Raw data were not disclosed in 95% of PubMed-indexed heart failure meta-analyses in 2021: A systematic analysis of transparency

BACKGROUND

The rising concern of irreproducible and non-transparent studies poses a significant challenge in modern medical literature. The impact of this issue on cardiology, particularly in the subfield of heart failure, remains poorly understood. To address this knowledge gap, we assessed the quality of evidence presented in recent heart failure meta-analyses by exploring several crucial transparency indicators.

METHODS

We conducted a cross-sectional study and searched PubMed for meta - analyses themed around heart failure. We included the 100 most recent publications from 2021 and investigated the presence of several indices that are associated with transparency and reproducibility.

RESULTS

The vast majority of the papers did not include their raw data (95/100, 95%) nor their analytic code (99/100, 99%). Less than half (42/100, 42%) preregistered their protocol, while only 65/100 (65%) adhered to a reporting guidelines method. Bias calculation for the respective studies included in each meta - analysis was present in 83/100 (83%) papers and publication bias was measured in approximately half (56/100, 56%).

CONCLUSIONS

Our study indicates that meta-analyses in the field of heart failure present important information of transparency infrequently. Therefore, reproduction and validation of their findings seems to be practically impossible.

A New Bibliometric Index: The Top 100 Most Disruptive and Developmental Publications in Colorectal Surgery Journals

BACKGROUND

A new bibliometric index called the disruption score was recently proposed to identify innovative and paradigm-changing publications.

OBJECTIVE

The goal was to apply the disruption score to the colorectal surgery literature to provide the community with a repository of important research articles.

DESIGN

This study is a bibliometric analysis.

SETTINGS

The 100 most disruptive and developmental publications in Diseases of the Colon & Rectum, Colorectal Disease, International Journal of Colorectal Disease, and Techniques in Coloproctology were identified from a validated data set of disruption scores and linked with the iCite National Institutes of Health tool to obtain citation counts.

MAIN OUTCOME MEASURES

The primary outcomes measured were the disruption score and citation count.

RESULTS

We identified 12,127 articles published in Diseases of the Colon & Rectum (n = 8109), International Journal of Colorectal Disease (n = 1912), Colorectal Disease (n = 1751), and Techniques in Coloproctology (n = 355) between 1954 and 2014. Diseases of the Colon & Rectum had the most articles in the top 100 most disruptive and developmental lists. The disruptive articles were in the top 1% of the disruption score distribution in PubMed and were cited between 1 and 671 times. Being highly cited was weakly correlated with high disruption scores (r = 0.09). Developmental articles had disruption scores that were more strongly correlated with citation count (r = 0.18).

LIMITATIONS

This study is subject to the limitations of bibliometric indices, which change over time.

DISCUSSION

The disruption score identified insightful and paradigm-changing studies in colorectal surgery. These studies include a wide range of topics and consistently identified editorials and case reports/case series as important research. This bibliometric analysis provides colorectal surgeons with a unique archive of research that can often be overlooked but that may have scholarly significance. See Video Abstract at http://links.lww.com/DCR/B639.UN NUEVO INDICE BIBLIOMÉTRICO: LAS 100 MAS IMPORTANTES PUBLICACIONES EN INNOVACIONES DESESTABILIZADORAS Y DE DESARROLLO EN LAS REVISTAS DE CIRUGÍA COLORRECTALANTECEDENTES:Un nuevo índice bibliométrico llamado innovación desestabilizadora y de desarrollo ha sido propuesto para identificar publicaciones de vanguardia y que pueden romper paradigmas.OBJETIVO:La meta fué aplicar el índice de desestabilización a la literature en cirugía colorectal para aportar a la comunidad con un acervo importante de artículos de investigación.DISEÑO:Un análisis bibliométrico.PARAMETROS:Las 100 publicaciones mas desestabilizadores y de desarrollo en las revistas: Diseases of the Colon and Rectum, Colorectal Disease, International Journal of Colorectal Disease, y Techniques in Coloproctology se recuperaron de una base de datos validada con puntuaciones de desestabilización y se ligaron con la herramienta iCite NIH para obtener la cuantificación de citas.PRINCIPAL MEDIDA DE RESULTADO:El índice desestabilizador y la cuantificación de citas.RESULTADOS:Se identificaron 12,127 articulos publicados en Diseases of the Colon and Rectum (n = 8,109), International Journal of Colorectal Disease (n = 1,912), Colorectal Disease (n = 1,751), y Techniques in Coloproctology (n = 355) de 1954-2014. Diseases of the Colon and Rectum representó la mayoría de las publicaciones dentro de la lista de los 100 mas desestabilizadores y de desarrollo. Esta literatura desestabilizadora se encuentra en el principal 1% de la distribución de la puntuacón desestabilizadora en PubMed y se citaron de 1 a 671 veces. El ser citado con frecuencia se relacionó vagamente con las puntuaciones de desastibilización (r = 0.09). Los artículos de desarrollo tuvieron puntuaciones de desestabilización que estuvieron muy correlacionados con la cuantificación de las citas (r = 0.18).LIMITACIONES:Las sujetas a las limitaciones de los índices bibliométricos, que se modifican en el tiempo.DISCUSION:La putuación de desestabilicación identificó trabajos perspicaces, pragmáticos y modificadores de paradigmas en cirugía colorrectal. Es de interés identificar que se incluyeron una gran variedad de temas y en forma consistente editoriales, reportes de casos y series de casos que representaron una investigación importante. Este análisis bibliométrico aporta a los cirujanos colorrectales de un acervo de investigación único que puede con frecuencia pasarse por alto, y sin embargo tener una gran importancia académica. Consulte Video Resumen en http://links.lww.com/DCR/B639. (Traducción- Dr. Miguel Esquivel-Herrera).

Analysis of 567,758 randomized controlled trials published over 30 years reveals trends in phrases used to discuss results that do not reach statistical significance

The power of language to modify the reader's perception of interpreting biomedical results cannot be underestimated. Misreporting and misinterpretation are pressing problems in randomized controlled trials (RCT) output. This may be partially related to the statistical significance paradigm used in clinical trials centered around a P value below 0.05 cutoff. Strict use of this P value may lead to strategies of clinical researchers to describe their clinical results with P values approaching but not reaching the threshold to be "almost significant." The question is how phrases expressing nonsignificant results have been reported in RCTs over the past 30 years. To this end, we conducted a quantitative analysis of English full texts containing 567,758 RCTs recorded in PubMed between 1990 and 2020 (81.5% of all published RCTs in PubMed). We determined the exact presence of 505 predefined phrases denoting results that approach but do not cross the line of formal statistical significance (P < 0.05). We modeled temporal trends in phrase data with Bayesian linear regression. Evidence for temporal change was obtained through Bayes factor (BF) analysis. In a randomly sampled subset, the associated P values were manually extracted. We identified 61,741 phrases in 49,134 RCTs indicating almost significant results (8.65%; 95% confidence interval (CI): 8.58% to 8.73%). The overall prevalence of these phrases remained stable over time, with the most prevalent phrases being "marginally significant" (in 7,735 RCTs), "all but significant" (7,015), "a nonsignificant trend" (3,442), "failed to reach statistical significance" (2,578), and "a strong trend" (1,700). The strongest evidence for an increased temporal prevalence was found for "a numerical trend," "a positive trend," "an increasing trend," and "nominally significant." In contrast, the phrases "all but significant," "approaches statistical significance," "did not quite reach statistical significance," "difference was apparent," "failed to reach statistical significance," and "not quite significant" decreased over time. In a random sampled subset of 29,000 phrases, the manually identified and corresponding 11,926 P values, 68,1% ranged between 0.05 and 0.15 (CI: 67. to 69.0; median 0.06). Our results show that RCT reports regularly contain specific phrases describing marginally nonsignificant results to report P values close to but above the dominant 0.05 cutoff. The fact that the prevalence of the phrases remained stable over time indicates that this practice of broadly interpreting P values close to a predefined threshold remains prevalent. To enhance responsible and transparent interpretation of RCT results, researchers, clinicians, reviewers, and editors may reduce the focus on formal statistical significance thresholds and stimulate reporting of P values with corresponding effect sizes and CIs and focus on the clinical relevance of the statistical difference found in RCTs.

