this is typically not formally required or practical in an academic setting, it is good practice for the primary investigator or laboratory manager to personally review and sign off on all lab members’ notebooks on a scheduled basis (either biweekly or monthly). During review and sign off, the primary investigator or laboratory manager should also make sure that all references to electronic data locations have been recorded properly and can be readily accessed. At the time of manuscript preparation, all data pertaining to a manuscript should be kept in a distinct file that is easily accessible or linked to the manuscript.

Electronic Laboratory Notebooks As mentioned above, large “omic” or high-throughput electronic datasets have essentially rendered the traditional paper laboratory notebook obsolete as a comprehensive record-keeping method. An electronic laboratory notebook (ELN) allows for consolidation of fragmented laboratory records into a single interface which may also directly link to large electronic datasets [3]. ELNs can be “specific ELNs” that are designed to work with specific applications, instruments, or data types, or

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they can be “generic ELNs” designed to support access to a variety of data types and information needs. A generic ELN aims to function similar to a modern-day version of the traditional laboratory notebook. ELNs may exist as web-based, free and open-source, or proprietary software. Some ELNs function similar to a blog, while others aim to represent an evolved interface based on a traditional lab notebook [4]. ELN software can be designed specifically for the management of scientific data, or more general note-taking software such as OneNote (Microsoft, Redmond, WA) or EverNote (Evernote Corp, Redwood City, CA) can be used as an ELN [5]. ELNs are also called by a variety of acronyms including ERN (Electronic Research Notebook), ERMS (Electronic Resource Management System), LIMS (Laboratory Information Management System), and SDMS (Scientific Data Management System). LIMS and SDMS are software that may aim not only to replace the traditional laboratory notebook but also to address broader laboratory management, inventory, cataloguing of experimental protocols, and sample storage issues [6]. Comprehensive lists of ELNs, associated costs, and product reviews are publicly available, and some are listed at the end of this chapter. The goal of nearly all ELNs is to document scientific data in a centralized, legible, easily searchable, historically accurate, and legally rigorous fashion. ELNs also can promote secure collaboration among investigators or lab members sharing the same program. The ELN can facilitate review of the laboratory record by the primary investigator or laboratory manager. A properly implemented ELN can decrease errors and potentially reduce total laboratory costs. Because data can be accessed or generated using a variety of electronic devices including computers, scientific instruments, and handheld devices, ELNs offer a secure way to integrate data between these devices using a single record. The ELN eliminates the need to remove the paper laboratory notebook from the laboratory. ELNs allow for easier backing up of data and enable efficient importing or exporting of data to facilitate collaborations or review. In industrial labs involved in medical device or drug development, ELNs are subject to Food and Drug Administration (FDA) regulations 21 CFR 820 and Title 21 CFR Part 11 which pertain to data security and integrity [7]. These regulations do not apply directly to academic laboratories, but similar assurances and protections should be sought from the manufacturer of the ELN being considered for use in the laboratory. ELN or LIMS also can offer the ability to integrate sample information and management into daily experimental notes. Samples can be catalogued and recorded within an experimental protocol. This can allow the investigator to quickly link to the data sheet for a reagent being used. The sample age, aliquots, and other background information can be readily referenced during the experiment. For example, the investigator can pull up the data sheet for an antibody, determine the number of remaining aliquots, and determine its expiration date readily during an experiment. These features of LIMS can be used to catalog and organize freezers and link to this information during the experiment. This can save time, prevent running out of reagents, and reduce the need to look through sample boxes to find an intended reagent [8]. Although ELN use has increased in scientific industry and despite the numerous advantages of ELNs, a small portion of academic scientific researchers currently

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utilize this format. Identified barriers to adoption of the ELN include budgetary concerns, time needed for conversion to an electronic format, disruption of existing workflow, concerns about data security, superfluous features, and software being offered in a limited number of languages. Concerns regarding Information Technology (IT) support also have limited adoption of ELNs [9]. Furthermore, because so many varieties of ELN exist, many academic researchers are concerned about adopting a particular type of ELN that is not universally utilized across their institution, thereby limiting the ability to share or transfer data. Therefore, adoption and support of the ELN may need to be considered on the departmental or institutional level to address these concerns.

