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1.  Developing the Critical Thinking Skills of Astrobiology Students through Creative and Scientific Inquiry 
Astrobiology  2015;15(1):89-99.
Abstract
Scientific inquiry represents a multifaceted approach to explore and understand the natural world. Training students in the principles of scientific inquiry can help promote the scientific learning process as well as help students enhance their understanding of scientific research. Here, we report on the development and implementation of a learning module that introduces astrobiology students to the concepts of creative and scientific inquiry, as well as provide practical exercises to build critical thinking skills. The module contained three distinct components: (1) a creative inquiry activity designed to introduce concepts regarding the role of creativity in scientific inquiry; (2) guidelines to help astrobiology students formulate and self-assess questions regarding various scientific content and imagery; and (3) a practical exercise where students were allowed to watch a scientific presentation and practice their analytical skills. Pre- and post-course surveys were used to assess the students' perceptions regarding creative and scientific inquiry and whether this activity impacted their understanding of the scientific process. Survey results indicate that the exercise helped improve students' science skills by promoting awareness regarding the role of creativity in scientific inquiry and building their confidence in formulating and assessing scientific questions. Together, the module and survey results confirm the need to include such inquiry-based activities into the higher education classroom, thereby helping students hone their critical thinking and question asking skill set and facilitating their professional development in astrobiology. Key Words: Scientific inquiry—Critical thinking—Curriculum development—Astrobiology—Microbialites. Astrobiology 15, 89–99.
doi:10.1089/ast.2014.1219
PMCID: PMC4290794  PMID: 25474292
2.  Scientific meeting abstracts: significance, access, and trends. 
Abstracts of scientific papers and posters that are presented at annual scientific meetings of professional societies are part of the broader category of conference literature. They are an important avenue for the dissemination of current data. While timely and succinct, these abstracts present problems such as an abbreviated peer review and incomplete bibliographic access. METHODS: Seventy societies of health sciences professionals were surveyed about the publication of abstracts from their annual meetings. Nineteen frequently cited journals also were contacted about their policies on the citation of meeting abstracts. Ten databases were searched for the presence of meetings abstracts. RESULTS: Ninety percent of the seventy societies publish their abstracts, with nearly half appearing in the society's journal. Seventy-seven percent of the societies supply meeting attendees with a copy of each abstract, and 43% make their abstracts available in an electronic format. Most of the journals surveyed allow meeting abstracts to be cited. Bibliographic access to these abstracts does not appear to be widespread. CONCLUSIONS: Meeting abstracts play an important role in the dissemination of scientific knowledge. Bibliographic access to meeting abstracts is very limited. The trend toward making meeting abstracts available via the Internet has the potential to give a broader audience access to the information they contain.
PMCID: PMC226328  PMID: 9549015
3.  Misrepresentation of Randomized Controlled Trials in Press Releases and News Coverage: A Cohort Study 
PLoS Medicine  2012;9(9):e1001308.
A study conducted by Amélie Yavchitz and colleagues examines the factors associated with “spin” (specific reporting strategies, intentional or unintentional, that emphasize the beneficial effect of treatments) in press releases of clinical trials.
Background
Previous studies indicate that in published reports, trial results can be distorted by the use of “spin” (specific reporting strategies, intentional or unintentional, emphasizing the beneficial effect of the experimental treatment). We aimed to (1) evaluate the presence of “spin” in press releases and associated media coverage; and (2) evaluate whether findings of randomized controlled trials (RCTs) based on press releases and media coverage are misinterpreted.
Methods and Findings
We systematically searched for all press releases indexed in the EurekAlert! database between December 2009 and March 2010. Of the 498 press releases retrieved and screened, we included press releases for all two-arm, parallel-group RCTs (n = 70). We obtained a copy of the scientific article to which the press release related and we systematically searched for related news items using Lexis Nexis.
“Spin,” defined as specific reporting strategies (intentional or unintentional) emphasizing the beneficial effect of the experimental treatment, was identified in 28 (40%) scientific article abstract conclusions and in 33 (47%) press releases. From bivariate and multivariable analysis assessing the journal type, funding source, sample size, type of treatment (drug or other), results of the primary outcomes (all nonstatistically significant versus other), author of the press release, and the presence of “spin” in the abstract conclusion, the only factor associated, with “spin” in the press release was “spin” in the article abstract conclusions (relative risk [RR] 5.6, [95% CI 2.8–11.1], p<0.001). Findings of RCTs based on press releases were overestimated for 19 (27%) reports. News items were identified for 41 RCTs; 21 (51%) were reported with “spin,” mainly the same type of “spin” as those identified in the press release and article abstract conclusion. Findings of RCTs based on the news item was overestimated for ten (24%) reports.
Conclusion
“Spin” was identified in about half of press releases and media coverage. In multivariable analysis, the main factor associated with “spin” in press releases was the presence of “spin” in the article abstract conclusion.
Editors' Summary
Background
The mass media play an important role in disseminating the results of medical research. Every day, news items in newspapers and magazines and on the television, radio, and internet provide the general public with information about the latest clinical studies. Such news items are written by journalists and are often based on information in “press releases.” These short communications, which are posted on online databases such as EurekAlert! and sent directly to journalists, are prepared by researchers or more often by the drug companies, funding bodies, or institutions supporting the clinical research and are designed to attract favorable media attention to newly published research results. Press releases provide journalists with the information they need to develop and publish a news story, including a link to the peer-reviewed journal (a scholarly periodical containing articles that have been judged by independent experts) in which the research results appear.
Why Was This Study Done?
In an ideal world, journal articles, press releases, and news stories would all accurately reflect the results of health research. Unfortunately, the findings of randomized controlled trials (RCTs—studies that compare the outcomes of patients randomly assigned to receive alternative interventions), which are the best way to evaluate new treatments, are sometimes distorted in peer-reviewed journals by the use of “spin”—reporting that emphasizes the beneficial effects of the experimental (new) treatment. For example, a journal article may interpret nonstatistically significant differences as showing the equivalence of two treatments although such results actually indicate a lack of evidence for the superiority of either treatment. “Spin” can distort the transposition of research into clinical practice and, when reproduced in the mass media, it can give patients unrealistic expectations about new treatments. It is important, therefore, to know where “spin” occurs and to understand the effects of that “spin”. In this study, the researchers evaluate the presence of “spin” in press releases and associated media coverage and analyze whether the interpretation of RCT results based on press releases and associated news items could lead to the misinterpretation of RCT results.
What Did the Researchers Do and Find?
The researchers identified 70 press releases indexed in EurekAlert! over a 4-month period that described two-arm, parallel-group RCTs. They used Lexis Nexis, a database of news reports from around the world, to identify associated news items for 41 of these press releases and then analyzed the press releases, news items, and abstracts of the scientific articles related to each press release for “spin”. Finally, they interpreted the results of the RCTs using each source of information independently. Nearly half the press releases and article abstract conclusions contained “spin” and, importantly, “spin” in the press releases was associated with “spin” in the article abstracts. The researchers overestimated the benefits of the experimental treatment from the press release as compared to the full-text peer-reviewed article for 27% of reports. Factors that were associated with this overestimation of treatment benefits included publication in a specialized journal and having “spin” in the press release. Of the news items related to press releases, half contained “spin”, usually of the same type as identified in the press release and article abstract. Finally, the researchers overestimated the benefit of the experimental treatment from the news item as compared to the full-text peer-reviewed article in 24% of cases.