Pharmacovigilance with Transformers: A Framework to Detect Adverse Drug Reactions Using BERT Fine-Tuned with FARM

Adverse drug reactions (ADRs) are the undesirable effects associated with the use of a drug due to some pharmacological action of the drug. During the last few years, social media has become a popular platform where people discuss their health problems and, therefore, has become a popular source to share information related to ADR in the natural language. This paper presents an end-to-end system for modelling ADR detection from the given text by fine-tuning BERT with a highly modular Framework for Adapting Representation Models (FARM). BERT overcame the predominant neural networks bringing remarkable performance gains. However, training BERT is a computationally expensive task which limits its usage for production environments and makes it difficult to determine the most important hyperparameters for the downstream task. Furthermore, developing an end-to-end ADR extraction system comprising two downstream tasks, i.e., text classification for filtering text containing ADRs and extracting ADR mentions from the classified text, is also challenging. The framework used in this work, FARM-BERT, provides support for multitask learning by combining multiple prediction heads which makes training of the end-to-end systems easier and computationally faster. In the proposed model, one prediction head is used for text classification and the other is used for ADR sequence labeling. Experiments are performed on Twitter, PubMed, TwiMed-Twitter, and TwiMed-PubMed datasets. The proposed model is compared with the baseline models and state-of-the-art techniques, and it is shown that it yields better results for the given task with the F-scores of 89.6%, 97.6%, 84.9%, and 95.9% on Twitter, PubMed, TwiMed-Twitter, and TwiMed-PubMed datasets, respectively. Moreover, training time and testing time of the proposed model are compared with BERT's, and it is shown that the proposed model is computationally faster than BERT.

Social Media and Research Publication Activity During Early Stages of the COVID-19 Pandemic: Longitudinal Trend Analysis

BACKGROUND

The COVID-19 pandemic has highlighted the importance of rapid dissemination of scientific and medical discoveries. Current platforms available for the distribution of scientific and clinical research data and information include preprint repositories and traditional peer-reviewed journals. In recent times, social media has emerged as a helpful platform to share scientific and medical discoveries.

OBJECTIVE

This study aimed to comparatively analyze activity on social media (specifically, Twitter) and that related to publications in the form of preprint and peer-reviewed journal articles in the context of COVID-19 and gastroenterology during the early stages of the COVID-19 pandemic.

METHODS

COVID-19-related data from Twitter (tweets and user data) and articles published in preprint servers (bioRxiv and medRxiv) as well as in the PubMed database were collected and analyzed during the first 6 months of the pandemic, from December 2019 through May 2020. Global and regional geographic and gastrointestinal organ-specific social media trends were compared to preprint and publication activity. Any relationship between Twitter activity and preprint articles published and that between Twitter activity and PubMed articles published overall, by organ system, and by geographic location were identified using Spearman's rank-order correlation.

RESULTS

Over the 6-month period, 73,079 tweets from 44,609 users, 7164 journal publications, and 4702 preprint publications were retrieved. Twitter activity (ie, number of tweets) peaked in March 2020, whereas preprint and publication activity (ie, number of articles published) peaked in April 2020. Overall, strong correlations were identified between trends in Twitter activity and preprint and publication activity (P<.001 for both). COVID-19 data across the three platforms mainly concentrated on pulmonology or critical care, but when analyzing the field of gastroenterology specifically, most tweets pertained to pancreatology, most publications focused on hepatology, and most preprints covered hepatology and luminal gastroenterology. Furthermore, there were significant positive associations between trends in Twitter and publication activity for all gastroenterology topics (luminal gastroenterology: P=.009; hepatology and inflammatory bowel disease: P=.006; gastrointestinal endoscopy: P=.007), except pancreatology (P=.20), suggesting that Twitter activity did not correlate with publication activity for this topic. Finally, Twitter activity was the highest in the United States (7331 tweets), whereas PubMed activity was the highest in China (1768 publications).

CONCLUSIONS

The COVID-19 pandemic has highlighted the potential of social media as a vehicle for disseminating scientific information during a public health crisis. Sharing and spreading information on COVID-19 in a timely manner during the pandemic has been paramount; this was achieved at a much faster pace on social media, particularly on Twitter. Future investigation could demonstrate how social media can be used to augment and promote scholarly activity, especially as the world begins to increasingly rely on digital or virtual platforms. Scientists and clinicians should consider the use of social media in augmenting public awareness regarding their scholarly pursuits.

ReCiter: An open source, identity-driven, authorship prediction algorithm optimized for academic institutions

Academic institutions need to maintain publication lists for thousands of faculty and other scholars. Automated tools are essential to minimize the need for direct feedback from the scholars themselves who are practically unable to commit necessary effort to keep the data accurate. In relying exclusively on clustering techniques, author disambiguation applications fail to satisfy key use cases of academic institutions. Algorithms can perfectly group together a set of publications authored by a common individual, but, for them to be useful to an academic institution, they need to programmatically and recurrently map articles to thousands of scholars of interest en masse. Consistent with a savvy librarian’s approach for generating a scholar’s list of publications, identity-driven authorship prediction is the process of using information about a scholar to quantify the likelihood that person wrote certain articles. ReCiter is an application that attempts to do exactly that. ReCiter uses institutionally-maintained identity data such as name of department and year of terminal degree to predict which articles a given scholar has authored. To compute the overall score for a given candidate article from PubMed (and, optionally, Scopus), ReCiter uses: up to 12 types of commonly available, identity data; whether other members of a cluster have been accepted or rejected by a user; and the average score of a cluster. In addition, ReCiter provides scoring and qualitative evidence supporting why particular articles are suggested. This context and confidence scoring allows curators to more accurately provide feedback on behalf of scholars. To help users to more efficiently curate publication lists, we used a support vector machine analysis to optimize the scoring of the ReCiter algorithm. In our analysis of a diverse test group of 500 scholars at an academic private medical center, ReCiter correctly predicted 98% of their publications in PubMed.

Quantifying the scientific interest in surgical training and education: numerical evidence of a PubMed analysis

The scientific interest (SI) for a given field can be ascertained by quantifying the volume of published research. We quantified the SI in surgical education to clarify the extent of worldwide efforts on this crucial factor required to improve health-care systems. A set of Medical Subject Headings (MeSH) was defined for the PubMed search. The number of Pubmed Indexed Papers (nPIP) relevant to the SI was extracted from database conception to December 2016 and their distribution and evolution by country were analyzed at 10-year intervals. Population Adjusted Index (PAI) and Medical School Adjusted Index (MSAI) analyses were performed for countries with the nPIP > 30. We identified 51,713 articles written in 33 different languages related to surgical education; 87.6% of these were written in English. General surgery was the leading surgical specialty. The overall nPIP doubled every 10 years from 1987 (from 6009 to 13,501, to 26,272) but stabilized at 3707, 3800 and 3433 in the past 3 years, respectively. The PAI and MSAI analyses showed that the USA, United Kingdom, New Zealand, Canada, Australia and Ireland are top producers of published research in surgical education, constituting a combined 62.88% of the nPIP. Our quantification of the change in SI in surgical education and training gives a clear picture of evolution, efforts and leadership worldwide over time. This picture mirrors an international academic society that should encourage all those involved in surgical education to improve efforts in educational research.

A systematic review and meta-analysis of published research data on COVID-19 infection fatality rates

An important unknown during the coronavirus disease-2019 (COVID-19) pandemic has been the infection fatality rate (IFR). This differs from the case fatality rate (CFR) as an estimate of the number of deaths and as a proportion of the total number of cases, including those who are mild and asymptomatic. While the CFR is extremely valuable for experts, IFR is increasingly being called for by policy makers and the lay public as an estimate of the overall mortality from COVID-19.

METHODS

Pubmed, Medline, SSRN, and Medrxiv were searched using a set of terms and Boolean operators on 25/04/2020 and re-searched on 14/05/2020, 21/05/2020 and 16/06/2020. Articles were screened for inclusion by both authors. Meta-analysis was performed in Stata 15.1 by using the metan command, based on IFR and confidence intervals extracted from each study. Google/Google Scholar was used to assess the grey literature relating to government reports.

RESULTS

After exclusions, there were 24 estimates of IFR included in the final meta-analysis, from a wide range of countries, published between February and June 2020. The meta-analysis demonstrated a point estimate of IFR of 0.68% (0.53%-0.82%) with high heterogeneity (p < 0.001).

CONCLUSION

Based on a systematic review and meta-analysis of published evidence on COVID-19 until July 2020, the IFR of the disease across populations is 0.68% (0.53%-0.82%). However, due to very high heterogeneity in the meta-analysis, it is difficult to know if this represents a completely unbiased point estimate. It is likely that, due to age and perhaps underlying comorbidities in the population, different places will experience different IFRs due to the disease. Given issues with mortality recording, it is also likely that this represents an underestimate of the true IFR figure. More research looking at age-stratified IFR is urgently needed to inform policymaking on this front.