Archiving of Scientific Data New trends in data availability are improving the sharing of scientific data among investigators across the globe. Funding agencies and an increasing number of high-­ impact peer-reviewed publications are requiring that primary scientific data be made available to the scientific community. For routine experiments with limited datasets, uncropped or primary images from which figures were generated are often required as supplementary files to be submitted at the time of peer review. Thus, it is important to keep track of the location of all unprocessed, raw data even after figures are generated. Spreadsheets containing raw data may also be required to accompany manuscript submission. These files may appear as online supplemental files associated with the primary publication. For larger “omic” datasets, requirements often mandate that raw data be deposited into a publicly available repository such as the database of phenotypes and genotypes (dbGAP; National Center for Biotechnology Information (NCBI), Bethesda, MD) for sequencing data or the Gene Expression Omnibus (GEO; NCBI, Bethesda MD) database for gene expression and functional genomic data [10, 11]. Specialized reagents, novel cell lines, patient-derived xenografts, and genetically engineered mouse models may also be required to be made available to the scientific community either directly from the investigator or by deposition of the model system into a commercially available repository such as The Jackson Laboratory (Bar Harbor, ME) or ATCC (American Type Culture Collection, Manassas, VA) [12, 13]. A statement attesting to the availability of data or reagents known as a data sharing plan is required for NIH grant submission and often required when a manuscript is submitted to a journal for publication [14]. Keeping reagents, models, and data meticulously organized is therefore critical in light of these requirements.

Rigor, Reproducibility, and Data Integrity A recent survey of 1576 researchers by the journal Nature determined that more than 70% of scientists have tried and failed to reproduce results from another laboratory and more than half have failed to reproduce their own work [15]. Moreover, 52%

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of researchers felt there was a significant crisis of reproducibility in the scientific community [15]. Scientific journals and funding agencies have adjusted policies and requirements to address this crisis of reproducibility and ensure the integrity of scientific data in the published literature. The National Institutes of Health (NIH) has recently revised the language of review instructions for research grants and mentored career development awards to promote rigorous and transparent research. While these changes are specifically designed to address rigor and transparency in NIH grant applications and progress reports, by extension these guidelines are indicative of increased emphasis on rigor and reproducibility by the scientific community overall [16, 17]. The NIH guidelines contain four areas of focus: scientific premise, scientific rigor (design), biological variables, and authentication (Table 4.1) [18]. These areas must be specifically addressed in each grant proposal to receive funding. It is worthwhile for the surgeon-scientist to consider each of these areas when designing and conducting research projects or applying for federal funding. Additionally, the NIH and journal editors from over 30 preclinical scientific journals including Science and Nature reached consensus in 2014 on required principles and guidelines for reporting preclinical research (Table 4.2). Ultimately, the desired product is data with integrity and that which most closely approximates the truth. The scientific premise for an application or research project is derived from prior published research or preliminary data justifying the scientific question and supporting the application. The investigator should consider and specifically discuss the strengths and weaknesses of the premise when prioritizing projects for grant application or scientific inquiry. If the original scientific premise is weak, researchers may be tempted to over-interpret or misinterpret data to align with preliminary findings and concur with a faulty scientific premise. A research career with long-­ term success cannot be based on a faulty premise, and thus it is important to consider and openly discuss the quality of observations that constitute the background or preliminary data for any research endeavor. Table 4.1  NIH requirements for rigor and transparency Area of focus Premise

Design Variables

Authentication

Description of requirement Discuss the strengths and weaknesses of the scientific background forming the basis of the proposal Discuss how the study is designed to achieve robust and unbiased results Discuss how relevant biological variables, including sex, are incorporated into the proposal. Provide justification if model systems (e.g., mice, cell lines) from only one sex are used Describe the methods used to validate and confirm the identity of key biological or chemical resources used in the proposal

Adapted from https://grants.nih.gov/reproducibility/index.htm

Section of grant Research strategy

Research strategy Research strategy

Attachment for authentication of key biological and/or chemical resources

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Table 4.2  NIH rigor and reproducibility guidelines for journals: principles and guidelines for reporting preclinical research Recommended journal requirements Rigorous statistical analysis Transparency in reporting: core standards Standards

Replicates Statistics Randomization Blinding Sample size estimation Inclusion and exclusion criteria Data and material sharing

Consider refutations Best practice guidelines Image-based data Antibodies Cell lines Animals

