When should potentially false research findings be considered acceptable?

Ioannidis estimated that most published research findings are false, but he did not indicate when, if at all, potentially false research results may be considered as acceptable to society. We combined our two previously published models to calculate the probability above which research findings may become acceptable. A new model indicates that the probability above which research results should be accepted depends on the expected payback from the research (the benefits) and the inadvertent consequences (the harms). This probability may dramatically change depending on our willingness to tolerate error in accepting false research findings. Our acceptance of research findings changes as a function of what we call "acceptable regret," i.e., our tolerance of making a wrong decision in accepting the research hypothesis. We illustrate our findings by providing a new framework for early stopping rules in clinical research (i.e., when should we accept early findings from a clinical trial indicating the benefits as true?). Obtaining absolute "truth" in research is impossible, and so society has to decide when less-than-perfect results may become acceptable.     

Computational knowledge integration in biopharmaceutical research

An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.     

2012年中国植物科学若干领域重要研究进展

2012年中国植物科学研究继续快速发展。中国科学家在植物科学多个领域中取得了大量的原创性、高水平研究成果, 包括植物基因组研究、植物天然免疫抗性及其应答环境的信号转导机制以及植物去甲基化作用和DNA双链断裂修复机制研究等, 受到国内外的高度评价。该文对2012年中国本土植物生命科学若干领域取得的重要研究进展进行概括性评述, 旨在全面追踪当前中国植物科学领域发展的最新前沿和热点事件, 并展现我国科学家所取得的杰出成就。     

2009年中国植物科学若干领域重要研究进展

2009年中国植物科学在水稻和拟南芥研究等方面取得“爆发性”的快速发展。中国科学家在植物科学各领域中取得了大量的原创性研究成果, 尤其是在基于新一代测序技术和计算生物学理论的基因组学、水稻功能基因挖掘、激素受体和信号转导以及转基因作物产业化和生态安全性研究等方面取得一系列重大进展, 受到了国内外广泛关注。该文对2009年中国本土植物生命科学若干领域取得的重要研究进展进行概括性评述, 旨在全面追踪当前中国植物科学领域发展的最新前沿和热点事件, 并展现我国科学家们所取得的杰出成就。     

Iranian human genome project: Overview of a research process among Iranian ethnicities

The Human Genome Project (HGP) refers to the international scientific research program, formally begun in October 1990 and completed in 2003, mainly designated to discover all the human genes, analyzing the structure of human DNA and determining the location of all human genes and also making them accessible for further biological and medical investigations. With the appropriate rationale approach, a similar study has been held in Iran. The study of human genome among Iranian ethnicities (IHGP) has been attempted formally in 2000 through a detailed and fully programmed research among all the major ethnic groups by more than 1,900 samples from all over Iran based on the main demographical and anthropological findings and formally known criteria considered for the international HGP. This paper overviewed the process of the research in the terms of program goals, primary data collection, research designation and methodology and also practical aspects and primary findings of the Iranian genome project and its progress during a nearly 5-year period.     

The Impact of Neuroscience on Music Education Advocacy and Philosophy

This content analysis examines how philosophy and advocacy articles published between 2005 and 2010 were influenced by current neuroscience research. The contents of twelve journals were explored, resulting in the inclusion of forty-five articles in this analysis. Recently, there has been a growing interest in neuroscientific research on music. Articles were coded for latent content and emerging themes to determine if this interest has begun to be expressed in philosophy and advocacy writings. The educational implications and issues of using neuroscientific findings are addressed, and recommendations are offered for using future research for advocacy purposes.     

Trends in health policy and systems research over the past decade: still too little capacity in low-income countries

BACKGROUND: The past decade has seen several high-level events and documents committing to strengthening the field of health policy and systems research (HPSR) as a critical input to strengthening health systems. Specifically, they called for increased production, capacity to undertake and funding for HPSR. The objective of this paper is to assess the extent to which progress has been achieved, an important feedback for stakeholders in this field. METHODS AND FINDING: Two sources of data have been used. The first is a bibliometric analysis to assess growth in production of HPSR between 2003 and 2009. The six building blocks of the health system were used to define the scope of this search. The second is a survey of 96 research institutions undertaken in 2010 to assess the capacity and funding availability to undertake HPSR, compared with findings from the same survey undertaken in 2000 and 2008. Both analyses focus on HPSR relevant to low-income and middle-income countries (LMICs). Overall, we found an increasing trend of publications on HPSR in LMICs, although only 4% were led by authors from low-income countries (LICs). This is consistent with findings from the institutional survey, where despite improvements in infrastructure of research institutions, a minimal change has been seen in the level of experience of researchers within LIC institutions. Funding availability in LICs has increased notably to institutions in Sub-Saharan Africa; nonetheless, the overall increase has been modest in all regions. CONCLUSION: Although progress has been made in both the production and funding availability for HPSR, capacity to undertake the research locally has grown at a much slower pace, particularly in LICs where there is most need for this research. A firm commitment to dedicate a proportion of all future funding for research to building capacity may be the only solution to turn the tide.     