Bibliometric Analysis of Pediatric Liver Transplantation Research in PubMed from 2014 to 2018

BACKGROUND Pediatric liver transplantation is used to treat children with end-stage liver disease. This study explored the research hotspots and bibliometric characteristics of pediatric liver transplantation through a variety of bibliometric analysis software. We conducted hotspot analysis to help determine important directions for future scientific research. MATERIAL AND METHODS The study samples were articles related to pediatric liver transplantation published in PubMed in the past 5 years. The high-frequency keywords are extracted by BICOMB software, and then a binary matrix and a common word matrix were constructed. Gcluto software was used to perform double-clustering and visual analysis on high-frequency words, and then we obtained hot area classification. Strategic coordinates are constructed using Excel. Citespace and VOSviewer software are used for further analysis and bibliometric data visualization. RESULTS A total of 36 high-frequency words were found in the 4118 studies. A peak map was drawn through double-cluster analysis. Biclustering analysis was used to calculate the concentricity and density of each hotspot. We obtained the top 10 countries/regions engaged in pediatric liver transplantation research. VOSviewer was used to visualize the co-author map. CONCLUSIONS We found 5 clusters and 7 aspects for pediatric liver transplantation. Additionally, calculation results showed that post-transplant lymphoproliferative disorder in pediatric patients and outcomes of multivisceral transplantation seem very promising. This conclusion is of great value for future exploratory research.

Quantifying Sex Bias in Clinical Studies at Scale With Automated Data Extraction

IMPORTANCE

Analyses of female representation in clinical studies have been limited in scope and scale.

OBJECTIVE

To perform a large-scale analysis of global enrollment sex bias in clinical studies.

DESIGN, SETTING, AND PARTICIPANTS

In this cross-sectional study, clinical studies from published articles from PubMed from 1966 to 2018 and records from Aggregate Analysis of ClinicalTrials.gov from 1999 to 2018 were identified. Global disease prevalence was determined for male and female patients in 11 disease categories from the Global Burden of Disease database: cardiovascular, diabetes, digestive, hepatitis (types A, B, C, and E), HIV/AIDS, kidney (chronic), mental, musculoskeletal, neoplasms, neurological, and respiratory (chronic). Machine reading algorithms were developed that extracted sex data from tables in articles and records on December 31, 2018, at an artificial intelligence research institute. Male and female participants in 43 135 articles (792 004 915 participants) and 13 165 records (12 977 103 participants) were included.

MAIN OUTCOMES AND MEASURES

Sex bias was defined as the difference between the fraction of female participants in study participants minus prevalence fraction of female participants for each disease category. A total of 1000 bootstrap estimates of sex bias were computed by resampling individual studies with replacement. Sex bias was reported as mean and 95% bootstrap confidence intervals from articles and records in each disease category over time (before or during 1993 to 2018), with studies or participants as the measurement unit.

RESULTS

There were 792 004 915 participants, including 390 470 834 female participants (49%), in articles and 12 977 103 participants, including 6 351 619 female participants (49%), in records. With studies as measurement unit, substantial female underrepresentation (sex bias ≤ -0.05) was observed in 7 of 11 disease categories, especially HIV/AIDS (mean for articles, -0.17 [95% CI, -0.18 to -0.16]), chronic kidney diseases (mean, -0.17 [95% CI, -0.17 to -0.16]), and cardiovascular diseases (mean, -0.14 [95% CI, -0.14 to -0.13]). Sex bias in articles for all categories combined was unchanged over time with studies as measurement unit (range, -0.15 [95% CI, -0.16 to -0.13] to -0.10 [95% CI, -0.14 to -0.06]), but improved from before or during 1993 (mean, -0.11 [95% CI, -0.16 to -0.05]) to 2014 to 2018 (mean, -0.05 [95% CI, -0.09 to -0.02]) with participants as the measurement unit. Larger study size was associated with greater female representation.

CONCLUSIONS AND RELEVANCE

Automated extraction of the number of participants in clinical reports provides an effective alternative to manual analysis of demographic bias. Despite legal and policy initiatives to increase female representation, sex bias against female participants in clinical studies persists. Studies with more participants have greater female representation. Differences between sex bias estimates with studies vs participants as measurement unit, and between articles vs records, suggest that sex bias with both measures and data sources should be reported.

Single screening versus conventional double screening for study selection in systematic reviews: a methodological systematic review

BACKGROUND

Stringent requirements exist regarding the transparency of the study selection process and the reliability of results. A 2-step selection process is generally recommended; this is conducted by 2 reviewers independently of each other (conventional double-screening). However, the approach is resource intensive, which can be a problem, as systematic reviews generally need to be completed within a defined period with a limited budget. The aim of the following methodological systematic review was to analyse the evidence available on whether single screening is equivalent to double screening in the screening process conducted in systematic reviews.

METHODS

We searched Medline, PubMed and the Cochrane Methodology Register (last search 10/2018). We also used supplementary search techniques and sources ("similar articles" function in PubMed, conference abstracts and reference lists). We included all evaluations comparing single with double screening. Data were summarized in a structured, narrative way.

RESULTS

The 4 evaluations included investigated a total of 23 single screenings (12 sets for screening involving 9 reviewers). The median proportion of missed studies was 5% (range 0 to 58%). The median proportion of missed studies was 3% for the 6 experienced reviewers (range: 0 to 21%) and 13% for the 3 reviewers with less experience (range: 0 to 58%). The impact of missing studies on the findings of meta-analyses had been reported in 2 evaluations for 7 single screenings including a total of 18,148 references. In 3 of these 7 single screenings - all conducted by the same reviewer (with less experience) - the findings would have changed substantially. The remaining 4 of these 7 screenings were conducted by experienced reviewers and the missing studies had no impact or a negligible on the findings of the meta-analyses.

CONCLUSIONS

Single screening of the titles and abstracts of studies retrieved in bibliographic searches is not equivalent to double screening, as substantially more studies are missed. However, in our opinion such an approach could still represent an appropriate methodological shortcut in rapid reviews, as long as it is conducted by an experienced reviewer. Further research on single screening is required, for instance, regarding factors influencing the number of studies missed.

A systematic review of phytocannabinoid exposure on the endocannabinoid system: Implications for psychosis

Cannabis, the most widely used illicit drug worldwide, produces psychoactive effects through its component cannabinoids, which act on the endocannabinoid system. Research on how cannabinoid exposure affects the endocannabinoid system is limited. Substantial evidence indicates cannabis use as a risk factor for psychosis, and the mechanism(s) by which this is occurring is/are currently unknown. Here, we conduct the first review of the effects of exogenous cannabinoids on the endocannabinoid system in humans with and without psychotic disorders. The most well established finding is the down-regulation of cannabinoid CB1 receptors (CB1R) after chronic and recent cannabis exposure, but it remains uncertain whether this effect is present in cannabis users with schizophrenia. We highlight where cannabis exposure affects the endocannabinoid system in a pattern that may mirror what is seen in psychosis, and how further research can push this field forward. In these times of changing cannabis legislation, research highlighting the biological effects of cannabinoids is greatly needed.

Study filters for non-randomized studies of interventions consistently lacked sensitivity upon external validation

BACKGROUND

Little evidence is available on searches for non-randomized studies (NRS) in bibliographic databases within the framework of systematic reviews. For instance, it is currently unclear whether, when searching for NRS, effective restriction of the search strategy to certain study types is possible. The following challenges need to be considered: 1) For non-randomized controlled trials (NRCTs): whether they can be identified by established filters for randomized controlled trials (RCTs). 2) For other NRS types (such as cohort studies): whether study filters exist for each study type and, if so, which performance measures they have. The aims of the present analysis were to identify and validate existing NRS filters in MEDLINE as well as to evaluate established RCT filters using a set of MEDLINE citations.

METHODS

Our analysis is a retrospective analysis of study filters based on MEDLINE citations of NRS from Cochrane reviews. In a first step we identified existing NRS filters. For the generation of the reference set, we screened Cochrane reviews evaluating NRS, which covered a broad range of study types. The citations of the studies included in the Cochrane reviews were identified via the reviews' bibliographies and the corresponding PubMed identification numbers (PMIDs) were extracted from PubMed. Random samples comprising up to 200 citations (i.e. 200 PMIDs) each were created for each study type to generate the test sets.

RESULTS

A total of 271 Cochrane reviews from 41 different Cochrane groups were eligible for data extraction. We identified 14 NRS filters published since 2001. The study filters generated between 660,000 and 9.5 million hits in MEDLINE. Most filters covered several study types. The reference set included 2890 publications classified as NRS for the generation of the test sets. Twelve test sets were generated (one for each study type), of which 8 included 200 citations each. None of the study filters achieved sufficient sensitivity (≥ 92%) for all of the study types targeted.

CONCLUSIONS

The performance of current NRS filters is insufficient for effective use in daily practice. It is therefore necessary to develop new strategies (e.g. new NRS filters in combination with other search techniques). The challenges related to NRS should be taken into account.

