Evaluating Chemical Interaction Studies for Mixture Risk Assessment

We describe a set of criteria to evaluate the quality of data and interpretations in chemical interaction studies. These criteria reflect the consensus of the literature on interaction analysis developed over decades of research in pharmacology, toxicology, and biometry; address common pitfalls in published interaction studies; and can be easily applied to common methods of interaction analysis. The criteria apply broadly to interaction data for drugs, pesticides, industrial chemicals, food additives, and natural products and are intended to assist risk assessors who must evaluate interaction studies for use in component-based mixture risk assessments. The criteria may also assist researchers interested in conducting interaction studies to inform mixture risk assessment. The criteria are also intended to serve larger scientific goals, including increasing the repeatability of results obtained in chemical interaction studies, enhancing the reliability of conclusions drawn from interaction data, providing greater consistency of interpretations among various analysts, and decreasing uncertainty in using interaction data in risk assessments. We describe the basis for each criterion and demonstrate their utility by using them to evaluate interaction studies from the recent toxicological and pharmacological literature, which serve as examples of different types of data sets that the risk assessor may encounter.     

No evidence of association or interaction between the IL4RA, IL4, and IL13 genes in type 1 diabetes

Attempts to identify susceptibility loci that, on their own, have marginal main effects by use of gene-gene interaction tests have increased in popularity. The results obtained from analyses of epistasis are, however, difficult to interpret. Gene-gene interaction, albeit only marginally significant, has recently been reported for the interleukin-4 and interleukin-13 genes (IL4 and IL13) with the interleukin-4 receptor A gene (IL4RA), contributing to the susceptibility of type 1 diabetes (T1D). We aimed to replicate these findings by genotyping both large family and case-control data sets and by using previously published data. Gene-gene interaction tests were performed using linear regression models in cases only. We did not find any single-locus associations with T1D and did not obtain evidence of gene-gene interaction. Additional support from independent samples will be even more important in the study of gene-gene interactions and other subgroup analyses.     

A Supervised Approach to Quantifying Sentence Similarity: With Application to Evidence Based Medicine

Following the Evidence Based Medicine (EBM) practice, practitioners make use of the existing evidence to make therapeutic decisions. This evidence, in the form of scientific statements, is usually found in scholarly publications such as randomised control trials and systematic reviews. However, finding such information in the overwhelming amount of published material is particularly challenging. Approaches have been proposed to automatically extract scientific artefacts in EBM using standardised schemas. Our work takes this stream a step forward and looks into consolidating extracted artefacts—i.e., quantifying their degree of similarity based on the assumption that they carry the same rhetorical role. By semantically connecting key statements in the literature of EBM, practitioners are not only able to find available evidence more easily, but also can track the effects of different treatments/outcomes in a number of related studies. We devise a regression model based on a varied set of features and evaluate it both on a general English corpus (the SICK corpus), as well as on an EBM corpus (the NICTA-PIBOSO corpus). Experimental results show that our approach performs on par with the state of the art on the general English and achieves encouraging results on the biomedical text when compared against human judgement.     

Visualizing clinical evidence: citation networks for the incubation periods of respiratory viral infections

Simply by repetition, medical facts can become enshrined as truth even when there is little empirical evidence supporting them. We present an intuitive and clear visual design for tracking the citation history of a particular scientific fact over time. We apply this method to data from a previously published literature review on the incubation period of nine respiratory viral infections. The resulting citation networks reveal that the conventional wisdom about the incubation period for these diseases was based on a small fraction of available data and in one case, on no retrievable empirical evidence. Overall, 50% of all incubation period statements did not provide a source for their estimate and 65% of original sources for incubation period data were not incorporated into subsequent publications. More standardized and widely available methods for visualizing these histories of medical evidence are needed to ensure that conventional wisdom cannot stray too far from empirically supported knowledge.     

