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John P.A. Ioannidis. Professor of Medicine (Stanford Prevention Research), of Epidemiology and Population Health and by courtesy, of Statistics and of. Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A.


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Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A. Robert Luben,16,,15,,,,, Maties Torrent,4,68,3,,,,, Yong-Mei Lv,3,,3,,,,, Cited for: IDENTIFICATION. Source: UniProtKB/TrEMBL (unreviewed). 5. "Molecular genetics of successful smoking cessation: convergent genome-wide association. TAXI 1 MOVIE DOWNLOAD TORENT FIFA It also provides is hard and. Tell FileZilla Server prompted to allow power-supply fan is not working, please in more than. The status of config file when it immediately disconnects, works good, so.

Defining functional DNA elements in the human genome. Drug discovery doi Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.

Archaic humans: Four makes a party. Birney E, Pritchard JK. The European Bioinformatics Institute's data resources Policy challenges of clinical genome sequencing. The Reactome pathway knowledgebase. Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.

Journey to the genetic interior. Interview by Stephen S Hall. Scientific American doi:. Analysis of variation at transcription factor binding sites in Drosophila and humans. Classification of human genomic regions based on experimentally determined binding sites of more than transcription-related factors.

An integrated encyclopedia of DNA elements in the human genome. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome research doi Sequence features and chromatin structure around the genomic regions bound by human transcription factors.

The future of DNA sequence archiving. GigaScience doi Modeling gene expression using chromatin features in various cellular contexts. Paralogous annotation of disease-causing variants in long QT syndrome genes. Human mutation doi The genomic basis of adaptive evolution in threespine sticklebacks.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell doi VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Major submissions tool developments at the European Nucleotide Archive.

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. A high-resolution map of human evolutionary constraint using 29 mammals. Mouse genomic variation and its effect on phenotypes and gene regulation. The variant call format and VCFtools. PLoS biology doi Chromatin and heritability: how epigenetic studies can complement genetic approaches. Trends in genetics : TIG doi Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses.

Efficient storage of high throughput DNA sequencing data using reference-based compression. Assemblies: the good, the bad, the ugly. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Reactome: a database of reactions, pathways and biological processes. The European Nucleotide Archive. Allele-specific and heritable chromatin signatures in humans. The BioPAX community standard for pathway data sharing.

Nature biotechnology doi An international bioinformatics infrastructure to underpin the Arabidopsis community. International Arabidopsis Informatics Consortium. The Plant cell doi Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

Genomic information infrastructure after the deluge. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. A database and API for variation, dense genotyping and resequencing data. BMC bioinformatics doi Ensembl variation resources.

BMC genomics doi A draft sequence of the Neandertal genome. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome medicine doi International network of cancer genome projects. Heritable individual-specific and allele-specific chromatin signatures in humans. An effective model for natural selection in promoters. Hoffman MM, Birney E.

The consequence of natural selection on genetic variation in the mouse. Genomics doi A new strategy for genome assembly using short sequence reads and reduced representation libraries. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.

A small-cell lung cancer genome with complex signatures of tobacco exposure. Improvements to services at the European Nucleotide Archive. Ensembl's 10th year. Sense from sequence reads: methods for alignment and assembly.

Flicek P, Birney E. Comptes rendus biologies doi Ensembl Genomes: extending Ensembl across the taxonomic space. EMMA--mouse mutant resources for the international scientific community. Prepublication data sharing. Nature protocols doi The consensus coding sequence CCDS project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome biology doi:. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. VectorBase: a data resource for invertebrate vector genomics. Reactome knowledgebase of human biological pathways and processes. Petabyte-scale innovations at the European Nucleotide Archive. MAPU 2. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome-wide nucleotide-level mammalian ancestor reconstruction. Advanced genomic data mining. Integrating biological data--the Distributed Annotation System.

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Arabidopsis reactome: a foundation knowledgebase for plant systems biology. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions tDMRs. Genome analysis of the platypus reveals unique signatures of evolution.

What everybody should know about the rat genome and its online resources. SNP and haplotype mapping for genetic analysis in the rat. Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.

Margulies EH, Birney E. Levers and fulcrums: progress in cis-regulatory motif models. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E. Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases doi Evolutionary genomics: come fly with us.

Double Dutch for duplications. ENFIN a network to enhance integrative systems biology. Kahlem P, Birney E. Annals of the New York Academy of Sciences doi Genome browsing with Ensembl: a practical overview. In vivo validation of a computationally predicted conserved Ath5 target gene set. Challenges and standards in integrating surveys of structural variation. Optimized design and assessment of whole genome tiling arrays.

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Genome sequence of Aedes aegypti, a major arbovirus vector. Evolutionary and biomedical insights from the rhesus macaque genome. Patterns of somatic mutation in human cancer genomes. Identification of novel peptide hormones in the human proteome by hidden Markov model screening.

Reactome: a knowledge base of biologic pathways and processes. BMC bioinformatics doi:. VectorBase: a home for invertebrate vectors of human pathogens. Estimating the neutral rate of nucleotide substitution using introns.

Molecular biology and evolution doi TranscriptSNPView: a genome-wide catalog of mouse coding variation. Dry work in a wet world: computation in systems biology. Molecular systems biology doi Picking pyknons out of the human genome. Meynert A, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Systems biology doi:. Gene finding in the chicken genome.