What Do These Findings Mean?
These findings show that “spin” in press releases and news reports is related to the presence of “spin” in the abstract of peer-reviewed reports of RCTs and suggest that the interpretation of RCT results based solely on press releases or media coverage could distort the interpretation of research findings in a way that favors experimental treatments. This interpretation shift is probably related to the presence of “spin” in peer-reviewed article abstracts, press releases, and news items and may be partly responsible for a mismatch between the perceived and real beneficial effects of new treatments among the general public. Overall, these findings highlight the important role that journal reviewers and editors play in disseminating research findings. These individuals, the researchers conclude, have a responsibility to ensure that the conclusions reported in the abstracts of peer-reviewed articles are appropriate and do not over-interpret the results of clinical research.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001308.
The PLOS Hub for Clinical Trials, which collects PLOS journals relating to clinical trials, includes some other articles on “spin” in clinical trial reports
EurekAlert is an online free database for science press releases
The UK National Health Service Choices website includes Beyond the Headlines, a resource that provides an unbiased and evidence-based analysis of health stories that make the news for both the public and health professionals
The US-based organization HealthNewsReview, a project supported by the Foundation for Informed Medical Decision Making, also provides expert reviews of news stories
doi:10.1371/journal.pmed.1001308
PMCID: PMC3439420  PMID: 22984354
4.  A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment 
BMC Bioinformatics  2011;12:69.
Background
Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple section-based scheme assigns individual sentences in abstracts under sections such as Objective, Methods, Results and Conclusions. Some schemes of textual information structure have proved useful for biomedical text mining (BIO-TM) tasks (e.g. automatic summarization). However, user-centered evaluation in the context of real-life tasks has been lacking.
Methods
We take three schemes of different type and granularity - those based on section names, Argumentative Zones (AZ) and Core Scientific Concepts (CoreSC) - and evaluate their usefulness for a real-life task which focuses on biomedical abstracts: Cancer Risk Assessment (CRA). We annotate a corpus of CRA abstracts according to each scheme, develop classifiers for automatic identification of the schemes in abstracts, and evaluate both the manual and automatic classifications directly as well as in the context of CRA.
Results
Our results show that for each scheme, the majority of categories appear in abstracts, although two of the schemes (AZ and CoreSC) were developed originally for full journal articles. All the schemes can be identified in abstracts relatively reliably using machine learning. Moreover, when cancer risk assessors are presented with scheme annotated abstracts, they find relevant information significantly faster than when presented with unannotated abstracts, even when the annotations are produced using an automatic classifier. Interestingly, in this user-based evaluation the coarse-grained scheme based on section names proved nearly as useful for CRA as the finest-grained CoreSC scheme.
Conclusions
We have shown that existing schemes aimed at capturing information structure of scientific documents can be applied to biomedical abstracts and can be identified in them automatically with an accuracy which is high enough to benefit a real-life task in biomedicine.
doi:10.1186/1471-2105-12-69
PMCID: PMC3060841  PMID: 21385430
5.  Selection in Reported Epidemiological Risks: An Empirical Assessment 
PLoS Medicine  2007;4(3):e79.
Background
Epidemiological studies may be subject to selective reporting, but empirical evidence thereof is limited. We empirically evaluated the extent of selection of significant results and large effect sizes in a large sample of recent articles.
Methods and Findings
We evaluated 389 articles of epidemiological studies that reported, in their respective abstracts, at least one relative risk for a continuous risk factor in contrasts based on median, tertile, quartile, or quintile categorizations. We examined the proportion and correlates of reporting statistically significant and nonsignificant results in the abstract and whether the magnitude of the relative risks presented (coined to be consistently ≥1.00) differs depending on the type of contrast used for the risk factor. In 342 articles (87.9%), ≥1 statistically significant relative risk was reported in the abstract, while only 169 articles (43.4%) reported ≥1 statistically nonsignificant relative risk in the abstract. Reporting of statistically significant results was more common with structured abstracts, and was less common in US-based studies and in cancer outcomes. Among 50 randomly selected articles in which the full text was examined, a median of nine (interquartile range 5–16) statistically significant and six (interquartile range 3–16) statistically nonsignificant relative risks were presented (p = 0.25). Paradoxically, the smallest presented relative risks were based on the contrasts of extreme quintiles; on average, the relative risk magnitude was 1.41-, 1.42-, and 1.36-fold larger in contrasts of extreme quartiles, extreme tertiles, and above-versus-below median values, respectively (p < 0.001).
Conclusions
Published epidemiological investigations almost universally highlight significant associations between risk factors and outcomes. For continuous risk factors, investigators selectively present contrasts between more extreme groups, when relative risks are inherently lower.
An evaluation of published articles reporting epidemiological studies found that they almost universally highlight significant associations between risk factors and outcomes.
Editors' Summary
Background.
Medical and scientific researchers use statistical tests to try to work out whether their observations—for example, seeing a difference in some characteristic between two groups of people—might have occurred as a result of chance alone. Statistical tests cannot determine this for sure, rather they can only give a probability that the observations would have arisen by chance. When researchers have many different hypotheses, and carry out many statistical tests on the same set of data, they run the risk of concluding that there are real differences where in fact there are none. At the same time, it has long been known that scientific and medical researchers tend to pick out the findings on which to report in their papers. Findings that are more interesting, impressive, or statistically significant are more likely to be published. This is termed “publication bias” or “selective reporting bias.” Therefore, some people are concerned that the published scientific literature might contain many false-positive findings, i.e., findings that are not true but are simply the result of chance variation in the data. This would have a serious impact on the accuracy of the published scientific literature and would tend to overestimate the strength and direction of relationships being studied.
Why Was This Study Done?
Selective reporting bias has already been studied in detail in the area of randomized trials (studies where participants are randomly allocated to receive an intervention, e.g., a new drug, versus an alternative intervention or “comparator,” in order to understand the benefits or safety of the new intervention). These studies have shown that very many of the findings of trials are never published, and that statistically significant findings are more likely to be included in published papers than nonsignificant findings. However, much medical research is carried out that does not use randomized trial methods, either because that method is not useful to answer the question at hand or is unethical. Epidemiological research is often concerned with looking at links between risk factors and the development of disease, and this type of research would generally use observation rather than experiment to uncover connections. The researchers here were concerned that selective reporting bias might be just as much of a problem in epidemiological research as in randomized trials research, and wanted to study this specifically.
What Did the Researchers Do and Find?
