bluuebunny/crossref_metadata_2025 huggingface dataset:
Parsing Metadata with R - A Package Story
Authors: Klebel Thomas
Published: September 2023

Every R package has its story. Some packages are written by experts, some bynovices. Some are developed quickly, others were long in the making. This is thestory of jstor, a package which I developed during my time as a student ofsociology, working in a research project on the scientific elite withinsociology.
All the Badges One Can Earn: Parsing Badges of CRAN Packages READMEs
Authors: Salmon Maëlle
Published: September 2023

A while ago weonboarded anexciting package, codemetarby Carl Boettiger. codemetar is an R specificinformation collector and parser for the CodeMetaproject. In particular, codemetar candigest metadata about an R package in order to fill the termsrecognized by CodeMeta. This meansextracting information from DESCRIPTION but also from e.g. continuousintegration

1

badges in the README!
The Antarctic/Southern Ocean rOpenSci community
Authors: Raymond Ben , Sumner Michael
Published: September 2023

Antarctic/Southern Ocean science and rOpenSci Collaboration and reproducibility are fundamental to Antarctic and Southern Ocean science, and the value of data to Antarctic science has long been promoted. The Antarctic Treaty (which came into force in 1961) included the provision that scientific observations and results from Antarctica should be openly shared.
Selecting the Best Phylogenetic Evolutionary Model
Authors: Bilderbeek Richèl J.C.
Published: September 2023

With this blog post, I show how to use the mcbette R packagein an informal way.A more formal introduction on mcbettecan be found in the Journal of Open Source Science

1

.After introducing a concrete problem, I will show how mcbettecan be used to solve it. After discussing mcbette, I will conclude withwhy I think rOpenSci is important and how enjoyablemy experiences have been so far.The problem Imagine you are a field biologist.
2 Months in 2 Minutes - rOpenSci News, October 2019
Authors: Butland Stefanie
Published: September 2023

rOpenSci HQ What would

you

like to hear about in an rOpenSci Community Call? We are soliciting your “votes” and new ideas for Community Call topics and speakers. Find out how you can influence us by checking out our new Community Calls repository. Videos, speaker’s slides, resources and collaborative notes from our Community Call on Reproducible Workflows at Scale with drake are posted. Help wanted!
Set Up Your Package to Foster a Community - Community Call Summary
Authors: Rüeger Sina , Salmon Maëlle , Gruson Hugo , LaZerte Steffi , Padgham Mark
Published: September 2023

Last Thursday we held a Community Call discussing how to set up a Package to Foster a Community. This call included speakers Maëlle Salmon, Hugo Gruson and Steffi LaZerte, and was moderated by Stefanie Butland.Summarizing the community call Scientific software development - and with that R packages - is a community effort.
2 Months in 2 Minutes - rOpenSci News, April 2020
Authors: Butland Stefanie
Published: September 2023

rOpenSci HQ The recording, collaborative notes and links to community discussion and resources are up for our latest Community Call on Maintaining an R package. Panel moderated by Julia Silge included Elin Waring, Erin Grand, Leonardo Collado-Torres, and Scott Chamberlain.  Software Peer Review 1 staff-contributed package passed software peer review.

parzer

- Parse messy geographic coordinates. Author: Scott Chamberlain;
rOpenSci Software Peer Review: Still Improving
Authors: Salmon Maëlle , Anderson Brooke , Chamberlain Scott , Krystalli Anna , Mullen Lincoln , Ram Karthik , Ross Noam , Vidoni Melina
Published: September 2023

rOpenSci’s suite of packages is comprised of contributions from staff engineers and the wider R community, bringing considerable diversity of skills, expertise and experience to bear on the suite. How do we ensure that every package is held to a high standard?
Community Captioning of rOpenSci Community Calls
Authors: Grenié Matthias , Gruson Hugo
Published: September 2023

Webinars and community calls are a great way to gather many people to discuss a specific topic, without the logistic hurdles of in-person events. But whether online or in-person, to reach the broadest audience, all events should work towards greater accessibility.
rOpenSci Dev Guide 0.3.0: Updates
Authors: Chamberlain Scott , Anderson Brooke , Krystalli Anna , Mullen Lincoln , Ram Karthik , Ross Noam , Salmon Maëlle , Vidoni Melina
Published: September 2023

As announced in February, we now have an online book containing all things related to rOpenSci software review. Our goal is to update it approximately quarterly - it’s time to present the third version. You can read the changelog or this blog post to find out what’s new in our dev guide 0.3.0!Updates to our policies and guidance Scope We’ve introduced an important change for anyone thinking of submitting a package.
Automatic Code Cleaning in R with Rclean
Authors: Lau M.K.
Published: September 2023

The R language has become very popular among scientists and analystsbecause it enables the rapid development of software and empowersscientific investigation. However, regardless of the language used,data analysis is usually complicated. Because of various projectcomplexities and time constraints, analytical software often reflectsthese challenges. “What did I measure? What analyses are relevant tothe study? Do I need to transform the data?
Generating and customizing badges in r-universe
Authors: Ooms Jeroen
Published: September 2023

