bluuebunny/crossref_metadata_2025 huggingface dataset:
Willingness-to-pay per quality-adjusted life year of patients with psoriasis: A study in Vietnam
Authors: Dinh Hoang Yen  , Nguyen Trong Hao  , Nguyen Thuy Hang
Published: December 2024

Background: The chronic nature and frequent recurrence of psoriasis reduce patients' quality of life and increase treatment costs. This study aimed to estimate the willingness-to-pay (WTP) per quality-adjusted life-year (QALY) of psoriasis patients in Vietnam. Patients and methods: A cross-sectional study was conducted based on face-to-face interviews with psoriasis patients at Ho Chi Minh City (HCMC) Hospital of Dermato-Venereology. The Euro Quality of Life 5-Dimension 5-Level (EQ-5D-5L) questionnaire was used, and questions about WTP were asked. Factors related to WTP per QALY were analysed statistically. Results: A total of 310 psoriasis patients (58.4% males; mean age of 48.84±16.27 years) were included. The mean disease and treatment durations were 11.51±9.82 and 9.69±8.87 years, respectively. The mean health-related quality of life was 0.787±0.128, and WTP/QALY was 7,726.86±4,506.82 USD (179,100,000±104,463,500 VND). Patients with university/college degrees had a significantly higher WTP/QALY (10,666.60 USD - 247.24 million VND) than patients with high school or under high school education (8,440.44 and 6,638.38 USD - 195.64 million and 153.87 million VND, p<0.05). There was a significant negative correlation between WTP/QALY and age (r=-0.247, p=0.000). Conclusions: The WTP per QALY of psoriasis patients was almost 3 times higher than GDP per capita of Vietnam in 2018. Education level, health-related quality of life and age are associated with WTP/QALY.
A comparison of Vietnamese, Malaysian, Thai and Indonesian EQ-5D-5L value sets using a Vietnamese sample of HER2 positive breast cancer patients
Authors: Vo Ngoc Yen Nhi  , Tran Thi Yen Nhi  , Nguyen Tran Nhu Y  , Nguyen Thi To Nga  , Nguyen Thi Thu Thuy
Published: December 2024

Background: Vietnamese value set was published in 2019, but so far there has been no assessment comparison of the Vietnamese value set with other value sets. Objectives: To compare the Vietnamese, Malaysian, Thai, Indonesian value sets and evaluate the appropriateness of the Vietnamese value set for Vietnamese people. Methods: A cross-sectional study was conducted on 338 HER2 positive breast cancer patients are treating at 6 hospitals in Vietnam. Data was collected by taking the entire sample from July to December in 2019. The EQ-5D-5L health states ratings were collected through interviews with patients and utility scores were calculated using the Vietnamese, Malaysian, Thai and Indonesian value sets. The difference in the mean values from 4 value sets was verified by the Wilcoxon signed rank test and the consistency between value sets was assessed by using intraclass correlation coefficients (ICCs). Spearman's test was used to evaluate the correlation between the patient's demographic characteristics with EQ-5D score (95% confidence interval). Results: The study was performed on 338 patients with the mean age of 53.870 ± 9.970 and weight of patients of 54.589 ± 7.698 kg. The Thai value set had the highest mean utility score (0.904 ± 0.142), followed by the Indonesian value set (0.881 ± 0.117), Malaysian value set (0.867 ± 0.143) and the Vietnamese value set had the smallest mean utility score (0.863 ± 0.142). There was a very high consistency between the value sets ( intraclass correlation coefficients > 0.900). The forecasting model of EQ-5D VAS utility score based on EQ-5D-5L utility score from the Vietnamese value set had the highest R square (R2 = 0.231). Conclusion: Vietnamese, Malaysian, Thai, Indonesian value sets have an overall high level of correlation and consistency, in which the correlation of Vietnamese and Malaysian value sets is highest. The Vietnamese value set is most suitable for the Vietnamese HER2-positive breast cancer patients, the Malaysian value set is the second-best option to be applied.
Policy Implications and Recommendations for Integrated Diabetes Care in Nigeria: Strengthening Healthcare Systems to Address Growing Diabetes Burden
Authors:   School of Natural and Applied Sciences Kampala International University Uganda, Achieng M. Nyambura
Published: December 2024

Diabetes has emerged as a significant public health concern in Nigeria, contributing to the growing burden of non-communicable diseases (NCDs) within the country. This review explores the policy implications and presents recommendations for strengthening integrated diabetes care in Nigeria, addressing the challenges posed by a healthcare system traditionally focused on infectious diseases. The rising prevalence of diabetes in Nigeria is driven by urbanization, lifestyle changes, and limited awareness of preventive healthcare, leading to inadequate management of the disease. The review critically examines the current policy landscape, highlighting gaps in diabetes-specific healthcare strategies and emphasizing the need for integration of diabetes care within primary healthcare (PHC) systems. The potential benefits of such integration are discussed, including improved accessibility, resource optimization, and enhanced patient outcomes. The review further explores key policy recommendations such as the development of a national diabetes policy, strengthening primary healthcare infrastructure, training healthcare providers, leveraging digital health tools, and implementing public health campaigns. Additionally, the review outlines challenges to policy implementation, including resource limitations, workforce shortages, and cultural barriers. The integration of diabetes care into PHC is seen as a vital strategy for improving care continuity and addressing the socioeconomic burden of diabetes in Nigeria. The review concludes with a call for multi-sectoral collaboration and comprehensive public health strategies to combat the diabetes epidemic, ensuring better health outcomes and a more resilient healthcare system.