A survey of homozygous deletions in human cancer genomes. Automated generation of heuristics for biological sequence comparison. Slater GS, Birney E. Reactome: a knowledgebase of biological pathways. Transcriptome analysis for the chicken based on 19, finished cDNA sequences and , expressed sequence tags.

The International Protein Index: an integrated database for proteomics experiments. Proteomics doi Genome information resources - developments at Ensembl. Hammond MP, Birney E. The Ensembl core software libraries. GeneWise and Genomewise. Sockeye: a 3D environment for comparative genomics. Comparison of human chromosome 21 conserved nongenic sequences CNGs with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.

An overview of Ensembl. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Biological database design and implementation. Birney E, Clamp M. Briefings in bioinformatics doi The Anopheles gambiae genome: an update. Trends in parasitology doi EnsMart: a generic system for fast and flexible access to biological data. Discovering novel cis-regulatory motifs using functional networks. Unrestricted free access works and must continue.

Comparative genomics: genome-wide analysis in metazoan eukaryotes. Ensembl accommodating comparative genomics. The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harbor symposia on quantitative biology doi The European Bioinformatics Institute's data resources.

Ensembl: a genome infrastructure. Birney E, Ensembl Team. Apollo: a sequence annotation editor. Analysis of the mouse transcriptome based on functional annotation of 60, full-length cDNAs. Initial sequencing and comparative analysis of the mouse genome. Immunity-related genes and gene families in Anopheles gambiae. The genome sequence of the malaria mosquito Anopheles gambiae.

The Bioperl toolkit: Perl modules for the life sciences. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. A physical map of the mouse genome. Genome annotation techniques: new approaches and challenges. Drug discovery today doi Databases and tools for browsing genomes. Annual review of genomics and human genetics doi The Pfam protein families database. The Ensembl genome database project.

Progress in sequencing the mouse genome. Hidden Markov models in biological sequence analysis Birney E. IBM journal of research and development doi:. Integration of cytogenetic landmarks into the draft sequence of the human genome. Initial sequencing and analysis of the human genome.

I have worked in the fields of evidence-based medicine, clinical investigation, clinical and molecular epidemiology, clinical research methodology, empirical research methods, statistics, and genomics. I have a strong interest in meta-research and in large-scale evidence in particular randomized trials and meta-analyses and in appraisal and control of diverse biases in biomedical research and beyond.

I am interested in developing and applying new research methods, and in the interdisciplinary enhancement of existing research methods for study design and analysis. Some of my most influential papers in terms of citations are those addressing issues of reproducibility, replication validity, biases in biomedical research and other fields, research synthesis methods, extensions of meta-analysis, genome-wide association studies and agnostic evaluation of associations, and validity of randomized trials and observational research.

I have also designed, steered and participated in influential randomized trials in particular, the major trials that changed decisively the management and outcome of HIV infection, but also trials in nephrology, and in antibiotic use in the community , and large international consortia that have helped transform the efficiency of research in diverse fields of genomic, molecular and clinical epidemiology.

I enjoy working with a diverse array of colleagues from very diverse disciplines and to have an opportunity to learn from both senior and junior investigators, and particularly students at all levels. The purpose of this study is to see if providing information to a person on their inherited genetic risk of cardiovascular disease CVD helps to motivate that person to change their diet, lifestyle or medication regimen to alter their risk.

Stanford is currently not accepting patients for this trial. For more information, please contact Josh Knowles, View full details. The COVID pandemic is a major global crisis and obtaining reliable evidence is essential for optimizing outcomes and saving lives. Here is a list of my published work on this major challenge. Misinformation and distortion of my work and of the work of other scientists unfortunately is rampant.

Evidence is accumulating rapidly and readers should try to consult always the most up-to-date and most reliable information. The end of the pandemic due to a new virus and the transition to endemicity may be defined based on a high proportion of the global population having some immunity from natural infection or vaccination. Other considerations include diminished death toll, diminished pressure on health systems, reduced actual and perceived personal risk, removal of restrictive measures, and diminished public attention.

Endemicity may still show major spikes of infections and seasonality, but typically less clinical burden, although some locations are still hit more than others. Personal risk for the vast majority of the global population was already very small by end , but perceived risk may still be grossly over-estimated. Restrictive measures of high stringency have persisted in many countries by early The gargantuan attention in news media, social media, and even scientific circles should be tempered.

Public health officials need to declare the end of the pandemic. Mid- and long-term consequences of epidemic waves and of adopted measures on health, society, economy, civilization, and democracy may perpetuate a pandemic legacy long after the pandemic itself has ended. View details for DOI View details for PubMedID This mixed design synthesis aimed to estimate the infection fatality rate IFR of Coronavirus Disease COVID in community-dwelling elderly populations and other age groups from seroprevalence studies.

We extracted the most fully adjusted if unavailable, unadjusted seroprevalence estimates; age- and residence-stratified cumulative COVID deaths until 1week after the seroprevalence sampling midpoint from official reports; and population statistics, to calculate IFRs adjusted for test performance.

Sample size-weighted IFRs were estimated for countries with multiple estimates. Thirteen seroprevalence surveys representing 11 high-income countries were included in the main analysis. Median IFR in community-dwelling elderly and elderly overall was 2. Multiple sensitivity analyses yielded similar results. Effective collaboration and mentorship are essential to success in a career of health research.

We summarize our conversation with Dr. John Ioannidis, professor at Stanford University, author of the most accessed manuscript in the history of the Public Library of Science, and one of the most cited scientists in history. Ioannidis was invited for a question and answer session as part of a graduate-level course on biostatistical collaboration hosted at McMaster University in December This text provides insight into the experiences and pearls he shared, that we hope will inspire and guide other researchers early or junior in their careers.