In this investigation, searches were carried out of PubMed, a database of biomedical research studies, to extract epidemiological studies that were published between January 2004 and October 2005. The researchers wanted to specifically look at studies reporting the effect of continuous risk factors and their effect on health or disease outcomes (a continuous risk factor is something like age or glucose concentration in the blood, is a number, and can have any value on a sliding scale). Three hundred and eighty-nine original research studies were found, and the researchers pulled out from the abstracts and full text of these papers the relative risks that were reported along with the results of statistical tests for them. (Relative risk is the chance of getting an outcome, say disease, in one group as compared to another group.) The researchers found that nearly 90% of these studies had one or more statistically significant risks reported in the abstract, but only 43% reported one or more risks that were not statistically significant. When looking at all of the findings reported anywhere in the full text for 50 of these studies, the researchers saw that papers overall reported more statistically significant risks than nonsignificant risks. Finally, it seemed that in the set of papers studied here, the way in which statistical analyses were done produced a bias towards more extreme findings: for datasets showing small relative risks, papers were more likely to report a comparison between extreme subsets of the data so as to report larger relative risks.
What Do These Findings Mean?
These findings suggest that there is a tendency among epidemiology researchers to highlight statistically significant findings and to avoid highlighting nonsignificant findings in their research papers. This behavior may be a problem, because many of these significant findings could in future turn out to be “false positives.” At present, registers exist for researchers to describe ongoing clinical trials, and to set out the outcomes that they plan to analyze for those trials. These registers will go some way towards addressing some of the problems described here, but only for clinical trials research. Registers do not yet exist for epidemiological studies, and therefore it is important that researchers and readers are aware of and cautious about the problem of selective reporting in epidemiological research.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040079.
Wikipedia entry on publication bias (note: Wikipedia is an internet encyclopedia that anyone can edit)
The International Committee of Medical Journal Editors gives guidelines for submitting manuscripts to its member journals, and includes comments about registration of ongoing studies and the obligation to publish negative studies
ClinicalTrials.gov and the ISRCTN register are two registries of ongoing clinical trials
doi:10.1371/journal.pmed.0040079
PMCID: PMC1808481  PMID: 17341129
6.  The Scientific Conferences Organized During War Time (1992-1995) in Sarajevo 
Materia Socio-Medica  2011;23(4):238-248.
Author of this paper spent 1479 days in the siege of Sarajevo, during the period of war time in Bosnia and Herzegovina (B&H). This siege, lasting from 1992 to 1995 (e.g. Dayton Piece agreement was signed in November, 1995) represents the longest siege in the history of the world. Besides usual daily work, as the associate professor of Health education, Medical deontology and Medical informatics for the students of the Faculty of medicine, Faculty of dental medicine, Faculty of Pharmacy and Nursing college of University of Sarajevo, the author organized by himself and contributors, 10 scientific conferences in a sieged Sarajevo. All presented papers at those conferences are published in Proceedings abstract books, as the proof of continuing scientific work, in Sarajevo and other cities in B&H. Additionally, the author continued to publish, in that time, unique PubMed/MedLine indexed journal, - Medical Archives, (i.e. established in 1947) and, in 1993 formed a new journal named - “Acta Informatica Medica” (AIM) , as the Journal of the Bosnian Society of Medical informatics. Bosnian Society of Medical Informatics, thus became the first scientific association from Bosnia and Herzegovina, included in 1994, in the European Federation of Medical Informatics (EFMI) and the International Medical Informatics Assiciation (IMIA) , which was “miracle” from the besieged Sarajevo and war time result of aggression on Bosnia and Herzegovina. It should be noted that the importance of maintaining these academic gatherings, in the circumstances of war, was multifaceted. First of all, thanks to these meetings, the continuity of scientific meetings and activities in the besieged city of Sarajevo was not broken, as well as the continuity of scientific publication, which was crucial for the maintenance of the teaching staff at the university and, finally, in the expansion of the “scientific truth” about what happened in Sarajevo and B&H in these difficult times. All of this was critical to the “survival” of B&H and its people. Some of the published articles, especially in the Medical Archives journal, which even in difficult war conditions did not break the continuity of its publication, and then it was the only scientific journal indexed in B&H, having been consequently cited in the major biomedical data bases in the world. Many scientists abroad have had the opportunity to learn about some of the wonders of Sarajevo “war medicine”, thanks to this journal. Finally, despite the fact that it is another way of expressing its resistance to the aggression on B&H, the organized symposia in the war represented the continuity of the scientific research activities. Bosnia and Herzegovina and Sarajevo under siege, in this way, kept in touch with the civilized world and modern achievements, despite the fact that they were victims of medieval barbarism. In addition, these meetings sent a powerful message to the world about the willingness to register and systematize all the war experiences, especially those related to medicine and medical practice, in terms of what Europe has not known, since the Second World War. Partially, we succeeded in that. The total number of 286 presentations were presented in seven war Conferences, as quantitative and qualitative contribution to the scientific activities, despite the inhuman conditions, in which these articles emerged. These presentations and Conferences testify to the enthusiasm of B&H community and academic institutions that have collaborated with it. Authors and co-authors presented the “war” articles that deserve to be mentioned in the monograph “1479 days of the siege of Sarajevo”. Unfortunately, many of these brave authors are not alive and cannot read this. The task for us remains to remember them by their own good. Old Persian proverb says; “The event which is not recorded is as like it had never happened”. Sapienti sat.
doi:10.5455/msm.2011.23.238-248
PMCID: PMC3633541  PMID: 23678305
Bosnia and Herzegovina; siege; scientific meetings during wartime.
7.  Don’t forget the posters! Quality and content variables associated with accepted abstracts at a national trauma meeting 
BACKGROUND
As a primary venue for presenting research results, abstracts selected for presentation at national meetings should be of the highest scientific merit and research quality. It is uncertain to what degree this is achieved as the methodological quality of abstracts submitted to national surgical meetings has not been previously described. The objective of this study was to evaluate abstracts presented at a leading trauma meeting for methodological quality.
METHODS
All abstracts accepted for the 2009 American Association for the Surgery of Trauma meeting were reviewed and scored for methodological quality based on 10 criteria (scores, 0–10; 10 being the highest). Criteria were based on nationally published methodology guidelines. Two independent reviewers who were blinded to institution, region, and author reviewed each abstract.
RESULTS
A total of 187 abstracts were accepted for presentation (67 oral and 120 posters). The most frequent clinical topics were shock/transfusion (23%), abdomen (12%), and nervous system (11%). Shock/transfusion abstracts were more common in the oral presentations (31% vs. 19%; p =0.06). Abstracts from the northeast and south regions were the most common in both oral (26% and 29%) and posters (25% and 24%). Basic science accounted for 12% of accepted studies, while 51% were clinical and 28% were health services/outcomes. Only 8% of abstracts presented randomized data and only 11% reported null findings. Overall abstract scores ranged from 3 to 10 (median, 7; mean, 7.4). Abstracts selected for poster presentation had an overall higher score than those selected for oral presentation (7.4 ±1.7 vs. 6.8 ±1.7; p =0.02).