Quality of Animal Experiments in Anti-Angiogenic Cancer Drug Development – A Systematic Review

Translation from preclinical animal research to clinical bedside has proven to be difficult to impossible in many fields of research (e.g. acute stroke, ALS and HIV vaccination development) with oncology showing particularly low translation rates (5% vs. 20% for cardiovascular diseases). Several investigations on published preclinical animal research have revealed that apart from plain species differences, translational problems can arise from low study quality (e.g. study design) or non-representative experimental conditions (e.g. treatment schedule).This review assessed the published experimental circumstances and quality of anti-angiogenic cancer drug development in 232 in vivo studies. The quality of study design was often insufficient; at least the information published about the experiments was not satisfactory in most cases. There was no quality improvement over time, with the exception of conflict of interest statements. This increase presumably arose mainly because journal guidelines request such statements more often recently.Visual inspection of data and a cluster analysis confirmed a trend described in literature that low study quality tends to overestimate study outcome. It was also found that experimental outcome was more favorable when a potential drug was investigated as the main focus of a study, compared to drugs that were used as comparison interventions. We assume that this effect arises from the frequent neglect of blinding investigators towards treatment arms and refer to it as hypothesis bias.In conclusion, the reporting and presumably also the experimental performance of animal studies in drug development for oncology suffer from similar shortcomings as other fields of research (such as stroke or ALS). We consider it necessary to enforce experimental quality and reporting that corresponds to the level of clinical studies. It seems that only clear journal guidelines or guidelines from licensing authorities, where failure to fulfill prevents publication or experimental license, can help to improve this situation.     

Consistency of financial interest disclosures in the biomedical literature: the case of coronary stents

Background

Disclosure of authors'' financial interests has been proposed as a strategy for protecting the integrity of the biomedical literature. We examined whether authors'' financial interests were disclosed consistently in articles on coronary stents published in 2006.

Methodology/Principal Findings

We searched PubMed for English-language articles published in 2006 that provided evidence or guidance regarding the use of coronary artery stents. We recorded article characteristics, including information about authors'' financial disclosures. The main outcome measures were the prevalence, nature, and consistency of financial disclosures. There were 746 articles, 2985 authors, and 135 journals in the database. Eighty-three percent of the articles did not contain disclosure statements for any author (including declarations of no interests). Only 6% of authors had an article with a disclosure statement. In comparisons between articles by the same author, the types of disagreement were as follows: no disclosure statements vs declarations of no interests (64%); specific disclosures vs no disclosure statements (34%); and specific disclosures vs declarations of no interests (2%). Among the 75 authors who disclosed at least 1 relationship with an organization, there were 2 cases (3%) in which the organization was disclosed in every article the author wrote.

Conclusions/Significance

In the rare instances when financial interests were disclosed, they were not disclosed consistently, suggesting that there are problems with transparency in an area of the literature that has important implications for patient care. Our findings suggest that the inconsistencies we observed are due to both the policies of journals and the behavior of some authors.     

Extraction of Pharmacokinetic Evidence of Drug–Drug Interactions from the Literature

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which are reported differently for distinct experimental goals. We focus on pharmacokinetic evidence for DDI, essential for identifying causal mechanisms of putative interactions and as input for further pharmacological and pharmacoepidemiology investigations. We used manually curated corpora of PubMed abstracts and annotated sentences to evaluate the efficacy of literature mining on two tasks: first, identifying PubMed abstracts containing pharmacokinetic evidence of DDIs; second, extracting sentences containing such evidence from abstracts. We implemented a text mining pipeline and evaluated it using several linear classifiers and a variety of feature transforms. The most important textual features in the abstract and sentence classification tasks were analyzed. We also investigated the performance benefits of using features derived from PubMed metadata fields, various publicly available named entity recognizers, and pharmacokinetic dictionaries. Several classifiers performed very well in distinguishing relevant and irrelevant abstracts (reaching F1≈0.93, MCC≈0.74, iAUC≈0.99) and sentences (F1≈0.76, MCC≈0.65, iAUC≈0.83). We found that word bigram features were important for achieving optimal classifier performance and that features derived from Medical Subject Headings (MeSH) terms significantly improved abstract classification. We also found that some drug-related named entity recognition tools and dictionaries led to slight but significant improvements, especially in classification of evidence sentences. Based on our thorough analysis of classifiers and feature transforms and the high classification performance achieved, we demonstrate that literature mining can aid DDI discovery by supporting automatic extraction of specific types of experimental evidence.     

Disentangling the interaction among host resources,the immune system and pathogens

The interaction between the immune system and pathogens is often characterised as a predator–prey interaction. This characterisation ignores the fact that both require host resources to reproduce. Here, we propose novel theory that considers how these resource requirements can modify the interaction between the immune system and pathogens. We derive a series of models to describe the energetic interaction between the immune system and pathogens, from fully independent resources to direct competition for the same resource. We show that increasing within‐host resource supply has qualitatively distinct effects under these different scenarios. In particular, we show the conditions for which pathogen load is expected to increase, decrease or even peak at intermediate resource supply. We survey the empirical literature and find evidence for all three patterns. These patterns are not explained by previous theory, suggesting that competition for host resources can have a strong influence on the outcome of disease.     