Badges in r-universe After creating your personal universe, the dashboard on https://{yourname}.r-universe.dev shows the version and other details for each package in your repository. We have also added a new tab that lists the available badges for the repository.
Introducing the 2018 rOpenSci Research Fellows!
Authors: Ram Karthik
Published: September 2023

rOpenSci’s mission is to enable and support a thriving community of researchers who embrace open and reproducible research practices as part of their work. Since our inception, one of the mechanisms through which we have supported the community is by developing high-quality open source tools that lower barriers to working with scientific data.
icon: web icons for rmarkdown
Authors: O'Hara-Wild Mitchell
Published: September 2023

Icons in R Icons can be added to your R Markdown documents using short prefixes which identify the font’s library.fa: Font Awesomeai: Academiconsii: ionicons For example, `r icon::fa("rocket")` can be used to add the rocket icon from Font Awesome. This interface is convenient if you are familiar with the icon you want, or if you are dynamically selecting your icon.
2 Months in 2 Minutes - rOpenSci News, October 2020
Authors: Butland Stefanie
Published: September 2023

rOpenSci HQ rOpenSci at R-Ladies Our community manager Stefanie Butland, and one of our software review editors Brooke Anderson, are speaking remotely at an R-Ladies East Lansing meetup Thursday, October 22nd.
Community Call - Maintaining an R Package
Authors: LaZerte Steffi
Published: September 2023

For this Community Call, we’re trying something different. We’ll start with a short talk by

Julia Silge

, then spend most of the time on Q & A with four panelists -

Elin Waring

,

Erin Grand

,

Leonardo Collado-Torres

, and

Scott Chamberlain

- moderated by Julia. Our panelists bring a wide range of perspectives so there’s something for everyone.
The Story Behind rspatialdata
Authors: Seimon Dilinie , Kumar Varsha Ujjinni Vijay
Published: September 2023

As two postgrad students on summer vacation but with no travel plans (during this global pandemic of course), we took up an internship at King Abdullah University of Science and Technology (KAUST) last summer and ended up collaborating on a really cool project with Paula Moraga! Did we mention that we worked in Saudi Arabia, while living in Australia? All is well when we have the internet. We also ended up presenting our project at useR!
Generating reasonable starting trees for complex phylogenetic analyses
Authors: Wright April
Published: September 2023

I never really thought I would write an R package. I use R pretty casually. Then, this year, I was invited to participate during the last week of the Analytical Paleobiology short course, an intensive month-long experience in quantitative paleontology. I was thrilled to be invited.
Covidpreprints.com: Automating Website Updates with the europepmc and rAltmetric Packages
Authors: Goh Zhang-He , Coates Jonny , Gruson Hugo
Published: September 2023

At the eLife Sprint in September 2020, we revamped the covidpreprints.com website, which aims at featuring landmark preprints on a timeline of the pandemic.The birth of the project The ongoing COVID-19 pandemic has led to about 35 million confirmed cases and over a million deaths worldwide.
How to Use System Commands in your R Script or Package
Authors: Ooms Jeroen , Salmon Maëlle
Published: September 2023

Have you ever found a command-line tool that’s perfect for getting your job done, and wanted to use it from an R script or package?E.g. some sort of scientific software providing a specific functionality made available though a command-line interface (CLI)? In this post, we have a look at a few options for writing such CLI wrappers in R.In particular, we compare the base R functions system() and system2(), the sys package and the processx
Thank You to the rOpenSci Community, 2021
Authors: Butland Stefanie , LaZerte Steffi
Published: September 2023

Can you think of an rOpenSci community member that you’d like to thank?A reviewer who helped you improve your package?Someone who answered your question?A community call speaker from whom you gained insight?Someone who encouraged you behind the scenes?
rnassqs: accessing USDA agricultural data via API
Authors: Potter Nicholas
Published: September 2023

The United States Deparment of Agriculture National AgriculturalStatistics Service (USDA-NASS) provides a wide range of agriculturaldata that includes animal, crop, demographic, economic, andenvironmental measures across a number of geographies and time periods.This data is available by direct download or queriable via theQuick Stats interface.
rOpenSci's new Code of Conduct
Authors: Butland Stefanie , Chamberlain Scott , Woo Kara
Published: September 2023

We are pleased to announce the release of our new Code of Conduct. rOpenSci’s community is our best asset and it’s important that we put strong mechanisms in place before we have to act on a report. As before, our Code applies equally to members of the rOpenSci team and to anyone from the community at large participating in in-person or online activities.
Want to Intern with rOpenSci’s Community Manager?
Authors: Butland Stefanie
Published: September 2023

Want to get some hands-on insights into running an open source community? Here’s an opportunity to work with me, rOpenSci’s Community Manager, on some non-code community-related work. I am looking for someone to work 1 day a week for 12 to 14 weeks. Working alongside rOpenSci’s Community Manager, Stefanie Butland, you will use guidelines and checklists to help run some of our established programs like our Blog and Community Calls.
rOpenSci 2019 Code of Conduct Transparency Report
Authors: Butland Stefanie , Chamberlain Scott , Woo Kara
Published: September 2023

