cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Clinical parameters associated with gastric portal hypertensive polyps
Creators: name: Hildenbrand, Florian Freimut
name: Wohlwend, Chantal
name: von Felten, Stefanie
name: Rodewald, Ann-Katrin
name: Murray, Fritz Ruprecht
name: Olivier The, Frans
name: Bütikofer, Simon
name: Gubler, Christoph
name: Morell, Bernhard
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 60506 Virology
subject: FOS: Biological sciences

description: Portal hypertensive polyps (PHPs) are incompletely characterized lesions that can be found in the distal stomach of patients with portal hypertension. We aimed to delineate clinical factors associated with the appearance of these rare polyps. We conducted a cross-sectional study of a cohort with 513 cirrhotic patients comparing patients with and without PHP using descriptive analyses and multivariable logistic regression. To address the problem of missing values, in particular for HVPG and liver stiffness, we used multiple imputation of missing values. The prevalence of macroscopically diagnosed PHP was 3.3% (95% confidence interval 2.0 − 5.4%). In 53% of cases, the correct classification was missed on index gastroscopy. Patients with PHP were older at gastroscopy (65 years vs. 59), had higher hepatic venous pressure gradients (HVPG, 28 mmHg vs. 19 mmHg), higher transient elastography (TE) measurements (50.7 kPa vs. 21.8 kPa) and more often had previous rubber band ligations (RBL, 64.7% vs. 25.8%). The multivariable logistic regression on the outcome macroscopically diagnosed PHP estimated an odds ratio (OR) for HPVG of 1.13 (CI 0.95–1.34), increased liver stiffness of 1.03 (1.00 − 1.07) and previous RBL of 3.84 (1.24 − 11.88), respectively. The prevalence of PHPs in the stomach was higher than assumed in previous studies and misclassification was commonly observed. The appearance of these rare polyps is associated with previous RBL and may correlate with severity of PH. Thus, PHPs may be regarded as marker for relevant PH, but clinical significance of these polyps is still uncertain.
Vitamin D inadequacy combined with high BMI affects paraspinal muscle atrophy and pain intensity in postmenopausal women
Creators: name: Chen, H.
name: Xu, H.-W.
name: Zhang, S.-B.
name: Yi, Y.-Y.
name: Wang, S.-J.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 111714 Mental Health
subject: FOS: Health sciences

description: This study was performed to assess the effects of vitamin D deficiency/insufficiency combined with a high body mass index (BMI) on paraspinal muscle (PSM) atrophy and pain intensity in postmenopausal women with lower back pain (LBP). In total, 365 postmenopausal women were analyzed in the study. We divided the women into four groups according to BMI and vitamin D status. Outcome measurements included PSM atrophy, fatty infiltration (FI) and severity of LBP. Binary logistic regression was used to analyze the odds ratio (OR), and the interaction between the BMI and vitamin D status was tested. Compared with the control group, the high BMI with vitamin D deficiency/insufficiency group had a significantly increased risk of FI > grade 2 (OR = 10.69, p < 0.001), hand grip strength of <16 kg (OR = 8.96, p < 0.001), Short Physical Performance Battery score of ≤8 (OR = 3.69, p < 0.001) and visual analog scale (VAS) score of >3 (OR = 4.76, p < 0.001). A significant positive additive interaction was found between the BMI and vitamin D status on PSM atrophy. Vitamin D deficiency/insufficiency combined with a high BMI was associated with PSM atrophy and LBP intensity in postmenopausal women. The interaction analysis showed a positive additive interaction between BMI and vitamin D status.
Relativistic frequency shifts in Cr, Ti, Fe, Ni, Ca, Na, and V to search for variation in the fine structure constant
Creators: name: Dzuba, V. A.
name: Flambaum, V. V.
name: Murphy, M. T.
name: Berke, D. A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Sensitivity of the frequencies of twenty two atomic transitions to the variation of the fine structure constant $α$ is calculated. The findings are to be used in search for possible variation of $α$ across our Galaxy using high quality spectroscopic data for stars similar to our Sun.
description: 4 pages, 2 tables
title: It’s not easy to spot disinformation on Twitter
Creators: name: Stier, Sebastian
name: Schoch, David
name: Keller, Franziska
name: Yang, JungHwan
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2020
Subjects: subject: Bots
subject: Campaign
subject: Disinformation
subject: Facebook
subject: Twitter