Animal Models of Tremor: Relevance to Human Tremor Disorders

Background

Tremor is the most common movement disorder; however, the pathophysiology of tremor remains elusive. While several neuropathological alterations in tremor disorders have been observed in post-mortem studies of human brains, a full understanding of the relationship between brain circuitry alterations and tremor requires testing in animal models. Additionally, tremor animal models are critical for our understanding of tremor pathophysiology, and/or to serve as a platform for therapy development.

Methods

A PubMed search was conducted in May 2018 to identify published papers for review.

Results

The methodology used in most studies on animal models of tremor lacks standardized measurement of tremor frequency and amplitude; instead, these studies are based on the visual inspection of phenotypes, which may fail to delineate tremor from other movement disorders such as ataxia. Of the animal models with extensive tremor characterization, harmaline-induced rodent tremor models provide an important framework showing that rhythmic and synchronous neuronal activities within the olivocerebellar circuit can drive action tremor. In addition, dopamine-depleted monkey and mouse models may develop rest tremor, highlighting the role of dopamine in rest tremor generation. Finally, other animal models of tremor have involvement of the cerebellar circuitry, leading to altered Purkinje cell physiology.

Discussion

Both the cerebellum and the basal ganglia are likely to play a role in tremor generation. While the cerebellar circuitry can generate rhythmic movements, the nigrostriatal system is likely to modulate the tremor circuit. Tremor disorders are heterogeneous in nature. Therefore, each animal model may represent a subset of tremor disorders, which collectively can advance our understanding of tremor.

Specificities of mental health problems in the countries of the Maghreb region, through scientific publications on the theme of suicide. A systematic review

BACKGROUND

In an article published in the journal "La Tunisie médicale" in 1972, Professor Sleim Ammar, a visionary North African psychiatrist, announced that "suicide is a public health problem" in the Maghreb.

OBJECTIVES

This work, on the one hand, aims to describe the profile of Maghreb publications indexed in the Medline database, on the topic of suicide during the last forty years, and on the other hand to extract the Maghreb specificities of the epidemiology and the suicide management, used as tracer of Maghreb mental health.

METHODS

This is a systematic medical review, combined with a bibliometric study, on the theme of "suicide" in Maghreb region. We submitted a distinct and clear search term to the Medline database, via its online interface, "PubMed", on May 16, 2018. In addition to the description of the bibliometric characteristics of these Maghreb studies, we synthesized the analysis of their content by tables detailing the documented facts and recommended proposals.

RESULTS

Out of 32 Maghreb articles on suicide, selected for this literature review, 18 were Moroccan and 13 were Tunisian. Two-thirds of them published after 2010. The snapshot of Maghreb research indexed on Medline, on suicide, was the following: a publication written in French, focused on the attempts of suicide, with a monocentric and descriptive methodological approach, written by a psychiatry team and published in an "open access" African journal. The recommendations of these North African publications on suicide were often general and not operational.

CONCLUSION

the North African scientific research on suicide remains unproductive and of low methodological quality. The focus of this research towards primary suicide prevention, as part of a comprehensive public health approach, would be essential for the promotion of mental health in the North African region.

Chronobiological theories of mood disorder

Major depressive disorder (MDD) remains the most prevalent mental disorder and a leading cause of disability, affecting approximately 100 million adults worldwide. The disorder is characterized by a constellation of symptoms affecting mood, anxiety, neurochemical balance, sleep patterns, and circadian and/or seasonal rhythm entrainment. However, the mechanisms underlying the association between chronobiological parameters and depression remain unknown. A PubMed search was conducted to review articles from 1979 to the present, using the following search terms: "chronobiology," "mood," "sleep," and "circadian rhythms." We aimed to synthesize the literature investigating chronobiological theories of mood disorders. Current treatments primarily include tricyclic antidepressants and selective serotonin reuptake inhibitors, which are known to increase extracellular concentrations of monoamine neurotransmitters. However, these antidepressants do not treat the sleep disturbances or circadian and/or seasonal rhythm dysfunctions associated with depressive disorders. Several theories associating sleep and circadian rhythm disturbances with depression have been proposed. Current evidence supports the existence of associations between these, but the direction of causality remains elusive. Given the existence of chronobiological disturbances in depression and evidence regarding their treatment in improving depression, a chronobiological approach, including timely use of light and melatonin agonists, could complement the treatment of MDD.

What Can Big Data on Academic Interest Reveal about a Drug? Reflections in Three Major US Databases

The different stages of the life cycle of a drug - 'prenatal' stage, birth of a drug, rapid growth, maturity and stability, decline, and status before 'death' - are reflected in the three following databases: journal articles (PubMed-www.ncbi.nlm.nih.gov/pubmed); patents (US Patent Office-http://partfl1.uspto.gov/netahtml/PTO/search-adv.htlm); and approved drugs (FDA - www.accessdata.fda.gov/scripts/cder/drugsatfda/index/cfm). These databases are huge, from authoritative sources, correctly classified, and they properly link different datasets. Analysis of such data can uncover hidden patterns important for the assessment of drug status and may also yield some predictions regarding its future prospects. Drug-related, publication-based academic bibliographic records are especially numerous and support the development of various scientometric indices. In combination with information from other types of databases, they can outline various trends in pharmacology. Scientometric indices can be classified into those indicating a change in the status of a drug, and those assessing the chances for success, or even drug discontinuation. Here, we present big data analytics on publication-based academic interest in two segments: (i) description of scientometric indices and (ii) their applications for the assessment of the status of a drug.

KCa3.1 Channels and Glioblastoma: In Vitro Studies

BACKGROUND

Several tumor entities including brain tumors aberrantly overexpress intermediate conductance Ca2+ activated KCa3.1 K+ channels. These channels contribute significantly to the transformed phenotype of the tumor cells.

METHOD

PubMed was searched in order to summarize our current knowledge on the molecular signaling upstream and downstream and the effector functions of KCa3.1 channel activity in tumor cells in general and in glioblastoma cells in particular. In addition, KCa3.1 expression and function for repair of DNA double strand breaks was determined experimentally in primary glioblastoma cultures in dependence on the abundance of proneural and mesenchymal stem cell markers.

RESULTS

By modulating membrane potential, cell volume, Ca2+ signals and the respiratory chain, KCa3.1 channels in both, plasma and inner mitochondrial membrane, have been demonstrated to regulate many cellular processes such as migration and tissue invasion, metastasis, cell cycle progression, oxygen consumption and metabolism, DNA damage response and cell death of cancer cells. Moreover, KCa3.1 channels have been shown to crucially contribute to resistance against radiotherapy. Futhermore, the original in vitro data on KCa3.1 channel expression in subtypes of glioblastoma stem(-like) cells propose KCa3.1 as marker for the mesenchymal subgroup of cancer stem cells and suggest that KCa3.1 contributes to the therapy resistance of mesenchymal glioblastoma stem cells.

CONCLUSION

The data suggest KCa3.1 channel targeting in combination with radiotherapy as promising new tool to eradicate therapy-resistant mesenchymal glioblastoma stem cells.

The Challenge of microRNA as a Biomarker of Epilepsy

BACKGROUND

Epilepsy is one of chronic severe neurological disorders possess to recurring seizures. And now anti-epileptic drugs are only effective in less than one third of epilepsy patients, and biomarkers predicting are not available when the specific antiepileptic drugs treated. Advanced studies have showed that miRNA may be a key in the pathogenesis of epilepsy beginning in the early 2000 years. Several target genes and pathways of miRNA which related to the therapeutic methods to epilepsy.

METHOD

We searched PubMed from Jan 1,2000 to Jan 1, 2017, using the terms "epilepsy AND microRNA AND biomarker" and "seizure AND microRNA AND biomarker". We selected articles that featured novel miRNAs in vivo epilepsy models and patients. We then selected the most relevant articles based on a subjective appraisal of their quality and mechanistic insight that could be relevant to epilepsy.

RESULTS

Decrease the expression of has-miR134 could be a potential non-invasive biomarker to use in diagnosis for the epilepsy patients for using hsa-miR-134 also be identified to distinguish patients with and without epilepsy. miR-181a show significant downregulation in the acute stage, but up regulation in the chronic stage and in the latent stage there is no changing and how about this phenomenon appearance in different stage still should be discussed in the future. Besides that, miR- 146a can down-regulated in the patients using genome-wide for serum in circulating miRNAs.miR- 124, miR-199a, and miR-128 etc. could be a candidate for the biomarker in future. miR-15a-5p and -194-5p down-regulated in epilepsy patients, in the future, it may be used as a novel biomarker for improve diagnosis.

CONCLUSION

These observations give a chance that new development for diagnosis and treatment of epilepsy patients. Advanced technique and miRNA combination may product more effective roles in epilepsy and other disease. These reports will be available to solve the application of miRNAs as biomarkers and novel therapy approaches for epilepsy. In summary, researcher who focus on miRNAs should be understanding of the causes, treatment, and diagnosis of epilepsy. exploration of any of these effects on the efficacy of these drugs is worthwhile.

