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Oral and Topical Insecticide response Bioassays and Associated Statistical Analyses Used Commonly in Veterinary and Medical Entomology

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JOUrNAL OF INSECT SCIENCE 2020年第6期20卷 p1-9页

作者： Burgess, Edwin r. King, Bethia H. Geden, Christopher J. Northern Illinois Univ Dept Biol Sci De Kalb IL 60115 USA ARS USDA Ctr Med Agr & Vet Entomol 1600 SW 23rd Dr Gainesville FL 32607 USA

Veterinary and medical entomologists who are involved in research on pest control often need to perform dose-response bioassays and analyze the results. This article is meant as a beginner's guide for doing this and includes instructions for using the free program r for the analyses. The bioassays and analyses are described using previously unpublished data from bioassays on house flies, Musca domestics Linnaeus (Diptera: Muscidae), but can be used on a wide range of pest species. Flies were exposed topically to beta-cyfluthrin, a pyrethroid, or exposed to spinosad or spinetoram in sugar to encourage consumption. LD, values for beta-cyfluthrin in a susceptible strain were similar regardless of whether mortality was assessed at 24 or 48 h, consistent with it being a relatively quick-acting insecticide. Based on LC50 values, spinetoram was about twice as toxic as spinosad in a susceptible strain, suggesting a benefit to formulating spinetoram for house fly control, although spinetoram was no more toxic than spinosad for a pyrethroid-resistant strain. results were consistent with previous reports of spinosad exhibiting little cross-resistance. For both spinosad and spinetoram, LC50 values were not greatly different between the pyrethroid-resistant strain and the susceptible strain.

关键词： toxicology r programming probit analysis pesticide house fly

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Vetsyn: An r package for veterinary syndromic surveillance

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PrEVENTIVE VETErINArY MEDICINE 2015年第1-2期122卷 21-32页

作者： Dorea, F. C. Widgren, S. Lindberg, A. Natl Vet Inst SVA Dept Dis Control & Epidemiol Swedish Zoonosis Ctr SE-75189 Uppsala Sweden

A recent inventory showed that several countries are exploring varied types of animal health sources for the development of veterinary syndromic surveillance (VSS), however, few systems have documented success after the phase of development or exploratory analysis of data. We suggest there are three main challenges in the current development of animal syndromic surveillance: (i) the lack of standards in disease recording and classification;(ii) the development of statistical methods appropriate to deal with animal data;and (iii) the creation of ready-to-use tools that employ these statistical methods. We address the latter two challenges and present an r package - vetsyn - which covers the steps of VSS implementation from classified data to interface. Detailed tutorials are included with the package. The goal is to provide ready-to-use codes to automatize the process of converting pre-classified animal health data into epidemiological information. The package functions are illustrated using real data and simulated outbreaks. Functions to monitor data daily and weekly are available. The main innovation offered by the package is ability to manage data streams, analyses, alarms and user interface in a continuous flow. We expect that this will facilitate the implementation of syndromic surveillance systems by veterinary epidemiologists and surveillance practitioners. (C) 2015 Elsevier B.V. All rights reserved.

关键词： Animal health Syndromic surveillance r programming

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Comparative study of granulometric and granule trend of pre- and post-tsunami sediments with recent beach sediments from Nagoor to Poompuhar, Tamil Nadu

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JOUrNAL OF EArTH SYSTEM SCIENCE 2024年第3期133卷 146页

作者： Sivanandam, Yamini Saranaathan, S. E. Loveson, V. J. SASTRA Deemed Be Univ Sch Civil Engn Thanjavur 613401 Tamil Nadu India CSIR Natl Inst Oceanog Dona Paula Geol Oceanog Div Panaji 403004 Goa India

The December 26, 2004 tsunami waves caused significant destruction that changed geomorphic characteristics in India's east coast. The article presents a comparative study of granulometric and granule trends of pre-tsunami (December, 2004) and post-tsunami (January, 2005) sediments with recent beach sediments (December, 2022) in eight locations, namely, Poompuhar, Chinnankudi, Kuttyandiyur, Chandrapadi, Kottucherimedu, Karaikal Beach, Vadakku Vanjiyur North, and Nagoor Beach. The study was conducted using r programming and aimed to understand the sediment transport and depositional processes. The textural parameters of the sediments imply that they are becoming relatively Bner, stating that the beaches are recovering and reclaiming their regular depositional environment after the disaster. The linear discriminate function plots of pre-tsunami sediments have the highest percentage of aeolian deposits, followed by post-tsunami. The recent sediments have the maximum deposition by the beach environment, and pre-tsunami sediments have the minimal. CM plots show that the transportation of sediments by rolling is more in recent days, whereas sediments were transported by bottom suspension and rolling and by graded suspension in pre- and post-tsunami environments. Further, this study compared sediment roundness between the pre- and post-tsunami periods and the recently deposited sediments. This paper highlights the sediment characteristics observed, especially in the aftermath of natural disasters such as tsunamis.