CONCLUSION
Although oral presentations traditionally receive the most attention and interest, the methodological quality of abstracts accepted for poster presentation equals (and sometimes exceeds) that of oral abstracts. Attendees of these national meetings should reconsider their time spent in viewing and visiting these poster sessions as with the oral presentations. In light of our findings, we highly encourage that all members and guests attend the American Association for the Surgery of Trauma Poster Rounds at each year’s scientific assembly.
doi:10.1097/TA.0b013e3182479c9b
PMCID: PMC4198948  PMID: 22673278
Trauma; abstract; meeting; quality; methodology
8.  Searching for Animal Sentience: A Systematic Review of the Scientific Literature 
Simple Summary
The emotional lives of animals is often doubted and questioned. Due to the subjective nature of animal emotions, many think that they are out of the reach of scientific measurement. In this systematic review, of over two decades of scientific literature, we found that this was not actually the case. By using a list of keywords, formed of both positive and negative emotions, and terminology relating to animal sentience, we reviewed the scientific literature. We found that the subjective lives of animals are not only a vital part of human medical research but are regularly measured and studied with scientific rigor.
Abstract
Knowledge of animal sentience is fundamental to many disciplines and imperative to the animal welfare movement. In this review, we examined what is being explored and discussed, regarding animal sentience, within the scientific literature. Rather than attempting to extract meaning from the many complex and abstract definitions of animal sentience, we searched over two decades of scientific literature using a peer-reviewed list of 174 keywords. The list consisted of human emotions, terminology associated with animal sentience, and traits often thought to be indicative of subjective states. We discovered that very little was actually being explored, and instead there was already much agreement about what animals can feel. Why then is there so much scepticism surrounding the science of animal sentience? Sentience refers to the subjective states of animals, and so is often thought to be impossible to measure objectively. However, when we consider that much of the research found to accept and utilise animal sentience is performed for the development of human drugs and treatment, it appears that measuring sentience is, after all, not quite as impossible as was previously thought. In this paper, we explored what has been published on animal sentience in the scientific literature and where the gaps in research lie. We drew conclusions on the implications for animal welfare science and argued for the importance of addressing these gaps in our knowledge. We found that there is a need for more research on positive emotional states in animals, and that there is still much to learn about taxa such as invertebrates. Such information will not only be useful in supporting and initiating legislative amendments but will help to increase understanding, and potentially positive actions and attitudes towards animals.
doi:10.3390/ani3030882
PMCID: PMC4494450  PMID: 26479539
animal sentience; animal welfare; attitudes; behaviour; cognitive ethology; consciousness; emotions; subjective states
9.  Preparing and presenting effective abstracts and posters in psychiatry 
Presenting an abstract and a poster gives scientists from all fields, including psychiatry, an important opportunity to introduce their research to others. Researchers and mental health professionals at all levels of career development can use several media resources to assist them with the technical aspects of preparing an abstract or a poster. This article will focus on major principles associated with preparing and presenting an abstract and a poster at a scientific meeting. A literature search using NIH PubMed was conducted to identify peer and non-peer-reviewed articles that provide methods for effective abstract and poster presentation for the period of 1966 to June 2014. First, we review the purpose and relative importance of abstracts and posters in academic settings. Next, we describe the qualities of an effective abstract and poster and common pitfalls that may occur. Finally, we present a systematic approach to preparing and presenting an abstract and a poster in a scientific setting. Several sources consistently suggest that readability, organization, and succinctness are qualities that make an effective and successful abstract and poster. Mental health professionals in all stages of their career development may benefit from following these guidelines in presenting their scientific work.
doi:10.1007/s40596-014-0190-z
PMCID: PMC4268042  PMID: 25085499
poster; presentation; academic; psychiatry; career development
10.  The Chilling Effect: How Do Researchers React to Controversy? 
PLoS Medicine  2008;5(11):e222.
Background
Can political controversy have a “chilling effect” on the production of new science? This is a timely concern, given how often American politicians are accused of undermining science for political purposes. Yet little is known about how scientists react to these kinds of controversies.
Methods and Findings
Drawing on interview (n = 30) and survey data (n = 82), this study examines the reactions of scientists whose National Institutes of Health (NIH)-funded grants were implicated in a highly publicized political controversy. Critics charged that these grants were “a waste of taxpayer money.” The NIH defended each grant and no funding was rescinded. Nevertheless, this study finds that many of the scientists whose grants were criticized now engage in self-censorship. About half of the sample said that they now remove potentially controversial words from their grant and a quarter reported eliminating entire topics from their research agendas. Four researchers reportedly chose to move into more secure positions entirely, either outside academia or in jobs that guaranteed salaries. About 10% of the group reported that this controversy strengthened their commitment to complete their research and disseminate it widely.
Conclusions
These findings provide evidence that political controversies can shape what scientists choose to study. Debates about the politics of science usually focus on the direct suppression, distortion, and manipulation of scientific results. This study suggests that scholars must also examine how scientists may self-censor in response to political events.
Drawing on interview and survey data, Joanna Kempner's study finds that political controversies shape what many scientists choose not to study.
Editors' Summary
Background.
Scientific research is an expensive business and, inevitably, the organizations that fund this research—governments, charities, and industry—play an important role in determining the directions that this research takes. Funding bodies can have both positive and negative effects on the acquisition of scientific knowledge. They can pump money into topical areas such as the human genome project. Alternatively, by withholding funding, they can discourage some types of research. So, for example, US federal funds cannot be used to support many aspects of human stem cell research. “Self-censoring” by scientists can also have a negative effect on scientific progress. That is, some scientists may decide to avoid areas of research in which there are many regulatory requirements, political pressure, or in which there is substantial pressure from advocacy groups. A good example of this last type of self-censoring is the withdrawal of many scientists from research that involves certain animal models, like primates, because of animal rights activists.
Why Was This Study Done?
Some people think that political controversy might also encourage scientists to avoid some areas of scientific inquiry, but no studies have formally investigated this possibility. Could political arguments about the value of certain types of research influence the questions that scientists pursue? An argument of this sort occurred in the US in 2003 when Patrick Toomey, who was then a Republican Congressional Representative, argued that National Institutes of Health (NIH) grants supporting research into certain aspects of sexual behavior were “much less worthy of taxpayer funding” than research on “devastating diseases,” and proposed an amendment to the 2004 NIH appropriations bill (which regulates the research funded by NIH). The Amendment was rejected, but more than 200 NIH-funded grants, most of which examined behaviors that affect the spread of HIV/AIDS, were internally reviewed later that year; NIH defended each grant, so none were curtailed. In this study, Joanna Kempner investigates how the scientists whose US federal grants were targeted in this clash between politics and science responded to the political controversy.
What Did the Researchers Do and Find?