[Scientific production from public hospitals of the City of Buenos Aires, 2017]

The number of publications in the scientific literature coming from an institution is an indicator of its scientific production. The scientific production of the hospitals of the Government of the City of Buenos Aires (GCBA) has been evaluated previously, but without discriminating how much of that production corresponded to other academic institutions settled there (University of Buenos Aires, UBA, National Council of Scientific Research and Techniques, CONICET). Our objective was to evaluate the publications included in PubMed that correspond to hospitals of the GCBA, describe their main characteristics, and discriminate the contribution of other academic institutions (UBA and CONICET). It is a cross-sectional study based on a PubMed search, using the name of each of the 34 GCBA hospitals, CONICET and UBA in the "affiliation" field. In total, 2727 publications from GCBA hospitals were identified (4.6% of Argentine publications); 73.9% in English, 78.9% in relation to humans, 37.2% in the last 5 years; 6.4% with high level of evidence (clinical trials and meta-analysis), and 28.4% including children. Compared to the national total, the GCBA publications include fewer works in English, more research in humans, more clinical trials and more research in children. Of the publications corresponding to hospitals of the GCBA, 90.4% did not share the affiliation with CONICET or with UBA. In conclusion, the GCBA hospitals generated 4.6% of the total Argentine publications in PubMed; and 90% of these was not shared with UBA or CONICET. Publications from GCBA institutions include more clinical trials and research in children.

Improving precision in concept normalization

Most natural language processing applications exhibit a trade-off between precision and recall. In some use cases for natural language processing, there are reasons to prefer to tilt that trade-off toward high precision. Relying on the Zipfian distribution of false positive results, we describe a strategy for increasing precision, using a variety of both pre-processing and post-processing methods. They draw on both knowledge-based and frequentist approaches to modeling language. Based on an existing high-performance biomedical concept recognition pipeline and a previously published manually annotated corpus, we apply this hybrid rationalist/empiricist strategy to concept normalization for eight different ontologies. Which approaches did and did not improve precision varied widely between the ontologies.

Meta-analysis of mismatch negativity to simple versus complex deviants in schizophrenia

Mismatch negativity (MMN) deficits in schizophrenia (SCZ) have been studied extensively since the early 1990s, with the vast majority of studies using simple auditory oddball task deviants that vary in a single acoustic dimension such as pitch or duration. There has been a growing interest in using more complex deviants that violate more abstract rules to probe higher order cognitive deficits. It is still unclear how sensory processing deficits compare to and contribute to higher order cognitive dysfunction, which can be investigated with later attention-dependent auditory event-related potential (ERP) components such as a subcomponent of P300, P3b. In this meta-analysis, we compared MMN deficits in SCZ using simple deviants to more complex deviants. We also pooled studies that measured MMN and P3b in the same study sample and examined the relationship between MMN and P3b deficits within study samples. Our analysis reveals that, to date, studies using simple deviants demonstrate larger deficits than those using complex deviants, with effect sizes in the range of moderate to large. The difference in effect sizes between deviant types was reduced significantly when accounting for magnitude of MMN measured in healthy controls. P3b deficits, while large, were only modestly greater than MMN deficits (d=0.21). Taken together, our findings suggest that MMN to simple deviants may still be optimal as a biomarker for SCZ and that sensory processing dysfunction contributes significantly to MMN deficit and disease pathophysiology.

Adult Pilocytic Astrocytoma: An Institutional Series and Systematic Literature Review for Extent of Resection and Recurrence

INTRODUCTION

Pilocytic astrocytoma is a classically benign tumor that most often affects pediatric patients. Rarely, it occurs during adulthood. We present a case series and systematic literature review of adult pilocytic astrocytoma (APA) to examine the clinical presentation, extent of resection, and recurrence rate associated with this tumor in this population.

MATERIALS AND METHODS

Our institutional records were retrospectively reviewed for cases of pilocytic astrocytoma in adults. A PubMed search identified English-language studies of pathology-proven APA. A meta-analysis was performed to determine the relationship between extent of tumor resection and recurrence.

RESULTS

Forty-six patients with APA were diagnosed at our institution (mean age 33.6 ± 13.3; 24 [52%] female). Twenty-four patients (52%) underwent gross total resection, 11 (24%) subtotal resection, 4 (9%) near total resection, 4 (9%) observation after biopsy, and 3 (6%) radiotherapy alone. Tumors recurred or progressed in 6 (13%) patients, of whom 4 were treated by STR and 2 were treated by radiotherapy alone. Thirty-nine (95%) patients were still alive at last follow-up. A systematic literature review identified 415 patients with APA in 38 studies. Including our case series, 7 studies reported extent of resection, follow-up, and recurrence. Of 254 patients with a weighted mean follow-up of 77.7 ± 49.6 (31-250) months, 129 (51%) were treated with gross total resection, and 125 (49%) underwent subtotal resection. Tumor recurred in 79 (31%) patients, 22 (27%) after gross total resection and 57 (73%) after subtotal resection (P < 0.001).

CONCLUSIONS

Pilocytic astrocytoma rarely presents during adulthood. Overall, prognosis is favorable and survival rates are high. APA recurrence is more likely after STR, and the goal of surgery should always be GTR when feasible.

Aripiprazole, A Drug that Displays Partial Agonism and Functional Selectivity

BACKGROUND

The treatment of schizophrenia is challenging due to the wide range of symptoms (positive, negative, cognitive) associated with the disease. Typical antipsychotics that antagonize D2 receptors are effective in treating positive symptoms, but extrapyramidal side-effects (EPS) are a common occurrence. Atypical antipsychotics targeting 5-HT2A and D2 receptors are more effective at treating cognitive and negative symptoms compared to typical antipsychotics, but these drugs also result in side-effects such as metabolic syndromes.

OBJECTIVE

To identify evidence in the literature that elucidates the pharmacological profile of aripiprazole.s.

METHODS

We searched PubMed for peer reviewed articles on aripiprazole and its clinical efficacy, side-effects, pharmacology, and effects in animal models of schizophrenia symptoms.

RESULTS

Aripiprazole is a newer atypical antipsychotic that displays a unique pharmacological profile, including partial D2 agonism and functionally selective properties. Aripiprazole is effective at treating the positive symptoms of schizophrenia and has the potential to treat negative and cognitive symptoms at least as well as other atypical antipsychotics. The drug has a favorable side-effect profile and has a low propensity to result in EPS or metabolic syndromes. Animal models of schizophrenia have been used to determine the efficacy of aripiprazole in symptom management. In these instances, aripiprazole resulted in the reversal of deficits in extinction, pre-pulse inhibition, and social withdrawal. Because aripiprazole requires a greater than 90% occupancy rate at D2 receptors to be clinically active and does not produce EPS, this suggests a functionally selective effect on intracellular signaling pathways.

CONCLUSION

A combination of factors such as dopamine system stabilization via partial agonism, functional selectivity at D2 receptors, and serotonin-dopamine system interaction may contribute to the ability of aripiprazole to successfully manage schizophrenia symptoms. This review examines these mechanisms of action to further clarify the pharmacological actions of aripiprazole.

Science and Facebook: The same popularity law!

The distribution of scientific citations for publications selected with different rules (author, topic, institution, country, journal, etc…) collapse on a single curve if one plots the citations relative to their mean value. We find that the distribution of “shares” for the Facebook posts rescale in the same manner to the very same curve with scientific citations. This finding suggests that citations are subjected to the same growth mechanism with Facebook popularity measures, being influenced by a statistically similar social environment and selection mechanism. In a simple master-equation approach the exponential growth of the number of publications and a preferential selection mechanism leads to a Tsallis-Pareto distribution offering an excellent description for the observed statistics. Based on our model and on the data derived from PubMed we predict that according to the present trend the average citations per scientific publications exponentially relaxes to about 4.

Genetic Landscape of Congenital Myasthenic Syndromes From Turkey: Novel Mutations and Clinical Insights

Congenital myasthenic syndromes are clinically and genetically heterogeneous disorders of neuromuscular transmission. Most are treatable, but certain subtypes worsen with cholinesterase inhibitors. This underlines the importance of genetic diagnosis. Here, the authors report on cases with genetically proven congenital myasthenic syndromes from Turkey. The authors retrospectively reviewed their experience of all patients with congenital myasthenic syndromes, referred over a 5-year period (2011-2016) to the Child Neurology Department of Dokuz Eylül University, Izmir, Turkey. In addition, PubMed was searched for published cases of genetically proven congenital myasthenic syndromes originating from Turkey. In total, the authors identified 43 (8 new patients, 35 recently published patients) cases. Defects in the acetylcholine receptor (n = 15; 35%) were the most common type, followed by synaptic basal-lamina associated (n = 14; 33%) and presynaptic syndromes (n = 10; 23%). The authors had only 3 cases (7%) who had defects in endplate development. One patient had mutation GFPT1 gene (n = 1; 2%). Knowledge on congenital myasthenic syndromes and related genes in Turkey will lead to prompt diagnosis and treatment of these rare neuromuscular disorders.