Meta-analysis of linkage data under worst-case conditions: a demonstration using the human OB region.

To date, few methods have been developed explicitly for meta-analysis of linkage analyses. Moreover, the methods that have been developed or suggested generally depend on certain ideal situations and have not been widely applied. In this article, we apply standard statistical theory and meta-analytic techniques in novel ways to five published papers discussing the evidence of linkage of body mass index (BMI) to the region of the human genome containing the OB gene. These methods are "inference based," meaning that they allow one to make statements about the statistical significance of the entire body of evidence. As currently developed, they do not allow specific statements to be made about the amount of variance explained by any putative locus or allow precise confidence intervals to be placed around the putative location of a linked locus. By applying these techniques to the literature on linkage in the human OB gene region, we are able to show that the evidence for linkage somewhere in the region is extremely strong (P = 1.5 x 10[-5]).     

Japanese guideline for the management of hyperuricemia and gout: second edition

Gout is a urate deposition disease caused by persistent hyperuricemia. Because gout patients present with a variety of clinical symptoms, it is necessary to have a guideline for the standard management and care of gout and hyperuricemia. The Japanese Society of Gout and Nucleic Acid Metabolism, a scientific society committed to study nucleic acid metabolism and related diseases, established the first edition of the "Guideline for the Management of Hyperuricemia and Gout" in 2002, and published the revised version in January 2010. This second edition is not only evidence based on a search of systemic literature, but also includes consensus levels by a Delphi exercise to determine the strength of the recommendations. A draft version of this guideline was reviewed by internal and external reviewers as well as a patient. In this guideline, key messages from each chapter are listed as statements together with the evidence level, consensus level, and strength of the recommendation. In this proceeding, several selected chapters on the clinical management of gout and hyperuricemia are described. We hope this guideline is appropriately used for the standard management and care of patients with hyperuricemia and gout in daily practice.     

Interactions among ecosystem stressors and their importance in conservation

Interactions between multiple ecosystem stressors are expected to jeopardize biological processes, functions and biodiversity. The scientific community has declared stressor interactions—notably synergies—a key issue for conservation and management. Here, we review ecological literature over the past four decades to evaluate trends in the reporting of ecological interactions (synergies, antagonisms and additive effects) and highlight the implications and importance to conservation. Despite increasing popularity, and ever-finer terminologies, we find that synergies are (still) not the most prevalent type of interaction, and that conservation practitioners need to appreciate and manage for all interaction outcomes, including antagonistic and additive effects. However, it will not be possible to identify the effect of every interaction on every organism''s physiology and every ecosystem function because the number of stressors, and their potential interactions, are growing rapidly. Predicting the type of interactions may be possible in the near-future, using meta-analyses, conservation-oriented experiments and adaptive monitoring. Pending a general framework for predicting interactions, conservation management should enact interventions that are robust to uncertainty in interaction type and that continue to bolster biological resilience in a stressful world.     

Malatesta转基因研究:引证分析及相关证据

发表多篇以转基因农产品饲喂动物而导致健康损害论文的维罗纳大学(University of Verona)学者Manuela Malatesta,是国际上采用实验方法研究转基因生物安全领域有影响力的学者之一。通过对美国Web of Science数据平台全部论文的检索,重点分析了其所发表的10篇转基因毒理学论文的研究内容、研究方法与结论,并追踪其研究的相关证据及学术界对其研究的评价,在此基础上,分析该研究方法与结论的可靠性。研究发现,Malatesta所发表转基因存在安全隐患的10篇研究论文,由于其研究材料及方法上所存在的问题除了个别存在明显错误的论文无法重现而被学术界所否定外,其余论文均被后续采用规范研究方法的同类研究所推翻。     