Kempner interviewed 30 of the 162 principal investigators (PIs) whose grants were reviewed. She asked them to describe their research, the grants that were reviewed, and their experience with NIH before, during, and after the controversy. She also asked them whether this experience had changed their research practice. She then used the information from these interviews to design a survey that she sent to all the PIs whose grants had been reviewed; 82 responded. About half of the scientists interviewed and/or surveyed reported that they now remove “red flag” words (for example, “AIDS” and “homosexual”) from the titles and abstracts of their grant applications. About one-fourth of the respondents no longer included controversial topics (for example, “abortion” and “emergency contraception”) in their research agendas, and four researchers had made major career changes as a result of the controversy. Finally, about 10% of respondents said that their experience had strengthened their commitment to see their research completed and its results published although even many of these scientists also engaged in some self-censorship.
What Do These Findings Mean?
These findings show that, even though no funding was withdrawn, self-censoring is now common among the scientists whose grants were targeted during this particular political controversy. Because this study included researchers in only one area of health research, its findings may not be generalizable to other areas of research. Furthermore, because only half of the PIs involved in the controversy responded to the survey, these findings may be affected by selection bias. That is, the scientists most anxious about the effects of political controversy on their research funding (and thus more likely to engage in self-censorship) may not have responded. Nevertheless, these findings suggest that the political environment might have a powerful effect on self-censorship by scientists and might dissuade some scientists from embarking on research projects that they would otherwise have pursued. Further research into what Kempner calls the “chilling effect” of political controversy on scientific research is now needed to ensure that a healthy balance can be struck between political involvement in scientific decision making and scientific progress.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050222.
The Consortium of Social Science Associations, an advocacy organization that provides a bridge between the academic research community and Washington policymakers, has more information about the political controversy initiated by Patrick Toomey
Some of Kempner's previous research on self-censorship by scientists is described in a 2005 National Geographic news article
doi:10.1371/journal.pmed.0050222
PMCID: PMC2586361  PMID: 19018657
11.  Study of the comprehension of the scientific method by members of a university health research laboratory 
In Brazil, scientific research is carried out mainly at universities, where professors coordinate research projects with the active participation of undergraduate and graduate students. However, there is no formal program for the teaching/learning of the scientific method. The objective of the present study was to evaluate the comprehension of the scientific method by students of health sciences who participate in scientific projects in an academic research laboratory. An observational descriptive cross-sectional study was conducted using Edgar Morin complexity as theoretical reference. In a semi-structured interview, students were asked to solve an abstract logical puzzle - TanGram. The collected data were analyzed using the hermeneutic-dialectic analysis method proposed by Minayo and discussed in terms of the theoretical reference of complexity. The students' concept of the scientific method is limited to participation in projects, stressing the execution of practical procedures as opposed to scientific thinking. The solving of the TanGram puzzle revealed that the students had difficulties in understanding questions and activities focused on subjects and their processes. Objective answers, even when dealing with personal issues, were also reflected on the students' opinions about the characteristics of a successful researcher. Students' difficulties concerning these issues may affect their scientific performance and result in poorly designed experiments. This is a preliminary study that should be extended to other centers of scientific research.
doi:10.1590/S0100-879X2012007500002
PMCID: PMC3854260  PMID: 22249427
Scientific method; Complexity; Academic scientific research
12.  Clinical pancreatic disorder I: Acute pancreatitis 
The Annual American Pancreas Club is an important event for communicating around clinical pancreatic disorders, just as the European, Japanese, Indian, and the International Pancreatic association. Even though the meeting is only 1½ day there were 169 different abstracts and a “How do I do it session.” Among all these abstracts on the pancreas there are some real pearls, but they are almost always well hidden, never highlighted – all abstracts are similarly presented – and will too soon be forgotten. The present filing of the abstracts is one way (not the way) to get the pancreatic abstracts a little more read and a little more remembered – and perhaps a little more cited. It should also be understood that most of the abstracts are short summaries of hundreds of working hours (evenings, nights, weekends, holidays, you name them …) in the laboratory or in the clinic, often combined with blood, sweat and tears. The authors should be shown at least some respect, and their abstracts should not only be thought of as “just another little abstract” – and the best respect they can be shown are that they will be remembered to be another brick in our scientific wall.
Now the pancreatic abstracts of American Pancreas Club 2011 are gathered and filed with the aim to give them a larger audience than they have had in their original abstract book. However, it is obvious that most of clinical fellows do not have time to read all the abstracts. For them I have made a “clinical highlight section” of 10 percent of all the pancreatic abstracts. If someone else should have done some collection of abstract, there should probably have been other selections, but as this is not the case, the editor's choices are the highlighted ones.
The article as series I of clinical highlight section is present, and more series will be present in the following issues. If readers will remember some of the abstracts better after reading this “abstract of abstracts”, it was worth the efforts – and without efforts there will be little progress.
doi:10.4297/najms.2011.3316
PMCID: PMC3336879  PMID: 22555122
Acute pancreatitis; accurate classification; clinical highlight; American pancreas club; international pancreatic association
13.  Analysis of full-text publication and publishing predictors of abstracts presented at an Italian public health meeting (2005–2007) 
BMC Research Notes  2015;8:492.
Background
In Public Health, a thorough review of abstract quality evaluations and the publication history of studies presented at scientific meetings has never been conducted. To analyse the long-term outcome of quality abstracts submitted to conferences of Italian Society of Hygiene and Public Health (SItI) from 2005 to 2007, we conducted a second analysis of previously published material aiming to estimate full-text publication rate of high quality abstract presented at Italian public health meetings, and to identify predictors of full-text publication.
Methods
The search was undertaken through scientific databases and search engines and through the web sites of the major Italian journals of Public Health. For each publication confirmed as a full text paper, the journal name, impact factor, year of publication, gender of the first author, type of study design, characteristics of the results and sample size were collected.
Results
The overall publication rate of the abstracts presented is 23.5 %; most of the papers were published in Public Health journals (average impact factor: 3.007). Non universitary affiliation had resulted in a lower probability of publication, while some of the Conference topics had predisposed the studies to an increased likelihood of publication as well as poster form presentation.
Conclusions
The method presented in this study provides a good framework for the evaluation of the scientific evidence. The findings achieved should be taken into consideration by the Scientific Societies during the contributions selection phase, with the aim of achieving a continuous improvement of work quality. In the future, it would be interesting to survey the abstract authors to identify reasons for unpublished data.
doi:10.1186/s13104-015-1463-7
PMCID: PMC4587780  PMID: 26415871
Scientific Societies; Publications; Conferences and congresses
14.  Is gastroenterology research in decline? A comparison of abstract publication rates from The British Society of Gastroenterology meetings between 1995 and 2005 
F1000Research  2013;2:59.
Background: Reports have suggested that academic medicine may be in decline within the UK. Further evidence suggests that rates of subsequent full publication of abstracts presented at major scientific meetings are low and may be declining. We have compared the publication rates of abstracts presented at meetings of the British Society of Gastroenterology (BSG) between 1995 and 2005 and examined factors associated with full paper publication. 
Methods: Abstracts presented at BSG meetings in 1995 and 2005 were assessed by cross-referencing with multiple databases. Abstract characteristics associated with publication were analysed.