Keywords: Integrated diabetes care, Nigeria healthcare system, Non-communicable diseases (NCDs), Diabetes management
Preventive Measures for Diarrhea in Communities Lacking Clean Water Supply: A Scientific Review
Authors:   School of Natural and Applied Sciences Kampala International University Uganda, Mwaura J. Ngugi
Published: December 2024

Diarrhea remains a leading cause of morbidity and mortality in communities with limited access to clean water, especially in low- and middle-income countries. This review highlights preventive measures aimed at reducing the incidence of diarrhea in populations lacking safe water supplies. The review explores the role of water quality improvements, sanitation infrastructure, hygiene promotion, and community engagement in minimizing diarrheal disease transmission. Key interventions include point-of-use water treatment methods such as solar disinfection (SODIS) and water purification tablets, improved sanitation practices to contain waste and prevent water contamination, and hygiene promotion with a focus on handwashing. Furthermore, the integration of food safety protocols and cholera vaccination programs complements water, sanitation, and hygiene (WASH) initiatives. The review also emphasizes the importance of community education and the involvement of local leaders and health workers in fostering sustainable health practices. Despite proven solutions, challenges to implementation—such as economic constraints, cultural barriers, political factors, and geographic limitations—persist. The review advocates for innovative financing models, culturally sensitive interventions, and policy support to address these obstacles and improve long-term health outcomes in resource-limited settings.

Keywords: Diarrhea, clean water supply, preventive measures, sanitation, hygiene practices, community engagement.
The Role of Oral Rehydration Therapy in Managing Diarrhea in Children
Authors:   School of Natural and Applied Sciences Kampala International Uganda, Kibibi J. Wambui
Published: December 2024

Diarrhea is a leading cause of illness and mortality among children under five, particularly in low- and middle-income countries (LMICs), with dehydration as the primary threat. Oral Rehydration Therapy (ORT), developed in the 1960s, remains a critical intervention, effectively replenishing fluids and electrolytes lost during diarrheal episodes. This review explores the mechanism, clinical efficacy, global implementation, and challenges associated with ORT in managing childhood diarrhea. Despite its proven impact in reducing mortality, global use of ORT remains inconsistent due to cultural, logistical, and educational barriers. Future directions include next-generation oral rehydration solutions, zinc supplementation, and mobile health interventions to increase ORT accessibility and improve outcomes. Global efforts to promote ORT adoption and address barriers to its use are crucial for reducing child mortality and morbidity from diarrheal diseases.

Keywords: Oral Rehydration Therapy, ORT, diarrhea management, childhood dehydration, electrolyte imbalance.
Tracing Malaria Incidence across West and East Africa: A Comparative Historical Analysis of Trends, Influences, and Regional Differences
Authors:   School of Natural and Applied Sciences Kampala International Uganda, Amina H. Katu
Published: December 2024

This review provides a comparative historical analysis of malaria incidence across West and East Africa, focusing on the unique trends, environmental influences, and socio-political conditions that shape malaria transmission dynamics in these regions. While malaria poses a pervasive public health burden across Africa, West and East Africa differ significantly in terms of climate, healthcare infrastructure, socio-economic status, and malaria control strategies, each influencing regional patterns of malaria incidence. West Africa’s tropical climate fosters year-round transmission, while East Africa, with its diverse topography, experiences seasonal and altitudinal variations in transmission patterns. Historical approaches to malaria control in both regions reveal numerous challenges, including limited healthcare access, economic constraints, and socio-political instability, all of which have impacted the effectiveness of interventions. Through comparative analysis, this review examines the successes and limitations of past and current malaria control efforts, emphasizing the need for region-specific approaches that address climate-adapted interventions, insecticide and drug resistance management, community engagement, and sustainable funding. By analyzing historical and contemporary malaria control strategies, this review highlights best practices and challenges, offering insights for future policies aimed at reducing malaria incidence sustainably and advancing regional public health.

Keywords: Malaria incidence, West Africa, East Africa, malaria transmission, public health.
Mujeres indígenas frente al cambio climático
Authors: Landa Amador Anahi Alejandra
Published: December 2024

El cambio climático no solo impacta el medio ambiente, sino que también afecta a la fauna, nuestros alimentos y la salud de la población mundial. En su libro "Mujeres indígenas frente al cambio climático", Rocío Silva Santisteban presenta las historias de mujeres que resuenan por las calles reclamando justicia, que se rigen por el respeto a la vida, que son evidencia viva de la sabiduria ancestral de las culturas indígenas. El libro se enfoca en las comunidades que habitan Brasil y Perú, busca evidenciar cómo el cambio climático afecta en sus tradiciones y saberes de aquellos que están al frente de la defensa de sus tierras y culturas.
Archival and analysis of #GI2013 Tweets
Authors: Turner Stephen
Published: December 2024