Weight Cycling: A Review of the Animal Literature

This review critically evaluates the animal literature concerning the effects of weight cycling on factors related to development of obesity, diabetes, hypertension, and hyperlipidemia. Although human studies have been used to retrospectively examine the relationship between fluctuations in body weight and a variety of disease markers, direct causal links between weight cycling and negative health effects have been inferred from a series of scientific publications using animals as subjects. We use data from 24 such publications to evaluate evidence for and against a series of hypotheses that have been suggested regarding weight cycling and health. Although there are some intriguing results, there is currently little evidence to support any of these hypotheses. However, methodological limitations were identified in many of these studies, and caution should be used in making definitive decisions about weight cycling. Weight cycling studies could be improved by including more appropriate controls, comparing controls to weight cycling animals at more appropriate time points, and giving more attention to potential effects of diet composition. While more careful research is needed, at this time we conclude that the published animal literature does not justify any warnings about the hazards of weight cycling.     

Aquatic invasive species: introduction to the Special Issue and dynamics of public interest

Hydrobiologia - Aquatic invasive species research has been surging in popularity, with the number of papers published in Hydrobiologia doubling since the previous decade. We overview contributions...     

A Systematic Review of the Role of Proprietary and Patent Medicine Vendors in Healthcare Provision in Nigeria

Background

Interventions to reduce the burden of disease and mortality in sub-Saharan Africa increasingly recognize the important role that drug retailers play in delivering basic healthcare services. In Nigeria, owner-operated drug retail outlets, known as patent and proprietary medicine vendors (PPMVs), are a main source of medicines for acute conditions, but their practices are not well understood. Greater understanding of the role of PPMVs and the quality of care they provide is needed in order to inform ongoing national health initiatives that aim to incorporate PPMVs as a delivery mechanism.

Objective and Methods

This paper reviews and synthesizes the existing published and grey literature on the characteristics, knowledge and practices of PPMVs in Nigeria. We searched published and grey literature using a number of electronic databases, supplemented with website searches of relevant international agencies. We included all studies providing outcome data on PPMVs in Nigeria, including non-experimental studies, and assessed the rigor of each study using the WHO-Johns Hopkins Rigor scale. We used narrative synthesis to evaluate the findings.

Results

We identified 50 articles for inclusion. These studies provided data on a wide range of PPMV outcomes: training; health knowledge; health practices, including drug stocking and dispensing, client interaction, and referral; compliance with regulatory guidelines; and the effects of interventions targeting PPMVs. In general, PPMVs have low health knowledge and poor health treatment practices. However, the literature focuses largely on services for adult malaria, and little is known about other health areas or services for children.

Conclusions

This review highlights several concerns with the quality of the private drug retail sector in Nigeria, as well as gaps in the existing evidence base. Future research should adopt a more holistic view of the services provided by PPMV shops, and evaluate intervention strategies that may improve the services provided in this sector.     

Relationship between psychopathological factors and metabolic control in children and adolescents with insulin-dependent diabetes mellitus

This paper provides a critical overview of the literature on the relationship between psychological/psychopathological factors and metabolic control in children and adolescents with insulin dependent diabetes mellitus (IDDM). We discuss studies on individual and family psychopathological factors, as well as reports on the effects of psychoeducational/psychotherapeutic interventions on glycemic control in patients with IDDM aged <18 years. The analysis of the literature indicates that while evidence on the relationship between individual factors and metabolic control is still mixed, in part due to methodological issues, results from family studies do suggest that patients in dysfunctional families and children of parents with high degrees of psychopathology present with poor glycemic control. As for the effects of psychoeducational/psychotherapeutic interventions, limited but increasing evidence shows that they can actually contribute to improve metabolic control. We finally suggest some future underexplored avenues of research in the field, including studies on the psychopathological and neurobiological mechanisms underlying the above mentioned findings. All this body of research should provide a strong empirical rationale for allocating resources in order to include psychiatrists within the interdisciplinary diabetes health care team.     