description: Dr. Sebastian Stier and his co-authors Franziska Keller, David Schoch, and JungHwan Yang examine so called “astroturfing” campaigns which aim at misleading the public by giving a false impression that there is genuine grass-roots support or opposition for a particular group or policy. Those campaigns don’t solely rely on automated “bots” or bot accounts — humans, not programmers or AI, are behind the “troll farms”.
description: GESIS Blog
Influence of coronal hole morphology on the solar wind speed at Earth
Creators: name: Samara, Evangelia
name: Magdalenic, Jasmina
name: Rodriguez, Luciano
name: Heinemann, Stephan G.
name: Georgoulis, Manolis K.
name: Hofmeister, Stefan J.
name: Poedts, Stefaan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: It has long been known that the high-speed stream (HSS) peak velocity at Earth directly depends on the area of the coronal hole (CH) on the Sun. Different degrees of association between the two parameters have been shown by many authors. In this study, we revisit this association in greater detail for a sample of 45 nonpolar CHs during the minimum phase of solar cycle 24. The aim is to understand how CHs of different properties influence the HSS peak speeds observed at Earth and draw from this to improve solar wind modeling. The characteristics of the CHs of our sample were extracted based on the Collection of Analysis Tools for Coronal Holes (CATCH) which employs an intensity threshold technique applied to extreme-ultraviolet (EUV) filtergrams. We first examined all the correlations between the geometric characteristics of the CHs and the HSS peak speed and duration at Earth, for the entire sample. The CHs were then categorized in different groups based on morphological criteria, such as the aspect ratio, the orientation angle and the geometric complexity, a parameter which is often neglected when the formation of the fast solar wind at Earth is studied. Our results, confirmed also by the bootstrapping technique, show that all three aforementioned morphological criteria play a major role in determining the HSS peak speed at 1 AU. Therefore, they need to be taken into consideration for empirical models that aim to forecast the fast solar wind at Earth based on the observed CH solar sources.
description: Accepted by the Astronomy & Astrophysics journal
title: Demographic inference and corrections for non-representativeness when working with multilingual social media data
Creators: name: Flöck, Fabian
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2020
Subjects: subject: Deep Learning
subject: Reweighting
subject: Social Media
subject: Twitter

description: Dr. Fabian Flöck introduces a new state of the art for inferring demographic attributes of social media profiles with deep learning in 32 languages. In his paper from last year he showed how to estimate the probabilities to be on Twitter for different socio-demographic strata in over 1000 regions in the EU. Read the blog post to learn more about the paper, the pretrained model or the Web demo.
description: GESIS Blog
When does a hypergeometric function ${}_{p\!}F_q$ belong to the Laguerre--Pólya class $LP^+$?
Creators: name: Sokal, Alan D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: 33C20 (Primary), 30B70, 30C15, 30D20, 30E05, 44A60 (Secondary)

description: I show that a hypergeometric function ${}_{p}F_q(a_1,\ldots,a_p;b_1,\ldots,b_q;\,\cdot\,)$ with $p \le q$ belongs to the Laguerre--Pólya class $LP^+$ for arbitrarily large $b_{p+1},\ldots,b_q > 0$ if and only if, after a possible reordering, the differences $a_i - b_i$ are nonnegative integers. This result arises as an easy corollary of the case $p=q$ proven two decades ago by Ki and Kim. I also give explicit examples for the case ${}_{1}F_2$.
description: 10 pages, LaTeX2e
title: Nachrichtenkonsum in digitalen Medien: Mehr Vielfalt durch Google, Facebook und Co
Creators: name: Zervos, Sophie
name: Umme, Linna
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2020
Subjects: subject: Diversity
subject: Facebook
subject: Social Media
subject: Google
subject: News
subject: Intermediaries

description: Social media and search engines - so-called intermediaries - promote individual news consumption and the diversity of news sources. This is the conclusion of a recent study by GESIS scientists Sebastian Stier and Johannes Breuer together with Michael Scharkow from Johannes Gutenberg University Mainz and Frank Mangold from the University of Hohenheim - and thus contradicts the widespread view that social media and other intermediaries have a negative impact on the diversity of news consumption.
description: Soziale Medien und Suchmaschinen – sogenannte Intermediäre – befördern den individuellen Nachrichtenkonsum und die Vielfalt der Nachrichtenquellen. Zu diesem Ergebnis kommt eine aktuelle Studie der GESIS-Wissenschaftler Sebastian Stier und Johannes Breuer gemeinsam mit Michael Scharkow von der Johannes Gutenberg Universität Mainz und Frank Mangold von der Universität Hohenheim – und widerspricht damit der weit verbreiteten Ansicht, dass sich soziale Medien und andere Intermediäre negativ auf die Vielfalt des Nachrichtenkonsums auswirken.
description: GESIS Blog
PRISMA 2020 checklist
Creators: name: Pramudyo, Miftah
name: Putra, Iwan Cahyo Santosa
name: Kamarullah, William
name: Prameswari, Hawani Sasmaya
name: Saboe, Aninka
name: Akbar, Mohammad Rizki
Publisher: name: figshare
Year: 2022
Subjects: subject: 110201 Cardiology (incl. Cardiovascular Diseases)
subject: FOS: Clinical medicine
subject: Cardiology