He emphasized the importance of passion, enthusiasm and a sincere pursuit for high quality research as being the cornerstones to success and continued productivity in this field. Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic.

We present an open-source, automated approach to identify 5 indicators of transparency data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration and apply it across the entire open access biomedical literature of 2. Our results indicate remarkable improvements in some e.

This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science. We aimed to empirically assess the current use of E-values in published literature.

METHODS: We conducted a systematic literature search for all publications, published up till the end of , which cited at least one of two inceptive E-value papers and presented E-values for original data. For these case publications we identified control publications, matched by journal and issue, where the authors had not calculated E-values.

Of the 87 papers, 14 concluded that residual confounding likely threatens at least some of the main conclusions. Seven of these 14 named potential uncontrolled confounders. The median E-value was 1. The 69 case-control publication pairs dealt with effect sizes of similar magnitude.

Facile automation in calculating E-values may compound the already poor handling of confounding. E-values should not be a substitute for careful consideration of potential sources of unmeasured confounding. If used, they should be interpreted in the context of expected confounding in specific fields. Many technology companies, including Airbnb, Amazon, Booking.

Originally derived from the same statistical roots, randomized controlled trials RCTs in medicine are now criticized for being expensive and difficult, while in technology, the marginal cost of such experiments is approaching zero and the value for data-driven decision-making is broadly recognized. This is an overview of key scaling lessons learned in the technology field. They include 1 a focus on metrics, an overall evaluation criterion and thousands of metrics for insights and debugging, automatically computed for every experiment; 2 quick release cycles with automated ramp-up and shut-down that afford agile and safe experimentation, leading to consistent incremental progress over time; and 3 a culture of 'test everything' because most ideas fail and tiny changes sometimes show surprising outcomes worth millions of dollars annually.

Technological advances, online interactions, and the availability of large-scale data allowed technology companies to take the science of RCTs and use them as online randomized controlled experiments at large scale with hundreds of such concurrent experiments running on any given day on a wide range of software products, be they web sites, mobile applications, or desktop applications.

Rather than hindering innovation, these experiments enabled accelerated innovation with clear improvements to key metrics, including user experience and revenue. As healthcare increases interactions with patients utilizing these modern channels of web sites and digital health applications, many of the lessons apply. The most innovative technological field has recognized that systematic series of randomized trials with numerous failures of the most promising ideas leads to sustainable improvement.

While there are many differences between technology and medicine, it is worth considering whether and how similar designs can be applied via simple RCTs that focus on healthcare decision-making or service delivery. Changes - small and large - should undergo continuous and repeated evaluations in randomized trials and learning from their results will enable accelerated healthcare improvements.

Epidemic forecasting has a dubious track-record, and its failures became more prominent with COVID Poor data input, wrong modeling assumptions, high sensitivity of estimates, lack of incorporation of epidemiological features, poor past evidence on effects of available interventions, lack of transparency, errors, lack of determinacy, looking at only one or a few dimensions of the problem at hand, lack of expertise in crucial disciplines, groupthink and bandwagon effects and selective reporting are some of the causes of these failures.

Nevertheless, epidemic forecasting is unlikely to be abandoned. Some but not all of these problems can be fixed. Careful modeling of predictive distributions rather than focusing on point estimates, considering multiple dimensions of impact, and continuously reappraising models based on their validated performance may help. If extreme values are considered, extremes should be considered for the consequences of multiple dimensions of impact so as to continuously calibrate predictive insights and decision-making.

When major decisions e. View details for Web of Science ID Citation metrics are widely used and misused. We have created a publicly available database of , top scientists that provides standardized information on citations, h-index, coauthorship-adjusted hm-index, citations to papers in different authorship positions, and a composite indicator.

Separate data are shown for career-long and single-year impact. Metrics with and without self-citations and ratio of citations to citing papers are given. Scientists are classified into 22 scientific fields and subfields. Field- and subfield-specific percentiles are also provided for all scientists who have published at least five papers. Career-long data are updated to end of and to end of for comparison.

Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of biomedical journals articles published in , the biomedical literature largely lacked transparency in important dimensions. We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed.

The majority of the studies disclosed some information regarding funding , Among the articles with empirical data in which protocols or data sharing would be pertinent, 19 Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts 5. Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed.

Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed. In the context of a recent proposal to exclude research from consideration at the Environmental Protection Agency, John Ioannidis points out that "perceived perfection is not a characteristic of science, but of dogma" and envisions how governments can promote a standard of openness in science.

Meta-research is the study of research itself: its methods, reporting, reproducibility, evaluation, and incentives. Given that science is the key driver of human progress, improving the efficiency of scientific investigation and yielding more credible and more useful research results can translate to major benefits. The research enterprise grows very fast. Both new opportunities for knowledge and innovation and new threats to validity and scientific integrity emerge.

Old biases abound, and new ones continuously appear as novel disciplines emerge with different standards and challenges. Meta-research uses an interdisciplinary approach to study, promote, and defend robust science. Major disruptions are likely to happen in the way we pursue scientific investigation, and it is important to ensure that these disruptions are evidence based.

Numerous biases are believed to affect the scientific literature, but their actual prevalence across disciplines is unknown. To gain a comprehensive picture of the potential imprint of bias in science, we probed for the most commonly postulated bias-related patterns and risk factors, in a large random sample of meta-analyses taken from all disciplines.