In January 2019, we announced the release of rOpenSci’s Code of Conduct version 2.0. This includes a named Committee, greater detail about unacceptable behaviors, instructions on how to make a report, and information on how reports are handled. We are committed to transparency with our community while upholding of victims and people who report incidents.
How to Cite R and R Packages
Authors: LaZerte Steffi
Published: September 2023

I teach R to a lot of scientists, those that are new to science (i.e. students)as well as more established scientists, new to R.I find that after all their struggles of dealing with dates,or remembering where to put the comma, they’re so grateful to actual have an analysis,that they often forget or aren’t aware of the next steps.
Community Call - Governance strategies for open source research software projects
Authors: Sholler Dan , Butland Stefanie
Published: September 2023

🎤 Dan Sholler, rOpenSci Postdoctoral Fellow 🕘 Tuesday, December 18, 2018, 10-11AM PST; 7-8PM CET (find your timezone) ☎️ Details for joining the Community Call. Everyone is welcome. No RSVP needed. Researchers use open source software for the capabilities it provides, such as streamlined data access and analysis and interoperability with other pieces of the scientific computing ecosystem.
2 Months in 2 Minutes - rOpenSci News, December 2019
Authors: Butland Stefanie
Published: September 2023

rOpenSci HQ rOpenSci Announces a New $896k Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R. We’re excited to announce a new member of our team! Introducing Mark Padgham, rOpenSci’s new Software Research Scientist NumFOCUS recognizes Melina Vidoni and Will Landau for their contributions to rOpenSci.
Introducing the rOpenSci Community Contributing Guide
Authors: Butland Stefanie , LaZerte Steffi
Published: September 2023

Many people in our community actively contribute to rOpenSci projects.
10 Things We Learned in Creating the Blog Guide with bookdown
Authors: Butland Stefanie , Salmon Maëlle
Published: September 2023

After soliciting, reviewing, and publishing over 100 blog posts and tech notes by rOpenSci community members, we have created the rOpenSci Blog Guide for Authors and Editors to address many frequently asked questions and frequently given suggestions. Technically, we structured the content as a bookdown gitbook.
rOpenSci Code of Conduct Annual Review
Authors: Butland Stefanie , Chamberlain Scott , Padgham Mark , Woo Kara
Published: September 2023

Our community is our best asset. It’s so important to us, it’s in our mission statement. We recognize that communities are not inclusive by default; they require deliberate attention, including an enforceable Code of Conduct. rOpenSci is committed to providing a safe, inclusive, welcoming, and harassment-free experience for everyone.
Unconf18 projects 1: mchtoolbox, pkginspector, dataspice, rOpenSciEd, rOpenInterviews
Authors: Salmon Maëlle
Published: September 2023

After Stefanie’s recap of unconf18, this week the blog will feature brief summaries of projects developed at the event: each day 4 to 5 projects will be highlighted. (Full set of project recaps: recap 1, recap 2, recap 3, recap 4) In the following weeks, a handful of groups will share more thorough posts about their work.
The Value of Welcome, part 2: How to prepare 40 new community members for an unconference
Authors: Butland Stefanie
Published: September 2023

I’ve raved about the value of extending a personalized welcome to new community members and I recently shared six tips for running a successful hackathon-flavoured unconference. Building on these, I’d like to share the specific approach and (free!) tools I used to help prepare new rOpenSci community members to be productive at our unconference.
The Fun of Building Things and the Challenge of Learning - the rOpenSci OzUnconf 2019
Authors: Stammel Steph
Published: September 2023

It was the best of times, it was the worst of times. Dickens might have meant it figuratively, but in the case of the rOpenSci OzUnconf 2019, we mean it literally. Set to the backdrop of a national emergency that is still ongoing from 11-13 December, our participants came from across Australia as well as New Zealand, Japan, India and Indonesia.
The 2018 author and reviewer survey
Authors: Ram Karthik , Ross Noam , Chamberlain Scott , Salmon Maëlle
Published: September 2023

rOpenSci’s package review system (akaonboarding) is one of our keyactivities to improve quality and sustainability of scientific Rpackages. Theeditorial team are constantly working towards improving the experiencefor both authors and reviewers. After our first year, we surveyedauthors andreviewers whoparticipated in our onboarding process to help us better understandwhat’s working well and where there is room for improvement.
ὕδωρ + σκοπῶ = water + observe
Authors: Vantas Konstantinos
Published: September 2023

That’s a lot alike Data Science, isn’t it? Hydrologic Processes evolve in space and time, are extremely complex and we may never comprehend them. For this reason Hydrologists use models where their inputs and outputs are measurable variables: climatic and hydrologic data, land uses, vegetation coverage, soil type etc.
Community Call - Involving Multilingual Communities
Authors: Butland Stefanie
Published: September 2023

rOpenSci’s community is increasingly international and multilingual. While we have operated primarily in English, we now receive submissions of packages from authors whose primary language is not. As we expand our community in this way, we want to learn from the experience of other organizations. How can we manage our peer-review process and open-source projects to be welcoming to non-native English speakers?
Make Your R Package Easier to Cite
Authors: Salmon Maëlle , Chamberlain Scott , Ram Karthik
Published: September 2023