关键词： Pre-tsunami post-tsunami granulometric granule trend r programming

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PeptCreatr: A Web App for Unique Peptides in Human

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INTErNATIONAL JOUrNAL OF PEPTIDE rESEArCH AND THErAPEUTICS 2022年第2期28卷 1-4页

作者： Arumugaperumal, Arun Krishna, Deepa Velayudhan Alaguponniah, Sathyalakshmi Nallaperumal, Krishnan Sivasubramaniam, Sudhakar Manonmaniam Sundaranar Univ Dept Biotechnol Tirunelveli 627012 Tamil Nadu India Manonmaniam Sundaranar Univ Ctr Informat Technol & Engn Tirunelveli 627012 Tamil Nadu India

The concept of unique peptides implies that a peptide of a certain length can be assigned uniquely to certain protein of the whole proteome. It originated in the field of peptide identification using mass spectrometer. The creation of a database of unique peptides for an organism will be useful when techniques develop to instantaneously identify a protein's identity based on its unique sequence. The unique proteome of human was downloaded from UniProt database. The unique peptides for the protein sequences were found out by a custom made script in r programming. The identified unique peptides were incorporated in an r shiny web application and is hosted at https://***/createpept/. This will serve as a useful reference for researchers in the field of proteomics. [GrAPHICS] .

关键词： Unique peptides r programming Shiny web application Human proteome

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qDATA - an r application implementing a practical framework for analyzing quantitative real-time PCr data

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BIOTECHNIQUES 2024年第12期76卷 559-573页

作者： Ionascu, Adrian Ecovoiu, Alexandru Al. Chifiriuc, Mariana Carmen ratiu, Attila Cristian Univ Bucharest Fac Biol Drosophila Lab Bucharest 060101 Romania Acad Romanian Scientists Ilfov 3 Bucharest 050044 Romania Univ Bucharest Fac Biol Dept Bot & Microbiol Bucharest 060101 Romania Univ Bucharest Res Inst Fac Biol Bucharest 050095 Romania Romanian Acad Bucharest Romania

Gene expression assays that are based on quantitative real-time PCr (qrT-PCr) method are still very popular, therefore, we developed qDATA, an open-source r-based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward data input consisting in Ct values and on other mandatory fields specifying the experimental and control groups. qDATA automatically performs descriptive statistics, normality and statistical testing on 2(-Delta Ct) (or Delta Ct) and 2(-Delta Delta Ct) terms calculated with Livak's method. We also propose a qrT-PCr data analysis framework that depends on performing exhaustive Delta Ct calculations within discrete biological replicates (Brs) and subsequently using the Livak formula for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. The efficiency of our computing approach was tested using input Ct values corresponding to immune related gene expression evaluated in experimental infection of Drosophila melanogaster and Apis mellifera workers. The presented results reveal that our working strategy is reliable and highlight the efficacy and performance of qDATA application.

关键词： Bioinformatics software data analysis qrT-PCr r programming statistics

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Aerobiology: The computational tool for biological data in the air

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METHODS IN ECOLOGY AND EVOLUTION 2019年第8期10卷 1371-1376页

作者： rojo, Jesus Picornell, Antonio Oteros, Jose Univ Castilla La Mancha Inst Environm Sci Bot Toledo Spain Tech Univ Munich Helmholtz Ctr Ctr Allergy & Environm ZAUM Munich Germany Tech Univ Munich Helmholtz Ctr German Ctr Lung Res DZL Munich Germany Univ Malaga Dept Plant Biol Malaga Spain

Aerobiological databases are constantly increasing. Many of them contain long and extensive time series of data which are very difficult and tedious to manage. The development of new real-time automatic sampling devices also requires new tools to reduce time of calculations and data management. In this sense, the Aerobiology r package has been implemented to accelerate and facilitate these tasks. This package was structured in three sections based on (a) the checking of the database, (b) calculation of the main aerobiological indexes and (c) visualization of the results. The Aerobiology package contains numerous functions which, in conjunction, solve the main general tasks that scientists must assume for the analysis of the biological data. The package is freely distributed under GNU General Public License and can directly be installed from CrAN (). The reference manual is available at . Contact: ***@***.

关键词： aerobiology automation bioaerosols bioinformatics computational biology pollen diversity r programming

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An open-source software for geodetic deformation analysis in GNSS networks

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EArTH SCIENCE INFOrMATICS 2022年第3期15卷 2051-2062页

作者： Bilgen, Burhaneddin Inal, Cevat Konya Tech Univ Dept Geomat Engn Konya Turkey

Measurements can be done with classical terrestrial techniques in geodetic deformation networks, as well as by using Global Navigation Satellite System (GNSS) technique, which is one of the most widely used modern techniques today. GNSS is a high-accuracy technique that is widely used today for monitoring and detecting deformations in the earth's crust and engineering structures. However, difficulties are encountered in the evaluation of measurements due to the intensive use of statistics in deformation analysis and the high numerical calculation load. Considering the possible consequences of deformations in the earth's crust and engineering structures, strategies and evaluation software are needed to determine them quickly. In this study, an open-source software that can be used in the analysis of deformation surveys carried out in campaigns with the static GNSS technique were developed by using r programming language since open-source deformation analysis software is missing in the field of deformation analysis. The method chosen for the determination of deformations is presented. The general features of the developed software are introduced, and a case study was carried out to test the computational performance of the software and to investigate which parameters are effective in determining the amount of deformation in GNSS networks correctly. As a result of the study, it was seen that ambiguity resolution rates and ionospheric activity affect the accuracy of the deformations determined in GNSS networks.

