PSS Health: como calcular tamanho de amostra para estimar média, proporção e correlação / PSS Health: how to calculate a sample size to estimate means, proportions, and correlations

A ferramenta PSS Health (Power and Sample Size for Health Researchers) foi desenvolvida com o propósito de facilitar o cálculo do tamanho amostral e do poder de testes de hipóteses para diferentes objetivos de estudo, usando interface amigável e terminologia comum à área da saúde. Este é o primeiro de uma série de artigos que pretendem orientar o usuário na utilização da ferramenta PSS Health para o planejamento de uma pesquisa. Neste artigo, se ensina como utilizar o PSS Health quando o objetivo principal do estudo é estimar uma média, estimar uma proporção (prevalência ou incidência) ou estimar uma correlação. São disponibilizados vídeos demonstrando o uso da ferramenta em cada um dos contextos citados. (AU)

The PSS Health (Power and Sample Size for Health Researchers) tool was developed with the purpose of facilitating the calculation of sample size and power of hypothesis tests for different study objectives, based on a user-friendly interface and common health care terminology. This is the first in a series of articles intending to guide the user in how to use the PSS Health tool for planning a research project. This article teaches how to use PSS Health when the main objective of the study is to estimate means, proportions (prevalence or incidence), or correlations. Videos showing how to use the tool in each of the mentioned contexts are available. (AU)

Development of tools for clinical trial information retrieval and Meta-analysis based on R-Shiny: Taking non-small cell lung cancer as an example / 中国临床药理学与治疗学

AIM: To develop a tool providing the graphical user interface (GUI), which can integrate Meta-analysis and information retrieval from clinical trials. METHODS: The Web application based on the Bootstrap framework was built with the Shiny package of R language, and the information retrieval and meta-analysis functions were implemented based on the R packages of DT, Meta, gemtc, etc. RESULTS: The tool could filter the articles and variables according to the user's requirements, and the information presented in the form of a table. Users can also select different experimental group drugs and control group drugs for classic meta-analysis, and add or subtract different studies to construct the network map between drugs for network meta-analysis. CONCLUSION: This tool has a friendly user interface, which is easy to use, accurate in analysis and drawing results, and can bring convenience to researchers.

PKconverter: R package to convert the pharmacokinetic parameters

Population pharmacokinetic analysis and modeling procedures typically require estimates of both population and individual pharmacokinetic parameters. However, only some of these parameters are contained in models and only parameters in the model can be estimated. In this paper, we introduce a new R package, PKconverter, to calculate pharmacokinetic parameters using the relationships among them. After fitting the model, other parameters can be calculated from the functional relationship among the parameters. PKconverter provides the functions to calculate whole parameters along with a Shiny application for converting the parameters. With this package, it is also possible to calculate the standard errors of the other parameters that are not in the model and estimate individual parameters simultaneously.

COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

Description of immature stages of Platycoelia valida Burmeister, 1844 (Coleoptera: Melolonthidae: Rutelinae: Anoplognathini)

Abstract Description of immature stages of Platycoelia valida Burmeister, 1844 (Coleoptera: Melolonthidae: Rutelinae: Anoplognathini). Third instar larva and pupa of P. valida are described for the first time based on specimens collected in soils of yucca and coffee fields in Cundinamarca, Colombia. Illustrations of diagnostic structures and keys to the known third-stage larvae of Rutelinae tribes and Platycoelia species are included. Data on the biology and distribution of P. valida in Colombia are also commented.

IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

Helminths of Molothrus bonariensis (Gmelin, 1789) (Passeriformes: Icteridae) from southernmost Brazil / Helmintos of Molothrus bonariensis (Gmelin, 1789) (Passeriformes: Icteridae) do extremo sul do Brasil

Abstract Information about helminths of Molothrus bonariensis (Gmelin, 1789) (Passeriformes: Icteridae) are scarce; in this sense the objective of this paper was to contribute to its knowledge. Five hosts of southern Brazil were examined and the helminths Prosthogonimus ovatus, Tanaisia valida (Digenea), Diplotriaena bargusinica and Synhimantus (Dispharynx) nasuta (Nematoda) were identified. The species T. valida, P. ovatus and S. (D.) nasuta are for the first time registered for the bird in Brazil. Prosthogonimus ovatus, T. valida, D. bargusinica e S. (D.) nasuta are first recorded in M. bonariensis in the southern Brazilian state Rio Grande do Sul.

Resumo Informações sobre helmintos de Molothrus bonariensis (Gmelin, 1789) (Passeriformes: Icteridae) são escassas, nesse sentido, o objetivo do trabalho foi contribuir para esse conhecimento. Foram examinados cinco hospedeiros do extremo sul do Brasil, identificou-se os helmintos Prosthogonimus ovatus, Tanaisia valida (Digenea), Diplotriaena bargusinica e Synhimantus (Dispharynx) nasuta (Nematoda). As espécies T. valida, P. ovatus e S. (D.) nasuta são pela primeira vez registradas para a ave no Brasil. Prosthogonimus ovatus, T. valida, D. bargusinica e S. (D.) nasuta são pela primeira vez registradas em M. bonariensis no estado do Rio Grande do Sul.

A new species of Callistethus from Mexico (Coleoptera, Melolonthidae, Rutelinae) / Una nueva especie de Callistethus de México (Coleoptera, Melolonthidae, Rutelinae)

Callistethus tlapanecus, a new species collected in pine forest located at 2160 meters of altitude in eastern mountains of the state of Guerrero, Mexico is described. The morphological characters that distinguish it from other Mexican and Central American species are discussed. The diagnostic characters are illustrated, and a key to Mexican species of Callistethus is also included.

Se describe Callistethus tlapanecus, nueva especie colectada en bosques de pino situados a 2160 metros de altitud en las montañas orientales del estado de Guerrero, México. Se comentan los caracteres morfológicos que distinguen a esta especie de otras especies mexicanas y centroamericanas de Callistethus. Se ilustran los caracteres diagnósticos y se incluye una clave para separar las especies mexicanas de Callistethus.