I archived and analyzed all Tweets containing #GI2013 from the recent Cold Spring Harbor Genome Informatics meeting, using my previously described code. Friday was the most Tweeted day.
Automated Archival and Visual Analysis of Tweets Mentioning #bog13, Bioinformatics, #rstats, and Others
Authors: Turner Stephen
Published: December 2024

Automatically Archiving Twitter Results

Ever since Twitter gamed its own API and killed off great services like IFTTT triggers, I've been looking for a way to automatically archive tweets containing certain search terms of interest to me. Twitter's built-in search is limited, and I wanted to archive interesting tweets for future reference and to start playing around with some basic text / trend analysis.
Friday fun: Abstract mad libs
Authors: Turner Stephen
Published: December 2024

For those of you writing abstracts that will get you to Hawaii this fall for IGES (due June 1) and ASHG (due June 2), just follow this template from Piled Higher and Deeper.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Seminar: Translating Disease-Associate Genetic Variants into Pathways
Authors: Turner Stephen
Published: December 2024

Soumya Raychaudhuri is the lead author on the GRAIL paper in Nature Genetics. GRAIL (Gene Relationships Across Implicated Loci) is software available from the Broad Institute and looks like an interesting way to prioritize SNPs for followup. I'll cover it here in the future, but in the meantime, check out this seminar this Wednesday.
"Document Design and Purpose, Not Mechanics"
Authors: Turner Stephen
Published: December 2024

If you ever write code for scientific computing (chances are you do if you're here), stop what you're doing and spend 8 minutes reading this open-access paper: Wilson et al. Best Practices for Scientific Computing.
RStudio Conference 2017 Recap
Authors: Turner Stephen
Published: December 2024

The first ever RStudio conference was held January 11-14, 2017 in Orlando, FL. For anyone else like me who spends hours each working day staring into an RStudio session, the conference was truly

excellent

. The speaker lineup was diverse and covered lots of areas related to development in R, including the tidyverse, the RStudio IDE, Shiny, htmlwidgets, and authoring with RMarkdown.
The Comics Grid’s 14th Volume (2024)
Authors: Priego Ernesto
Published: December 2024

We have wrapped up The Comics Grid’s 14th volume, corresponding to 2024.
X-cess of variants in XLMR
Authors: Turner Stephen
Published: December 2024

From a News and Views article in Nature Genetics, following up the recently mentioned sequencing effort for X-linked mental retardation:Nature Genetics: X-cess of variants in XLMRGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
The Utility of Network Analysis
Authors:   Unknown
Published: December 2024

Like most bioinformatics nerds (or anyone with a facebook account), I’m fascinated by networks. Most people immediately think of protein-protein interaction networks, or biological pathways when thinking about networks, but sometimes representing a problem as a network makes solving problems easier. Recently, some collaborators from the PAGE study had a list of a few hundred SNPs gathered from multiple loci across the genome.
Hierarchical Clustering in R
Authors:   Unknown
Published: December 2024

Hierarchical clustering is a technique for grouping samples/data points into categories and subcategories based on a similarity measure. Being the powerful statistical package it is, R has several routines for doing hierarchical clustering. The basic command for doing HC is Nearly all clustering approaches use a concept of distance.
Five articles on the success/failure of GWAS
Authors: Turner Stephen
Published: December 2024

Here are four interesting and provocative articles in New England Journal of Medicine:David Goldstein: Common Genetic Variation and Human TraitsJoel Hirschhorn: Genomewide Association Studies — Illuminating Biologic PathwaysPeter Kraft and David Hunter: Genetic Risk Prediction — Are We There Yet?John Hardy &
Do your "data janitor work" like a boss with dplyr
Authors: Turner Stephen
Published: December 2024

Data “janitor-work” The New York Times recently ran a piece on wrangling and cleaning data: “For Big-Data Scientists, ‘Janitor Work’ Is Key Hurdle to Insights” Whether you call it “janitor-work,” wrangling/munging, cleaning/cleansing/scrubbing, tidying, or something else, the article above is worth a read (even though it implicitly denigrates the important work that your housekeeping staff does). It’s one of the few “Big Data” pieces that
Use meaningful color schemes in your figures
Authors: Turner Stephen
Published: December 2024

Some of the best figure design ideas come from cartographers. If you've ever read a Tufte book you've seen lots of examples. Let's talk about using color effectively. Penn State geography professor Cindy Brewer's ColorBrewer tool for selecting color schemes for figures has been conveniently packaged into an R library called RColorBrewer.
Sequencing is Not (Yet) the Silver Bullet
Authors: Turner Stephen
Published: December 2024

Amidst the fallout of an academic discussion over the worth of GWA studies followed by several gloomy and scathing articles in the popular press, came this paper in Nature Genetics. In summary, the investigators sequenced all the coding DNA on the X-chromosome in families affected with an evidently X-linked mental retardation phenotype.
Redesign by Subtraction
Authors: Turner Stephen
Published: December 2024

GGD has a new look. I was inspired by Gina Trapani (Smarterware, Lifehacker) to remove any extra lines, links, and other "ink" that doesn't serve any purpose, and I hope the site appears cleaner and easier to read. I also wanted the extra horizontal space for larger images and avoid the dreaded side-scrolling in posts with lots of code like this one.
Using the microbenchmark package to compare the execution time of R expressions
Authors: Turner Stephen
Published: December 2024

I recently learned about the microbenchmark package while browsing through Hadley’s advanced R programming book. I’ve done some quick benchmarking using system.time() in a for loop and taking the average, but the microbenchmark function in the microbenchmark package makes this much easier.
De Novo Transcriptome Assembly with Trinity: Protocol and Videos
Authors: Turner Stephen
Published: December 2024

One of the clearest advantages RNA-seq has over array-based technology for studying gene expression is not needing a reference genome or a pre-existing oligo array.

