Research Integrity in Greater China: Surveying Regulations,Perceptions and Knowledge of Research Integrity from a Hong Kong Perspective

In their 2010 article ‘Research Integrity in China: Problems and Prospects’, Zeng and Resnik challenge others to engage in empirical research on research integrity in China. Here we respond to that call in three ways: first, we provide updates to their analysis of regulations and allegations of scientific misconduct; second, we report on two surveys conducted in Hong Kong that provide empirical backing to describe ways in which problems and prospects that Zeng and Resnik identify are being explored; and third, we continue the discussion started by Zeng and Resnik, pointing to ways in which China's high‐profile participation in international academic research presents concerns about research integrity. According to our research, based upon searches of both English and Chinese language literature and policies, and two surveys conducted in Hong Kong, academic faculty and research post‐graduate students in Hong Kong are aware of and have a positive attitude towards responsible conduct of research. Although Hong Kong is but one small part of China, we present this research as a response to concerns Zeng and Resnik introduce and as a call for a continued conversation.     

Feature ranking based on synergy networks to identify prognostic markers in DPT-1

Interaction among different risk factors plays an important role in the development and progress of complex disease, such as diabetes. However, traditional epidemiological methods often focus on analyzing individual or a few ‘essential’ risk factors, hopefully to obtain some insights into the etiology of complex disease. In this paper, we propose a systematic framework for risk factor analysis based on a synergy network, which enables better identification of potential risk factors that may serve as prognostic markers for complex disease. A spectral approximate algorithm is derived to solve this network optimization problem, which leads to a new network-based feature ranking method that improves the traditional feature ranking by taking into account the pairwise synergistic interactions among risk factors in addition to their individual predictive power. We first evaluate the performance of our method based on simulated datasets, and then, we use our method to study immunologic and metabolic indices based on the Diabetes Prevention Trial-Type 1 (DPT-1) study that may provide prognostic and diagnostic information regarding the development of type 1 diabetes. The performance comparison based on both simulated and DPT-1 datasets demonstrates that our network-based ranking method provides prognostic markers with higher predictive power than traditional analysis based on individual factors.     

Status and Exchange in the Profession of Anthropology

This is a study of the distribution of Ph.D.s in anthropology who obtained their degrees from and who are teaching in Ph.D.-granting departments in the United States and Canada. 1358 graduates of 80 departments are considered. A quantitative method of ranking departments, based upon exchange theory principles, is applied to this universe and its results compared to the results of a qualitative ranking carried out by the American Council of Education (A.C.E.) based upon personal evaluation of departments by anthropologists themselves. An elite is designated and the degree to which that elite dominates the academic profession is expressed in terms of the distribution of its graduates as faculty of elite schools, other Ph.D.-granting schools, and non-Ph.D.-granting schools as compared with the distribution of nonelite graduates among those same faculties. A suggestion is made concerning the social structure of the academic profession of anthropology based on the results of the study.     

Opportunities for web-based indicators in environmental sciences

This paper proposes a set of web-based indicators for quantifying and ranking the relevance of terms related to key-issues in Ecology and Sustainability Science. Search engines that operate in different contexts (e.g. global, social, scientific) are considered as web information carriers (WICs) and are able to analyse; (i) relevance on different levels: global web, individual/personal sphere, on-line news, and culture/science; (ii) time trends of relevance; (iii) relevance of keywords for environmental governance. For the purposes of this study, several indicators and specific indices (relational indices and dynamic indices) were applied to a test-set of 24 keywords. Outputs consistently show that traditional study topics in environmental sciences such as water and air have remained the most quantitatively relevant keywords, while interest in systemic issues (i.e. ecosystem and landscape) has grown over the last 20 years. Nowadays, the relevance of new concepts such as resilience and ecosystem services is increasing, but the actual ability of these concepts to influence environmental governance needs to be further studied and understood. The proposed approach, which is based on intuitive and easily replicable procedures, can support the decision-making processes related to environmental governance.     