Patients with schizophrenia show aberrant patterns of basal ganglia activation: Evidence from ALE meta-analysis

The diverse circuits and functional contributions of the basal ganglia, coupled with known differences in dopaminergic function in patients with schizophrenia, suggest they may be an important contributor to the etiology of the hallmark symptoms and cognitive dysfunction experienced by these patients. Using activation-likelihood-estimation meta-analysis of functional imaging research, we investigated differences in activation patterns in the basal ganglia in patients with schizophrenia, relative to healthy controls across task domains. This analysis included 42 functional neuroimaging studies, representing a variety of behavioral domains that have been linked to basal ganglia function in prior work. We provide important new information about the functional activation patterns and functional topography of the basal ganglia for different task domains in healthy controls. Crucially however, we demonstrate that across task domains, patients with schizophrenia show markedly decreased activation in the basal ganglia relative to healthy controls. Our results provide further support for basal ganglia dysfunction in patients with schizophrenia, and the broad dysfunction across task domains may contribute to the symptoms and cognitive deficits associated with schizophrenia.

Evolutionary Considerations on the Emerging Subculture of the E-psychonauts and the Novel Psychoactive Substances: A Comeback to the Shamanism?

BACKGROUND

Evolutionary research on drug abuse has hitherto been restricted to proximate studies, considering aetiology, mechanism, and ontogeny. However, in order to explain the recent emergency of a new behavioral pattern (e.g. 'the e-psychonaut style') of novel psychoactive substances' (NPS) intake, a complementary evolutionary model may be needed.

OBJECTIVE

A range of evolutionary interpretations on the 'psychonaut style' and the recent emergency of NPS were here considered.

METHOD

The PubMed database was searched in order to elicit evolutionary theory-based documents commenting on NPS/NPS users/e-psychonauts.

RESULTS

The traditional 'shamanic style' use of entheogens/plant-derived compounds may present with a range of similarities with the 'e-psychonauts' use of mostly of hallucinogen/psychedelic NPS. These users consider themselves as 'new/technological' shamans.

CONCLUSION

Indeed, a range of evolutionary mechanisms, such as: optimal foraging, costly signaling, and reproduction at the expense of health may all cooperate to explain the recent spread and diffusion of the NPS market, and this may represent a reason of concern.

[Acupoints Selection Exploring for Acupuncture Treatment of Insulin Resistance Based on Data Mining]

OBJECTIVE

To analyze the characteristics and rules of acupoint selection for acupuncture treatment of insulin resistance.

METHODS

Data collections were conducted by searching references on acupuncture treatment of insulin resistance in PubMed, CNKI, VIP data base from 1991 to 2016, and acupuncture prescription data base for acupuncture treatment of insulin resistance was established. Data mining was applied to analyze the characteristics and rules of acupoint selection.

RESULTS

A total of 64 papers were recruited, and 73 acupoints were selected in these papers. It was found that the acupoints as Zusanli (ST 36), Sanyinjiao (SP 6), Fenglong (ST 40) and Taichong (LR 3) were used with highest frequencies. All acupoints selected distributed in 13 meridians, especially Foot Yangming Stomach Meridian, Foot Taiyin Bladder Meridian, and Conception Vessel with a total frequency of 58.07%. The special acupoints including five-shu points, eight confluent points and back-shu points, accounted for 56.71%.

CONCLUSIONS

This study excavated the regular acupoint selection and acupoints compatibility for acupuncture treatment in patients with insulin resistance, giving evidence based confirming and direction for acupuncture clinical treatment.

Presymptomatic cortical thinning in familial Alzheimer disease: A longitudinal MRI study

OBJECTIVE

To identify a cortical signature pattern of cortical thinning in familial Alzheimer disease (FAD) and assess its utility in detecting and tracking presymptomatic neurodegeneration.

METHODS

We recruited 43 FAD mutation carriers-36 PSEN1, 7 APP (20 symptomatic, 23 presymptomatic)-and 42 healthy controls to a longitudinal clinical and MRI study. T1-weighted MRI scans were acquired at baseline in all participants; 55 individuals (33 mutation carriers; 22 controls) had multiple (mean 2.9) follow-up scans approximately annually. Cortical thickness was measured using FreeSurfer. A cortical thinning signature was identified from symptomatic FAD participants. We then examined cortical thickness changes in this signature region in presymptomatic carriers and assessed associations with cognitive performance.

RESULTS

The cortical signature included 6 regions: entorhinal cortex, inferior parietal cortex, precuneus, superior parietal cortex, superior frontal cortex, and supramarginal gyrus. There were significant differences in mean cortical signature thickness between mutation carriers and controls 3 years before predicted symptom onset. The earliest significant difference in a single region, detectable 4 years preonset, was in the precuneus. Rate of change in cortical thickness became significantly different in the cortical signature at 5 years before predicted onset, and in the precuneus at 8 years preonset. Baseline mean signature thickness predicted rate of subsequent thinning and correlated with presymptomatic cognitive change.

CONCLUSIONS

The FAD cortical signature appears to be similar to that described for sporadic AD. All component regions showed significant presymptomatic thinning. A composite signature may provide more robust results than a single region and have utility as an outcome measure in presymptomatic trials.

Associated Microscale Spine Density and Macroscale Connectivity Disruptions in Schizophrenia

BACKGROUND

Schizophrenia is often described as a disorder of dysconnectivity, with disruptions in neural connectivity reported on the cellular microscale as well as the global macroscale level of brain organization. How these effects on these two scales are related is poorly understood.

METHODS

First (part I of this study), we collated data on layer 3 pyramidal spine density of the healthy brain from the literature and cross-analyzed these data with new data on macroscale connectivity as derived from diffusion imaging. Second (part II of this study), we examined how alterations in regional spine density in schizophrenia are related to changes in white matter connectivity. Data on group differences in spine density were collated from histology reports in the literature and examined in a meta-regression analysis in context of alterations in macroscale white matter connectivity as derived from diffusion imaging data of a (separately acquired) group of 61 patients and 55 matched control subjects.

RESULTS

Densely connected areas of the healthy human cortex were shown to overlap with areas that display high pyramidal complexity, with pyramidal neurons that are more spinous (p = .0027) compared with pyramidal neurons in areas of low macroscale connectivity. Cross-scale meta-regression analysis showed a significant association between regional variation in level of disease-related spine density reduction in schizophrenia and regional level of decrease in macroscale connectivity (two data sets examined, p = .0028 and p = .0011).

CONCLUSIONS

Our study presents evidence that regional disruptions in microscale neuronal connectivity in schizophrenia go hand in hand with changes in macroscale brain connectivity.

Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists

We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of Health (NIH). In doing so, we exploited established unique identifiers—Principal Investigator (PI) IDs—that the NIH assigns to funded scientists. Analyzing a set of 36,987 NIH scientists who received their first R01 grant between 1985 and 2009, we identified 355,921 articles appearing in PubMed that would allow us to evaluate the precision and recall of the Author-ity disambiguation. We found that Author-ity identified the NIH scientists with 99.51% precision across the articles. It had a corresponding recall of 99.64%. Precision and recall, moreover, appeared stable across common and uncommon last names, across ethnic backgrounds, and across levels of scientist productivity.

A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome

Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, “conronavirus”, “case”, “transmission” and “detection” were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened.

[An analysis of Chilean biomedical publications in PubMed in the years 2008-2009]

BACKGROUND

During the years 2008 and 2009, 1,191 biomedical articles authored by Chilean investigators working in Chile were indexed in PubMed.

AIMS

To evaluate the potential visibility of those articles, according to scientometric indexes of the journals where they were published.

METHODS

Those journals where the articles had been published were identified and each journal’s Impact Factor (JIF), 5-year JIF, SCImago Journal Rank (SJR), SCImago Quartiles (Q) for 2010 and the Source Normalized Impact per Paper (SNIP) for 2008-2009 were identified.

RESULTS

Three hundred and twelve articles (26,2%) were dedicated to experimental studies in animals, tissues or cells and they were classified as “Biomedicine”, while 879 (73,8%) were classified as “Clinical Medicine”; in both areas the main type of articles were original reports (90% and 73.6%, respectively). Revista Médica de Chile and Revista Chilena de Infectología concentrated the greater number of publications. Articles classified in Biomedicine were published more frequently in English and in journals with higher scientometric indexes than those classified in Clinical Medicine.