De novo

transcriptome assembly allows you to study non-model organisms, cancer cells, or environmental metatranscriptomes.
I can has power calculations?
Authors: Turner Stephen
Published: December 2024

What's your power to detect a recessive effect with an odds ratio of 1.2 for a disease with 4.2% prevalence using 1200 cases and 2900 controls? What if the allele is rare? Is it worth it, in terms of power gain, to genotype 1000 more individuals? How small of an effect can you detect with 80% power using the data you have? These questions and others can be answered by power and sample size calculations.
All code on GGD is Free and Open-Source (GPLv2)
Authors: Turner Stephen
Published: December 2024

At the request of a commenter I just wanted to clarify that any code released here for R or anything else is free and open source unless specifically stated otherwise. The open source (GPLv2) license for any code on GGD can be found on this page.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Efficient Mixed-Model Association eXpedited (EMMAX) to Simutaneously Account for Relatedness and Stratification in Genome-Wide Association Studies
Authors: Turner Stephen
Published: December 2024

A few months ago I covered an algorithm called EMMA (Efficient Mixed-Model Association) implemented in R for simultaneously correct for both population stratification and relatedness in an association study.
Curoverse raises $1.5M to develop & support an open-source bioinformatics data analysis platform
Authors: Turner Stephen
Published: December 2024

Boston-based startup Curoverse has announced $1.5 million in funding to develop and support the open-source Arvados platform for cloud-based bioinformatics & genomics data analysis. The Arvados platform was developed in George Church's lab by scientists and engineers led by Alexander Wait Zaranek, now scientific director at Curoverse.
Francis Collins: Computational biologists are "breakthrough artists"
Authors: Turner Stephen
Published: December 2024

Just caught this on the OpenHelix Blog. In an interview with Charlie Rose, NIH director Francis Collins said Computational biologists will be the "breakthrough" artists of the future. Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Unsuck your writing
Authors: Turner Stephen
Published: December 2024

I recently found this little gem of a web app that analyzes the clarity of your writing. Hemingway highlights long, complex, and hard to read sentences. It also highlights complex words where a simple one would do, and highlights adverbs, suggesting you use a stronger verb instead. It highlights passive voice (bad!), and tells you the minimum reading grade level necessary to understand your writing.
Evolutionary Computation and Data Mining in Biology
Authors:   Unknown
Published: December 2024

For over 15 years, members of the computer science, machine learning, and data mining communities have gathered in a beautiful European location each spring to share ideas about biologically-inspired computation.  Stemming from the work of John Holland who pioneered the field of genetic algorithms, multiple approaches have been developed that exploit the dynamics of natural systems to solve computational problems.
R Commander: A Basic Statistics GUI for R
Authors: Turner Stephen
Published: December 2024

R is a great tool with lots of resources for genetics, genome-wide association studies, and many other biological applications.  We've covered several places to find help in R in the past, but if you're still apprehensive about diving into R's command-line interface, fear not.  The R commander is a graphical user interface (GUI) for R that works under Windows, Linux, and Mac.
Analysis of #ASHG2013 Tweets
Authors: Turner Stephen
Published: December 2024

I archived and anlayzed all Tweets with the hashtag #ASHG2013 using my previously mentioned code. Number of Tweets by date shows Wednesday was the most Tweeted day: The top used hashtags other than #ASHG2013: The most prolific users: And what Twitter analysis would be complete without the widely loved, and more widely hated word cloud:

Edit 8:24am

: I have gotten notes that some Tweets were not captured in this archive.
Goncalo Abecasis "Sequencing 1000s of Human Genomes" Faculty Candidate Seminar
Authors: Turner Stephen
Published: December 2024

Vanderbilt Center for Human Genetics Research faculty candidate Goncalo Abecasis will be interviewing for a faculty position here this week. Come check out his seminar - "Sequencing Thousands of Human Genomes" - Friday June 11th, 2-3pm in 512 Light Hall.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Screen How-to
Authors:   Unknown
Published: December 2024

`screen` is one of the most useful system tools I've ever used. It allows you to begin a process and then detach from the process to let it continue to run in the background.
Query a MySQL Database from R using RMySQL
Authors: Turner Stephen
Published: December 2024

I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser's public MySQL instance), set up a function to make querying easier, and query the database to return results as a data frame. Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Syntax Highlight Code in Keynote or Powerpoint
Authors: Turner Stephen
Published: December 2024

