scholarly journals Coalescent: an open-science framework for importance sampling in coalescent theory

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1203
Author(s):  
Susanta Tewari ◽  
John L. Spouge
Keyword(s):  
Importance Sampling ◽  
Open Science ◽  
Coalescent Theory ◽  
Science Framework

scholarly journals Coalescent: an Open-Science framework for Importance Sampling in Coalescent theory

2014 ◽  
Author(s):  
Susanta Tewari ◽  
John L Spouge
Keyword(s):  
Importance Sampling ◽  
User Interaction ◽  
Open Science ◽  
Maximum Likelihood Estimates ◽  
Effective Sample Size ◽  
Data Sets ◽  
Coalescent Theory ◽  
Target Distribution ◽  
Compute Data ◽  
Infinite Sites Model

Importance sampling is widely used in coalescent theory to compute data likelihood. Efficient importance sampling requires a trial distribution close to the target distribution of the genealogies conditioned on the data. Moreover, an efficient proposal requires intuition about how the data influence the target distribution. Different proposals might work under similar conditions, and sometimes the corresponding concepts overlap extensively. Currently, there is no framework available for coalescent theory that evaluates proposals in an integrated manner. Typically, problems are not modeled, optimization is performed vigorously on limited datasets, user interaction requires thorough knowledge, and programs are not aligned with the current demands of open science. We have designed a general framework (http://coalescent.sourceforge.net) for importance sampling, to compute data likelihood under the infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. The framework computes the data likelihood and provides maximum likelihood estimates of the mutation parameter. Well-known benchmarks in the coalescent literature validate the framework’s accuracy. We evaluate several proposals in the coalescent literature, to discover that the order of efficiency among three standard proposals changes when running time is considered along with the effective sample size. The framework provides an intuitive user interface with minimal clutter. For speed, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework accessible to a large community.

scholarly journals Coalescent: an Open-Science framework for Importance Sampling in Coalescent theory

2014 ◽  
Author(s):  
Susanta Tewari ◽  
John L Spouge
Keyword(s):  
Importance Sampling ◽  
User Interaction ◽  
Open Science ◽  
Maximum Likelihood Estimates ◽  
Effective Sample Size ◽  
Data Sets ◽  
Coalescent Theory ◽  
Target Distribution ◽  
Compute Data ◽  
Infinite Sites Model

Importance sampling is widely used in coalescent theory to compute data likelihood. Efficient importance sampling requires a trial distribution close to the target distribution of the genealogies conditioned on the data. Moreover, an efficient proposal requires intuition about how the data influence the target distribution. Different proposals might work under similar conditions, and sometimes the corresponding concepts overlap extensively. Currently, there is no framework available for coalescent theory that evaluates proposals in an integrated manner. Typically, problems are not modeled, optimization is performed vigorously on limited datasets, user interaction requires thorough knowledge, and programs are not aligned with the current demands of open science. We have designed a general framework (http://coalescent.sourceforge.net) for importance sampling, to compute data likelihood under the infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. The framework computes the data likelihood and provides maximum likelihood estimates of the mutation parameter. Well-known benchmarks in the coalescent literature validate the framework’s accuracy. We evaluate several proposals in the coalescent literature, to discover that the order of efficiency among three standard proposals changes when running time is considered along with the effective sample size. The framework provides an intuitive user interface with minimal clutter. For speed, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework accessible to a large community.

Publikasi Akademik Sepanjang 2019

2019 ◽  
Author(s):  
Adib Rifqi Setiawan
Keyword(s):  
Open Science ◽  
Research Papers ◽  
Science Framework

Berikut ini beberapa publikasi saya pada 2019 ini. Penting atau tidak, saya menganggap bahwa publikasi hanyalah efek samping riset. Di luar publikasi ini, saya juga masih aktif sebagai penulis media daring, seperti Qureta.com, Selasar.com, dan SantriMilenial.net serta mengunggah beberapa artikel preprint melalui layanan Open Science Framework (OSF), EdArxiv.org, dan Research Papers in Economics (RePEc).

scholarly journals Genetic and Transcriptomic Biomarkers in Neurodegenerative Diseases: Current Situation and the Road Ahead

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1030
Author(s):  
Julie Lake ◽  
Catherine S. Storm ◽  
Mary B. Makarious ◽  
Sara Bandres-Ciga
Keyword(s):  
Neurodegenerative Diseases ◽  
Large Scale ◽  
Disease Diagnosis ◽  
Open Science ◽  
Future Directions ◽  
The Road ◽  
Current State ◽  
Molecular Complexity ◽  
Science Framework ◽  
Lateral Sclerosis

Neurodegenerative diseases are etiologically and clinically heterogeneous conditions, often reflecting a spectrum of disease rather than well-defined disorders. The underlying molecular complexity of these diseases has made the discovery and validation of useful biomarkers challenging. The search of characteristic genetic and transcriptomic indicators for preclinical disease diagnosis, prognosis, or subtyping is an area of ongoing effort and interest. The next generation of biomarker studies holds promise by implementing meaningful longitudinal and multi-modal approaches in large scale biobank and healthcare system scale datasets. This work will only be possible in an open science framework. This review summarizes the current state of genetic and transcriptomic biomarkers in Parkinson’s disease, Alzheimer’s disease, and amyotrophic lateral sclerosis, providing a comprehensive landscape of recent literature and future directions.