CONCLUSIONS

Biomedical articles dealing with clinical topics, particularly case reports, were published mostly in national journals or in foreign journals with low scientometric indexes. It can be partly attributable to the authors’ interest in reaching local readers. The evaluation of research productivity should combine several scientometric indexes, selected according to the field of research, the institution's and investigators’ interests, with a qualitative and multifactorial assessment.

Appraisal of the Quality of Neurosurgery Clinical Practice Guidelines

OBJECTIVE

The rate of neurosurgery guidelines publications was compared over time with all other specialties. Neurosurgical guidelines and quality of supporting evidence were then analyzed and compared by subspecialty.

METHODS

The authors first performed a PubMed search for "Neurosurgery" and "Guidelines." This was then compared against searches performed for each specialty of the American Board of Medical Specialties. The second analysis was an inventory of all neurosurgery guidelines published by the Agency for Healthcare Research and Quality Guidelines clearinghouse. All Class I evidence and Level 1 recommendations were compared for different subspecialty topics.

RESULTS

When examined from 1970-2010, the rate of increase in publication of neurosurgery guidelines was about one third of all specialties combined (P < 0.0001). However, when only looking at the past 5 years the publication rate of neurosurgery guidelines has converged upon that for all specialties. The second analysis identified 49 published guidelines for assessment. There were 2733 studies cited as supporting evidence, with only 243 of these papers considered the highest class of evidence (8.9%). These papers were used to generate 697 recommendations, of which 170 (24.4%) were considered "Level 1" recommendations.

CONCLUSION

Although initially lagging, the publication of neurosurgical guidelines has recently increased at a rate comparable with that of other specialties. However, the quality of the evidence cited consists of a relatively low number of high-quality studies from which guidelines are created. Wider implications of this must be considered when defining and measuring quality of clinical performance in neurosurgery.

[Research progress and prospect of acupuncture for low-risk mild hypertension]

The low-risk mild hypertension constitutes a considerable proportion in hypertension. Through searching CNKI, Wanfang database, VIP database and PubMed database, literature during the last 10 years was collected and reviewed. It was indicated that excessive diagnosis, insufficient evidence of drug treatment, and poor drug adherence existed in low-risk mild hypertension, however, acupuncture at Renying (ST 9) and other therapies had remarkable effects. This paper mainly expounded the diagnosis and treatment status of low-risk mild hypertension as well as the research summary of acupuncture for low-risk mild hypertension.

Reviewing the Osteotropism in Neuroendocrine Tumors: The Role of Epithelial-Mesenchymal Transition

BACKGROUND

Neuroendocrine tumors (NETs) metastasize to the bone. However, the incidence, clinical features, management and pathogenesis of bone involvement in NET patients have been poorly investigated.

METHODS

We reviewed all published reports of histologically confirmed bone metastatic NETs and explored clinical, radiological, prognostic and therapeutic characteristics in a population of 152 patients. We then evaluated immunohistochemical expression of a panel of eight epithelial-mesenchymal transition (EMT)-related factors including SNAIL, TGF-β1, CTGF, IL-11, PTHrP, EpCAM, CXCR4 and RANK in an independent cohort of 44 archival primary NETs. Biomarker expression was correlated with clinicopathological variables, including skeletal involvement, and tested for survival prediction.

RESULTS

We found that 55% of NET patients with bone metastases were male, with a median age of 55 years at diagnosis. Metastases were restricted to the skeleton in 34% of the NET population, and axial and osteoblastic lesions were prevalent. NETs differently expressed proteins involved in EMT activation. High CXCR4 (p < 0.0001) and low TGF-β1 levels (p = 0.0015) were significantly associated with increased risk of skeletal metastases, suggesting that EMT is implicated in NET osteotropism. By applying an algorithm measuring distinct immunohistochemical predictors of osteotropism on primary tumors, we were able to identify NET patients with bone metastases with a sensitivity and specificity of 91 and 100%, respectively (p < 0.0001). Patients whose primary tumors expressed CTGF (p = 0.0007) as well as the truncated form of EpCAM (p = 0.06) showed shorter survival.

CONCLUSION

Although underestimated, bone metastases are a prominent feature of NETs, and the tumor expression of EMT markers at diagnosis may predict concurrent or subsequent skeleton colonization.

Computational Analysis of Missense Variants of G Protein-Coupled Receptors Involved in the Neuroendocrine Regulation of Reproduction

INTRODUCTION

Many missense variants in G protein-coupled receptors (GPCRs) involved in the neuroendocrine regulation of reproduction have been identified by phenotype-driven or large-scale exome sequencing. Computational functional prediction analysis is commonly performed to evaluate their impact on receptor function.

METHODS

To assess the performance and outcome of functional prediction analyses for these GPCRs, we performed a statistical analysis of the prediction performance of SIFT and PolyPhen-2 for variants with documented biological function as well as variants retrieved from Ensembl. We obtained missense variants with documented biological function testing from patients with reproductive disorders from a comprehensive literature search. Missense variants from individuals with known reproductive disorders were retrieved from the Human Gene Mutation Database. Missense variants from the general population were retrieved from the Ensembl genome database.

RESULTS

The accuracies of SIFT and PolyPhen-2 were 83 and 85%, respectively. The performance of both prediction tools was greater in predicting loss-of-function variants (SIFT: 92%; PolyPhen-2: 95%) than in predicting variants that did not affect function (SIFT: 54%; PolyPhen-2: 57%). Concordance between SIFT and PolyPhen-2 did not improve accuracy. Surprisingly, approximately half of the variants retrieved from Ensembl were predicted as loss-of-function variants by SIFT (47%) and PolyPhen-2 (54%).

CONCLUSION

Our findings provide new guidance for interpreting the results and limitations of computational functional prediction analyses for GPCRs and will help to determine which variants require biological function testing. In addition, our findings raise important questions regarding the link between genotype and phenotype in the general population.

Interactome of the hepatitis C virus: Literature mining with ANDSystem

A study of the molecular genetics mechanisms of host-pathogen interactions is of paramount importance in developing drugs against viral diseases. Currently, the literature contains a huge amount of information that describes interactions between HCV and human proteins. In addition, there are many factual databases that contain experimentally verified data on HCV-host interactions. The sources of such data are the original data along with the data manually extracted from the literature. However, the manual analysis of scientific publications is time consuming and, because of this, databases created with such an approach often do not have complete information. One of the most promising methods to provide actualisation and completeness of information is text mining. Here, with the use of a previously developed method by the authors using ANDSystem, an automated extraction of information on the interactions between HCV and human proteins was conducted. As a data source for the text mining approach, PubMed abstracts and full text articles were used. Additionally, external factual databases were analyzed. On the basis of this analysis, a special version of ANDSystem, extended with the HCV interactome, was created. The HCV interactome contains information about the interactions between 969 human and 11 HCV proteins. Among the 969 proteins, 153 'new' proteins were found not previously referred to in any external databases of protein-protein interactions for HCV-host interactions. Thus, the extended ANDSystem possesses a more comprehensive detailing of HCV-host interactions versus other existing databases. It was interesting that HCV proteins more preferably interact with human proteins that were already involved in a large number of protein-protein interactions as well as those associated with many diseases. Among human proteins of the HCV interactome, there were a large number of proteins regulated by microRNAs. It turned out that the results obtained for protein-protein interactions and microRNA-regulation did not depend on how well the proteins were studied, while protein-disease interactions appeared to be dependent on the level of study. In particular, the mean number of diseases linked to well-studied proteins (proteins were considered well-studied if they were mentioned in 50 or more PubMed publications) from the HCV interactome was 20.8, significantly exceeding the mean number of associations with diseases (10.1) for the total set of well-studied human proteins present in ANDSystem. For proteins not highly poorly-studied investigated, proteins from the HCV interactome (each protein was referred to in less than 50 publications) distribution of the number of diseases associated with them had no statistically significant differences from the distribution of the number of diseases associated with poorly-studied proteins based on the total set of human proteins stored in ANDSystem. With this, the average number of associations with diseases for the HCV interactome and the total set of human proteins were 0.3 and 0.2, respectively. Thus, ANDSystem, extended with the HCV interactome, can be helpful in a wide range of issues related to analyzing HCV-host interactions in the search for anti-HCV drug targets. The demo version of the extended ANDSystem covered here containing only interactions between human proteins, genes, metabolites, diseases, miRNAs and molecular-genetic pathways, as well as interactions between human proteins/genes and HCV proteins, is freely available at the following web address: http://www-bionet.sscc.ru/psd/andhcv/.