The magnitude of these biases varied widely across fields and was overall relatively small. However, we consistently observed a significant risk of small, early, and highly cited studies to overestimate effects and of studies not published in peer-reviewed journals to underestimate them. We also found at least partial confirmation of previous evidence suggesting that US studies and early studies might report more extreme effects, although these effects were smaller and more heterogeneously distributed across meta-analyses and disciplines.

Authors publishing at high rates and receiving many citations were, overall, not at greater risk of bias. However, effect sizes were likely to be overestimated by early-career researchers, those working in small or long-distance collaborations, and those responsible for scientific misconduct, supporting hypotheses that connect bias to situational factors, lack of mutual control, and individual integrity.

Some of these patterns and risk factors might have modestly increased in intensity over time, particularly in the social sciences. Our findings suggest that, besides one being routinely cautious that published small, highly-cited, and earlier studies may yield inflated results, the feasibility and costs of interventions to attenuate biases in the literature might need to be discussed on a discipline-specific and topic-specific basis.

We have empirically assessed the distribution of published effect sizes and estimated power by analyzing 26, statistical records from 3, cognitive neuroscience and psychology papers published recently. Median power to detect small, medium, and large effects was 0. This is so because sample sizes have remained small. Assuming similar true effect sizes in both disciplines, power was lower in cognitive neuroscience than in psychology.

Journal impact factors negatively correlated with power. In light of our findings, the recently reported low replication success in psychology is realistic, and worse performance may be expected for cognitive neuroscience. Many published randomized clinical trials RCTs make claims for subgroup differences.

The language and conceptual framework of "research reproducibility" are nonstandard and unsettled across the sciences. In this Perspective, we review an array of explicit and implicit definitions of reproducibility and related terminology, and discuss how to avoid potential misunderstandings when these terms are used as a surrogate for "truth. The use and misuse of P values has generated extensive debates. To evaluate in large scale the P values reported in the abstracts and full text of biomedical research articles over the past 25 years and determine how frequently statistical information is presented in ways other than P values.

Reporting of P values in English-language core clinical journals and specific article types as classified by PubMed also was evaluated. A random sample of MEDLINE abstracts was manually assessed for reporting of P values and other types of statistical information; of those abstracts reporting empirical data, articles were also assessed in full text. P values reported. Reporting of P values in abstracts increased from 7. In , P values were reported in The distribution of reported P values in abstracts and in full text showed strong clustering at P values of.

Over time, the "best" most statistically significant reported P values were modestly smaller and the "worst" least statistically significant reported P values became modestly less significant. In abstracts that were manually reviewed, were from articles reporting empirical data; P values were reported in Rather than reporting isolated P values, articles should include effect sizes and uncertainty metrics.

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest.

In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of biomedical journal articles published in Only one study provided a full protocol and none made all raw data directly available. The majority of studies did not mention anything about funding or conflicts of interest. The percentage of articles with no statement of conflict decreased substantially between and Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding.

This study provides baseline data to compare future progress in improving these indicators in the scientific literature. As the scientific enterprise has grown in size and diversity, we need empirical evidence on the research process to test and apply interventions that make it more efficient and its results more reliable.

Meta-research is an evolving scientific discipline that aims to evaluate and improve research practices. It includes thematic areas of methods, reporting, reproducibility, evaluation, and incentives how to do, report, verify, correct, and reward science. Much work is already done in this growing field, but efforts to-date are fragmented. We provide a map of ongoing efforts and discuss plans for connecting the multiple meta-research efforts across science worldwide.

Model specification-what adjusting variables are analytically modeled-may influence results of observational associations. We present a standardized approach to quantify the variability of results obtained with choices of adjustments called the "vibration of effects" VoE. We estimated the VoE for clinical, environmental, and physiological variables in association with all-cause mortality using National Health and Nutrition Examination Survey data. We selected 13 variables as adjustment covariates and computed 8, Cox models for each of variables' associations with all-cause mortality.

We present the VoE by assessing the variance of the effect size and in the -log10 P-value obtained by different combinations of adjustments. We present whether there are multimodality patterns in effect sizes and P-values and the trajectory of results with increasing adjustments. Estimating VoE offers empirical estimates of associations are under different model specifications. When VoE is large, claims for observational associations should be very cautious. We systematically evaluated evidence from randomized controlled trials RCTs as to whether screening decreases mortality from diseases where death is a common outcome.

We extracted recommendation status, category of evidence and RCT availability on mortality for screening tests for diseases on asymptomatic adults excluding pregnant women and children from USPSTF. Screening is recommended for 6 diseases 12 tests out of the We assessed 9 non-overlapping meta-analyses and 48 individual trials for these 19 diseases. Among currently available screening tests for diseases where death is a common outcome, reductions in disease-specific mortality are uncommon and reductions in all-cause mortality are very rare or non-existent.

Their conclusions were correlated with study design features. The ten most recent citations for the most-cited article on each index intervention were examined on whether they were critical to the highly-cited study. Altmetric scores were also obtained. Citation counts correlated strongly with Altmetric scores, especially news items. Early observational studies and small randomized trials may cause spurious claims of effectiveness that get perpetuated.

Non-randomised studies assessing COVID vaccine effectiveness need to consider multiple factors that may generate spurious estimates due to bias or genuinely modify effectiveness. These include pre-existing immunity, vaccination misclassification, exposure differences, testing, disease risk factor confounding, hospital admission decision, treatment use differences, and death attribution.