scholarly journals Published patterns of spin in biomedical literature: a protocol for a meta-research study

BMJ Open ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. e043784
Author(s):  
Naichuan Su ◽  
Michiel van der Linden ◽  
Geert JMG van der Heijden ◽  
Stefan Listl ◽  
Stefan Schandelmaier ◽  
...  
Keyword(s):  
Systematic Reviews ◽  
Scientific Journal ◽  
Open Science ◽  
Biomedical Literature ◽  
Measurement Tool ◽  
Delphi Consensus ◽  
Reporting Practices ◽  
Literature Reviews ◽  
Science Framework ◽  
Meta Analyses

IntroductionSpin is defined as reporting practices that distort the interpretation of results and create misleading conclusions by suggesting more favourable results. Such unjustifiable and misleading misrepresentation may negatively influence the development of further studies, clinical practice and healthcare policies. Spin manifests in various patterns in different sections of publications (titles, abstracts and main texts). The primary aim of this study is to identify reported spin patterns and assess the prevalence of spin in general, and the prevalence of spin patterns reported in biomedical literature based on previously published systematic reviews and literature reviews on spin.Methods and analysisPubMed, EMBASE and SCOPUS will be searched to identify systematic or literature reviews on spin in biomedicine. To improve the comprehensiveness of the search, the snowballing method will be used to broaden the search. The data on spin-related outcomes and characteristics of the included studies will be extracted. The methodological quality of the included studies will be assessed with selective items of the A MeaSurement Tool to Assess systematic Reviews-2 checklist. A new classification scheme for spin patterns will be developed if the classifications of spin patterns identified in the included studies vary. The prevalence of spin and spin patterns will be pooled based on meta-analyses if the classification schemes for spin are comparable across included studies. Otherwise, the prevalence will be described qualitatively. The seriousness of spin patterns will be assessed based on a Delphi consensus study.Ethics and disseminationThis study has been approved by the Academic Centre for Dentistry Amsterdam Ethics Review Committee (2020250). The study will be submitted to a peer-reviewed scientific journal.RegistrationOpen Science Framework: osf.io/hzv6e

Overview of current legislation, experiences and existing scenarios on allowing the sale of tobacco products only in tobacco stores: a scoping review protocol

2021 ◽  
Vol 10 (16) ◽  
pp. e402101621884
Author(s):  
Lucas Manoel da Silva Cabral ◽  
Fernando Nagib Jardim ◽  
Maria José Domingues da Silva Giongo ◽  
Andréa Ramalho Reis Cardoso ◽  
Maria Raquel Fernandes da Silva ◽  
...  
Keyword(s):  
Scoping Review ◽  
Passive Smoking ◽  
Smoking Prevalence ◽  
Methodological Approach ◽  
Open Science ◽  
Tobacco Products ◽  
Scoping Reviews ◽  
Review Protocol ◽  
Science Framework

This article presents the scoping review protocol on allowing the sale of tobacco products only in tobacco stores in Brazil. It is based on the hypothesis that limiting the sale of tobacco products only in tobacco shops would significantly prevent initiation and encourage cessation, thus reducing smoking prevalence and passive smoking in Brazil. The protocol aims to document the processes involved in the planning and methodological approach of an extensive scoping review, guided by Joanna Briggs Institute’s manual. The review protocol was prepared following PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation. It was registered in the Open Science Framework.

Psychophysiology, cognition, and political differences

2021 ◽  
Vol 40 (2) ◽  
pp. 137-141 ◽  
Author(s):  
Jordan Mansell ◽  
Allison Harell ◽  
Elisabeth Gidengil ◽  
Patrick A. Stewart
Keyword(s):  
Political Science ◽  
Life Sciences ◽  
Science Research ◽  
Open Science ◽  
Common Theme ◽  
Special Issue ◽  
The Future ◽  
Research Questions ◽  
Political Differences ◽  
Science Framework

AbstractWe introduce the Politics and the Life Sciences special issue on Psychophysiology, Cognition, and Political Differences. This issue represents the second special issue funded by the Association for Politics and the Life Sciences that adheres to the Open Science Framework for registered reports (RR). Here pre-analysis plans (PAPs) are peer-reviewed and given in-principle acceptance (IPA) prior to data being collected and/or analyzed, and are published contingent upon the preregistration of the study being followed as proposed. Bound by a common theme of the importance of incorporating psychophysiological perspectives into the study of politics, broadly defined, the articles in this special issue feature a unique set of research questions and methodologies. In the following, we summarize the findings, discuss the innovations produced by this research, and highlight the importance of open science for the future of political science research.

scholarly journals Interventions to Promote a Healthy Sexuality among School Adolescents: A Scoping Review