Scientists rarely cite research software they use as part of a research project. As a consequence, the software and the time spent developing and maintaining it becomes an invisible scholarly contribution. Furthermore, this lack of visibility means that incentives to produce high quality, sustainable software are missing. Among many reasons why software is not cited, one is the lack of a clear citation information from package developers.
Firm value determinants: Panel evidence from European listed companies
Authors: Vuković Bojana , Tica Teodora , Jakšić Dejan
Published: September 2023

Background: To manage growth opportunities effectively and to make a significant impact on superior longterm performance, it is necessary to analyze firm value and diagnose its determinants. Increasing profit, providing prosperity to the company's stakeholders, and improving company value are the goals of every company's business. Purpose: The paper aims to build a model of the company's optimal value by assessing company performance based on financial statement analysis of European companies over the period 2015-2020. Study design/methodology/approach: The impact of financial indicators such as financial leverage, profitability, size, liquidity, growth, and asset tangibility on company value was thoroughly considered. The empirical research was founded on a sample of 158 Eastern and Western European companies, generating 948 observations. Panel regression analysis was conducted. Findings/conclusions: The obtained results revealed that debt-to-assets ratio, return on equity, and assets tangibility have a significant adverse effect on company value, whereas the return on assets and firm size have a significant favorable effect. The obtained conclusions should serve as a beneficial tool for the strategy of reaching the targeted market company's value and ensuring the company's future viability by the market. Hence, stakeholders could assess the perspective of the future company's development and strengthen the importance and influence of financial variables on the company's value. Limitations/future research: The research limitations, which are also opportunities for future research, are aimed at the investigation of company value indicators at the level of individual European economies or industries. One should look at the company's value factors before and after the Covid-19 pandemic and consider a longer time in the company's business. Other financial determinants that affect the value of the company could be considered, and the company value could be measured by some other indicators. Also, the influence of nonfinancial determinants on the company value could be researched.
Biomaterials in Maxillofacial Surgery: Membranes and Grafts
Authors:   Department of Biomedical Sciences and Biotechnology, Section of Human Anatomy, University of Brescia, Viale Europa 11, 25123 Brescia, Italy, Rodella Luigi F. , Favero Gaia , Labanca Mauro
Published: September 2023

Today, significant differences in the use of biomaterials (membranes and grafts) of animal or synthetic origin have yet to be reported. Nevertheless, some evidences suggest that synthetic materials have a lower risk of disease transmission. This review aims to assess the available informations on regenerative bone technique using reasorbable membranes and bone grafts. In particular, biocompatibility, immunological response, tissue reaction, reabsorption time and histological features of materials daily use in dentistry and in maxillofacial surgery were emphasized.
Global Water Dances em Viçosa/MG: dança e ativismo ambiental
Authors: Silveira Juliana Carvalho Franco da , Fialho Vinicius Macena Santiago
Published: September 2023

Esta pesquisa teve como objetivo analisar os impactos das ações de um projeto de extensão em dança, cuja proposta foi participar do evento internacional Global Water Dances 2021 – envolvendo os participantes no processo de planejamento, ensaios, produção e apresentação –, no intuito de conscientizar e sensibilizar sobre a importância da água para a preservação da vida. A dança foi abordada nesse contexto como articuladora da relação corpo-ambiente e em seu caráter político, no sentido de possibilitar abertura para novas configurações sociais. A partir da análise dos impactos das ações do projeto, a dança foi reconhecida como uma epistemologia que possibilitou sensibilização e mobilização social, assim como a construção de um sentido de comunidade.
A dramaturgia de um puerpério: uma videodança a partir da Técnica Klauss Vianna
Authors: Silva Jaqueline Barbosa Pinto , Miller Jussara
Published: September 2023

Este artigo apresenta o processo criativo e a construção da dramaturgia da videodança parTida, por meio da Técnica Klauss Vianna (TKV) de dança e educação somática. A videodança foi realizada por ambas as autoras, uma que dança em processo de maternagem e a outra que a orienta no processo de criação. O processo criativo na TKV considera a processualidade como princípio, a improvisação como técnica e a labilidade como característica da coreografia. A dramaturgia emerge a partir da mobilidade e combinação desses fatores e dos demais elementos cênicos, incorporando a vivência singular de cada corpo que dança. A videodança revela a partida lenta de um corpo que foi parido de outro, e o aprendizado de ambos os corpos a viverem partidos. A pesquisa criativa em TKV se mostra aqui como uma ação política e a revela como metodologia possível para um artivismo materno.
Pengaruh Penggunaan Media Pembelajaran Video Fragmen Terhadap Motivasi Belajar Pendidikan Agama Kristen Siswa Kelas VIII SMP Negeri 1 Onanrunggu Kabupaten Samosir Tahun Pembelajaran 2023/2024
Authors: Gultom Mesi , Siagian Albiner , Samosir Taripar Aripin
Published: September 2023