description: This PRISMA 2020 checklist was used to improve the transparency of our manuscript entitled Elevated shock index and modified shock index are associated with mortality and major adverse cardiac events in patients with acute myocardial infarction: A systematic review and meta-analysis. .
title: The missing link? Linking surveys with geospatial and digital behavioral data
Creators: name: Breuer, Johannes
name: Jünger, Stefan
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2021
Subjects: subject: Data Linking
subject: Social Media
subject: Geospatial Data
subject: Digital Behavioral Data
subject: Survey Methodology
subject: Research Data Management

description: Survey data are the most widely used type of data in the quantitative social sciences. They have been used to investigate a huge range of societally relevant topics. However, they also have specific limitations. An effective way of addressing those is linking survey data with other types of data, such as geospatial or digital behavioral data. This blog post discusses the benefits of linking survey data with other types of data as well as what researchers need to consider if they want to do this. To address the latter, we introduce a general framework for organizing the data linking workflow.
description: Umfragedaten sind die in den quantitativen Sozialwissenschaften am häufigsten verwendete Datenart. Sie wurden für die Untersuchung einer Vielzahl gesellschaftlich relevanter Themen verwendet. Sie haben jedoch auch spezifische Einschränkungen. Ein effektiver Weg, diese zu überwinden, ist die Verknüpfung von Umfragedaten mit anderen Datentypen, z. B. mit Geodaten oder digitalen Verhaltensdaten. In diesem Blogbeitrag werden die Vorteile der Verknüpfung von Umfragedaten mit anderen Datentypen erörtert, aber auch, was Forschende beachten müssen, wenn sie dies tun wollen. Daher stellen wir einen allgemeinen Rahmen für die Organisation des Datenverknüpfungsworkflows vor.
description: GESIS Blog
Estimates for the Kolmogorov widths of weighted Sobolev classes with conditions on the $0$th and the greatest derivatives
Creators: name: Vasil'eva, A. A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics

description: In this article, we obtain the order estimates for the Kolmogorov widths of sets with conditions on the norm in the weighted Sobolev space $W^r_{p_1}$ and in the weighted space $L_{p_0}$.
title: The “Call Me Sexist But” Dataset
Creators: name: Samory, Mattia
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2021
Subjects: subject: Sexism
subject: Psychometrics
subject: NLP
subject: Dataset
subject: CSS
subject: Computational Social Science

description: Have you ever wondered if a message you sent may be received as sexist? Did you ask yourself how could you have made it better? To take concrete steps towards understanding what, really, is sexist, a group of researchers curated a dataset of over 10.000 tweets to enable researchers to study the multiple ways sexism appears in day-to-day communication.
description: Haben Sie sich jemals gefragt, ob eine von Ihnen gesendete Nachricht als sexistisch empfunden werden könnte? Haben Sie sich gefragt, wie Sie es besser machen könnten? Um konkrete Schritte zu unternehmen, um zu verstehen, was wirklich sexistisch ist, hat eine Gruppe von Forschenden einen Datensatz von über 10.000 Tweets zusammengestellt, um Forschenden die Möglichkeit zu geben, die verschiedenen Arten von Sexismus in der alltäglichen Kommunikation zu untersuchen.
description: GESIS Blog
title: World Toilet Day – What Bathrooms Have To Do With Social Equity
Creators: name: Link, Emma
name: Repke, Lydia
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2021
Subjects: subject: ISSP
subject: Eurobarometer
subject: Toilets
subject: Water
subject: Sanitation
subject: Hygiene
subject: WASH
subject: Sustainable Development Goals
subject: UN

description: The provision of water, sanitation, and hygiene (also referred to as WASH) for all people is one of the most pressing issues in our world, and it is closely intertwined with other problems, such as social injustice and climate change. Globally, 4.2 billion people lack access to safe sanitation – this is more than half of humanity. Every year on November 19, the United Nations celebrate World Toilet Day to raise awareness of the issue.
description: Die Bereitstellung von Wasser, Sanitärversorgung und Hygiene (auch als WASH bezeichnet) für alle Menschen gehört zu den drängendsten Themen in unserer Welt und ist eng mit anderen Problemfeldern wie sozialer Ungerechtigkeit und Klimawandel verbunden. Weltweit fehlt 4,2 Milliarden Menschen der Zugang zu sicheren Sanitäreinrichtungen – das ist mehr als die Hälfte der Menschheit. Jedes Jahr am 19. November halten die Vereinten Nationen den Welttoilettentag ab, um dem Thema mehr Aufmerksamkeit zu verschaffen.
description: GESIS Blog
title: Zur Regierungsablösung nach 16 Jahren Angela Merkel: Die Meinung der deutschen Wähler:innen im Datencheck
Creators: name: Riebe, Frauke
name: Hetzer, Lukas
name: Wenker, Jonas
Publisher: name: GESIS - Leibniz Institute for the Social Sciences
publisherIdentifier: https://ror.org/018afyw53
Year: 2021
Subjects: subject: GLES
subject: Federal Election
subject: BTW21
subject: Ampel
subject: Merkel
subject: Election