2021 ◽  
Vol 11 (11) ◽  
pp. 1155
Author(s):  
Fernanda Loureiro ◽  
Margarida Ferreira ◽  
Paula Sarreira-de-Oliveira ◽  
Vanessa Antunes
Keyword(s):  
Open Science ◽  
Multidisciplinary Teams ◽  
Adolescent Sexual Behavior ◽  
Scoping Reviews ◽  
Key Factor ◽  
Nurses Role ◽  
Healthy Sexuality ◽  
Science Framework ◽  
Meta Analyses

Schools are particularly suitable contexts for the implementation of interventions focused on adolescent sexual behavior. Sexual education and promotion have a multidisciplinary nature. Nurses’ role and the spectrum of the carried-out interventions is not clear. We aimed to identify interventions that promote a healthy sexuality among school adolescents. Our review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews and was registered in the Open Science Framework. Published articles on sexuality in adolescents in school contexts were considered. The research limitations included primary studies; access in full text in English, Spanish, or Portuguese; and no data publication limitation. Research was carried out on the EBSCOhost, PubMed, SciELO, and Web of Science platforms; gray literature and the bibliographies of selected articles were also searched. A total of 56 studies were included in the sample. The studies used a broad range of research methods, and 10 types of interventions were identified. Multi-interventional programs and socio-emotional interventions showed a greater impact on long-term behavioral changes, and continuity seemed to be a key factor. Long-term studies are needed to reach a consensus on the effectiveness of interventions. Nurses’ particular role on the multidisciplinary teams was found to be a gap in the research, and must be further explored.

scholarly journals A free and publicly available stimuli set for statistical learning experiments in language and music

2020 ◽  
Author(s):  
Dominique T Vuvan ◽  
Erica H Wojcik
Keyword(s):  
Statistical Learning ◽  
Open Science ◽  
Research Progress ◽  
Cognitive Representations ◽  
Language And Music ◽  
Continuous Stream ◽  
Science Framework ◽  
Segmentation Task ◽  
Current Report ◽  
Validation Experiments

The ability to encode regularities from the environment and abstract these patterns into structured cognitive representations is called statistical learning. Currently, one of the most studied paradigms of statistical learning is a word segmentation task originally introduced in a landmark paper by Saffran, Newport, and Aslin (1996). In this paradigm, participants hear a continuous stream of artificial words without acoustic cues to the boundaries separating the words. Then, they are asked to discriminate between words and non-words in the artificial language. One of the barriers that has impeded research progress using this paradigm is the lack of stimulus standardization. This lack of standardization is inefficient, causing researchers to create new stimuli for each new line of experiments. Furthermore, it makes the comparison of methods and results between different experiments difficult, if not impossible. The goal of the current report is to introduce a publically available stimuli set for language (syllable) and music (tone) segmentation experiments of statistical learning. All stimuli, data, and code associated with the current report are available for download on Open Science Framework, and we report here our validation experiments for both sets of stimuli.

scholarly journals Lesões orais em idosos que fazem uso de prótese dentária: um protocolo de revisão de escopo

2021 ◽  
Vol 10 (14) ◽  
pp. e521101422252
Author(s):  
Júlio César Guimarães Freire ◽  
Jessyka Hellem de Melo Pereira ◽  
Paulo Henrique Lucas do Nascimento ◽  
Pedro Antônio Medeiros da Silva ◽  
Aparecida Borges ◽  
...  
Keyword(s):  
Web Of Science ◽  
Open Science ◽  
Dental Prosthesis ◽  
Google Scholar ◽  
Oral Manifestations ◽  
Medical Subject Headings ◽  
Subject Headings ◽  
Science Framework

O envelhecimento da população faz surgir a necessidade de cuidados especiais com a saúde. O edentulismo, por exemplo, é uma condição bucal que afeta, principalmente, os idosos, sendo comum o uso de próteses dentárias que muitas vezes geram lesões orais. Este protocolo propõe uma revisão de escopo sobre a prevalência de lesões na mucosa oral em decorrência do uso de prótese dentária na população idosa. Desse modo, o objetivo do referido protocolo é apresentar a metodologia que será adotada, de acordo com as recomendações de estruturação do Joanna Briggs Institute para revisões de escopo, sendo este documento previamente registrado no repositório Open Science Framework. A estratégia de busca será elaborada de modo a identificar as possíveis fontes de evidências publicadas nas seguintes bases de dados: Cochrane, PubMed via MEDLINE, LILACS, Web of Science e Scopus. No que se refere à literatura cinzenta, serão feitas buscas através do Google Scholar. Serão utilizados os seguintes descritores do vocabulário controlado Descritores em Ciências da Saúde/Medical Subject Headings: idoso/aged, prótese dentária/dental prosthesis e manifestações bucais/oral manifestations, seus sinônimos e variações ortográficas. A estratégia PCC (População, Conceito, Contexto) servirá de base para elaboração da pergunta de pesquisa e definição dos critérios de inclusão e exclusão. Os resultados da revisão de escopo proposta deverão mostrar os fatores que influenciam a prevalência de lesões em mucosa oral de pessoas idosas que fazem uso de prótese dentária.

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