This research aims to determine whether the learning motivation of students who are taught with fragment video media is higher than the learning motivation of students who are taught without fragment video media in Class VIII of SMP Negeri 1 Onanrunggu, Samosir Regency.  The method used in this research is a quantitative method, a True-Experimental approach with a Posttest-Only Control Design form.  The population was all 90 students in class VIII of SMP Negeri 1 Onanrunggu and the sample was determined to be 30 in the experimental class and 30 in the control class using purposive sampling techniques.  The results of the analysis show that the average learning motivation of students who were taught using video fragment media (3.518) was higher than the learning motivation of students who were taught without video fragment media (3.345).  Data analysis uses the variance pool t test formula, according to the test analysis requirements, namely n1 = n2 and the variance of the two sample groups is homogeneous.  The results of data analysis show the value of tcount = 3.991 > ttable (α = 0.01; dk = n1+n2-2 = 58) = 2.392, so H0 is rejected and H1 is accepted.  Thus, the researchers concluded that the learning motivation of students who were taught with fragment video media was higher than the learning motivation of students who were taught without fragment video media in class VIII of SMP Negeri 1 Onanrunggu, Samosir Regency, Academic Year 2023/2024.
The Trinity of Trauma: Ignorance, Fragility, and Control (Three Volumes) by Ellert R. S. Nijenhuis 🇩🇪
Authors: Schwab Matthias
Published: September 2023

This opus magnum comprises three weighty volumes in which Ellert R. S. Nijenhuis comprehensively presents his experiences, insights and ideas on dealing with trauma and dissociation. These have grown out of many years of practical and scientific work. The choice of the title Trinity of Trauma –with its allusion to the Christian religious trinity– may alienate some, but it points to one of the most challenging parts of dealing and coping with traumatic experiences: the paradox of separated and dissociated agents in the unity of an embodied person. Additionally the three basic action tendencies of “ignorance”, “fragility” and “control” that Nijenhuis describes actually seem to be something like a universal dynamic pattern of interaction when people are forced to deal with difficult-to-process experiences.
VERBAL HUMOR IN TRANSLATION: MENAECHMI OF PLAUTUS
Authors:   SOFIA UNIVERSITY ST. KLIMENT OHRIDSKI, Jakimova-Zheleva Katrin
Published: September 2023

The text examines selected comic moments from Plautus' comedy Menaechmi with a main focus on verbal humor and the translation of those excerpts into Bulgarian in Alexander Nichev's translation. The translation model of Jean-Paul Vinаy and Jean Darbelnet with its strategies and procedures is applied to each of the cited examples, briefly examining the relationships between its structural elements and illustrating what entail those among them, necessary for this analysis. The study's purpose is to establish to what extent this model, with its great influence in the field of translation studies and its hierarchical structure, is applicable to the translation of verbal humor and which aspects of comic display remain possibly unattainable for transfer into the target language and culture and for what reason.
A projektív rajzteszt néhány aspektusának vizsgálata a polgári pereket érintő igazságügyi szakértői munkában
Authors: Törő Krisztina , Kovács Borbála , Bor Luca , Sófi Gyula
Published: September 2023

Háttér: Pszichológusi/pszichiáteri munkánk kapcsán gyakran végzünk különböző hatóságok és bíróságok részére vizsgálatot. Kutatásunkban igazságügyi szakvéleményeket elemeztünk adott szempont mentén. Tanulmányunkban a fókuszt a projektív rajztesztekre és a szakvélemények tartalmának összevetésére helyeztük. Célkitűzés: Jelen kutatásunk célja, hogy feltárjuk a projektív rajztesztben megjelenő adott jellemzők összefüggéseit egymással, és a szakértői véleményben szereplő megállapításokkal. Módszer: Vizsgálatunkban 67 fő vett részt. A szakvéleményeket egyszerű tartalomelemzés módszerével tekintettük át. A családrajzokon pedig a Main és Caplan által leírt 24 itemes kötődési „leltárt” alkalmaztuk a kötődés és disszonancia jegyeinek kódolására (Main & Kaplan, 1986). Eredmények: A rajztesztekben talált rajzjegyek és a szakvéleményben vizsgált szülői magatartás nem mutatott egyértelmű összefüggést. A rajzjegyek vizsgálatakor a vizsgálati csoport és a kontrollcsoport kötődési sérülés jegyeinek számában nem volt szignifikáns különbség. A disszonancia jegyei viszont elvárásunkkal ellentétben a kontrollcsoportban fordultak elő többször. Diszkusszió: A projektív tesztek fontos információkat hordoznak a kötődéssel, a családi disszonanciával kapcsolatban, de rá szeretnénk mutatni a korlátokra is, és ezáltal érzékeny témaként felvetni a szakértői véleményekkel kapcsolatos szülői prekoncepció problematikáját is.
Determining the efficacy of N-acetyl cysteine in treatment of pneumonia in COVID-19 hospitalized patients: A meta-analysis
Authors: E.A Shaaban Mohamed , I.M Mohamed Ahmed
Published: September 2023