I came across this awesome gist explaining how to syntax highlight code in Keynote. The same trick works for Powerpoint. Mac only. Install homebrew if you don’t have it already and brew install highlight. highlight -O rtf myfile.ext | pbcopy to highlight code to a formatted text converter in RTF output format, and copy the result to the system clipboard. Paste into Keynote or Powerpoint.
New Year's Resolution: Learn How to Code
Authors: Turner Stephen
Published: December 2024

Farhad Manjoo at Slate has a good article on why you need to learn how to program. Chances are, if you're reading this post here you're already fairly adept at some form of programming. But if you're not, you should give it some serious thought.
Software from CSHL Genome Informatics 2015
Authors: Turner Stephen
Published: December 2024

I just returned from the Genome Informatics meeting at Cold Spring Harbor. This was, hands down, the best scientific conference I've been to in years. The quality of the talks and posters was excellent, and it was great meeting in person many of the scientists and developers whose tools and software I use on a daily basis.
DESeq vs edgeR Comparison
Authors: Turner Stephen
Published: December 2024

Update (Dec 18, 2012): Please see this related post I wrote about differential isoform expression analysis with Cuffdiff 2.

DESeq and edgeR are two methods and R packages for analyzing quantitative readouts (in the form of counts) from high-throughput experiments such as RNA-seq or ChIP-seq.
PCG Journal Club Articles, 5/13 & 5/27
Authors:   Unknown
Published: December 2024

Hi! I'm Julia Wall, the Technical Writer in Vanderbilt's CHGR. Every two weeks or so, I'll be posting citation links to the articles that the students in our Program for Computational Genomics (PCG) Journal Club discuss in their bimonthly meetings.
Rebecca Skloot (HeLa) to speak at Vanderbilt September 7
Authors: Turner Stephen
Published: December 2024

Rebecca Skloot, author of bestselling

The Immortal Life of Henrietta Lacks

(Amazon, $14), will be speaking here at Vanderbilt next Tuesday at noon in 208 Light Hall. This is one you don't want to miss. Be sure to get there a few minutes early. When 208 fills up they'll have overflow in 202 with a live webcast. RSVP to jane...@vanderbilt.edu for a free lunch.
Mycoplasma Contamination in Cell-Line Based Experiments
Authors:   Unknown
Published: December 2024

For a few years now, my EvoSTAR colleague, Bill Langdon, has been exploring the degree to which Mycoplasma bacteria have contaminated experimental systems and even "infected" online databases with the contents of their genomes.
Using R, LaTeX, and Sweave for Reproducible Research: Handouts, Templates, & Other Resources
Authors: Turner Stephen
Published: December 2024

Several readers emailed me or left a comment on my previous announcement of Frank Harrell's workshop on using Sweave for reproducible research asking if we could record the seminar. Unfortunately we couldn't record audio or video, but take a look at the Sweave/Latex page on the Biostatistics Dept Wiki.
Russ Altman's Translational Bioinformatics Year in Review
Authors:   Unknown
Published: December 2024

A few weeks ago the 2014 AMIA Translational Bioinformatics Meeting (TBI) was held in beautiful San Francisco.  This meeting is full of great science that spans the divide between molecular and clinical research, but a true highlight of this meeting is the closing keynote, traditionally given by Russ Altman.
Has anyone ever used Galaxy?
Authors: Turner Stephen
Published: December 2024

Has anyone ever used Galaxy? I saw their presentation at last year's ASHG. Seems like a great way to do collaborate on and keep a record of analyses in an easy web-GUI interface without having to download any software.
Gene regulation: A new toolbox for mapping regulatory sites
Authors: Turner Stephen
Published: December 2024

Here's a paper in Nature Reviews Genetics highlighting two recently published methods for mapping regulatory sites. Most currently used procedures rely on ChIP, where you can only examine sites one protein at a time.
Genomics and the Consumer: The Present and Future of Personalized Medicine
Authors: Turner Stephen
Published: December 2024

For those of you not following GGD on Twitter you may not have seen this - California State Senator Alex Padilla and 23andMe are hosting a policy forum entitled "Genomics and the Consumer: The Present and Future of Personalized Medicine" today in San Francisco.
Linux Command Line Cheat Sheet
Authors: Turner Stephen
Published: December 2024

Whenever we have new students rotating through our lab who've never used Linux I always end up scrounging around the world wide series-of-tubes only to find some command line reference that's not really useful for students. So I made my own one-page reference guide that gives a basic description of most of the commands most of you will use. Feel free to distribute.
Vanderbilt Genetics Symposium: Beyond Disease Dichotomy - Quantitative Traits and Intermediate Phenotypes
Authors: Turner Stephen
Published: December 2024

About a year ago I reiterated a point made nicely in a Nature Reviews Genetics article, that there is no such thing as a common disorder - only extremes of quantitative traits. Such is the theme of this year's Annual Vanderbilt Genetics Symposium, "Beyond Disease Dichotomy - Quantitative Traits and Intermediate Phenotypes." This is a day-long event held at the Vanderbilt Student Life Center on Wednesday October 13, 8am-4pm.
Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application
Authors: Turner Stephen
Published: December 2024