description: These were eventful and crisis-ridden years in office during which Angela Merkel was Chancellor of the Federal Republic of Germany from 2005 to 2021: the financial/euro crisis, the "refugee crisis," the climate crisis and, most recently, the Corona pandemic. Times of crisis are often accompanied by change. But how is this change reflected in the attitudes of the German population toward the most important social issues? How have Angela Merkel and the German government been perceived over the years? And how has the desire for a traffic light coalition changed over the past 16 years? Answers to these questions are provided by data from the German Longitudinal Election Study (GLES), the central polling program for the 2009, 2013, 2017 and 2021 federal elections in Germany, with surveys of the population and candidates.
description: Es waren ereignis- und krisenreiche Amtsjahre, in denen Angela Merkel von 2005 bis 2021 Bundeskanzlerin der Bundesrepublik Deutschland war: die Finanz‑/Eurokrise, die „Flüchtlingskrise“, die Klimakrise und zuletzt die Corona-Pandemie. Zeiten der Krise gehen oft mit Wandel einher. Doch wie spiegelt sich dieser Wandel in den Einstellungen der deutschen Bevölkerung zu den wichtigsten gesellschaftlichen Themen wider? Wie wurden Angela Merkel und die Bundesregierung im Verlauf der Jahre wahrgenommen? Und wie hat sich der Wunsch nach einer Ampel-Koalition in den letzten 16 Jahren verändert? Antworten auf diese Fragen erlauben die Daten der German Longitudinal Election Study (GLES), das zentrale Umfrageprogramm zu den Bundestagswahlen 2009, 2013, 2017 und 2021 in Deutschland, mit Befragungen der Bevölkerung und der Kandidierenden.
description: GESIS Blog
lineagespot: Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater
Creators: name: Pechlivanis, Nikolaos
name: Tsagiopoulou, Maria
name: Maria-Christina Maniou
name: Anastasis Togkousidis
name: Mouchtaropoulou, Evangelia
name: Chassalevris, Taxiarchis
name: Chaintoutis, Serafeim C.
name: Petala, Maria
name: Kostoglou, Margaritis
name: Thodoris Karapantsios
name: Laidou, Stamatia
name: Vlachonikola, Elisavet
name: Chatzidimitriou, Anastasia
name: Papadopoulos, Agis
name: Papaioannou, Nikolaos
name: Dovas, Chrysostomos I.
name: Anagnostis Argiriou
name: Psomopoulos, Fotis
Publisher: name: F1000 Research Limited
Year: 2022

description: Nearly two years after the first report of SARS-CoV-2 in Wuhan, China, the virus has caused an unprecedented global crisis. The COVID-19 pandemic has affected more the four million people, making it necessary for the emergence of new approaches able to monitor its spread. Most laboratories rely on PCR-based methods for epidemiological investigation and early mutation detection of the virus. Yet, these methods are not easily scalable, especially in large urban areas, or in cases where new mutations arise. Recently, the detection of SARS-CoV-2 RNA in wastewater turned into a useful tool to study the prevalence of the virus in the community. To this end, a novel methodology, called lineagespot, has been developed for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). The tool accepts as input a VCF file, which contains all nucleotide (and the corresponding amino acid) mutations identified in a sample, along with a file containing all lineage-assignment mutations. After analyzing all inputs, a tab-delimited file (TSV file) is produced containing the identified mutations that are related to SARS-CoV-2 lineages. In addition, it computes the average allele frequencies to quantify lineage abundance metrics. lineagespot is dependent on the source used for retrieving lineage definitions; currently, the package supports two potential sources, i.e. the lineage-characteristic mutation profiles pre-calculated by outbreak.info and the lineage-characteristic mutation profiles derived from the trained Pangolin models. So far, the tool has been evaluated through application to NGS data produced to cover a six-month period for the municipality of Thessaloniki, Greece. The results revealed the presence of SARS-CoV-2 variants in wastewater data, and have been recently published at scientific reports. It is worth noting that lineagespot was able to record the evolution and rapid domination of the Alpha variant (B.1.1.7) in the community, and identified a strong correlation between the mutations evident through our approach and the mutations observed in patients from the same area and time periods. lineagespot has been developed as an open-source tool, implemented in R, and is freely available through GitHub and the Bioconductor repository.
title: Increasing the structural and compositional diversity of ion-track templated 1D nanostructures through multistep etching, plastic deformation, and deposition
Creators: name: Hossain, Umme Habiba
name: Jantsen, Gennadi
name: Muench, Falk
name: Kunz, Ulrike
name: Ensinger, Wolfgang
Publisher: name: IOP Publishing
Year: 2022