Confirmation bias in studies of fluctuating asymmetry

Fluctuating asymmetry (FA) represents small, non-directional deviations from perfect symmetry in morphological characters. FA is generally accepted to increase in response to stress; therefore, FA is frequently used in ecological studies as an index of stress experienced by an organism, in particular due to environmental pollution. We experimentally tested the hypothesis that the outcomes of studies based on FA measurements may have been influenced by confirmation bias, i.e. the tendency of humans to seek out evidence in a manner that confirms their hypotheses and beliefs. We collected 100 leaves of downy birch (Betula pubescens) from a single tree, grouped them haphazardly into ten samples, scanned every sample, and then asked each of 31 scientists (experienced in studying FA) to measure FA from the scanned images of all 100 leaves. Three groups of participants were provided with false information about the origin of each sample and about the hypothesis to be tested, and one group (control) was provided with true information. The participants who believed that the leaves originated from a heavily polluted site reported significantly higher values of FA when compared to the participants who believed that the leaves were collected from an unpolluted site. When the participants were told that half the samples originated from a polluted site and half from a clean site and were asked to attribute each sample to either of these sites based on leaf FA, the differences in FA between samples classified as ‘polluted’ and ‘unpolluted’ were much higher than the differences obtained from measurements of the same sets of samples made by the control group. We conclude that when scientists expected to find high FA in some samples, the results of their measurements confirmed their expectations. This effect, classified as confirmation bias, may considerably influence the outcomes of the research on FA. This confirmation bias can be avoided by using a blind method, where the person conducting measurements is not aware of the origin of samples being measured. We argue that the use of blind methods is critically important for any study addressing environmental or genetic impacts on FA.     

Ethics in Science

Ethics are a set of moral principles and values a civilized society follows. Doing science with principles of ethics is the bedrock of scientific activity. The society trusts that the results and the projected outcome of any scientific activity is based on an honest and conscientious attempt by the scientific community. However, during the last few decades, there has been an explosion of knowledge and the advent of digital age. We can access the publications of competitors with just a “click”. The evaluation parameters have evolved a lot and are based on impact factors, h-index and citations. There is a general feeling that the scientific community is under a lot of pressure for fulfilling the criteria for upward growth and even retention of the positions held. The noble profession of scientific research and academics has been marred by the temptation to falsify and fabricate data, plagiarism and other unethical practices. Broadly speaking, the breach of ethics involves: plagiarism, falsification of data, redundant (duplicate) publication, drawing far-fetched conclusions without hard data, for early publicity, gift authorship (receiving as well as giving), not giving sufficient attention and consideration to scholars and post-docs as per the norms, self promotion at the cost of team-members, treating colleagues (overall all juniors) in a feudal way and Machiavellianism (cunningness and duplicity in general conduct and push to positions of power and pelf). Misconduct in Indian academics and science is also under a lot of focus. It is important and urgent that science, engineering, and health departments and institutions in our country have in place systems for education and training in pursuit of science with ethics by sound and professional courses in Responsible Conduct of Research. All research and academic institution must have the Office of Ethics for information, guidelines, training and professional oversight of conduct of research with the ethos and ethics of research.     

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete‐case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete‐case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.     

Integrating data‐deficient species in analyses of evolutionary history loss

There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary relationships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data‐deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness. We aimed to explore the potential bias caused by data‐deficient species in estimating four widely used indices: HEDGE, EDGE, PDloss, and Expected PDloss. Second, we tested four different widely applicable and multitaxa imputation methods and their potential to minimize the bias for those four indices. Two methods are based on a best‐ vs. worst‐case extinction scenarios, one is based on the frequency distribution of threat status within a taxonomic group and one is based on correlates of extinction risks. We showed that data‐deficient species led to important bias in predictions of evolutionary history loss (especially high underestimation when they were removed). This issue was particularly important when data‐deficient species tended to be clustered in the tree of life. The imputation method based on correlates of extinction risks, especially geographic range size, had the best performance and enabled us to improve risk assessments. Solving threat status of DD species can fundamentally change our understanding of loss of phylogenetic diversity. We found that this loss could be substantially higher than previously found in amphibians, squamate reptiles, and carnivores. We also identified species that are of high priority for the conservation of evolutionary distinctiveness.     

民办高校科研导师制的探索、实践与成效

大学生创新能力的培养是高等教育的重要内容之一.我院开展了基于大学生科技创新项目的科研导师制,以培养学生的创新实践能力和科研的"工匠精神",并帮助学生进行学业规划.科研导师还将项目成果转化为教学案例引入课堂,扩大受益面.科研导师制的实施得到了学生的普遍认可,人才培养质量明显提高.本文还探讨了科研导师制实施中需要关注的问题...     

