1、Dr. Daniel McGowan 论文写作系列第五讲Good study design and forward planning如何做好研究设计和预先规划工作Rejection following peer review can mean a considerable amount of additional work for many authors to get their studies published. In the worst cases, their studies may be simply un-publishable. Much heartbreak and hard
2、 work can be avoided by simply planning and designing your study properly in advance. In the long run, this will save you time, allowing you to get on with the research for your next big paper.No-one wants to have to repeat experiments because the controls were inappropriate or the case/sample numbe
3、rs were insufficient to provide enough statistical power. Frequently though, researchers rush into experiments without making all the proper considerations, and this can result in delays when their manuscripts reach the peer review stage. Remembering a few basic principles of study design can help t
4、o reduce the risk of outright rejection and repeated experimentation.1. Have a hypothesis or research questionHaving a hypothesis or appropriate research question enables you to frame your research within an appropriate context, which in turn will help you apply the appropriate controls. It will als
5、o help you describe the rationale for your study when it is time to write it up. Having a hypothesis also means that the objectives of the study are clearly defined, thus reducing the chance that your study will be open-ended and possibly criticised for being incomplete. You can then logically work
6、through these objectives and, importantly, present your results in a logical manner rather than haphazardly.2. Ensure that the appropriate methods are usedOnce you have a clear idea of the aims of your study, and the specific research question you are setting out to answer, you will need able to det
7、ermine what methods would be appropriate to achieve these. Important considerations include deciding whether subjective, qualitative data will be sufficient to address your question, or whether there is a need for more quantitative methods. For basic science studies, such considerations might includ
8、e the following questions. Will the combination of RT-PCR and in situ data be enough, or is there a need for qPCR? Is Western blotting alone sufficiently sensitive or do you need to also perform immunohistochemistry and cell counting experiments to show a difference between groups? For clinical stud
9、ies, important considerations include the choice of controls, sample sizes, statistical tests and approach, all of which are described in more detail in the points below.3. Ensure that the appropriate controls are usedControls are included in experiments to rule out alternative hypotheses. Theres an
10、 old saying that “nothing can be proven, only disproved”, and this is precisely why appropriate controls are necessary: to disprove any feasible alternative interpretations of the data you obtain and/or to eliminate or minimize the effects of extraneous variables. Consider what alternative hypothese
11、s exist, and systematically rule them out by performing experiments that disprove them. There are generally two types of controls: positive and negative. Positive controls show that a negative result is not due to a failure of the experimental system. Negative controls provide an indication of the b
12、ackground noise or baseline value with which to compare values from your experimental sample. In quantitative studies, a “relative control” or “housekeeping control” is required to show that changes in the apparent levels of a target gene or protein are not caused by differences in the amounts of pr
13、otein or DNA in the sample. These levels can be used as a baseline to measure changes in relative levels of a target gene or protein. Common housekeeping molecules include -actin and GAPDH. In clinical trials, subjects in a placebo group in intervention trials, and normal control subjects in observa
14、tional trials, need to be matched as closely as possible to those in the treatment or disease group in terms of age, sex and numerous other potential confounding factors. In randomized controlled trials, accepted procedures for assignment to groups also need to be followed (see, for example, the ICH
15、 good clinical practice guidelines at: http:/www.ich.org/LOB/media/MEDIA482.pdf).4. Use sample sizes large enough to provide a definitive resultMany studies fail to achieve the desired impact or to fully support a given hypothesis because the effect is too small or the variability too large to show
16、statistical significance. Often this can be simply overcome by increasing the sample size. However, once a study has been performed and the data analyzed, it can be impossible to go back and increase the numbers without starting all over again. For this reason, pilot studies are often performed in a
17、dvance of larger scale studies. Talk to a statistician. Determine the size of the effect of your treatment and/or the variability in your population before starting large-scale studies, and use this information to determine the sample size required to give you statistical power. Doing this can save
18、you time, money and potential disappointment later.5. Use appropriate statistical tests to analyze your dataStatistical analysis of your data is essential to show that an effect is genuine and significant. Tests of significance demonstrate the robustness of your findings, essentially showing how unl
19、ikely it is that your findings were obtained by chance. Are your data continuous or discrete? Are they normally distributed or non-normally distributed? The nature of your data will determine how they should be analyzed and what tests are appropriate. If in doubt, consult a statistician who will be
20、able to advise you on the most appropriate tests to use and what these tests indicate. Determining the right tests to use in advance will save you having to repeat your analyses if you got it wrong first time round, with the distinct possibility that no significant effect will be observed when the a
21、ppropriate tests are used. For clinical trials, the following guidelines may be useful: http:/www.ich.org/LOB/media/MEDIA485.pdf.6. Remove investigator and patient biasMany experiments involve subjective measurements or assessments performed by the investigators, as opposed to objective results prov
22、ided by the experimental system. If the investigator has prior knowledge of the groups to which individuals/samples belong, then investigator bias is a distinct possibility, and this can invalidate any of the findings obtained. In such cases, where the investigator is a factor inherent in the experi
23、mental system, it is essential that the investigator is blinded to the groups to which individuals or samples belong. Doing so ensures the objectivity of the findings and improves their reliability. Such blinding can refer to treatment in an intervention trial, or to assessment or interpretation of
24、clinical findings in an observational trial. Similarly, the outcome of a treatment could be influenced if a patient knows if they are receiving a placebo or drug; such patient bias should be avoided, by blinding the patient to the nature of the treatment. Being aware of the potential for bias before
25、 commencing experimentation can again save the need for time- and resource-consuming repeats.7. Comply with ethical requirementsThere are strict regulations regarding the use of human and animal subjects, and in many countries, regarding the use of stem cells, cell lines and genetically modified mat