It is useful to separate whether the impact of each factor admission decision, treatment use differences, and death attribution. Steps and measures to consider for improving vaccine effectiveness estimation include registration of studies and of analysis plans; sharing of raw data and code; background collection of reliable information; blinded assessment of outcomes, e. The public health community and health agencies should consider the evolving evidence in their recommendations and statements, and work to issue relational occupational guidelines.

Evidence coming from the current epidemiological and experimental research is expected to add knowledge about virus diffusion, COVID severity in most polluted areas, inter-personal distance requirements and need for wearing face masks in indoor or outdoor environments. Indoor environments represent even a more crucial challenge to cope with, as it is easier for the SARS-COV2 to spread, remain vital and infect other subjects in closed spaces in the presence of already infected asymptomatic or mildly symptomatic people.

Overstated generalizability external validity is common in research. It may coexist with inflation of the magnitude and statistical support for effects and dismissal of internal validity problems. Generalizability may be secured before attempting replication of proposed discoveries or replication may precede efforts to generalize.

These opposite approaches may decrease or increase, respectively, the use of inferential statistics with advantages and disadvantages. The current analysis aimed to examine whether the prevailing narrative that GBD is a minority view among experts is true. Citation data were obtained from Scopus using a previously validated composite citation indicator that incorporated also coauthorship and author order and ranking was against all authors in the same Science-Metrix scientific field with at least five full papers.

Random samples of scientists from the longer lists of signatories were also assessed. The number of Twitter followers for all key signatories was also tracked. For comparison, among the 34 key JSM signatories, 11, 14 and 15, respectively, were top cited. Key signatories represented 30 different scientific fields 9 represented in both documents, 17 only in GBD and 4 only in JSM. Mental disorders represent a worldwide public health concern. Psychotherapies and pharmacotherapies are recommended as first line treatments.

However, evidence has emerged that their efficacy may be overestimated, due to a variety of shortcomings in clinical trials e. We performed an umbrella review of recent meta-analyses of randomized controlled trials RCTs of psychotherapies and pharmacotherapies for the main mental disorders in adults. We selected meta-analyses that formally assessed risk of bias or quality of studies, excluded weak comparators, and used effect sizes for target symptoms as primary outcome.

We searched PubMed and PsycINFO and individual records of the Cochrane Library for meta-analyses published between January and March comparing psychotherapies or pharmacotherapies with placebo or treatment-as-usual TAU , or psychotherapies vs. Across disorders and treatments, the majority of effect sizes for target symptoms were small. A random effect meta-analytic evaluation of the effect sizes reported by the largest meta-analyses per disorder yielded a standardized mean difference SMD of 0.

The SMD for head-to-head comparisons of psychotherapies vs. The SMD for the combined treatment compared with either monotherapy was 0. Risk of bias was often high. After more than half a century of research, thousands of RCTs and millions of invested funds, the effect sizes of psychotherapies and pharmacotherapies for mental disorders are limited, suggesting a ceiling effect for treatment research as presently conducted. A paradigm shift in research seems to be required to achieve further progress.

Large effects are rare and there is no clear threshold for dramatic effects that would obviate future RCTs. Pre-registration is a research practice where a protocol is deposited in a repository before a scientific project is performed. Deviations from the original plan, may still often be desirable, but pre-registration makes them transparent. While pre-registration has been advocated and used to variable extent in diverse types of research, there has been relatively little attention given to the possibility of pre-registration for mathematical modeling studies.

Feasibility of pre-registration depends on the type of modeling and the ability to pre-specify processes and outcomes. In some types of modeling, in particular those that involve forecasting or other outcomes that can be appraised in the future, trust in model performance would be enhanced through pre-registration.

Pre-registration can also be seen as a component of a largest suite of research practices that aim to improve documentation, transparency, and sharing - eventually allowing better reproducibility of the research work. The current commentary discusses the evolving landscape of the concept of pre-registration as it relates to different mathematical modeling activities, the potential advantages and disadvantages, feasibility issues, and realistic goals. Seroprevalence surveys suggest that more than a third and possibly more than half of the global population has been infected with SARS-CoV-2 by early As large numbers of people continue to be infected, the efficacy and duration of natural immunity in terms of protection against SARS-CoV-2 reinfections and severe disease is of crucial significance for the future.

This narrative review provides an overview on epidemiological studies addressing this issue. National surveys covering documented that a previous SARS-CoV-2 infection is associated with a significantly reduced risk of reinfections with efficacy lasting for at least one year and only relatively moderate waning immunity.

Importantly, natural immunity showed roughly similar effect sizes regarding protection against reinfection across different SARS-CoV-2 variants, with the exception of the Omicron variant for which data are just emerging before final conclusions can be drawn.

Observational studies indicate that natural immunity may offer equal or greater protection against SARS-CoV-2 infections compared to individuals receiving two doses of an mRNA vaccine, but data are not fully consistent. The combination of a previous SARS-CoV-2 infection and a respective vaccination, termed hybrid immunity, seems to confer the greatest protection against SARS-CoV-2 infections, but several knowledge gaps remain regarding this issue. The coronavirus disease COVID pandemic incited a global clinical trial research agenda of unprecedented speed and high volume.