Description Provide guidelines for statistical analysis. Check statistical accuracy of submissions when appropriate Eliminate unreasonable limitations on length of methods sections. Provide a submission checklist including core standards to authors Encourage or require use of standards in scientific community (nomenclature standards, animal research reporting standards such as ARRIVE guidelines) Indicate number of times experiments repeated. Distinguish between biologic and technical replicates Require full reporting of statistics: test used, value of N, mean, median, SD, SEM, confidence intervals State whether samples were randomized and methods used for randomization State whether investigators were blinded to group assignment during outcome assessment Report power analysis if used. If not, describe how sample size was determined Indicate criteria for exclusion of any data or subjects All de-identified datasets must be made available upon request. Recommend submission of data to public repositories and link between manuscript to this data. Encourage submission of all data within manuscript or as supplemental material If a paper is published, the journal must consider publication of refutations subject to the same standards

Journals encouraged to establish explicit guidelines for image-based data in author instructions Report source, characteristics, dilutions, and validation methods Report source, authentication, rule out mycoplasma contamination Report source, species, strain, sex, age, breeding strategy, inbred and strain characteristics of transgenic animals

Adapted from https://www.nih.gov/research-training/rigor-reproducibility/principles-guidelinesreporting-preclinical-research. ARRIVE Animal Research: Reporting of In Vivo Experiments, N number of samples, SD standard deviation, SEM standard error of the mean

Scientific rigor is the stringent application of the scientific method to ensure robust experimental design and eliminate bias from the interpretation and reporting of results. Thus, the objective, hypothesis, specific aims, long-term goals, inclusion and exclusion criteria, experimental methods, variables, statistical methods, potential problems, and alternative approaches should be determined and documented a priori. Plans to repeat experiments should be made from the outset of the project. If possible, results should be confirmed by two or more experimental assays. When

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appropriate, formal statistical power calculations should be employed to determine the number of replicates or animals that should be used for a given experiment [17]. These calculations are also often required by institutional review boards and animal care and use committees. The research plan should also explicitly consider relevant biological variables, including sex. Sex is a biological variable that has not often been considered in studies using vertebrate animal models or cell lines. This has resulted in a paucity of data in the basic science literature related to sex-based differences in disease development, disease phenotype, and treatment responses. Specifically, both male and female mice should be included in an experimental design unless there is strong scientific justification (e.g., the study of ovarian development or testicular cancer) for limiting the study to only one sex. Cell lines established from both males and females should also be utilized when available [19, 20]. In addition, other variables including age, weight, and medical comorbidities should be appropriately considered when they could be relevant to the scientific question. Authentication of key resources is important to ensure that proper, intended reagents are being utilized for experiments and that they are achieving their targeted chemical or biologic effect. These resources must also be free from contamination. Authentication is particularly important for cell lines, specialty chemicals, antibodies, and other biological reagents used for experiments. Both the method and frequency of authentication should be specified at the outset of a project. Short tandem repeat DNA profiling of all cell lines should be performed at the outset of an experiment and after significant passaging has occurred to ensure the profile matches the parent cell line [21, 22]. Cell lines should be tested to ensure absence of mycoplasma contamination [23]. Genetically modified animals or cells should be validated by confirming the genomic alteration using PCR amplification or other genotyping assays. Chemical reagents that are key to the research plan should be obtained from reputable manufacturers and/or also may need to be validated by liquid or gas chromatography or mass spectrometry. Validation of antibodies involves showing that the antibody is specific, selective, and reproducible in the desired experimental context. Adopting algorithms for antibody validation can facilitate this process in the laboratory setting [24].

Conclusions The complexity of data generated in the modern scientific laboratory setting presents a significant challenge to the principles of proper record keeping and data integrity. Efficient, organized, and detailed data maintenance are the cornerstones of a successful laboratory. These processes may be facilitated by a variety of electronic laboratory notebook or lab management software designed to accommodate and manage the large datasets and procedures typical in today’s laboratory. A data sharing plan including appropriate archiving of large datasets is often required for federally funded studies and by many high-impact journals. There is recent increased emphasis on measures to ensure experimental rigor and reproducibility supported by

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the scientific community and National Institutes of Health. The academic surgeon-­ scientist conducting basic research can benefit from stringently incorporating these measures into their research projects from the outset of their career. Requirements pertaining to data archiving and data integrity should be reviewed when planning applications for funding or manuscript submission.