26、erials. Failure to comply with these regulations will prevent publication of your findings and could lead to legal issues; at best, it will limit the range of journals to which you can submit your findings. Make yourself aware of these regulations before you commence your study and ensure that all r
27、equirements are complied with so you dont encounter problems later on. As well as ethical requirements regarding experimentation, there are also strict guidelines provided by most journals regarding the requirements for authorship, and these also need to be complied with. Clinical trials should comp
28、ly with the Declaration of Helsinki (http:/ in addition to any local requirements. Informed consent is essential for most trials involving human subjects. Animal studies should comply with local and national regulations, although many journals are now aligning themselves with standards such as the N
29、IH “Guidelines for the Care and Use of Animals” (http:/oacu.od.nih.gov/regs/guide/guide.pdf). Finally, many journals require a statement describing who gave ethical approval for the study.8. Clinical study registrationMany top-tier journals now request that prospective clinical trials involving huma
30、n participants should be registered online in an accessible database. Many journals will instantly reject studies of this type that have not been registered. More information on this can be found at http:/www.icmje.org/faq.pdf. International clinical trial registries include the Chinese Clinical Tri
31、als Register (http:/www.chictr.org/), the Japanese Primary Registries Network (http:/rctportal.niph.go.jp/), The International Standard Randomised Control Trial Number database (http:/isrctn.org/) and Clinical Trials.gov (http:/www.clinicaltrials.gov/). Registration should be done before the first p
32、articipant is enrolled, but many of the databases do allow retrospective registration. However, by registering the trial once you receive ethical consent you will save time and overcome a major obstacle to publication.All studies are different and therefore have different requirements regarding appr
33、opriate study design. The points above are just a few of the important considerations that should be made prior to the commencement of experimentation, and the general principles apply to a variety of different study types. It is true that sometimes even peer review fails to detect flaws in study de
34、sign, as shown, for example, in the following report on randomized controlled clinical trials published in Chinese journals: http:/ However, if you want your study to stand the test of time, be published in a top-tier journal and to be widely accepted by the international research community, then pl
35、anning ahead and designing your study to make it robust and reliable will only serve to save you time, money and heartbreak later on.Overcoming the language barrierDr. Daniel McGowan 论文写作系列第四讲Overcoming the language barrier: writing in English for non-native authorsDr. Daniel McGowan 将向大家展示“ 克服语言障碍，
36、非英语母语科研人员如何写作?”“Journal editors, overloaded with quality manuscripts, may make decisions on manuscripts based on formal criteria, like grammar or spelling. Dont get rejected for avoidable mistakes; make sure your manuscript looks perfect” (quote from a senior executive at a large international publi
37、shing house).Scientific writing is difficult enough for many authors who have English as their first language; for non-native English-speaking authors, writing a paper in English represents a massive challenge that can make or break their papers chances of publication. With increased pressure on pub
38、lication space and increased demands on editors time many journals are introducing language screening protocols to check submissions before they reach the editors desk; some editors simply choose to overlook papers that are too poorly written to consider or send for review in the knowledge that, amo
39、ng the submissions they receive, will be well written studies containing interesting and robust science. However, all is not lost for non-native English-speaking authors: by being aware of some of the most common scientific writing language errors and how to avoid them, you can improve the quality o
40、f your paper and increase its chances of being accepted.It is helpful to think of the writing process in the same way that you think about performing experiments; that is, the language needs to be easily and accurately understood by the reader, without multiple possible interpretations arising. In e
41、xperiments, we use controls to rule out alternative hypotheses. In language, we must avoid ambiguities and unnecessary text (such as repetition and redundancies) to get our message across clearly. Scientific writing should possess what I call the three “C”s: clarity, conciseness and correctness (acc
42、uracy). The key to achieving this is to be as brief and specific as possible without omitting any details that might be essential for the reader to fully understand your meaning. In other words, say no more than you need to accurately convey your message. Although writing that fails to meet this sta
43、ndard is sometimes described as “sloppy” or “lazy” writing, authors are frequently unaware that what they have written is unclear and ambiguous. Thus, attention to detail and an appreciation of how your writing could be misinterpreted are essential. What follows is just a small selection of error ty
44、pes that, when present in large numbers, could result in your paper going straight to the rejected pile.Articles/Plural vs singularArticles (a/the) are adjectives that modify nouns. Where they are used incorrectly the reader can be left wondering if you are referring to a specific thing or to a non-
45、specific item or category. Worse, they could interpret the text incorrectly and make a wrong assumption. Incorrect use of articles can also lead to confusion relating to singular vs plural senses. The word “the” should be used in conjunction with a noun referring to a particular item or group of ite
46、ms (it can be used with both plural and singular nouns); for example, “the sections were/the section was then stained with H for example, “a section was then stained” infers that a single section, any section, was stained. “A” should only be used to refer to a single item or category, and should not
47、 be used in conjunction with plural nouns; that is, “a sections” would be incorrect. Asian authors frequently leave articles out of sentences making them sound awkward and unnatural, which would be the case when omitting the “the” in “adenovirus was injected into the fourth ventricle”.1. “The antibo
48、dy was injected into the hippocampus” (articles required to specify a particular antibody, presumably already referred to in the text, and a specific hippocampus, belonging to a subject already described).2. “A new method of extraction was devised” (“a” used rather than “the” because this statement
49、introduces this method to the reader; therefore it is non-specific at that time. Once introduced to the reader, “the new method of extraction” should be used to refer to that method in the specific sense).Nouns are used in the plural sense by adding an “s” to the end (in most cases). In the absence of an article, it can sometimes be unclear if the wrong sense (plural vs singular) has been used. For example, in the sentence “Acetyl group was added”, the reader is not clear whether the author means “An