Background
Most patients infected with COVID-19 experienced cold-like symptoms. Some other patients developed more serious symptoms such as pneumonia. N-Acetylcysteine ​​(NAC) is known to be effective against acute respiratory distress syndrome (ARDS) due to its anti-inflammatory and antioxidant properties. The effect of NAC on hospitalized COVID-19 patients was unknown. Therefore, this meta-analysis aimed to establish a relationship between the effects of NAC and non-NAC protocols in inpatients with COVID-19.
Method
By March 2022, a systemic review was conducted to assess the effects of NAC and non-NAC in inpatients with COVID-19. The clinical trials were identified in 20553 subjects admitted with COVID-19 at baseline. 2909 was treated with NAC and 17644 was treated without NAC. This study attempts to compare the effects of NAC and non-NAC in COVID-19 patients hospitalized with pneumonia. Statistical analysis uses the dichotomous method as a tool for odds ratio (OR) at  95% confidence interval (CI) to assess the effectiveness of NAC and non-NAC in COVID-19 patients hospitalized with pneumonia in random or fixed-effect model.
Results
Patients managed with NAC had fewer days in the ICU (OR, 2.79; 95% CI, -1.11-6.69, p = 0.16), lower mortality (OR, 0.69; 95% CI, 0.40-1.20, p = 0.19), and fewer number needed mechanical ventilation (OR, 0.74; 95% CI, 0.25-2.21, p = 0.59) compared with non-NAC in COVID-19 subjects hospitalized with pneumonia.
Conclusion
NAC has decreased the days stayed in the ICU, number of deaths, and number of patients needed mechanical ventilation in COVID-19 hospitalized with pneumonia, although, this difference was insignificant. Further studies are required that could affect the level of significance.
A comparative study of three methods to detect the upper atmospheric wind speed by DASH
Authors: Li Wen-Wen , Hui Ning-Ju , Li Cun-Xia , Liu Yang-He , Fang Yan , Li Ling-Qing , Wang Yan-Long , Tang Yuan-He ,   School of Science, Xi’an University of Technology, Xi’an 710048, China
Published: September 2023

The DASH (Doppler asymmetric spatial heterodyne) is used to detect the upper atmospheric wind speed by its imaging Fizeau interference fringes. There are two wind measurement methods: Fourier series method (FSM) and popular Fourier transform method (FTM). However, the wind speed measurement accuracy of FTM is greatly influenced by window function, and the calculation is relatively complicated. The Four-point algorithm (FPA) for DASH’s wind speed measurement is proposed in this paper. The contents of wind speed measurement principle, forward modeling, noise and inversion by the FSM, FTM and FPA are wholly compared and studied. The three wind speed measurement methods are all derived from the phase difference transformation of DASH Fizeau interference fringes. The Fizeau interference fringes with wind speed of 0–100 m/s at the interval of 10 m/s are simulated, and the forward wind speeds are obtained by FSM, FTM and FPA, and the corresponding wind measurement errors are 2.93%, 4.67% and 3.00%, respectively. After artificially adding Gaussian noise with a mean value of 0 and a standard deviation of 0.1, FSM, FTM and FPA are used to forward the Fizeau interference fringes after flat field, and the corresponding relative errors are 2.30%, 11.66% and 2.27%, respectively. After artificially adding Gaussian noise, the Fizeau interference fringes of wind speeds of 31–39 m/s with 1 m/s interval and 30.1–30.9 m/s with 0.1 m/s interval are simulated, and the forward wind speeds are obtained by FSM and FPA. In both cases, the wind speed measurement errors of FSM are 3.55% and 4.15% higher than those of FPA. The O(1S) 557.7 nm airglow at peak altitude of 98 km in Xi’an was photographed by using our GBAII (ground based airglow imaging interferometer)-DASH, and the imaging interferograms with zenith angles of 0° and 45° were obtained. Then by the methods of Fourier series, Fourier transform and FPA are used to obtain the inversion wind speed of 32.21 m/s, 43.55 m/s and 32.17 m/s, respectively. From the forward and inversion results of DASH, we can see that the FPA has a better result for detecting the upper atmospheric wind due to its simple calculation and smaller wind measurement error.
Single molecule analysis of CENP-A chromatin by high-speed atomic force microscopy
Authors: Melters Daniël P , Neuman Keir C , Bentahar Reda S , Rakshit Tatini , Dalal Yamini
Published: September 2023

Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated of the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamics in vitro inform us about transcriptional potential in vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the mean square displacement and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, we found that an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. From these data, we speculate that factors altering nucleosome mobility in vitro, also correspondingly alter transcription in vivo. Subsequently, we propose a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance nucleosome mobility.
Inhibition of microtubule detyrosination by parthenolide facilitates functional CNS axon regeneration
Authors: Leibinger Marco , Zeitler Charlotte , Paulat Miriam , Gobrecht Philipp , Hilla Alexander , Andreadaki Anastasia , Guthoff Rainer , Fischer Dietmar
Published: September 2023