Websites for ELN • List of ELN software packages. https://en.wikipedia.org/wiki/List_of_ELN_ software_packages. Accessed 19 July 2018. • Harvard biomedical data management: best practices and support services for research data lifecycles: electronic lab notebooks. https://datamanagement.hms. harvard.edu/electronic-lab-notebooks. Accessed 19 July 2018.

NIH Website for Rigor and Reproducibility • National Institutes of Health Rigor and Reproducibility. https://grants.nih.gov/ reproducibility/index.htm. Accessed 30 July 302018.

References 1. Schreier AA, Wilson K, Resnik D. Academic research record-keeping: best practices for individuals, group leaders, and institutions. Acad Med. 2006;81(1):42–7. 2. Rachinsky T, Sullivan C, Ghosh S, Resnick DS, Burton C, Armstrong M, Hanish JP, Sklan A.  First-to-invent versus first-to-file: impact of the AIA.  Pharm Pat Anal. 2014;3(4):353–9. https://doi.org/10.4155/ppa.14.28. 3. Giles J.  Going paperless: the digital lab. Nature. 2012;481(7382):430–1. https://doi. org/10.1038/481430a. 4. Dirnagl U, Przesdzing I. A pocket guide to electronic laboratory notebooks in the academic life sciences. F1000Res. 2016;5:2. https://doi.org/10.12688/f1000research.7628.1. 5. Guerrero S, Dujardin G, Cabrera-Andrade A, Paz YMC, Indacochea A, Ingles-Ferrandiz M, Nadimpalli HP, Collu N, Dublanche Y, De Mingo I, Camargo D.  Analysis and implementation of an electronic laboratory notebook in a biomedical research institute. PLoS One. 2016;11(8):e0160428. https://doi.org/10.1371/journal.pone.0160428. 6. Hull C. Editorial: Laboratory Information Management Systems (LIMS). Comb Chem High Throughput Screen. 2011;14(9):741. 7. U.S. Food and Drug Administration CFR – Code of Federal Regulations Title 21. https://www. accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=820. Accessed 30 July 2018. 8. Macneil R. The benefits of integrated systems for managing both samples and experimental data: an opportunity for labs in universities and government research institutions to lead the way. Autom Exp. 2011;3(1):2. https://doi.org/10.1186/1759-4499-3-2. 9. Kanza S, Willoughby C, Gibbins N, Whitby R, Frey JG, Erjavec J, Zupancic K, Hren M, Kovac K. Electronic lab notebooks: can they replace paper? J Cheminform. 2017;9(1):31. https://doi. org/10.1186/s13321-017-0221-3.