This expedited research activity in a time of crisis produced both successes and failures that offer valuable learning opportunities for the scientific community to consider. Successes include the implementation of large adaptive and pragmatic trials as well as burgeoning efforts toward rapid data synthesis and open science principles. Conversely, notable failures include: 1 inadequate study design and execution; 2 data reversal, fraud, and retraction; and 3 research duplication and waste.

Other challenges that became highlighted were the need to find unbiased designs for investigating complex, nonpharmaceutical interventions and the use of routinely collected data for outcomes assessment. This article discusses these issues juxtaposing the COVID trials experience against trials in anesthesiology and other fields. These lessons may serve as a positive catalyst for transforming future clinical trial research.

Prophylactic corticosteroids in singleton preterm pregnancies accelerate lung maturation and reduce the incidence of respiratory complications. It is unclear whether administration at term gestations, prior to caesarean section, improves the respiratory outcomes for these babies without causing any unnecessary morbidity to the mother or the infant.

We also assessed the impact of the treatment on the child in later life. Quasi-randomised and cluster-randomised controlled trials were also eligible for inclusion. Two review authors independently assessed trials for inclusion, assessed risk of bias, evaluated trustworthiness based on predefined criteria developed by Cochrane Pregnancy and Childbirth , extracted data and checked them for accuracy andassessed the certainty of the evidence using the GRADE approach.

Our primary outcomes were respiratory distress syndrome RDS , transient tachypnoea of the neonate TTN , admission to neonatal special care for respiratory morbidity and need for mechanical ventilation. We planned to perform subgroup analyses for the primary outcomes according to gestational age at randomisation and type of corticosteroid betamethasone or dexamethasone.

We also planned to perform sensitivity analysis, including only studies at low risk of bias. The trial included women and neonates recruited from 10 UK hospitals between and This review includes only trials that met predefined criteria for trustworthiness. We removed three trials from the analysis that were included in the previous version of this review. The risk of bias was low for random sequence generation, allocation concealment and incomplete outcome data.

The risk of bias for selective outcome reporting was unclear because there was no published trial protocol, and therefore it is unclear whether all the planned outcomes were reported in full. Due to a lack of blinding we judged there to be high risk of performance bias and detection bias. Antenatal corticosteroids probably reduce the risk of admission to neonatal special care for respiratory complications, compared with usual care RR 0.

The proportion of infants admitted to neonatal special care for respiratory morbidityafter treatment with antenatal corticosteroids was 2. It is uncertain if antenatal steroids have any effect on the risk of needing mechanical ventilation, compared with usual care RR 4.

It is uncertain if administration of antenatal corticosteroids reduces the rates of respiratory distress syndrome RDS or transient tachypnoea of the neonate TTN. The overall certainty of the evidence for the primary outcomes was found to be low or very low, apart from the outcome of admission to neonatal special care all levels for respiratory morbidity, for which the evidence was of moderate certainty.

Therefore, there is currently insufficient data to draw any firm conclusions. More evidence is needed to investigate the effect of prophylactic antenatal corticosteroids on the incidence of recognised respiratory morbidity such as RDS. Any future trials should assess the balance between respiratory benefit and potential immediate adverse effects e. There is very limited information on maternal health outcomes to provide any assurances that corticosteroids do not pose any increased risk of harm to the mother.

Further research should consider investigating the effectiveness of antenatal steroids at different gestational ages prior to caesarean section. There are nine potentially eligible studies that are currently ongoing and could be included in future updates of this review.

Investigators of trials registered by March 1, , without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID patients, regardless of setting or treatment schedule.

Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. The combined risk ratio for all-cause mortality was 0. These results provide strong evidence that convalescent plasma treatment for patients with COVID should not be used outside of randomized trials.

Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care. Florian Naudet and co-authors discuss strengthening requirements for sharing clinical trial data. Recent, high-profile, large-scale, preregistered failures to replicate uncover that many highly-regarded experiments are 'false positives;' that is, statistically significant results of underlying null effects.

Large surveys of research reveal that statistical power is often low and inadequate. At the core of research credibility lies the relation of statistical power to the rate of false positives. When median retrospective power is low View details for DOI With the establishment of large biobanks, discovery of single nucleotide variants SNVs, also known as single nucleotide polymorphisms SNVs associated with various phenotypes has accelerated.

Strategies for the use of COVID vaccines in children and young adults in particular university students are hotly debated and important to optimize. As of late August , recommendations on the use of these vaccines in children vary across different countries. Recommendations are more uniform for vaccines in young adults, but vaccination uptake in this age group shows a large range across countries.

Mandates for vaccination of university students are a particularly debated topic with many campuses endorsing mandates in the USA in contrast to European countries, at least as of August The commentary discusses the potential indirect impact of vaccination of youth on the COVID burden of disease for other age groups and societal functioning at large, estimates of direct impact on reducing fatalities and non-lethal COVIDrelated events in youth, estimates of potential lethal and non-lethal adverse events from vaccines, and differential considerations that may exist in the USA, European countries, and non-high-income countries.

Decision-making for deploying COVID vaccines in young people is subject to residual uncertainty on the future course of the pandemic and potential evolution towards endemicity. Rational recommendations would also benefit from better understanding of the clinical and sociodemographic features of COVID risk in young populations, and from dissecting the role of re-infections and durability of natural versus vaccine-induced immunity.

We examined the extent to which the scientific workforce in different fields was engaged in publishing COVIDrelated papers. The rapid and massive involvement of the scientific workforce in COVIDrelated work is unprecedented and creates opportunities and challenges. There is evidence for hyper-prolific productivity. Biological disease-modifying antirheumatic drugs bDMARDs and targeted synthetic disease-modifying antirheumatic drugs tsDMARDs , respectively, reduce the effects of proinflammatory cytokines and immune cells to ameliorate disease.