Injured axons in the central nervous system (CNS) usually fail to regenerate, causing permanent disabilities. However, the knockdown of PTEN or treatment of neurons with hyper-IL-6 (hIL-6) transforms neurons into a regenerative state, allowing them to regenerate axons in the injured optic nerve and spinal cord. Transneuronal delivery of hIL-6 to the injured brain stem neurons enables functional recovery after severe spinal cord injury. Here we demonstrate that the beneficial hIL-6 and PTEN knockout effects on axon growth are limited by the induction of tubulin detyrosination in axonal growth cones. Hence, cotreatment with parthenolide, a compound blocking microtubule detyrosination, synergistically accelerates neurite growth of cultured murine and primary RGCs isolated from adult human eyes. Systemic application of the prodrug dimethylamino-parthenolide (DMAPT) enables axon regeneration in the injured optic nerve and spinal cord. Moreover, combinatorial treatment further improves hIL-6-induced axon regeneration and locomotor recovery after severe SCI. Thus, DMAPT facilitates functional CNS regeneration and reduces the limiting effects of pro-regenerative treatments, making it a promising drug candidate for treating CNS injuries.Injured axons in the CNS usually fail to regenerate, causing permanent disabilities. No clinically approved drugs are currently available to improve or accelerate axon regeneration. We demonstrate that pro-regenerative treatments’ induced tubulin detyrosination in axonal growth cones limits axon growth. Hence, cotreatment with parthenolide, a compound blocking detyrosination, synergistically accelerates neurite growth of primary murine and, demonstrated for the first time,
human
retinal ganglion cells. Furthermore, systemic application of the parthenolide’s prodrug DMAPT accelerates hIL-6-mediated optic nerve regeneration and locomotor recovery after severe spinal cord injury. Thus, DMAPT facilitates functional CNS regeneration and reduces the limiting effects of pro-regenerative treatments, making it a potential (adjuvant) drug candidate for treating CNS injuries.
Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization
Authors: Nguyen Van Thien Chi , Nguyen Trong Hieu , Doan Nhu Nhat Tan , Pham Thi Mong Quynh , Nguyen Giang Thi Huong , Nguyen Thanh Dat , Tran Thuy Thi Thu , Vo Duy Long , Phan Thanh Hai , Jasmine Thanh Xuan , Nguyen Van Chu , Nguyen Huu Thinh , Nguyen Trieu Vu , Nguyen Thi Hue Hanh , Huynh Le Anh Khoa , Tran Trung Hieu , Dang Quang Thong , Doan Thuy Nguyen , Tran Anh Minh , Nguyen Viet Hai , Nguyen Vu Tuan Anh , Ho Le Minh Quoc , Tran Quang Dat , Pham Thi Thu Thuy , Ho Tan Dat , Nguyen Bao Toan , Nguyen Thanh Nhan Vo , Nguyen Thanh Dang , Phu Dung Thai Bieu , Phan Boi Hoan Huu , Vo Thi Loan , Nai Thi Huong Thoang , Tran Thuy Trang , Truong My Hoang , Tran Ngan Chau , Le Trung Kien , Tran Thanh Huong Thi , Duong Minh Long , Bach Hoai Phuong Thi , Kim Van Vu , Pham The Anh , Tran Duc Huy , Le Trinh Ngoc An , Pham Truong Vinh Ngoc , Le Minh Triet , Vo Dac Ho , Tran Thi Minh Thu , Nguyen Minh Nguyen , Van Thi Tuong Vi , Nguyen Anh Nhu , Tran Thi Trang , Tran Vu Uyen , Le Minh Phong , Do Thi Thanh , Phan Thi Van , Nguyen Luu Hong Dang , Nguyen Duy Sinh , Cao Van Thinh , Do Thanh Thuy Thi , Truong Dinh Kiet , Tang Hung Sang , Giang Hoa , Nguyen Hoai Nghia , Phan Minh Duy , Tran Le Son
Published: September 2023

Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (Screening for the Presence Of Tumor by Methylation And Size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (∼0.55X) of cell-free DNA. We applied SPOT-MAS to 738 nonmetastatic patients with breast, colorectal, gastric, lung and liver cancer, and 1,550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 62.3% and 73.9% for stage I and II, respectively, increasing to 88.3% for nonmetastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.
The MODY-associated TALK-1 L114P mutation causes islet α-cell overactivity and β-cell inactivity resulting in transient neonatal diabetes and glucose dyshomeostasis in adults
Authors: Nakhe Arya Y. , Dadi Prasanna K. , Kim Jinsun , Shrestha Shristi , Cartailler Jean-Philippe , Sampson Leesa , Magnuson Mark A. , Jacobson David A.
Published: September 2023

A gain-of-function mutation in the TALK-1 K
+
channel (p.L114P) associated with maturity-onset diabetes of the young (MODY) was recently reported in two distinct families. TALK-1 is a key regulator of β-cell electrical activity and glucose-stimulated insulin secretion (GSIS).
KCNK16
, the gene that encodes TALK-1, is the most abundant and β-cell– restricted K
+
channel transcript; polymorphisms in the
KCNK16
locus are also associated with an increased risk of type-2 diabetes. To investigate the impact of TALK-1-L114P on glucose homeostasis and confirm its association with MODY, a mouse model containing the
Kcnk16
L114P mutation was generated. Heterozygous and homozygous
Kcnk16
L114P mice exhibit increased neonatal lethality in the C57BL/6J and the mixed C57BL/6J:CD-1(ICR) genetic background, respectively. Lethality is likely a result of severe hyperglycemia observed in the homozygous
Kcnk16
L114P neonates due to lack of GSIS and can be reduced with insulin treatment. TALK-1-L114P drastically increased whole-cell β-cell K
+
currents resulting in blunted glucose-stimulated Ca
2+
entry and loss of glucose-induced Ca
2+
oscillations. Thus, adult
Kcnk16
L114P mice have reduced GSIS and plasma insulin levels, which significantly impaired glucose homeostasis. Taken together, this study determined that the MODY-associated TALK-1-L114P mutation disrupts glucose homeostasis in adult mice resembling a MODY phenotype and causes neonatal lethality by altering islet hormone secretion during development. These data strongly suggest that TALK-1 is an islet-restricted target for the treatment of diabetes.
Heat stress impairs centromere structure and segregation of meiotic chromosomes in Arabidopsis
Authors: Khaitova Lucie Crhak , Mikulkova Pavlina , Pecinkova Jana , Kalidass Manikandan , Heckmann Stefan , Lermontova Inna , Riha Karel
Published: September 2023