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10. The database of Genotypes and Phenotypes (dbGaP). https://www.ncbi.nlm.nih.gov/gap. Accessed 18 July 2018. 11. Gene Expression Omnibus (GEO) database. https://www.ncbi.nlm.nih.gov/geo/. Accessed 18 July 2018. 12. The Jackson Laboratory: donate a strain. https://www.jax.org/jax-mice-and-services/cryo-andstrain-donation/donate-a-strain. Accessed 18 July 2018. 13. ATCC deposit services. https://www.atcc.org/en/Services/Deposit_Services.aspx. Accessed 18 July 2018. 14. NIH Data Sharing Policy and Implementation Guidance. 2003. https://grants.nih.gov/grants/ policy/data_sharing/data_sharing_guidance.htm. Accessed 18 July 2018. 15. Baker M. 1,500 scientists lift the lid on reproducibility. Nature. 2016;533(7604):452–4. https:// doi.org/10.1038/533452a. 16. McNutt M. Journals unite for reproducibility. Science. 2014;346(6210):679. 17. Landis SC, Amara SG, Asadullah K, Austin CP, Blumenstein R, Bradley EW, Crystal RG, Darnell RB, Ferrante RJ, Fillit H, Finkelstein R, Fisher M, Gendelman HE, Golub RM, Goudreau JL, Gross RA, Gubitz AK, Hesterlee SE, Howells DW, Huguenard J, Kelner K, Koroshetz W, Krainc D, Lazic SE, Levine MS, Macleod MR, McCall JM, Moxley RT 3rd, Narasimhan K, Noble LJ, Perrin S, Porter JD, Steward O, Unger E, Utz U, Silberberg SD. A call for transparent reporting to optimize the predictive value of preclinical research. Nature. 2012;490(7419):187–91. https://doi.org/10.1038/nature11556. 18. National Institutes of Health Policy and Compliance: Rigor and Reproducibility. 2018. https:// grants.nih.gov/reproducibility/index.htm. Accessed 19 July 2018. 19. Tannenbaum C, Schwarz JM, Clayton JA, de Vries GJ, Sullivan C. Evaluating sex as a biological variable in preclinical research: the devil in the details. Biol Sex Differ. 2016;7:13. https:// doi.org/10.1186/s13293-016-0066-x. 20. Clayton JA, Collins FS.  Policy: NIH to balance sex in cell and animal studies. Nature. 2014;509(7500):282–3. 21. Almeida JL, Cole KD, Plant AL. Standards for cell line authentication and beyond. PLoS Biol. 2016;14(6):e1002476. https://doi.org/10.1371/journal.pbio.1002476. 22. Lorsch JR, Collins FS, Lippincott-Schwartz J. Cell biology. Fixing problems with cell lines. Science. 2014;346(6216):1452–3. https://doi.org/10.1126/science.1259110. 23. Uphoff CC, Drexler HG. Detection of mycoplasma contamination in cell cultures. Curr Protoc Mol Biol. 2014;106:28.4.1–14. https://doi.org/10.1002/0471142727.mb2804s106. 24. Bordeaux J, Welsh A, Agarwal S, Killiam E, Baquero M, Hanna J, Anagnostou V, Rimm D.  Antibody validation. Biotechniques. 2010;48(3):197–209. https://doi. org/10.2144/000113382.

5

Statistics for Bench Research Timothy W. King

Abstract

Success in academic surgery requires a basic understanding of statistics. Without this understanding a surgeon-scientist will not be able to interpret scientific articles, develop a hypothesis, or analyze the data they collect in their research program. The purpose of this chapter is to provide a brief overview of the statistical methods which are used in bench and clinical research. Keywords

Statistics · t Test · Type 1 error · Type 2 error · ANOVA · Correlation · Parametric Nonparametric

Introduction The use of statistics is a fundamental part of any research program. Without statistics, a scientist is unable to appropriately interpret their data. Therefore, in order to be a successful scientist, a thorough understanding of statistics is critical. While a thorough review is beyond the scope of this text, the goal of this chapter is to give you a basic overview of the statistics needed for success in your laboratory and provide resources to further explore this topic as it pertains to your research. Since there are multiple statistical computer programs currently available, it is very easy to enter data into a program and erroneously select a statistical test which provides a “significant” result. Thus, before you ever start an experiment, you need T. W. King (*) Departments of Surgery and Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA Birmingham VA Hospital, Birmingham, AL, USA e-mail: [email protected] © Springer Nature Switzerland AG (outside the USA) 2019 G. Kennedy et al. (eds.), Success in Academic Surgery: Basic Science, Success in Academic Surgery, https://doi.org/10.1007/978-3-030-14644-3_5

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to formulate a hypothesis. Your experiment will then test this hypothesis. The “null hypothesis” assumes that there is no difference between the two groups, and the “alternative hypothesis” assumes that a difference exists. You are trying to prove the alternative hypothesis. Formulating your hypothesis will define what the controls and variables of the experiment are and will lead you to the statistical analysis that is most appropriate for that experimental dataset. The first step of the analysis is to understand the types of data and variables that you are investigating. Therefore, the first question to ask is what types of data are you collecting?

Types of Data There are two types of data: continuous and discrete. Continuous data are quantitative and can have any value within a defined range (e.g., age, heart rate, tumor size). There are three types of discrete data, which are all qualitative: 1. Nominal: the data falls into defined categories with no implied order (e.g., eye color, gender, race). 2. Binary: the data is a yes/no and is usually coded as a 1 or 0 (e.g., disease present (diabetes/no diabetes), family history of cancer). 3. Ordinal: the data falls into defined categories with an implied order (e.g., tumor staging, GCS score). For example, if you were studying melanoma, Breslow depth would be a continuous dataset and Clark staging would be an ordinal discrete dataset. Applying a discrete statistical analysis to the Breslow depth would be inappropriate. Once you have defined the type of data, you need to determine the independent variable(s) from the dependent variable(s). The independent variable is what you control and change in the experiment, while the dependent variable is what happens as a result of the change you made (e.g., a drug treatment would be the independent variable, and the survival after treatment would be the dependent variable).