2010年中国植物科学若干领域重要研究进展

2010年中国植物科学研究继续快速发展。中国科学家在植物科学各领域中取得了大量的具有原创意义的研究成果,尤其是在水稻产量决定的遗传机制和作物基因组研究方面获得了一系列突破,农业生态学研究等方面也取得了重大进展,获得国内外的高度评价。该文对2010年中国本土植物生命科学若干领域取得的重要研究进展进行概括性评述,旨在全面追踪当前中国植物科学领域发展的最新前沿和热点事件,并展现我国科学家所取得的杰出成就。     

病毒性肝炎树鼩动物模型研究与建模策略

病毒性肝炎是由肝炎病毒引起的肝脏疾病。在我国,病毒性肝炎高度流行,其中又以乙型肝炎病毒(Hepatitis B virus,HBV)和丙型肝炎病毒(Hepatitis C virus,HCV)危害较大。动物模型是研究疾病感染与发病机制,进行药物与疫苗研究的必要工具。目前病毒性肝炎实验动物模型的研究已取得长足的发展,主要集中于病毒在动物体内的感染特性及发病规律方面。本文仅就病毒性肝炎动物模型,尤其乙型、丙型肝炎树鼩动物模型的研究及建模策略进行综述。     

中国非人灵长类物种的行为偏侧研究进展

行为偏侧是指动物进行某一行为时偏好使用某一侧肢体或感觉器官。行为偏侧作为脑偏侧所对应的可观测的行为指标,是动物行为适应性进化的代表性特征之一,它在个体水平上影响着个体适合度,在群体水平上是社会性物种的一种进化稳定策略,具有重要的生态和进化意义。中国非人灵长类资源丰富,而中国非人灵长类的行为偏侧研究起步较晚,始于二十世纪八十年代。本文系统归纳中国非人灵长类物种的行为偏侧研究进展,并基于当前研究现状,为今后发展提出积极建议。     

2010年中国植物科学若干领域重要研究进展

2010年中国植物科学研究继续快速发展。中国科学家在植物科学各领域中取得了大量的具有原创意义的研究成果, 尤其是在水稻产量决定的遗传机制和作物基因组研究方面获得了一系列突破, 农业生态学研究等方面也取得了重大进展, 获得国内外的高度评价。该文对2010年中国本土植物生命科学若干领域取得的重要研究进展进行概括性评述, 旨在全面追踪当前中国植物科学领域发展的最新前沿和热点事件, 并展现我国科学家所取得的杰出成就。     

Some recent advances in basic neuroscience research in China

Neuroscience as a distinct discipline or research programme has been a rather recent event in most Chinese universities and in the Chinese Academy of Sciences. However, the last few years have witnessed increased funding and an improved research environment for neuroscience, both of which facilitated an influx of Chinese neuroscientists trained abroad. In this review, we have highlighted some recent research advances made by neuroscientists in China. Based on our own expertise, this review is focused mainly on findings that have contributed to our understanding of the mechanisms underlying brain development, neural plasticity and cognitive processes, and neural degeneration.     

MLPA-based evidence for sequence gain: pitfalls in confirmation and necessity for exclusion of false positives

Multiplex ligation-dependent probe amplification (MLPA) has become a standard method for identifying copy number mutations in diagnostic and research settings. The occurrence of false-positive deletion findings and the underlying causes are well recognized, whereas false-positive duplication/amplification findings have not been appreciated so far. We here present three pertinent cases which were only identified on extended, nonstandard secondary analyses. We also offer and experimentally validate a potential explanation. Our findings imply that MLPA data indicating gain of genomic sequence require validation on an independent sample or by an independent method.     

Understanding landholder management of river frontages: The Goulburn Broken

Summary In this paper we discuss the findings of research exploring landholder adoption of practices expected to improve the management of river frontages. This research was part of a larger project undertaken by the Goulburn Broken Catchment Management Authority (GBCMA) to assess the impacts of grazing on the condition of riparian zones in the GBCMA region. Our research employed a postal survey to a random selection of all river frontage owners in the GBCMA. Research findings highlighted the limited adoption of most current recommended practices (CRP) such as watering stock off‐stream and fencing to manage stock access to river frontages. Higher adoption of CRP (in particular fencing) was correlated with greater knowledge of river frontage function and factors affecting river frontage condition; higher importance attached to the environmental, social and economic values of frontages; non‐farming occupations; and higher confidence in the efficacy of CRP. These findings have important implications for managers and scientists. There has been a large investment in community education in the GBCMA and survey findings suggest this has been an effective strategy. At the same time, there should be changes in the approach to community education. It seems there is much to be done to improve the acceptability of fencing frontages along large rivers. Appeals to adopt CRP also need to move beyond a narrow focus on farmers and the benefits of increased agricultural production and embrace the range of landholders and the different values they attach to their frontages. Most respondents had no on‐property profit and survey data indicated that financial constraints were an important factor limiting the adoption of CRP, particularly among farmers. There was considerable interest in taking up a grant scheme that would provide a higher level of support than is usually offered by government. These findings highlight the important role of economic incentives in assisting private landholders undertake conservation work along river frontages.     