description: Ion-track etching represents a highly versatile way of introducing artificial pores with diameters down into the nm-regime into polymers, which offers considerable synthetic flexibility in template-assisted nanofabrication schemes. While the mechanistic foundations of ion-track technology are well understood, its potential for creating structurally and compositionally complex nano-architectures is far from being fully tapped. In this study, we showcase different strategies to expand the synthetic repertoire of ion-track membrane templating by creating several new 1D nanostructures, namely metal nanotubes of elliptical cross-section, funnel-shaped nanotubes optionally overcoated with titania or nickel nanospike layers, and concentrical as well as stacked metal nanotube-nanowire heterostructures. These nano-architectures are obtained solely by applying different wet-chemical deposition methods (electroless plating, electrodeposition, and chemical bath deposition) to ion-track etched polycarbonate templates, whose pore geometry is modified through plastic deformation, consecutive etching steps under differing conditions, and etching steps intermitted by spatially confined deposition, providing new motifs for nanoscale replication.
Making biomedical research software findable, accessible, interoperable, reusable (FAIR) with FAIRshare
Creators: name: Bhavesh Patel
name: Soundarajan, Sanjay
Publisher: name: F1000 Research Limited
Year: 2022

description: We present here FAIRshare, an open-source and free (MIT license) cross-platform desktop software that helps biomedical researchers in making their research software Findable, Accessible, Interoperable, and Reusable (FAIR) in line with the FAIR for research software (FAIR4RS) guiding principles. The FAIR4RS principles, established by the FAIR4RS Working group, provide a foundation for optimizing the reusability of research software and encourage open science. The FAIR4RS principles are, however, aspirational. Practical guidelines that biomedical researchers can easily follow for making their research software FAIR are still lacking. To fill this gap, we established the first minimal and actionable step-by-step guidelines for researchers to make their biomedical research software FAIR. We designate these guidelines as the FAIR Biomedical Research Software (FAIR-BioRS) guidelines. FAIRshare walks the users step-by-step into implementing the FAIR-BioRS guidelines for their research software (including metadata such as codemeta.json, choosing a license – preferably open source, sharing on a suitable repository such as Zenodo, etc.). The process is streamlined through an intuitive graphical user interface and automation such as to minimize researchers’ time and effort. We believe that the FAIR-BioRS guidelines and FAIRshare will empower and encourage biomedical researchers into adopting FAIR and open practices for their research software.
Decomprolute: a proteomic tumor deconvolution benchmarking framework
Creators: name: Feng, Song
name: Calinawan, Anna
name: Petralia, Francesca
name: Wang, Pei
name: Pugliese, Pietro
name: Ceccarelli, Michele
name: Gosline, Sara
Publisher: name: F1000 Research Limited
Year: 2022

description: Tumor deconvolution algorithms are a reliable way to disentangle the diverse cell types that comprise solid tumors. To date, however, both the algorithms developed to deconvolve tumor data and the gold standard datasets used to assess the algorithms are geared toward the analysis of gene expression rather than protein levels of a tumor. While gene expression is more inexpensive to measure, protein levels provide a more accurate view of immune markers. To encourage more development of multiomic deconvolution algorithms, we introduce Decomprolute, a Common Workflow Language framework that leverages Docker to compare tumor deconvolution algorithms across multiomic data sets. Decomprolute leverages the large-scale multi-omic data sets produced by the Clinical Proteomics Tumor Analysis Consortium (CPTAC), which include matched mRNA expression and proteomics data from thousands of tumors across multiple cancer types to build a fully open-source, containerized proteomic tumor deconvolution benchmarking platform. The platform is available for access and use at http://pnnl-compbio.github.io/decomprolute. 
Constructive alignment and the Research Skills Development Framework: using theory to practically align graduate attributes, learning experiences, and assessment tasks in undergraduate midwifery
Creators: name: Pretorius, Lynette
name: Bailey, Carolyn
name: Miles, Maureen
Publisher: name: Monash University
Year: 2021
Subjects: subject: 130103 Higher Education
subject: FOS: Educational sciences
subject: Education
subject: 111006 Midwifery
subject: FOS: Health sciences
subject: Health Care

description: Midwifery educators have to provide students with stimulating curricula that teach academic and vocational content, as well as transferable skills. The Research Skills Development (RSD) framework provides a conceptual model that allows educators to explicitly scaffold the development of their students’ research skills. This paper aims to demonstrate the effective use of the RSD framework and constructive alignment theory to redesign a second-year Midwifery assessment task. The assessment task was changed into a scenario-based question to better reflect the unit learning objectives and expected graduate attributes. Students were provided with extra time in class to explore the assessment task in a peer environment. Following the return of their assessments, students were asked to complete a questionnaire to evaluate the effectiveness of the assessment redesign. We show that using a constructively aligned scenario-based assessment task in a second year unit more successfully articulated the expected graduate attributes of midwives. Qualitative and quantitative feedback suggested that students and staff appreciated a more clinically-relevant assessment task. This paper demonstrates that the use of the RSD framework to constructively align graduate attributes, learning experiences, and assessment tasks allows for the transformation of undergraduate assessment into a learning experience relevant to clinical practice.
Using JBrowse 2 for a model organism database: a WormBase case study
Creators: name: Cain, Scott
name: Holmes, Ian
name: Buels, Robert
name: Diesh, Colin
name: Xie, Peter
name: Martinez, Teresa
name: Stevens, Garrett
name: Hershberg, Elliot
name: Dider, Shihab
name: Stein, Lincoln
name: Harris, Todd
name: Nuin, Paulo
name: Wright, Adam
name: Bridge, Caroline
name: Junjun Zhang
name: Leung, Angel
name: Haw, Robin
name: Hogue, Greg
name: Duncan, Andrew
Publisher: name: F1000 Research Limited
Year: 2022