Descriptive Statistics Descriptive statistics are what we use to analyze the data that has been collected. Commonly, we then use this data as a sample of the whole population to make generalizations about the populations from which the samples were drawn. This is called inferential statistics. If we want to make inferences about a population, then it is important to ensure that the sample we are analyzing is a fair representation of the population we want to study. Measures of central tendency help us determine if this is true. The mean (average), median (middle value), and mode (most common value) are three commonly used measures of central tendency. Determining the distribution of the data is also very important as this will determine the statistical analysis

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100 80 60 40 20 0 0

20

40

60

80

100

Fig. 5.1  A normally distributed bell-shaped curve. The mean, median, and mode are all equal to 50

that you used to analyze that data. If the data follows a “bell-shaped curve,” you can conclude that it has a normal distribution. In a normally distributed (or parametric) data, the mean, median, and mode will all be the same value (Fig. 5.1). The mean can be affected by the sample size and outliers within the data. As the sample size increases, the effect of the outliers will decrease. If the data is not normally distributed, it is considered skewed. A positive-skewed dataset has the long tail of the curve on the positive side of the peak. This is also called a right-skewed distribution and will have the mean to the right of the median. A negative-skewed (or leftskewed) distribution will have the long tail on the negative side of the peak, and the mean will be to the left of the median. It is also important to measure the variability of the data. The range is the difference between largest and smallest values. In a normally distributed dataset, the variance (S2) is a measurement of dispersion and is derived by taking the difference of each individual variable (x) from the mean, squaring this difference, summing all the differences together, and then dividing the sum by the total number of data points (n). Mathematically, it is represented by the following formula:



S2 =

å ( x - mean ) n

2



The standard deviation (SD) is defined as the square root of the variance, and the standard error of the mean (SEM) is the standard deviation divided by the square root of the n. SEM is commonly used in calculating confidence intervals and in studies with a smaller sample size. For a normally distributed dataset, 68% of the data will be within one SD of the mean; 95% will be within two SDs of the mean; and 99.7% will be within three SDs of the mean. If the data is not normally distributed, then it should be analyzed with nonparametric methods.

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Table 5.1  Summary of Type 1 and Type 2 errors

Study results Difference (Reject null hypothesis) No difference (Accept null hypothesis)

Truth/reality Difference (null hypothesis false) Correct decision (Power) Type 2 error (β)

No difference (null hypothesis true) Type 1 error (α) Correct decision

Type 1 and Type 2 Errors When testing a hypothesis, there is a risk that the wrong conclusion is made from the interpretation of the data. The probability of a scientist concluding that a difference exists and in reality it does not (i.e., incorrectly rejecting the null hypothesis in favor of the alternative hypothesis) is called a Type 1 error (α) (Table 5.1). The probability that the scientist concludes that a difference doesn’t exist when in reality it does (i.e., incorrectly failing to rejecting the null hypothesis) is called a Type 2 (β) error. In general, a Type 1 error is set at 5% and a Type 2 error is set at 20%.

Sample Size and Power The power of a study is the probability of detecting an effect when there is an effect to be detected. It is defined as 1 − β. In general, scientists want the power of a study to be at least 80%. As the power of a study increases, the risk of making a Type 2 error, or concluding there is no effect when, in fact, there is one, decreases. The power of a study is directly related to the sample size because the larger the sample size, the smaller the SEM. Power also depends on the how much of a difference the investigator is trying to detect. If you are trying to detect very small difference, you will need a very large sample size to find that difference. This is important to determine before beginning an investigation to ensure that the study is feasible. For example, if you were trying to detect a small difference in tumor growth (e.g., 2 mm) after a drug treatment, you may need a very large sample size which might make the study impractical or too costly to do. However, if you changed the outcome to be a moderate difference (e.g., 2 cm), the sample size would go down significantly while maintaining the same amount of power, and the study could be done.

Data Analysis P Value The P value is the probability of concluding a difference exists due to chance. In most studies the P value is set at