While writing my thesis I came across this nice review by Rita Cantor, Kenneth Lange, and Janet Sinsheimer at UCLA, "Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application." Skip the introduction unless you're new to GWAS, in which case you'll probably want to start with this more recent review by Teri Manolio.
I'm Hiring!
Authors: Turner Stephen
Published: December 2024

I direct the Bioinformatics Core at the University of Virginia, and I'm hiring. Visit this link on the UVA Jobs website for more information. Here's the description: I'm Hiring - Bioinformatics Analyst in the UVA Bioinformatics CoreGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
GRUPO: Shiny App For Benchmarking Pubmed Publication Output
Authors: Turner Stephen
Published: December 2024

This is a guest post from VP Nagraj, a data scientist embedded within UVA’s Health Sciences Library, who runs our Data Analysis Support Hub (DASH) service.

The What GRUPO (Gauging Research University Publication Output) is a Shiny app that provides side-by-side benchmarking of American research university publication activity.
Hadley Wickham's ggplot2 / Data Visualization Course Materials
Authors: Turner Stephen
Published: December 2024

Hadley Wickham, creator of ggplot2, an immensely popular framework for Tufte-friendly data visualization using R, is teaching two short courses at Vanderbilt this week. Once we opened registration to Vanderbilt students and staff we instantly filled all the available seats, so unfortunately I wasn't able to announce the course here. But the good news is that Hadley's made all the data, code, and slides from the course available online here.
More on the McClellan / King GWAS essay
Authors: Turner Stephen
Published: December 2024

First, if you haven't taken a look at the comments on my previous post on this paper, go take a look. Thanks to everyone for sharing your thoughts and pointing out some of my own oversight regarding this paper. There was one issue in particular that deserves more attention than just another comment thread.
Annotating limma Results with Gene Names for Affy Microarrays
Authors: Turner Stephen
Published: December 2024

Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won't contain any featureData annotation. Consequentially, when I run topTable to get a list of differentially expressed genes, there's no annotation information other than the Affymetrix probeset IDs or transcript cluster IDs.
Genetic diversity in African populations
Authors: Turner Stephen
Published: December 2024

An international team led by Sarah Tishkoff, in collaboration with our own Scott Williams, and former CHGR member Jason Moore, published yesterday in Science the largest, most comprehensive characterization of genetic variation in over 100 different African populations.
Free tutorials on bioinformatics and model organisms resources
Authors: Turner Stephen
Published: December 2024

OpenHelix offers free access to a handful of their tutorials on genomics and bioinformatics resources, including the UCSC Genome Browser, Seattle SNPs, Genome Variation Server, and the VISTA Comparative Genomics tools.
Split, apply, and combine in R using PLYR
Authors: Turner Stephen
Published: December 2024

While flirting around with previously mentioned ggplot2 I came across an incredibly useful set of functions in the plyr package, made by Hadley Wickham, the same guy behind ggplot2.  If you've ever used MySQL before, think of "GROUP BY", but here you can arbitrarily apply any R function to splits of the data, or write one yourself.
Highlight all the acronyms in a Word document
Authors: Turner Stephen
Published: December 2024

A tip of the hat to Lifehacker for pointing this out.Ever been nailed by a reviewer or a thesis committee for using too many acronyms without defining them well? There's an easy way built into MS Word to find and highlight all the acronyms in a document.
Course Materials from useR! 2013 R/Bioconductor for Analyzing High-Throughput Genomic Data
Authors: Turner Stephen
Published: December 2024

At last week's 2013 useR! conference in Albacete, Spain, Martin Morgan and Marc Carlson led a course on using R/Bioconductor for analyzing next-gen sequencing data, covering alignment, RNA-seq, ChIP-seq, and sequence annotation using R. The course materials are online here, including R code for running the examples, the PDF vignette tutorial, and the course material itself as a package. Course Materials from useR!
RNA-Seq Methods & March Twitter Roundup
Authors: Turner Stephen
Published: December 2024

There were lots of interesting developments this month that didn't work their way into a full blog post. Here is an incomplete list of what I've been tweeting about over the last few weeks.
Investigating the economic sustainability of Social Welfare Non-Governmental Organizations: A Multiple Case Study Approach
Authors: Malambo Joseph , Bupe Mutono Mwanza Getrude , Mwange Mwange
Published: December 2024

This study investigates the economic sustainability of social welfare NGOs in Lusaka, Zambia, addressing a critical gap in understanding the challenges these organizations face. Despite their pivotal role in supporting vulnerable populations, many social welfare NGOs struggle with financial viability, leading to operational inefficiencies and closures. While existing literature identifies financial sustainability as a major hurdle, it lacks a comprehensive analysis of the specific economic challenges confronting these organizations. Through thematic analysis, the study explores organizational structure, financial management, human resources, program delivery, partnerships, and external factors affecting sustainability. Key findings highlight that NGOs face limited funding sources, rising operational costs, competition for resources, regulatory barriers, and external pressures such as economic instability and political unrest. In response, NGOs adopt diverse strategies, including diversifying funding through grants and partnerships, enhancing financial management, advocating for supportive government policies, and fostering collaborations with stakeholders. The study concludes that achieving economic sustainability requires a multifaceted approach tailored to the unique needs of each NGO and the socio-economic context. Recommendations include capacity-building programs for NGO staff to improve financial literacy and management skills, creating an enabling policy environment, and encouraging donors to adopt flexible funding models. This research provides valuable insights for policymakers, donors, and NGOs, enabling them to address structural barriers, align funding strategies, and refine operational practices to enhance their impact on vulnerable populations.
Simulaçao do escoamento de misturas de refrigerantes em tubos capilares utilizando modelo de fases separadas
Authors: Sanzovo Fiorelli Flávio Augusto , De Mattos Silvares Otávio
Published: December 2024