Results: There were no differences in overall publication rates, impact factors or time to publication between 1995 and 2005. Overall, basic-science abstracts were twice as likely to achieve full publication than non-basic science. There was a significant fall in the publication rates for case series and audits, and significantly increased rates for fundamental/basic-science abstracts over the study period. There were non-significant increases in publication rates for controlled trials and systematic reviews. In general, publication rates for all predominantly clinically orientated abstracts reduced between the two periods with the most notable fall occurring in nutrition. 
Conclusions: There was no evidence of a decline in overall abstract publication rates between 1995 and 2005. There seemed to be trend for increased publication rates of abstracts using perceived high-quality study methodologies with a corresponding decrease in those with lower quality methods. The proportion of basic-science abstracts is likely to be a determinant of overall full publication rates following scientific meetings.
doi:10.12688/f1000research.2-59.v1
PMCID: PMC3752733  PMID: 24327877
15.  Are Men More Likely than Women To Commit Scientific Misconduct? Maybe, Maybe Not 
mBio  2013;4(2):e00156-13.
ABSTRACT
In their study published in January 2013 in mBio, Fang et al. reviewed records from the Office of Research Integrity (ORI) and found more cases of scientific misconduct committed by men than women, particularly by faculty (F. C. Fang, J. W. Bennett, and A. Casadevall, mBio 4:1–3, 2013). Powerful social norms shape the way men and women behave, and implicit gender schemas can lead to different evaluation standards for men and women for tasks stereotypically linked to one gender. It is possible that norms for acceptable male and female behavior could lead to a lower threshold for men than women to engage in the risky behavior of scientific misconduct. It is also possible that women and men commit scientific fraud at the same rate but that, because crime is a male-gendered domain, evaluators require more proof of the criminal “competence” of women for an investigation to rise to the level of an ORI case or that female gender norms for likeability and a lower apology threshold more often prevent escalation of women’s fraud beyond a local level. Male scientists also have more opportunity to commit fraud than female scientists because they receive more NIH research funding—a finding that may also be influenced by gender schemas. We cannot conclude from the ORI data that men are more likely than women to risk the consequences of committing scientific misconduct simply because risk taking aligns with male gender stereotypes. Neither can we conclude that because men are more likely than women to commit fraud in other contexts, men are also more likely than women to commit scientific fraud. We can conclude, however, that scientific misconduct, regardless of who commits it, diminishes all who contribute to the scientific enterprise.
doi:10.1128/mBio.00156-13
PMCID: PMC3622921  PMID: 23532977
16.  EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts 
BMC Bioinformatics  2009;10(Suppl 8):S2.
Background
A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes' databases are currently available, scientific literature still remains at large for up-to-date source of learning the effects of a mutation on an enzyme. However, going through vast amounts of scientific documents to extract the information on desired mutation has always been a time consuming process. In this paper, therefore, we describe an unique method, termed as EnzyMiner, which automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability and/or the activity of a given enzyme.
Results
We present an automated system which identifies the abstracts that contain an amino-acid-level mutation and then classifies them according to the mutation's effect on the enzyme. In the case of mutation identification, MuGeX, an automated mutation-gene extraction system has an accuracy of 93.1% with a 91.5 F-measure. For impact analysis, document classification is performed to identify the abstracts that contain a change in enzyme's stability or activity resulting from the mutation. The system was trained on lipases and tested on amylases with an accuracy of 85%.
Conclusion
EnzyMiner identifies the abstracts that contain a protein mutation for a given enzyme and checks whether the abstract is related to a disease with the help of information extraction and machine learning techniques. For disease related abstracts, the mutation list and direct links to the abstracts are retrieved from the system and displayed on the Web. For those abstracts that are related to non-diseases, in addition to having the mutation list, the abstracts are also categorized into two groups. These two groups determine whether the mutation has an effect on the enzyme's stability or functionality followed by displaying these on the web.
doi:10.1186/1471-2105-10-S8-S2
PMCID: PMC2745584  PMID: 19758466
17.  Publication rates of abstracts presented at the 2007 and 2010 Canadian Association of Radiation Oncology meetings 
Current Oncology  2014;21(2):e250-e254.
Background
We set out to determine the rate, time-trend, and defining factors associated with publication of abstracts presented at two annual scientific meetings of the Canadian Association of Radiation Oncology (caro).
Methods
All abstracts accepted for oral presentation in 2007 and 2010 were obtained from the caro program archives and searched using the PubMed database. Variables in the dataset included the year of presentation at caro and of publication in a scientific journal, time to publication (in months), publishing journal, impact factor of publishing journal, abstract research type (clinical, technical, or basic science) and disease site, country of origin, and university of the first author.
Results
Overall, 88 of 172 abstracts from the 2007 (n = 102) and 2010 (n = 70) caro meetings were published in peer-reviewed journals (publication rate: 51.2%). Mean time to publication was 18.5 months. Among research types, clinical research (62.5%) and, among disease sites, prostate cancer (40.4%) were most likely to be published. Of all the abstracts, 50.1% were contributed by only 2 universities, a proportion that resembles the overall abstract publication rate of 51.2%. The conversion rate for those 2 universities (51.1%) is very similar to that for all abstracts presented at the two meetings.
Conclusions
Half the abstracts presented at the 2007 and 2010 caro meetings were ultimately published in journals indexed in PubMed by about 1.5 years after presentation. Half the abstracts and publications came from just 2 universities; more must to be done to close the gap.
doi:10.3747/co.21.1764
PMCID: PMC3997458  PMID: 24764710
Abstracts; annual meetings; Canada; conversion rate; radiation oncology
18.  Publication outcomes of the abstracts presented at the 2011 European Congress on Osteoporosis, Osteoarthritis and Musculo-Skeletal Diseases (ECCEO-IOF11) 
Summary
The publication outcomes of the abstracts presented during the ECCEO-IOF 2011 reflect a high research productivity, support the robustness of the selection process conducted by the Scientific Advisory Committee and suggest that IOF-ESCEO WCO is successful in its mission to promote and disseminate research.
Background and Objective
The European (now World) Congress on Osteoporosis, Osteoarthritis and Musculo-Skeletal Diseases (IOF-ESCEO WCO, formerly ECCEO-IOF) is the largest worldwide event fully dedicated to the clinical, epidemiological, translational and economic aspects of bone, joint and muscle diseases. The role of the Scientific Advisory Committee is to select abstracts for oral communication or poster presentation based on a short summary of the research. The aim of the present survey was to determine the publication rate in international peer reviewed journals of abstracts accepted at the IOF-ESCEO WCO 2011 Meeting (formerly ECCEO-IOF11), the relationship, if any, between the presentation format of the abstract and its subsequent full publication and the impact factor of the journal in which research was published.