关键词： Bernese v5 2 Geodetic deformation analysis GNSS IWST Periodic deformation surveys r programming S-transformation

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Analyzing Multivariate Generalizability Theory Designs within Structural Equation Modeling Frameworks

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STrUCTUrAL EQUATION MODELING-A MULTIDISCIPLINArY JOUrNAL 2024年第3期31卷 552-570页

作者： Vispoel, Walter P. Lee, Hyeryung Hong, Hyeri Univ Iowa Iowa City IA USA Calif State Univ Fresno Fresno CA USA Univ Iowa 361 Lindquist Ctr Iowa City IA 52242 USA

We demonstrate how to analyze complete multivariate generalizability theory (GT) designs within structural equation modeling frameworks that encompass both individual subscale scores and compo-sites formed from those scores. results from numerous analyses of observed scores obtained from respondents who completed the recently updated form of the Big Five Inventory (BFI-2) revealed that the lavaan SEM package in r produced results virtually identical to those obtained from the mGENOVA package, which historically has served as the gold standard for conducting multivariate GT analyses. We further extended lavaan analyses beyond what mGENOVA allows to produce Monte Carlo based confidence intervals for key GT parameters and correct score consistency and correlational indi-ces for effects of scale coarseness characteristic of binary and ordinal data. Our comprehensive online Supplemental Material includes code for performing all illustrated analyses using lavaan and mGENOVA.

关键词： Generalizability theory multivariate analysis r programming structural equation modeling

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Dissemination and Symptoms of Monkeypox Virus Infection

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ASIA-PACIFIC JOUrNAL OF PUBLIC HEALTH 2023年第2-3期35卷 175-178页

作者： Yang, San-Duk Park, Hyun-Seok Kyung Hee Cyber Univ Sch Integrated Software & Design Dept Cyber Secur & AI technol Seoul South Korea Ewha Womans Univ ELTEC Coll Engn Bioinformat Lab Seoul South Korea Ewha Womans Univ Ctr Convergence Res Adv Technol Seoul South Korea Kyung Hee Cyber Univ Sch Integrated Software & Design Dept Cyber Secur & AI technol Seoul 02447 South Korea Ewha Womans Univ ELTEC Coll Engn Bioinformat Lab Seoul 03760 South Korea

The monkeypox virus is endemic in Africa. However, the virus has spread worldwide since May 2022, and it has now been confirmed in 109 countries (as of September 22, 2022). Thus, an urgent investigation of the outbreak patterns of confirmed cases and evidence of viral infection is needed. This study investigated the spread of monkeypox in 109 countries, including 15 Asian-Pacific countries, by examining the number of cases, symptoms of infection, and the period between diagnosis and death.

关键词： monkeypox virus data analysis r programming big data analytics public health

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Calculating risk and prevalence ratios and differences in r: developing intuition with a hands-on tutorial and code

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ANNALS OF EPIDEMIOLOGY 2023年 86卷 104-109页

作者： Yorlets, rachel r. Lee, Youjin Gantenberg, Jason r. Brown Univ Sch Publ Hlth Dept Epidemiol 121 South Main StBox G-S121-3 Providence RI 02903 USA Brown Univ Populat Studies & Training Ctr Providence RI 02903 USA Brown Univ Sch Publ Hlth Dept Biostat Providence RI 02903 USA Brown Univ Dept Hlth Serv Policy & Practice Sch Publ Hlth Providence RI 02903 USA

Epidemiologic research questions often focus on evaluating binary outcomes, yet curricula and scientific literature do not always provide clear guidance or examples on selecting and calculating an appropriate measure of association in these scenarios. reporting inappropriate measures may lead to misleading sta-tistical conclusions. We present a hands-on tutorial that includes annotated code written in an open-source statistical programming language (r) showing readers how to apply, compare, and understand four methods used to estimate a risk or prevalence ratio (or difference), rather than presenting an odds ratio. We will provide guidance on when to use each method, discussing the strengths and limitations of each ap-proach, and compare the results obtained across them. Ultimately, we aim to help trainees, public health researchers, and interdisciplinary professionals develop an intuition for these methods and empower them to implement and interpret these methods in their own research.(c) 2023 Elsevier Inc. All rights reserved.

关键词： risk ratio risk difference r programming Log -binomial Modified poisson Logistic regression

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