Heat stress is a major threat to global crop production, and understanding its impact on plant fertility is crucial for developing climate-resilient crops. Despite the known negative effects of heat stress on plant reproduction, the underlying molecular mechanisms remain poorly understood. Here, we investigated the impact of elevated temperature on centromere structure and chromosome segregation during meiosis in
Arabidopsis thaliana
. Our findings reveal that heat stress causes a significant decline in fertility and leads to the formation of micronuclei in pollen mother cells, along with an extended duration of meiotic division. We also demonstrate a reduction in the amounts of centromeric histone and the kinetochore protein BMF1 at meiotic centromeres with increasing temperature. Furthermore, we show that heat stress prolongs the activity of the spindle assembly checkpoint during meiosis I, indicating impaired efficiency of the kinetochore attachments to spindle microtubules. Our analysis of mutants with reduced amounts of centromeric histone suggests that weakened centromeres sensitize plants to elevated temperature, resulting in meiotic defects and reduced fertility even at moderate temperatures. These results indicate that the structure and functionality of meiotic centromeres in
Arabidopsis
are highly sensitive to heat stress, and suggest that centromeres and kinetochores may represent a crucial bottleneck in plant adaptation to increasing temperatures.
Neutrophils actively swell to potentiate rapid migration
Authors: Nagy Tamas L , Strickland Jack , Weiner Orion D
Published: September 2023

While the involvement of actin polymerization in membrane protrusion is well-established, we have a more limited understanding of the role of transmembrane water flow in cell motility. Here we investigate the role of water influx in neutrophil migration. These cells undergo directed movement to sites of injury and infection. Chemoattractant exposure increases cell volume and potentiates neutrophil migration, but the causal link between these processes is not known. Using a genome-wide CRISPR screen, we identify the regulators of the chemoattractant-induced neutrophil swelling, including NHE1, AE2, PI3K-gamma, and CA2. Through NHE1 inhibition in primary human neutrophils, we show that cell swelling is both necessary and sufficient for rapid migration following chemoattractant stimulation. Our data demonstrate that cell swelling complements cytoskeletal inputs for chemoattractant-induced potentiation of migration.
Producción de un espacio híbrido en las áreas de expansión de Santiago-Chile 1990-2017: una aproximación desde los márgenes como espacios otros
Authors:   ,   Pontificia Universidad Católica de Chile. Instituto de Geografía, Robles Robles María Sarella
Published: September 2023

Se estudia la producción del espacio en las áreas de expansión de la ciudad de Santiago a partir del desarrollo de un marco teórico y metodológico alternativo. La tesis plantea como hipótesis la producción de un espacio diferenciado de la periferia y del periurbano, categorías espaciales y conceptuales prevalentes en la literatura relacionadas con el área de expansión de la ciudad de Santiago. Para desarrollar la hipótesis, se estudia la producción del espacio desde los márgenes como espacios otros, lo que significó, por una parte, desarrollar la categoría de márgenes como espacios otros, tomando para esto las reflexiones surgidas desde la geografía, además de las reflexiones surgidas desde las humanidades y ciencias sociales. Por otro lado, también significó desarrollar un método que permitiera abordar la producción del espacio desde los márgenes como espacios otros, retomando para esto la discusión producida desde la geografía crítica y radical respecto de cómo abordar la producción social del espacio. La aplicación de la perspectiva y método evidenció la producción de un espacio diferenciado de la periferia y el periurbano en el área de expansión. Este espacio diferenciado es de tipo híbrido, dado que retoma elementos urbanos y rurales, produciéndose una categoría espacial diferenciada de la urbana y de la urbana-rural. El reconocimiento de este espacio se traduce en la ruptura completa del la dicotomía urbana-rural, dado que la ruptura ya no solo tendría una naturaleza social, sino, además, física. Reconocer la producción de un espacio híbrido, y específicamente, del proceso específico que da forma a la hibridación, permite conocer en profundidad los diversos procesos espaciales que se producen en el área de expansión, las relaciones que se producen entre ellos, y las consecuencias sociales que implica su producción y relaciones. Finalmente, se plantea que la investigación alimenta el desarrollo de una geografía decolonial, y contribuye a dar cuenta de la singularidad de la espacialidad latinoamericana.