Results
Of 619 abstracts accepted at the 2011 ECCEO-IOF11 annual meeting, 45 were accepted for oral communication and 574 accepted for poster presentation. In the subsequent 3 years (2011–2014), 191 abstracts were published as a full-length manuscript (30.9 %). The publication rate was significantly higher for oral communications (75.6 %) than for poster presentations (27.4 %; p < 0.0001). Publications derived from oral communications were published in journals with a higher impact factor (8.3 ± 10.1) than those arising from poster presentations (4.0 ± 2.3; p < 0.0001), but there was no difference in the time to publication (OC 16.3 [IQR 8.4–23.3] months vs PP 11.3 [IQR 5.3–21.4]; p = 0.14).
Conclusion
These results indicate a high research productivity and an appropriate selection of oral communication by the Scientific Advisory Committee of ESCEO-IOF.
doi:10.1007/s11657-015-0216-5
PMCID: PMC4412599  PMID: 25910868
Publication outcomes; ECCEO-IOF Meeting; Oral communication; Poster; Presentation format
19.  PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts 
Nucleic Acids Research  2005;33(Web Server issue):W774-W778.
Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder () is a publicly available web tool designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine.
doi:10.1093/nar/gki429
PMCID: PMC1160190  PMID: 15980583
20.  Does direction of results of abstracts submitted to scientific conferences on drug addiction predict full publication? 
Background
Data from scientific literature show that about 63% of abstracts presented at biomedical conferences will be published in full. Some studies have indicated that full publication is associated with the direction of results (publication bias). No study has looked into the occurrence of publication bias in the field of addiction.
Objectives
To investigate whether the significance or direction of results of abstracts presented at the major international scientific conference on addiction is associated with full publication
Methods
The conference proceedings of the US Annual Meeting of the College on Problems of Drug Dependence (CPDD), were handsearched for abstracts of randomized controlled trials and controlled clinical trials that evaluated interventions for prevention, rehabilitation and treatment of drug addiction in humans (years searched 1993–2002). Data regarding the study designs and outcomes reported were extracted. Subsequent publication in peer reviewed journals was searched in MEDLINE and EMBASE databases, as of March 2006.
Results
Out of 5919 abstracts presented, 581 met the inclusion criteria; 359 (62%) conference abstracts had been published in a broad variety of peer reviewed journals (average time of publication 2.6 years, SD +/- 1.78). The proportion of published studies was almost the same for randomized controlled trials (62.4%) and controlled clinical trials (59.5%) while studies that reported positive results were significantly more likely to be published (74.5%) than those that did not report statistical results (60.9%.), negative or null results (47.1%) and no results (38.6%), Abstracts reporting positive results had a significantly higher probability of being published in full, while abstracts reporting null or negative results were half as likely to be published compared with positive ones (HR = 0.48; 95%CI 0.30–0.74)
Conclusion
Clinical trials were the minority of abstracts presented at the CPDD; we found evidence of possible publication bias in the field of addiction, with negative or null results having half the likelihood of being published than positive ones.
doi:10.1186/1471-2288-9-23
PMCID: PMC2674061  PMID: 19356245
21.  Something going on in Milan: a review of the 4th International PhD Student Cancer Conference 
ecancermedicalscience  2010;4:198.
The 4th International PhD Student Cancer Conference was held at the IFOM-IEO-Campus in Milan from 19–21 May 2010 http://www.semm.it/events_researchPast.php
The Conference covered many topics related to cancer, from basic biology to clinical aspects of the disease. All attendees presented their research, by either giving a talk or presenting a poster. This conference is an opportunity to introduce PhD students to top cancer research institutes across Europe.
The core participanting institutes included: European School of Molecular Medicine (SEMM)—IFOM-IEO Campus, MilanBeatson Institute for Cancer Research (BICR), GlasgowCambridge Research Institute (CRI), Cambridge, UKMRC Gray Institute of Radiation Biology (GIROB), OxfordLondon Research Institute (LRI), LondonPaterson Institute for Cancer Research (PICR), ManchesterThe Netherlands Cancer Institute (NKI), Amsterdam
‘You organizers have crushed all my prejudices towards Italians. Congratulations, I enjoyed the conference immensely!’ Even if it might have sounded like rudeness for sure this was supposed to be a genuine compliment (at least, that’s how we took it), also considering that it was told by a guy who himself was the fusion of two usually antithetical concepts: fashion style and English nationality.
The year 2010 has marked an important event for Italian research in the international scientific panorama: the European School of Molecular Medicine (SEMM) had the honour to host the 4th International PhD Student Cancer Conference, which was held from 19–21 May 2010 at the IFOM-IEO-Campus (http://www.semm.it/events_researchPast.php) in Milan.
The conference was attended by more than one hundred students, coming from a selection of cutting edge European institutes devoted to cancer research. The rationale behind it is the promotion of cooperation among young scientists across Europe to debate about science and to exchange ideas and experiences. But that is not all, it is also designed for PhD students to get in touch with other prestigious research centres and to create connections for future post docs or job experiences. And last but not least, it is a golden chance for penniless PhD students to spend a couple of extra days visiting a foreign country (this motivation will of course never be voiced to supervisors).
The network of participating institutes has a three-nation core, made up of the Netherlands Cancer Institute, the Italian European School of Molecular Medicine (SEMM) and five UK Cancer Research Institutes (The London Research Institute, The Cambridge Research Institute, The Beatson Institute for Cancer Research in Glasgow, The Patterson Institute for Cancer Research in Manchester and the MRC Gray Institute for Radiation Oncology and Biology in Oxford).
The conference is hosted and organised every year by one of the core institutes; the first was in Cambridge in 2007, Amsterdam in 2008 and London in 2009, this year was the turn of Milan.
In addition to the core institutes, PhD students from several other high-profile institutes are invited to attend the conference. This year participants applied from the Spanish National Cancer Centre (CNIO, Madrid), the German Cancer Research Centre (DKFZ, Heidelberg), the European Molecular Biology Labs (EMBL, Heidelberg) and the San Raffaele Institute (HSR, Milan). Moreover four ‘special guests’ from the National Centre for Biological Sciences of Bangalore (India) attended the conference in Milan. This represents a first step in widening the horizons beyond Europe into a global worldwide network of talented PhD students in life sciences.
The conference spread over two and a half days (Wednesday 19th to Friday 21st May) and touched on a broad spectrum of topics: from basic biology to development, from cancer therapies to modelling and top-down new generation global approaches. The final selection of presentations has been a tough task for us organisers (Chiara Segré, Federica Castellucci, Francesca Milanesi, Gianluca Varetti and Gian Maria Sarra Ferraris), due to the high scientific level of the abstracts submitted. In the end, 26 top students were chosen to give a 15-min oral presentation in one of eight sessions: Development & Differentiation, Cell Migration, Immunology & Cancer, Modelling & Large Scale approaches, Genome Instability, Signal Transduction, Cancer Genetics & Drug Resistance, Stem Cells in Biology and Cancer.