The behavioral profile of spice and synthetic cannabinoids in humans

The use of synthetic cannabinoids (spice) is increasing. The number of descriptions of (new) clinical side effects is also increasing. We screened relevant publications for articles about spice with a focus on the clinical manifestations of the use of this drug. Spice creates diffuse psychiatric and somatic effects that are only partially similar to those of natural cannabinoids. Most of the observed effects are related to sympathomimetic-cardiac effects and neuropsychiatric manifestations. Clinical treatment is primarily based on intensive apparative and laboratory monitoring and supportive therapy. Because the exact active ingredients of spice are often difficult to determine with standard specific toxicology testing, the assessment and analysis of consumed substances by specialized laboratories is recommended.

Examining the Impact of the National Institutes of Health Public Access Policy on the Citation Rates of Journal Articles

Purpose

To examine whether National Institutes of Health (NIH) funded articles that were archived in PubMed Central (PMC) after the release of the 2008 NIH Public Access Policy show greater scholarly impact than comparable articles not archived in PMC.

Methods

A list of journals across several subject areas was developed from which to collect article citation data. Citation information and cited reference counts of the articles published in 2006 and 2009 from 122 journals were obtained from the Scopus database. The articles were separated into categories of NIH funded, non-NIH funded and whether they were deposited in PubMed Central. An analysis of citation data across a five-year timespan was performed on this set of articles.

Results

A total of 45,716 articles were examined, including 7,960 with NIH-funding. An analysis of the number of times these articles were cited found that NIH-funded 2006 articles in PMC were not cited significantly more than NIH-funded non-PMC articles. However, 2009 NIH funded articles in PMC were cited 26% more than 2009 NIH funded articles not in PMC, 5 years after publication. This result is highly significant even after controlling for journal (as a proxy of article quality and topic).

Conclusion

Our analysis suggests that factors occurring between 2006 and 2009 produced a subsequent boost in scholarly impact of PubMed Central. The 2008 Public Access Policy is likely to be one such factor, but others may have contributed as well (e.g., growing size and visibility of PMC, increasing availability of full-text linkouts from PubMed, and indexing of PMC articles by Google Scholar).

A decade of Rural Clinical School research: a PubMed review

INTRODUCTION

One parameter of the operational framework of the Australian Rural Clinical Training & Support Program (RCTS) is rural health research, yet there are no published reports of the research outcomes generated by these hallmarks of Australian rural medical education. To assess the contribution of RCTS to rural health research, their MEDLINE-indexed research publications over the last decade was analysed, using a bibliometric method.

METHODS

MEDLINE-indexed RCTS publications from 2004 to 2013 were retrieved using validated PubMed queries. Two authors independently checked all retrieved RCTS publications for validity. Australian rural health (ARH) publications from RCTS were selectively enumerated and their proportion among all Australian rural health publications in each year was determined. ARH publications were defined as Australian publications that explore issues relevant to the health of the regional, rural or remote Australian population.RCTS publications related to medical education, Indigenous health, rural service areas, National Health Priority Areas (NHPA), and National Rural Health Alliance Priority Areas (NRHAPA) were analysed. Frequency of publication in different journals was also compared.

RESULTS

A total of 280 RCTS publications were retrieved, increasing from 10 in 2004 to 49 in 2013. ARH topics dominated (177 articles; 67%). RCTS rural health publications increased as a proportion of all ARH publications from 3.4% in 2004 to 7.7% in 2013. Other RCTS publications increased from 2 (20% of total) in 2004 to 19 (39% of total) in 2013, and covered topics such as mental health, cancer, diabetes, obesity and asthma. RCTS medical education publications increased from 3 in 2004 to 14 in 2013. In total, 81 articles were retrieved comprising 28.9% of all RCTS publications. Indigenous health (18; 6%), rural populations (37; 13%) and rural health services (83; 29%) were the other important categories relevant to the RCTS funding parameters. RCTS publications also included NHPA (57; 20%) and NRHAPA (61; 22%). The main journals publishing RCTS research in this time period were Rural and Remote Health (16%), Australian Journal of Rural Health (13%) and Australian Family Physician (9%).

RESULTS

This first study to report on the research efforts of RCTS researchers has shown that they are making a valuable contribution to rural health research and increasingly so within the research parameters indicated. These data represent a benchmark of research strengths and highlight research areas that should be strengthened with targeted research to best promote the health of rural Australians.

Association between rs6812193 polymorphism and sporadic Parkinson's disease susceptibility

Recently, the association of a single nucleotide polymorphism rs6812193 C/T with sporadic Parkinson's disease (PD) susceptibility has been widely evaluated, but the results remained inconsistent. This association should be clarified because of the importance of it on human health and quality of life. We performed a comprehensive meta-analysis to evaluate the association between the rs6812193 polymorphism and sporadic PD. PubMed was used to retrieve articles published up to June 2014 for all studies evaluating the rs6812193 polymorphism and PD in humans. Ethnicity-specific subgroup analysis was also performed based on ethnicity susceptibility. A total of 17 independent study samples (15 Caucasians and 2 Asians) including 17,956 cases and 52,751 controls were used in the presented study. The MAFT (minor allele T frequency) in PD patients of European descent is obviously higher than Asian cases (p < 0.01). The results suggested the rs6812193 polymorphism (allele T vs. C) is significantly associated with PD susceptibility among overall samples (OR 0.882, 95 % CI 0.856-0.908) and Caucasian population (OR 0.881, 95 % CI 0.856-0.907), but not in Asian samples (OR 0.918, 95 % CI 0.721-1.168). No evidence of publication bias was observed. Throughout our analysis, the rs6812193 polymorphism is significantly associated with sporadic PD susceptibility in Caucasian samples, and ethnicity might be the key point of inconsistency in rs6812193 studies. Further studies are warranted to re-examine the observed associations, especially in different ethnicities.

Evaluating historical candidate genes for schizophrenia

Prior to the genome-wide association era, candidate gene studies were a major approach in schizophrenia genetics. In this invited review, we consider the current status of 25 historical candidate genes for schizophrenia (for example, COMT, DISC1, DTNBP1 and NRG1). The initial study for 24 of these genes explicitly evaluated common variant hypotheses about schizophrenia. Our evaluation included a meta-analysis of the candidate gene literature, incorporation of the results of the largest genomic study yet published for schizophrenia, ratings from informed researchers who have published on these genes, and ratings from 24 schizophrenia geneticists. On the basis of current empirical evidence and mostly consensual assessments of informed opinion, it appears that the historical candidate gene literature did not yield clear insights into the genetic basis of schizophrenia. A likely reason why historical candidate gene studies did not achieve their primary aims is inadequate statistical power. However, the considerable efforts embodied in these early studies unquestionably set the stage for current successes in genomic approaches to schizophrenia.

Gene hunting in autism spectrum disorder: on the path to precision medicine

Autism spectrum disorder is typical of the majority of neuropsychiatric syndromes in that it is defined by signs and symptoms, rather than by aetiology. Not surprisingly, the causes of this complex human condition are manifold and include a substantial genetic component. Recent developments in gene-hunting technologies and methods, and the resulting plethora of genetic findings, promise to open new avenues to understanding of disease pathophysiology and to contribute to improved clinical management. Despite remarkable genetic heterogeneity, evidence is emerging for converging pathophysiology in autism spectrum disorder, but how this notion of convergent pathways will translate into therapeutics remains to be established. Leveraging genetic findings through advances in model systems and integrative genomic approaches could lead to the development of new classes of therapies and a personalised approach to treatment.

Searching for randomized controlled trials and systematic reviews on exercise. A descriptive study

CONTEXT AND OBJECTIVE

The current paradigm of science is to accumulate as much research data as possible, with less thought given to navigation or synthesis of the resulting mass, which hampers locating and using the research. The aim here was to describe the number of randomized controlled trials (RCTs) and systematic reviews (SRs) focusing on exercise, and their journal sources, that have been indexed in PubMed over time.

DESIGN AND SETTING

Descriptive study conducted at Bond University, Australia.

METHOD

To find RCTs, a search was conducted in PubMed Clinical Queries, using the category "Therapy" and the Medical Subject Headings (MeSH) term "Exercise". To find SRs, a search was conducted in PubMed Clinical Queries, using the category "Therapy", the MeSH term "Exercise" and various methodological filters.

RESULTS

Up until 2011, 9,354 RCTs about exercise were published in 1,250 journals and 1,262 SRs in 513 journals. Journals in the area of Sports Science published the greatest number of RCTs and journals categorized as belonging to "Other health professions" area (for example nursing or psychology) published the greatest number of SRs. The Cochrane Database of Systematic Reviews was the principal source for SRs, with 9.8% of the total, while the Journal of Strength and Conditioning Research and Medicine & Science in Sports & Exercise published 4.4% and 5.0% of the RCTs, respectively.

CONCLUSIONS

The rapid growth and resulting scatter of RCTs and SRs on exercise presents challenges for locating and using this research. Solutions for this issue need to be considered.