Correcting the estimated level of differential expression for gene selection bias: application to a microarray study

The level of differential gene expression may be defined as a fold change, a frequency of upregulation, or some other measure of the degree or extent of a difference in expression across groups of interest. On the basis of expression data for hundreds or thousands of genes, inferring which genes are differentially expressed or ranking genes in order of priority introduces a bias in estimates of their differential expression levels. A previous correction of this feature selection bias suffers from a lack of generality in the method of ranking genes, from requiring many biological replicates, and from unnecessarily overcompensating for the bias. For any method of ranking genes on the basis of gene expression measured for as few as three biological replicates, a simple leave-one-out algorithm corrects, with less overcompensation, the bias in estimates of the level of differential gene expression. In a microarray data set, the bias correction reduces estimates of the probability of upregulation or downregulation from 100% to as low as 60%, even for genes with estimated local false discovery rates close to 0. A simulation study quantifies both the advantage of smoothing estimates of bias before correction and the degree of overcompensation.     

Node centrality indices in food webs: Rank orders versus distributions

Network analysis examines the role of species in ecological communities. The most common approach involves measurement of centrality of species or other groups of individuals based on their topological positions in food webs, followed by establishing the rank order of importance of these groups. However, ranking may differ considerably with indices of centrality and therefore comparison of rank orders is essential to obtain more meaningful results on species performance. Since ranking ignores absolute differences between centrality values, species orders may neglect important structural information in food webs. Consequently, simultaneous examination of the distribution of index values is inevitable. Hierarchical clustering and consensus generation revealed that rank orders of centrality exhibit a similar pattern over six example food webs, while distributions differ not only with indices because their relationships are largely inconsistent with food webs as well. Therefore, optimal analysis of networks and the selection of keystone species in any ecological study should rely upon both of these procedures. Similar conclusions are drawn from the detailed evaluation of a sample food web from the Florida Bay.     

Productivity in Physical and Chemical Science Predicts the Future Economic Growth of Developing Countries Better than Other Popular Indices

Scientific productivity of middle income countries correlates stronger with present and future wealth than indices reflecting its financial, social, economic or technological sophistication. We identify the contribution of the relative productivity of different scientific disciplines in predicting the future economic growth of a nation. Results show that rich and poor countries differ in the relative proportion of their scientific output in the different disciplines: countries with higher relative productivity in basic sciences such as physics and chemistry had the highest economic growth in the following five years compared to countries with a higher relative productivity in applied sciences such as medicine and pharmacy. Results suggest that the economies of middle income countries that focus their academic efforts in selected areas of applied knowledge grow slower than countries which invest in general basic sciences.     

Functional characteristics of hemodynamics in adolescents under the conditions of different motor activities

The formation of functional systems in correspondence with the conditions of natural activity is the most important issue of developmental physiology. In this study, data on the assessment of the state of central and cerebral hemodynamics, as well as indices of spectral analysis of the heart rate’s variability (HRV) in adolescents depending on the level of motor activity has been collected and systematized. The possibility of integration of methods of rheoencephallography and cardiorythmography for the assessment of the characteristics of the ontogenetic formation of the cardiovascular system has been studied. Analysis of the formation of indices of hemodynamics during an academic year and the training cycle in swimmers and healthy adolescents who do not enroll in sports classes has been made. Changes in, and correlations between, the parameters of central hemodynamics and cerebral circulation, as well as parameters of HRV, have been detected. Analysis of the changes in the statistical indices of the cardiac rhythm in adolescents during an academic year on the basis of the qualitative and quantitative characteristics of the state of regulatory systems, as well as the determination of the direction of the response to the combination of academic loads and the factor of physical training, permitted a detailed study of changes that take place in some hemodynamic parameters in athletes and students, which is of particular importance for the diagnosis of their functional state.     

A project-based approach to the use of biological literature

A course is described which has been designed to increase students' ability and willingness to use and read the scientific literature, and ultimately to enable them to make their own contributions to the literature in an acceptable style and format. The objectives and methods of the course differ from those of traditional library-use courses by concentrating on making students read and evaluate the literature rather than on information retrieval per se. Reactions have been favourable. Students make more and better use of the literature and the standard of presentation of written work has improved. The work habits generated by the course assist students throughout their academic careers. The course may have considerable implications for other library user-education programmes.     