The scientific programme was further enriched by two scientific special sessions, held by Professor Pier Paolo di Fiore and Dr Giuseppe Testa, Principal Investigators at the IFOM-IEO-Campus and by a bioethical round table on human embryonic stem cell research moderated by Silvia Camporesi, a senior PhD student in the SEMM PhD Programme ‘Foundation of Life Science and their Bioethical Consequences’.
On top of everything, we had the pleasure of inviting, as keynote speakers, two leading European scientists in the fields of cancer invasion and biology of stem cells, respectively: Dr Peter Friedl from The Nijmegen Centre for Molecular Life (The Netherlands) and Professor Andreas Trumpp from The Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Heidelberg).
All the student talks have distinguished themselves for the impressive quality of the science; an encouraging evidence of the high profile level of research carried out in Europe. It would be beyond the purposes of this report to summarise all 26 talks, which touched many different and specific topics. For further information, the Conference Abstract book with all the scientific content is available on the conference Web site (http://www.semm.it/events_researchPast.php). In what follows, the special sessions and the keynote lectures will be discussed in detail.
doi:10.3332/ecancer.2010.198
PMCID: PMC3234021  PMID: 22276043
22.  When Ethics Constrains Clinical Research: Trial Design of Control Arms in “Greater Than Minimal Risk” Pediatric Trials 
Human Gene Therapy  2011;22(9):1121-1127.
Abstract
For more than three decades clinical research in the United States has been explicitly guided by the idea that ethical considerations must be central to research design and practice. In spite of the centrality of this idea, attempting to balance the sometimes conflicting values of advancing scientific knowledge and protecting human subjects continues to pose challenges. Possible conflicts between the standards of scientific research and those of ethics are particularly salient in relation to trial design. Specifically, the choice of a control arm is an aspect of trial design in which ethical and scientific issues are deeply entwined. Although ethical quandaries related to the choice of control arms may arise when conducting any type of clinical trials, they are conspicuous in early phase gene transfer trials that involve highly novel approaches and surgical procedures and have children as the research subjects. Because of children's and their parents' vulnerabilities, in trials that investigate therapies for fatal, rare diseases affecting minors, the scientific and ethical concerns related to choosing appropriate controls are particularly significant. In this paper we use direct gene transfer to the central nervous system to treat late infantile neuronal ceroid lipofuscinosis to illustrate some of these ethical issues and explore possible solutions to real and apparent conflicts between scientific and ethical considerations.
In this article, de Melo-Martín and colleagues discuss the real and apparent conflicts between scientific and ethical considerations surrounding the choice of controls in clinical trials for rare and fatal diseases affecting children.
doi:10.1089/hum.2010.230
PMCID: PMC3177948  PMID: 21446781
23.  Automated Cognome Construction and Semi-automated Hypothesis Generation 
Journal of Neuroscience Methods  2012;208(1):92-100.
Modern neuroscientific research stands on the shoulders of countless giants. PubMed alone contains more than 21 million peer-reviewed articles with 40–50,000 more published every month. Understanding the human brain, cognition, and disease will require integrating facts from dozens of scientific fields spread amongst millions of studies locked away in static documents, making any such integration daunting, at best. The future of scientific progress will be aided by bridging the gap between the millions of published research articles and modern databases such as the Allen Brain Atlas (ABA). To that end, we have analyzed the text of over 3.5 million scientific abstracts to find associations between neuroscientific concepts. From the literature alone, we show that we can blindly and algorithmically extract a “cognome”: relationships between brain structure, function, and disease. We demonstrate the potential of data-mining and cross-platform data-integration with the ABA by introducing two methods for semiautomated hypothesis generation. By analyzing statistical “holes” and discrepancies in the literature we can find understudied or overlooked research paths. That is, we have added a layer of semi-automation to a part of the scientific process itself. This is an important step toward fundamentally incorporating data-mining algorithms into the scientific method in a manner that is generalizable to any scientific or medical field.
doi:10.1016/j.jneumeth.2012.04.019
PMCID: PMC3376233  PMID: 22584238
24.  Sentence retrieval for abstracts of randomized controlled trials 
Background
The practice of evidence-based medicine (EBM) requires clinicians to integrate their expertise with the latest scientific research. But this is becoming increasingly difficult with the growing numbers of published articles. There is a clear need for better tools to improve clinician's ability to search the primary literature. Randomized clinical trials (RCTs) are the most reliable source of evidence documenting the efficacy of treatment options. This paper describes the retrieval of key sentences from abstracts of RCTs as a step towards helping users find relevant facts about the experimental design of clinical studies.
Method
Using Conditional Random Fields (CRFs), a popular and successful method for natural language processing problems, sentences referring to Intervention, Participants and Outcome Measures are automatically categorized. This is done by extending a previous approach for labeling sentences in an abstract for general categories associated with scientific argumentation or rhetorical roles: Aim, Method, Results and Conclusion. Methods are tested on several corpora of RCT abstracts. First structured abstracts with headings specifically indicating Intervention, Participant and Outcome Measures are used. Also a manually annotated corpus of structured and unstructured abstracts is prepared for testing a classifier that identifies sentences belonging to each category.
Results
Using CRFs, sentences can be labeled for the four rhetorical roles with F-scores from 0.93–0.98. This outperforms the use of Support Vector Machines. Furthermore, sentences can be automatically labeled for Intervention, Participant and Outcome Measures, in unstructured and structured abstracts where the section headings do not specifically indicate these three topics. F-scores of up to 0.83 and 0.84 are obtained for Intervention and Outcome Measure sentences.
Conclusion
Results indicate that some of the methodological elements of RCTs are identifiable at the sentence level in both structured and unstructured abstract reports. This is promising in that sentences labeled automatically could potentially form concise summaries, assist in information retrieval and finer-grained extraction.
doi:10.1186/1472-6947-9-10
PMCID: PMC2657779  PMID: 19208256
25.  Publication Rate of Abstracts Presented at the Shoulder and Elbow Session of the American Academy of Orthopaedic Surgery 
Many shoulder and elbow abstracts presented at the American Academy of Orthopaedic Surgeons (AAOS) annual meeting are cited in the orthopaedic literature or are used to guide orthopaedic practice, but not all of these abstracts are submitted, survive peer review, or eventually are published. Presuming unpublished works have not been scientifically confirmed, one could question whether it is academically responsible to cite abstracts presented at the AAOS before they are peer-reviewed and published. To partly address this issue we determined the peer-reviewed publication rate for 558 abstracts (233 papers and 325 posters) presented at the shoulder and elbow sessions of the AAOS from 1999 to 2004. In April 2007, we searched the computerized database MEDLINE® and PubMed® for published articles based on these abstracts. We examined the published articles to assess publication rate, time to publication, change in contents, change in authors, and change in conclusions of abstracts. The overall publication rate in peer-reviewed journals was 58% (321 of 558), similar to other orthopaedic meetings and medical disciplines. We believe it is unacceptable to cite shoulder and elbow abstracts submitted to the AAOS because only slightly more than ½ (58%) of them are authenticated scientifically.
doi:10.1007/s11999-008-0474-2
PMCID: PMC2674152  PMID: 18769988

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