However, immunosuppression can be associated with high rates of serious adverse events SAEs , including serious infections, and maybe an increased risk of malignancies and cardiovascular events. Currently, there is no empirical evidence on the extent to which contextual factors and risk of bias RoB domains may modify these harm signals in randomised trials. A predefined form will be used for extracting data on population characteristics eg, baseline characteristics or eligibility criteria, such as medication background and specific harm outcome measures, such as number of withdrawals, numbers of patients discontinuing due to adverse events and number of patients having SAEs.

RoB in individual trials will be assessed using a modified Cochrane RoB tool. We will estimate the potentially causal harm effects related to the experimental intervention compared with control comparator as risk ratios, and heterogeneity across randomised comparisons will be assessed statistically and evaluated as inconsistency using the I2 Index. Our metaregression analyses will designate population and trial characteristics and each RoB domain as independent variables, whereas the three harm domains will serve as dependent variables.

Results will be disseminated through publication in international peer-reviewed journals. We analyzed the funding sources, countries, outcomes, publication status, and correlation with the pediatric global burden of disease GBD for eligible trials. They did not evaluate the adjusted values relative to measured BMI values for the same individuals.

The proposed method was used to adjust the BMI values in one group to the measured data from the other group. The adjusted values were then compared with the measured values for the same individuals. The variance of the difference was unchanged. The adjustments reduced some errors and introduced new errors.

At an individual level, results were unpredictable. State-level estimates and projections of obesity prevalence from values adjusted by this method may be incorrect. The ratio of COVIDattributable deaths versus "true" COVID deaths depends on the synchronicity of the epidemic wave with population mortality; duration of test positivity, diagnostic time window, and testing practices close to and at death; infection prevalence; the extent of diagnosing without testing documentation; and the ratio of overall all-cause population mortality rate and infection fatality rate.

A nomogram is offered to assess the potential extent of over- and under-counting in different situations. Finally, excess death estimates are subject to substantial annual variability and include also indirect effects of the pandemic and the effects of measures taken. Here, we aimed to appraise thousands of meta-analyses of observational studies using a pre-specified set of quantitative criteria that assess the significance, amount, consistency, and bias of the evidence.

We also aimed to compare results from meta-analyses of observational studies against meta-analyses of randomized controlled trials RCTs and Mendelian randomization MR studies. METHODS: We retrieved from PubMed last update, November 19, umbrella reviews including meta-analyses of observational studies assessing putative risk or protective factors, regardless of the nature of the exposure and health outcome.

We extracted information on 7 quantitative criteria that reflect the level of statistical support, the amount of data, the consistency across different studies, and hints pointing to potential bias. These criteria were level of statistical significance pre-categorized according to , 0.

RESULTS: associations in 57 umbrella reviews assessed by a median number of 7 interquartile range 4 to 11 observational studies were eligible. We introduce and evaluate three tests for publication selection bias based on excess statistical significance. The proposed tests incorporate heterogeneity explicitly in the formulas for expected and excess statistical significance. We calculate the expected proportion of statistically significant findings in the absence of selective reporting or publication bias based on each study's standard error and meta-analysis estimates of the mean and variance of the true-effect distribution.

Comparing the expected to the observed proportion of statistically significant results leads to a simple proportion of statistical significance test PSST. Alternatively, we propose a direct test of excess statistical significance TESS. Simulations show that these excess statistical significance tests often outperform the conventional Egger test for publication selection bias and the three-parameter selection model.

This article is protected by copyright. All rights reserved. Data were screened and extracted by 6 investigators. Redundant meta-analyses were removed. Whenever possible for each comparison we extracted one meta-analysis on mortality with the most events, and one meta-analysis on a non-mortality outcome with the most studies. From each meta-analysis we extracted all individual study effects; outcomes were converted to odds ratios and placed on a common scale where an odds ratio View details for DOI Preventive approaches have latterly gained traction for improving mental health in young people.

In this paper, we first appraise the conceptual foundations of preventive psychiatry, encompassing the public health, Gordon's, US Institute of Medicine, World Health Organization, and good mental health frameworks, and neurodevelopmentally-sensitive clinical staging models. We then review the evidence supporting primary prevention of psychotic, bipolar and common mental disorders and promotion of good mental health as potential transformative strategies to reduce the incidence of these disorders in young people.

Within indicated approaches, the clinical high-risk for psychosis paradigm has received the most empirical validation, while clinical high-risk states for bipolar and common mental disorders are increasingly becoming a focus of attention. Selective approaches have mostly targeted familial vulnerability and non-genetic risk exposures.

Selective physical exercise may reduce the incidence of anxiety disorders. The approach to promotion of good mental health is currently fragmented. These goals can only be achieved through an urgent individual, societal, and global level response, which promotes a vigorous collaboration across scientific, health care, societal and governmental sectors for implementing preventive psychiatry, as much is at stake for young people with or at risk for emerging mental disorders.

Small randomized trials and observational, non-randomized analyses have not had a successful track record and have generated misleading expectations. Different large trials on the same intervention have generally been far more efficient in producing timely and consistent evidence. The rapid generation of evidence and accelerated dissemination of results have led to new challenges for systematic reviews and meta-analyses e.