Decision-Making in Research Tasks with Sequential Testing

Background

In a recent controversial essay, published by JPA Ioannidis in PLoS Medicine, it has been argued that in some research fields, most of the published findings are false. Based on theoretical reasoning it can be shown that small effect sizes, error-prone tests, low priors of the tested hypotheses and biases in the evaluation and publication of research findings increase the fraction of false positives. These findings raise concerns about the reliability of research. However, they are based on a very simple scenario of scientific research, where single tests are used to evaluate independent hypotheses.

Methodology/Principal Findings

In this study, we present computer simulations and experimental approaches for analyzing more realistic scenarios. In these scenarios, research tasks are solved sequentially, i.e. subsequent tests can be chosen depending on previous results. We investigate simple sequential testing and scenarios where only a selected subset of results can be published and used for future rounds of test choice. Results from computer simulations indicate that for the tasks analyzed in this study, the fraction of false among the positive findings declines over several rounds of testing if the most informative tests are performed. Our experiments show that human subjects frequently perform the most informative tests, leading to a decline of false positives as expected from the simulations.

Conclusions/Significance

For the research tasks studied here, findings tend to become more reliable over time. We also find that the performance in those experimental settings where not all performed tests could be published turned out to be surprisingly inefficient. Our results may help optimize existing procedures used in the practice of scientific research and provide guidance for the development of novel forms of scholarly communication.     

A knowledgebase system to enhance scientific discovery: Telemakus

BACKGROUND: With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. Efforts to improve and speed up scientific discovery are being explored on a number of fronts. However, much of this work is based on traditional search and retrieval approaches and the bibliographic citation presentation format remains unchanged. METHODS: Case study. RESULTS: The Telemakus KnowledgeBase System provides flexible new tools for creating knowledgebases to facilitate retrieval and review of scientific research reports. In formalizing the representation of the research methods and results of scientific reports, Telemakus offers a potential strategy to enhance the scientific discovery process. While other research has demonstrated that aggregating and analyzing research findings across domains augments knowledge discovery, the Telemakus system is unique in combining document surrogates with interactive concept maps of linked relationships across groups of research reports. CONCLUSION: Based on how scientists conduct research and read the literature, the Telemakus KnowledgeBase System brings together three innovations in analyzing, displaying and summarizing research reports across a domain: (1) research report schema, a document surrogate of extracted research methods and findings presented in a consistent and structured schema format which mimics the research process itself and provides a high-level surrogate to facilitate searching and rapid review of retrieved documents; (2) research findings, used to index the documents, allowing searchers to request, for example, research studies which have studied the relationship between neoplasms and vitamin E; and (3) visual exploration interface of linked relationships for interactive querying of research findings across the knowledgebase and graphical displays of what is known as well as, through gaps in the map, what is yet to be tested. The rationale and system architecture are described and plans for the future are discussed.     

Revealing Variations in Perception of Mental States from Dynamic Facial Expressions: A Cautionary Note

Although a great deal of research has been conducted on the recognition of basic facial emotions (e.g., anger, happiness, sadness), much less research has been carried out on the more subtle facial expressions of an individual''s mental state (e.g., anxiety, disinterest, relief). Of particular concern is that these mental state expressions provide a crucial source of communication in everyday life but little is known about the accuracy with which natural dynamic facial expressions of mental states are identified and, in particular, the variability in mental state perception that is produced. Here we report the findings of two studies that investigated the accuracy and variability with which dynamic facial expressions of mental states were identified by participants. Both studies used stimuli carefully constructed using procedures adopted in previous research, and free-report (Study 1) and forced-choice (Study 2) measures of response accuracy and variability. The findings of both studies showed levels of response accuracy that were accompanied by substantial variation in the labels assigned by observers to each mental state. Thus, when mental states are identified from facial expressions in experiments, the identities attached to these expressions appear to vary considerably across individuals. This variability raises important issues for understanding the identification of mental states in everyday situations and for the use of responses in facial expression research.     

‘Culture shock’: Black students account for their distinctiveness at an elite college

Previous research on black students attending predominantly white colleges has emphasized race-based differences with white students while downplaying differences in social class. This research indicates that class-based differences are an important component of many black students’ discomfort at ‘Northern College’, a school that has traditionally served wealthy white students. Drawing on interviews and participant observation done on campus, I apply cultural capital theory to explain how differences in class-specific cultural styles make campus life difficult for non-affluent blacks and discuss the implications of the findings for future research on black college experiences.     

Autism in infants: an update

Although autism is a disorder of very early onset, knowledge on how it is first expressed in infancy has, until recently, remained limited. In recent years new strategies of research, including prospective studies, have substantially increased our knowledge regarding autism in infants. Research findings have suggested the very early emergence of significant differences in social information processes. In addition to having important implications for research, these findings also offer new opportunities for screening and early identification and, hopefully, for improved outcome.     

Bacterial elicitation and evasion of plant innate immunity

Recent research on plant responses to bacterial attack has identified extracellular and intracellular host receptors that recognize conserved pathogen-associated molecular patterns and more specialized virulence proteins, respectively. These findings have shed light on our understanding of the molecular mechanisms by which bacteria elicit host defences and how pathogens have evolved to evade or suppress these defences.