description: Short talk describing initial efforts to add JBrowse 2 components to the model organism database for C. elegans and related nematodes, Wormbase.org. Included elements are an embedded linear genome view for feature pages and a synteny browser.
NICER monitoring of supersoft X-ray sources
Creators: name: Orio, M.
name: Gendreau, K.
name: Giese, M.
name: Luna, J. G. M.
name: Magdolen, J.
name: Pei, S.
name: Sun, B.
name: Behar, E.
name: Dobrotka, A.
name: Mikolajewska, J.
name: Pasham, D. R.
name: Strohmayer, T. E.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We monitored four supersoft sources - two persistent ones, CAL 83 and MR Vel, and the recent novae YZ Ret (Nova Ret 2020) and V1674 Her (Nova Her 2021) - with NICER. The two persistent SSS were observed with unvaried X-ray flux level and spectrum, respectively, 13 and 20 years after the last observations. Short period modulations of the supersoft X-ray source (SSS) appear where the spectrum of the luminous central source was fully visibl (in CAL 83 and V1674 Her) and were absent in YZ Ret and MR Vel, in which the flux originated in photoionized or shocked plasma, while the white dwarf (WD) was not observable. We thus suggest that the pulsations occur on, or very close to, the WD surface. The pulsations of CAL 83 were almost unvaried after 15 years, including an irregular drift of the $\simeq$67 s period by 2.1 s. Simulations, including previous XMM-Newton data, indicate actual variations in period length within hours, rather than an artifact of the variable amplitude of the pulsations. Large amplitude pulsations with a period of 501.53$\pm$0.30 s were always detected in V1674 Her, as long as the SSS was observable. This period seems to be due to rotation of a highly magnetized WD.We cannot confirm the maximum effective temperature of ($\simeq$145,000 K) previously inferred for this nova, and discuss the difficulty in interpreting its spectrum. The WD appears to present two surface zones, one of which does not emit SSS flux.
description: in press in the Astrophysical Journal
Lagrangian reverse engineering for regular black holes
Creators: name: Bokulić, Ana
name: Franzin, Edgardo
name: Jurić, Tajron
name: Smolić, Ivica
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Nonlinear extensions of classical Maxwell's electromagnetism are among the prominent candidates for theories admitting regular black hole solutions. A quest for such examples has been fruitful, but mostly unsystematic and littered by the introduction of physically unrealistic Lagrangians. We provide a procedure which admits the reconstruction of a nonlinear electromagnetic Lagrangian, consistent with the Euler--Heisenberg Lagrangian in the weak-field limit, from a given metric representing a regular, magnetically charged black hole.
description: 8 pages; ver.2: one sentence added, version accepted for publication in Physics Letters B
RPhenoscape: Semantic computing with morphological traits and ontologies
Creators: name: Lapp, Hilmar
name: Bradley, John
name: Xu, Hong
name: Amandeep Rathee
name: Balhoff, James
name: Wasila Dahdul
Publisher: name: F1000 Research Limited
Year: 2022

description: We present RPhenoscape, a package for the R programming language to provide convenient and robust access to the ontologies and ontology-liked morphological trait data (phenotypes) within the Phenoscape Knowledgebase (KB), as well as to several algorithms for computing with the semantics of traits based on formal logic reasoning. Among the major aims of the package is to enable the computational integration of trait semantics into evolutionary models for comparative trait analysis, which have traditionally treated traits simply as independent characters and character states. To this end, RPhenoscape provides access to the computational inference of presence/absence trait matrices, the presence/absence-based inference of trait dependence, evidence-based mutual trait compatibility/exclusivity, and a variety of semantic similarity metrics for phenotypes. RPhenoscape is currently in the last steps of a new major release series, which adds some of the features presented here and once complete will be made available on the Comprehense R Archive Network.
Applications of the dynamical generator coordinate method to quadrupole excitations
Creators: name: Hizawa, N.
name: Hagino, K.
name: Yoshida, K.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Theory (nucl-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We apply the dynamical generator coordinate method (DGCM) with a conjugate momentum to a nuclear collective excitation. To this end, we first discuss how to construct a numerically workable scheme of the DGCM for a general one-body operator. We then apply the DGCM to the quadrupole vibration of $^{16}$O using the Gogny D1S interaction. We show that both the ground state energy and the excitation energies are lowered as compared to the conventional GCM with the same number of basis functions. We also compute the sum rule values for the quadrupole and monopole operators, and show that the DGCM yields more consistent results than the conventional GCM to the values from the double commutator. These results imply that the conjugate momentum is an important and relevant degree of freedom in collective motions.
description: 9 pages, 4 figures
title: Numerical modelling of field vane shear test in sensitive clay
Creators: name: Kundu, Pritam
Publisher: name: Memorial University of Newfoundland
Year: 2022