Pressure to regulatory agencies has also mounted with massive emergency authorizations, but some of them have had to be revoked. Pandemic circumstances have disrupted the way trials are conducted; therefore, new methods have been developed and adopted more widely to facilitate recruitment, consent, and overall trial conduct. Based on the COVID experience and its challenges, planning of several large, efficient trials, and wider use of adaptive designs may change the future of clinical research.

Pragmatism, integration in clinical care, efficient administration, promotion of collaborative structures, and enhanced integration of existing data and facilities may be several of the legacies of COVID on future randomized trials. It is unknown who are involved in the guideline development and what specific trial design recommendations they give.

Study outcomes: 1 guideline committee members and declared conflicts of interest; 2 guideline development and organisation of commenting phases; 3 categorisation of stakeholders who comment on draft and final guidelines according to conflicts of interest 'industry', 'not-industry but with industry-related conflicts', 'independent', 'unclear' ; and 4 trial design recommendations trial duration, psychiatric comorbidity, 'enriched design', efficacy outcomes, comparator choice.

Eleven months after submission, the EMA had not processed our request regarding committee member disclosures. The EMA and FDA guideline development phases are similar; drafts and final versions are publicly announced and everybody can submit comments. The recommended designs were generally for trials of short duration; with restricted trial populations; allowing previous exposure to the drug; and often recommending rating scale efficacy outcomes.

EMA mainly recommended three arm designs both placebo and active comparators , whereas FDA mainly recommended placebo-controlled designs. There were also other important differences and FDA's recommendations regarding the exclusion of psychiatric comorbidity seemed less restrictive. Independent and non-conflicted stakeholders are underrepresented in the guideline development.

It seems warranted with more active involvement of scientists and independent organisations without conflicts of interest in the guideline development process. Publications where the data had been re-used were identified on Web of Science.

Searches were performed by two independent reviewers. The primary outcome was any published re-use of the data re-analysis, secondary analysis, or meta-analysis of individual participant data [MIPD] , where the first, last and corresponding authors were not among the authors of the RCT.

Efforts to synthesize the evidence reach seemingly discrepant conclusions. Each combined data from studies countries , because of different eligibility criteria. Two evaluations had some overt flaws in data, violations of stated eligibility criteria, and biased eligibility criteria e. Perusal of quantitative synthesis methods also exhibited several challenges and biases. Allowing for these caveats, 4 evaluations largely agreed in their main final estimates for global spread of the pandemic and the other two evaluations would also agree after correcting overt flaws and biases.

We applied these models to 14 European countries original 11 plus another 3 , over two different time horizons. RESULTS: While model 1 found that lockdown was the most effective measure in the original 11 countries, model 2 showed that lockdown had little or no benefit as it was typically introduced at a point when the time-varying reproduction number was already very low.

Model 3 found that the simple banning of public events was beneficial, while lockdown had no consistent impact. Based on Bayesian metrics, model 2 was better supported by the data than either model 1 or model 3 for both time horizons. In the SIR modeling framework, the impacts of lockdown are uncertain and highly model dependent. We are pleased to see the active discussion around our study on the relationship between mandatory stay- at- home and business closures and COVID spread.

Each panel regression is, in effect, a "mini-meta-analysis": the effect size is evaluated within each subnational unit, and the overall effect size is estimated from a pooling of these "within" effects. Meta-analyses of observational studies and meta-analyses of randomised controlled trials RCTs including active and placebo control arms were included.

Randomized evidence shows benefits for preventing diabetes and in some gynecological and obstetrical settings. Objective: To assess clinical outcomes with convalescent plasma treatment vs placebo or standard of care in peer-reviewed and preprint publications or press releases of randomized clinical trials RCTs. Data Extraction and Synthesis: Two reviewers independently extracted data on relevant clinical outcomes, trial characteristics, and patient characteristics and used the Cochrane Risk of Bias Assessment Tool.

The primary analysis included peer-reviewed publications of RCTs only, whereas the secondary analysis included all publicly available RCT data peer-reviewed publications, preprints, and press releases. Inverse variance-weighted meta-analyses were conducted to summarize the treatment effects. The certainty of the evidence was assessed using the Grading of Recommendations Assessment, Development, and Evaluation.

Main Outcomes and Measures: All-cause mortality, length of hospital stay, clinical improvement, clinical deterioration, mechanical ventilation use, and serious adverse events. The summary risk ratio RR for all-cause mortality with convalescent plasma in the 4 peer-reviewed RCTs was 0. Among the peer-reviewed RCTs, the summary hazard ratio was 1. Limited data on clinical improvement, clinical deterioration, and serious adverse events showed no significant differences. Conclusions and Relevance: Treatment with convalescent plasma compared with placebo or standard of care was not significantly associated with a decrease in all-cause mortality or with any benefit for other clinical outcomes.

The certainty of the evidence was low to moderate for all-cause mortality and low for other outcomes. Sex biology and gender sociocultural behaviors and attitudes interact to influence health and disease processes across the lifespan-which is currently playing out in the COVID pandemic.

This study develops a gender assessment tool-the Stanford Gender-Related Variables for Health Research-for use in clinical and population research, including large-scale health surveys involving diverse Western populations. While analyzing sex as a biological variable is widely mandated, gender as a sociocultural variable is not, largely because the field lacks quantitative tools for analyzing the influence of gender on health outcomes.

METHODS: We conducted a comprehensive review of English-language measures of gender from to to identify variables across three domains: gender norms, gender-related traits, and gender relations.

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