Este artigo apresenta um programa de simulação do escoamento de misturas de fluidos refrigerantes através de tubos capilares utilizando o modelo de fases separadas para a região de escoamento bifásico, validado experimentalmente. Obteve-se uma boa concordância entre os dados experimentais e os resultados de simulação. As principais diferenças estão relacionadas com a ocorrência do fenômeno do atraso de vaporização, experimentalmente verificada pelos autores.
Influência das tensões interlaminares nas características modais de vibração de uma placa laminada compósita
Authors: Reina J. Pedro , Marques A. T.
Published: December 2024

O recurso aos laminados compósitos na construção de estruturas como placas e cascas deve-se às suas propriedades mais atractivas como são a elevada rigidez e a extrema leveza. Porém, estes factores potenciam problemas de vibração pelo que se torna necessária a previsão das características de vibração destes laminados. As tensões na direcção transversa podem assumir primordial importância no comportamento dinâmico dos laminados compósitos, devido à heterogeneidade transversal típica das estruturas laminadas e à forte aniso tropia ao nível da camada, 30LGLT=E . Consequentemente é fundamental considerar um estado tridimensio nal de tensão pelo que foi desenvolvida uma ferramenta numérica que recorre a um elemento finito baseado numa teoria de camada discreta, a DLT (Discrete Layer Theory), que permite uma correcta descontinuidade das deformações transversas nas interfaces com camadas de diferentes características materiais. A validação dos va lores das tensões transversas obtidas por este modelo é realizada por comparação com as obtidas por um modelo baseado no uso de elementos finitos de interface para problemas tridimensionais. Neste trabalho pretende-se es tudar a influência das tensões interlaminares transversas nas características modais das vibrações das placas la minadas compósitas.
Reduçao dos tempos de intervençao
Authors: Julião Jorge , Greenough Richard
Published: December 2024

Tradicionalmente as técnicas de redução de tempos de paragem são fundamentadas na prevenção de falhas. Apesar do inegável sucesso destas técnicas, é impossível prever todas as falhas. Deste modo este artigo apresenta um proposta para minimizar tempos de paragem através da redução dos tempos de intervenção (acções correctivas). É sugerido que fornecendo aos técnicos de manutenção um fácil acesso a informação sobre experiências de falha, as intervenções de manutenção serão efectuadas de modo mais eficaz e eficiente. Por forma a tornar esta informação acessível, é proposto um modelo para classificar registos de falha. Este modelo irá servir de base à criação de um modelo de apoio à decisão para assistir a manutenção correctiva, em particular os técnicos de manutenção. O artigo apresenta ainda os resultados quer de uma pesquisa bibliográfica quer de um caso de estudo, de modo a caracterizar situação actual da gestão de informação sobre registos de falha. A pesquisa bibliográfica é centrada nos métodos e utilização de informação sobre falhas, e evidencia algumas das suas deficiências. O caso de estudo apresenta os principais resultados de uma investigação realizado com especialistas de manutenção, e visa complementar os resultados da literatura.
Furação de laminados epóxidos reforçados
Authors: Davim João Paulo , Reis Pedro
Published: December 2024

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Simulaçao do problema do degrau com RANS e LES
Authors: Abrunhosa José D. M. , Nieckele Angela O. Nieckele
Published: December 2024

No presente trabalho, é realizada a comparação das previsões do escoamento bidimensional turbulento em degrau (‘backstep’), utilizando-se modelos κ−ε para baixo número de Reynolds (RANS) e o modelo de Smagorinsky em uma simulação bidimensional tipo grandes escalas (LES). Os resultados mostraram que a simulação de grandes escalas utilizando modelagem bidimensional é inadequada, resultando em previsões mais pobres das estatísticas de turbulência, além de requerer um maior esforço computacional.
Efeito de sucessivas reparaçoes por soldadura
Authors: Veiga C. , García Loureiro Antonio Jesus , Batista A. C.
Published: December 2024