description: The undrained shear strength of clay is one of the key parameters in geotechnical design, which can be determined from laboratory or field tests. The disturbance of soil samples during sampling, transporting, storing and trimming could influence the laboratory test result, which could be significantly high for sensitive clay because the structure of the soil might be changed. Therefore, the field vane shear test (VST) is commonly used to determine the undrained shear strength of sensitive clay. Although the test is relatively simple, the interpretation of the VST results is challenging, as the failure mechanisms are still not well understood and cannot be observed in the field. Therefore, numerical simulation might be a viable option to examine such mechanisms. Some attempts have been made previously using Lagrangian-based finite element (FE) analysis but not could model the complete process, because large shear strains develop along the thin shear plane, which causes mesh distortion and numerical issues. In the present study, VST is simulated using an Eulerian-based FE approach. In this approach, the Eulerian material (soil) flows through the fixed mesh; therefore, the simulation can be continued for a large penetration and rotation. A nonlinear strain-softening and strain-rate dependent soil model for the undrained shear strength of sensitive clays is incorporated in the FE simulation. The first set of simulations is performed for only one element of thickness (i.e., two-dimensional conditions) by applying rotation to a rigid vane. Three-dimensional simulations are then performed by penetrating the vane to the desired depth, followed by a rotation. The rotation initiates the formation of a rounded square-shaped failure block which turns into a circular one after the peak torque. The penetration of the vane can significantly disturb the surrounding sensitive clay and thereby reduce the maximum torque during rotation. The extent of disturbance depends on several factors, such as blade thickness, soil sensitivity, and post-peak strength degradation parameters.
title: The Scope and Feasibility of Hydrogen Fuel Cell Vehicles as an Alternative Sustainable Mode of Transport
Creators: name: Chenthadiyil, Jens
Publisher: name: TU Wien
Year: 2022
Subjects: subject: Hydrogen Vehicles
subject: Alternate Energy source
subject: HFCV
subject: Fuel Cell Vehicles

description: In the face of the world's environmental crises, a movement for sustainable energy sources in the transportation industry has gained traction. As a zero-emission alternative to conventional automobiles, hydrogen fuel cell vehicles (HFCVs) provide a unique mix of advantages. The integration of HFCVs into the automobile sector, onthe other hand, is currently behind and has a lot of room for development. It is criticalto assess the technology's potential and comprehend the scope and feasibility of HFCVs. This study examines the existing literature to answer these research questions.In addition, statistical studies of global HFCV data were analyzed, as well as a surveyto determine the present degree of public awareness and understanding of thisHydrogen technology. According to the research, HFCVs have a lot of potential aspart of a forthcoming, sustainable transportation solution. However, infrastructure improvements, as well as additional promotional campaigns, are required to gain customer confidence in the new technology. Governments and major automotive manufacturers must work together to develop tools that will allow them to make the best strategic decisions possible when it comes to improving and integrating HFCVs into the road system.
Making biomedical research software FAIR with FAIRshare
Creators: name: Bhavesh Patel
name: Soundarajan, Sanjay
Publisher: name: F1000 Research Limited
Year: 2022