Personality in nonhuman primates: a review and evaluation of past research

Scientific reports of personality in nonhuman primates are now appearing with increasing frequency across a wide range of disciplines, including psychology, anthropology, endocrinology, and zoo management. To identify general patterns of research and summarize the major findings to date, we present a comprehensive review of the literature, allowing us to pinpoint the major gaps in knowledge and determine what research challenges lay ahead. An exhaustive search of five scientific databases identified 210 relevant research reports. These articles began to appear in the 1930s, but it was not until the 1980s that research on primate personality began to gather pace, with more than 100 articles published in the last decade. Our analyses of the literature indicate that some domains (e.g., sex, age, rearing conditions) are more evenly represented in the literature than are others (e.g., species, research location). Studies examining personality structure (e.g., with factor analysis) have identified personality dimensions that can be divided into 14 broad categories, with Sociability, Confidence/Aggression, and Fearfulness receiving the most research attention. Analyses of the findings pertaining to inter‐rater agreement, internal consistency, test–retest reliability, generally support not only the reliability of primate personality ratings scales but also point to the need for more psychometric studies and greater consistency in how the analyses are reported. When measured at the level of broad dimensions, Extraversion and Dominance generally demonstrated the highest levels of inter‐rater reliability, with weaker findings for the dimensions of Agreeableness, Emotionality, and Conscientiousness. Few studies provided data with regard to convergent and discriminant validity; Excitability and Dominance demonstrated the strongest validity coefficients when validated against relevant behavioral criterion measures. Overall, the validity data present a somewhat mixed picture, suggesting that high levels of validity are attainable, but by no means guaranteed. Discussion focuses on delineating major theoretical and empirical questions facing research and practice in primate personality. Am. J. Primatol. 72:653–671, 2010. © 2010 Wiley‐Liss, Inc.     

Landscape,Climate and Hantavirus Cardiopulmonary Syndrome Outbreaks

We performed a literature review in order to improve our understanding of how landscape and climate drivers affect HCPS outbreaks. Anthropogenic landscape changes such as forest loss, fragmentation and agricultural land uses are related with a boost in hantavirus reservoir species abundance and hantavirus prevalence in tropical areas, increasing HCPS risk. Additionally, higher precipitation, especially in arid regions, favors an increase in vegetational biomass, which augments the resources for reservoir rodents, also increasing HCPS risk. Although these relationships were observed, few studies described it so far, and the ones that did it are concentrated in few places. To guide future research on this issue, we build a conceptual model relating landscape and climate variables with HCPS outbreaks and identified research opportunities. We point out the need for studies addressing the effects of landscape configuration, temperature and the interaction between climate and landscape variables. Critical landscape thresholds are also highly relevant, once HCPS risk transmission can increase rapidly above a certain degree of landscape degradation. These studies could be relevant to implement preventive measures, creating landscapes that can mitigate disease spread risk.     

Embryonic stem cells: are useful in clinic treatments?

It is not uncommon to find statements in the social media and even in some scientific journals declaring that embryonic stem cells can be used in human medicine for therapeutic purposes. In our opinion, this statement does not fit the medical reality. To go into this subject in depth, and if possible to clarify it, we reviewed the most recent literature on clinical trials conducted with embryonic stem cells, concluding that up to the present time, there is only one ongoing clinical trial being carried out with these types of cells to treat a small group of patients with spinal cord injury. The results of this trial have still not been published. In conclusion, at present, there is only evidence of one phase I clinical trial conducted with embryonic stem cells, in comparison to the numerous trials conducted with adult stem cells.     

A Proposed Working Definition for the Novel Concept of Neurobehavioral Hormesis

It is proposed that a novel concept, neurobehavioral hormesis, be considered for integration into the field of toxicology. Hormesis results in a non-linear dose response where low dose exposures to toxicants cause beneficial effects, and detrimental effects at higher doses. Hormesis has not been systematically incorporated into traditional risk assessment methodologies, yet there is recent evidence that this pattern of results is relatively prevalent. In this paper, hormesis is applied to neurobehavioral toxicology, and an operational definition is proposed for application to putative examples of neurobehavioral hormesis. The two primary criteria used for the operational definition are: (1) performance is enhanced with low dose exposure and denigrated at higher doses, and (2) the change in behavior persists following a recovery period. In recent research from our laboratory it was reported that rats exposed to JP-8 jet fuel vapor demonstrated such a pattern of neurobehavioral performance on tests of learning and memory. Specifically, animals with long-term exposure to low concentrations of jet fuel demonstrated enhanced performance on specific operant tasks as compared both to controls and to animals exposed to higher concentrations. The effect was most apparent during complex versus simple operant tests, and was observed months following the last exposure to jet fuel. The effects meet both criteria for the proposed working definition of neurobehavioral hormesis, and thus provide evidence of the validity for considering neurobehavioral hormesis in published and future research, and suggests a more systematic investigation of existing literature may be warranted. Also, it provides additional support for the overall proposal to include hormetic effects in formal risk assessment paradigms.