O objectivo deste trabalho é a análise da evolução da microestrutura, das propriedades mecânicas e das tensões residuais em juntas soldadas de um aço carbono-manganês, quando submetidas a duas reparações sucessivas por soldadura. Para isso foram utilizadas chapas de dimensões 400x180x11mm, as quais forammontadas na forma de junta de bordos direitos, submetidas a um tratamento térmico de alívio de tensões residuais e seguidamente soldadas topo a topo pelo processo MAG robotizado, usando duas camadas de soldadura. Após a deposição das camadas de soldadura foram realizadas duas reparações sucessivas, também através do processo MAG robotizado. As tensões residuais foram medidas após a deposição das camadas de soldadura, bem como após cada reparação. As medições foram realizadas à superfície em linhas transversais ao cordão e ao longo do seu eixo. Finalmente foram preparados provetes a partir do material da junta, nos quais foram realizados exames metalográficos, medição de dureza e ensaios de tracção. Verificou-se que as reparações induziram alterações ao nível da microestrutura, das propriedades mecânicas e do campo de tensões residuais preexistentes na zona reparada. Ocorreram aumentos de estruturas refinadas tanto na zona afectada pelo calor como, e sobretudo, na zona fundida. As reparações provocaram uma ligeira diminuição da dureza e do limite elástico da zona fundida. Provocaram ainda, essencialmente na zona reparada, um aumento das tensões residuais longitudinais e transversais. Porém, as tensões residuais não atingiram o limite elástico do material na zona onde ocorrem.
WVSU’s Physical Activity for Health and Fitness and the Global Action Plan for Physical Activity
Authors: Malones Eva Rose
Published: December 2024

PATHFit or Physical Activity for Health and Fitness is a new program designed by CHED for tertiary level physical education. The unique features of this program lie along its standards for (1) active and healthy living that is characterized by progressively intensifying student’s physical activity and (2) advocacy and action plan where college students are encouraged to share their learning to their community. Both standards express CHED’s support of the Global Action Plan for Physical Activity (GAPPA) initiated by the WHO in 2018 to reduce physical inactivity and sedentary lifestyle by 15% before the year 2030. The purpose of this paper is to look into the 2-year trial implementation of PATHFit at West Visayas State University (WVSU) to investigate on the curriculum practices that were used to deliver the new PE program and see how these practices aligned with CHED’s standards and outcomes in order to contribute to the GAPPA. Results revealed that the new program ushered in a new era of teaching PE. The blending of PATHFit standards with the university’s hallmarks resulted in the delivery of kinesthetic intelligence, intensified physical fitness, nurturance of creative minds, awareness of health and social responsibilities, student independent learning, and empowerment of student leaders. This kind of physical literacy supports attributes of lifelong independent learning and real life experiences for future engagement to recreation to lower sedentary lifestyle that sets GAPPA in progress.
Effect of Different Organic and Inorganic Fertilizers on the Flower Yield of Roses
Authors: Penpillo Rubin , Ballano Monica
Published: December 2024

This study was conducted in the Ornamental Garden Bank of West Visayas State University from February 1998 to January 2000. The objectives are to: determine the number of flowers produced and classified as to size and length of stalk; determine the average monthly and yearly production of rose flowers, and find out the cost and return of each treatment.
Two hundred marcotted roses were planted in pots and were grown for two years under five fertilizer treatments. The treatments used were: A. Control (alternate foliar spray of 15-15-30+ME at the rate of 1.5g/l of water every 15 days); B, Control + ring application of 60 g chicken dung every 45 days; C, Control + ring application of 60 g chicken dung every 45 days; D, Control + ring application of 60 g hog manure every 45 days; and E, Control +1/2 ring application of 2.5 g of Inorganic fertilizer + 1/2 30 g of Chicken Dung + 1/2 30 g hog manure every 45 days. The experiment was laid in RCBD replicated four times with 10 potted plants per replicate. Results indicated that foliar spray plus the application of 14-1414, chicken dung and hog manure in the soil every 15 days, singly or in combination significantly produced more quality flowers than those that received foliar spray alone. Growing of roses in pots can be profitable as indicated by Return on Investment (ROI) The highest ROI of 140.07% was obtained in treatment E (foliar spray of inorganic fertilizer + ring application of 2.5 g of 14-14-14, ring application of 30 g each of chicken dung and hog manure every 45 day
Relación Entre el Estado Argentino y la Iglesia Católica entre 1943-1955 y sus Consecuencia en la Educación Superior
Authors: Reguera María Griselda
Published: December 2024

El presente ensayo analiza cómo fue la relación entre Perón y la Iglesia Católica entre 1943 hasta 1955 y como ese enfrentamiento trasciende en el Sistema de Educación en todos los niveles, pero este estudio abordará principalmente el nivel superior universitario.
En la primera parte se realiza un recorrido general por el contexto histórico desde la revolución de 1918 con la conformación de “La Universidad Reformista”, pasando por los gobiernos militares y el enfrentamiento entre el gobierno represivo y las Universidades, para continuar con las medidas que toma Perón al respecto, la conformación de la Universidad Obrera y el nuevo modelo de política en la educación superior.  
En este documento se intenta evidenciar cronológicamente como fue la mutación producida en el Estado a medida que el presidente va adquiriendo más poder, hasta el punto de pretender supeditar a la Iglesia para sus fines políticos, al no conseguirlo, inicia una campaña de desacreditación de los dogmas Católicos y hasta pretende crear una doctrina cristiana peronista que la reemplace. 
Todo esto va desencadenando una serie de medidas que acrecientan la brecha entre peronistas y antiperonistas, que terminara con el golpe de Estado que pondrá fin a su segundo gobierno.