Critical evaluation of scientific articles and other sources of information: an introduction to evidence-based veterinary medicine

The purpose of this paper is to briefly review key concepts regarding critical reading of the scientific literature to make informed decisions, in the context of evidence-based veterinary medicine. Key concepts are reviewed, based on the broader experience in human medicine, with adaptations, as indicated, to veterinary medicine. That a paper has been published in a peer-reviewed journal does not guarantee its credibility; guidelines are given regarding the general merit of different kinds of articles, as well as checklists and criteria that can be used to assess a paper. Specific study designs, their merits and limitations, are briefly discussed. Standard numerical indices for assessment of studies involving treatments and for assessments of diagnostic tests are summarized. Criteria for assessing drug trials are presented. The principles of statistical analysis are described, including practical considerations and common errors. Finally, numerous sources of bias are reviewed.     

医学生科研创新能力培养“3+X”模式的探索与实践

针对长期以来培养医学生的科研创新能力主要依靠零散的课外科研活动、受众面窄、没有系统性课程教学及其相关制度保障、致使对医学生科研创新能力培养明显乏力低效这一共性瓶颈教学问题,自2002年起,汕头大学医学院生物化学与分子生物学教学团队,在“科教相辅相佐”、“以学生为中心”、“以问题为导向”等先进教育理念指导下,倚重汕头大学医学院“医者之心”系列课程与书院育人文化之特色,发挥汕头大学的生物学、基础医学和临床医学一级学科均拥有本/硕/博/博后完整人才培养体系之优势,联合其他相关专业教学团队,在建立充分体现医学生科研创新能力培养内涵,覆盖医学本科5年全过程的核心课程体系的基础之上,历经20载的不懈努力,补充修善,成功构建了“3+X”模式,着力培养医学生的科研创新能力。所谓“3”意指对医学生的“全人培养”、“全程培养”和“全方位培养”。所谓“X”意指针对“3+X”模式运行效能的若干个验证性维度,主要包括组织医学生参加各种形式的全国大学生创新实验研究大赛、国际大学生学术研讨会,由医学本科生作为第一作者撰写发表学术论文等。培养医学生科研创新能力的成效十分显著,为有效解决上述共性瓶颈教学问题提供了一个有重要借鉴价值的范例。     

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models

Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and the codon usage, use this bias to predict the expression level of genes. When these indices were first introduced, they were based on fairly simple assumptions about which genes are most highly expressed: the CAI was originally based on the codon composition of a set of only 24 highly expressed genes, and the codon usage on assumptions about which functional classes of genes are highly expressed in fast-growing bacteria. Given the recent advent of genome-wide expression data, we should be able to improve on these assumptions. Here, we measure, in yeast, the degree to which consideration of the current genome-wide expression data sets improves the performance of both numerical indices. Indeed, we find that by changing the parameterization of each model its correlation with actual expression levels can be somewhat improved, although both indices are fairly insensitive to the exact way they are parameterized. This insensitivity indicates a consistent codon bias amongst highly expressed genes. We also attempt direct linear regression of codon composition against genome-wide expression levels (and protein abundance data). This has some similarity with the CAI formalism and yields an alternative model for the prediction of expression levels based on the coding sequences of genes. More information is available at http://bioinfo.mbb.yale.edu/expression/codons.     

In Defense of Indices: The Case of Bird Surveys

Abstract: Indices to population size have come under increasing criticism in recent years, on the grounds that indices might not faithfully represent the entire population. Most criticisms involve surveys of birds, particularly those based on point counts, which is my focus here. A variety of quantitative methods have been developed to reduce the bias of point counts, such as distance sampling, multiple-observer surveys, and time-of-detection methods. I argue that these developments are valuable, in that they enhance understanding of the detection process, but that their practical application may well be limited, likely to intensive studies focusing on a small number of species. These quantitative methods are not generally applicable to extensive, multiple-species surveys. Although criticism of the thoughtless use of indices is welcome, their wholesale rejection is not.     

A photographic method and a ranking procedure for estimating numbers of the rose aphid,Macrosiphum rosae (L.), on rose buds

Two sampling methods for aphids are described. The first is a photographic method that allows sampling with replacement for use in field experiments and in which a linear regression technique is used to estimate the errors of sampling. The second method is a ranking procedure for sampling natural populations in which regressions of aphid numbers on ‘colony length’ are used to minimize bias.