description: We present here FAIRshare, an open-source and free (MIT license) cross-platform desktop software that helps biomedical researchers in making their research software Findable, Accessible, Interoperable, and Reusable (FAIR) in line with the FAIR for research software (FAIR4RS) guiding principles. The FAIR4RS principles, established by the FAIR4RS Working group, provide a foundation for optimizing the reusability of research software and encourage open science. The FAIR4RS principles are, however, aspirational. Practical guidelines that biomedical researchers can easily follow for making their research software FAIR are still lacking. To fill this gap, we established the first minimal and actionable step-by-step guidelines for researchers to make their biomedical research software FAIR. We designate these guidelines as the FAIR Biomedical Research Software (FAIR-BioRS) guidelines. FAIRshare walks the users step-by-step into implementing the FAIR-BioRS guidelines for their research software (including metadata such as codemeta.json, choosing a license – preferably open source, sharing on a suitable repository such as Zenodo, etc.). The process is streamlined through an intuitive graphical user interface and automation such as to minimize researchers’ time and effort. We believe that the FAIR-BioRS guidelines and FAIRshare will empower and encourage biomedical researchers into adopting FAIR and open practices for their research software.
Variable mass accretion and failed wind explain changing look phenomena in NGC 1365
Creators: name: Mondal, Santanu
name: Adhikari, Tek P.
name: Hryniewicz, Krzysztof
name: Stalin, C. S.
name: Pandey, Ashwani
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Changing look active galactic nuclei (CLAGNs) show complex nature in their X-ray spectral shape and line of sight column density variation. The physical mechanisms responsible for these variations are unclear. Here, we study the spectral properties of a CLAGN, NGC\,1365 using combined {\it XMM-Newton} and {\it NuSTAR} observations to understand the CL behavior. The model fitted mass accretion rate varied between $0.003\pm 0.001$ and $0.009\pm0.002$ $\dot M_{\rm Edd}$ and the dynamic corona changed from $28\pm 3$ to $10\pm1$ $r_g$. We found that the variable absorption column density correlates with the mass accretion rate and the geometry of the corona. The derived wind velocity was sufficiently low compared to the escape velocity to drive the wind away from the disc for the epochs when column densities were high. This suggests that the high and variable absorption can be due to failed winds from the disc. Our estimated ratio of mass outflow to inflow rate from the inner region of the disc lies between $0.019\pm0.006$ and $0.12\pm0.04$. From spectral fitting of the combined data, we found the mass of the central black hole to be constant $4.38\pm0.34 - 4.51\pm0.29 \times10^{6} M_\odot$, consistent with earlier findings. The confidence contours of $N_H$ with other model parameters show that the model fitted parameters are robust and non-degenerate. Our study construed that the changing accretion rate, which is a fundamental physical quantity and the geometry of the corona driving the CL phenomena in NGC\,1365. The physical picture considered in this work connects both variable continuum and variable absorbing medium scenarios.
description: 8 pages, 7 figures, 1 table, accepted for publication in A&A, comments welcome
Moiré band structures of twisted phosphorene bilayers
Creators: name: Soltero, Isaac
name: Guerrero-Sánchez, Jonathan
name: Mireles, Francisco
name: Ruiz-Tijerina, David A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We report on the theoretical electronic spectra of twisted phosphorene bilayers exhibiting moiré patterns, as computed by means of a continuous approximation to the moiré superlattice Hamiltonian. Our model is constructed by interpolating between effective $Γ$-point conduction- and valence-band Hamiltonians for the different stacking configurations approximately realized across the moiré supercell, formulated on symmetry grounds. We predict the realization of three distinct regimes for $Γ$-point electrons and holes at different twist angle ranges: a Hubbard regime for small twist angles $θ< 2^\circ$, where the electronic states form arrays of quantum-dot-like states, one per moiré supercell; a Tomonaga-Luttinger regime at intermediate twist angles $2^\circ < θ\lesssim 10^\circ$, characterized by the appearance of arrays of quasi-1D states; and finally, a ballistic regime at large twist angles $θ\gtrsim 10^\circ$, where the band-edge states are delocalized, with dispersion anisotropies modulated by the twist angle. Our method correctly reproduces recent results based on large-scale ab initio calculations at a much lower computational cost, and with fewer restrictions on the twist angles considered.
description: Journal accepted version. 20 pages, including 11 figures and 5 appendices
Gas phase Elemental abundances in Molecular cloudS (GEMS) VI. A sulphur journey across star-forming regions: study of thioformaldehyde emission
Creators: name: Esplugues, G.
name: Fuente, A.
name: Navarro-Almaida, D.
name: Rodriguez-Baras, M.
name: Majumdar, L.
name: Caselli, P.
name: Wakelam, V.
name: Roueff, E.
name: Bachiller, R.
name: Spezzano, S.
name: Riviere-Marichalar, P.
name: Martin-Domenech, R.
name: Caro, G. M. Muñoz
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: In the context of the IRAM 30m Large Program GEMS, we present a study of thioformaldehyde in several starless cores located in star-forming filaments of Taurus, Perseus, and Orion. We investigate the influence of the environmental conditions on the abundances of these molecules in the cores, and the effect of time evolution. We have modelled the observed lines of H2CS, HDCS, and D2CS using the radiative transfer code RADEX. We have also used the chemical code Nautilus to model the evolution of these species depending on the characteristics of the starless cores. We derive column densities and abundances for all the cores. We also derive deuterium fractionation ratios, Dfrac, to determine and compare the evolutionary stage between different parts of each star-forming region. Our results indicate that the north region of the B213 filament in Taurus is more evolved than the south, while the north-eastern part of Perseus presents an earlier evolutionary stage than the south-western zone. Model results also show that Dfrac decreases with the cosmic-ray ionisation rate, while it increases with density and with the degree of sulphur depletion. In particular, we only reproduce the observations when the initial sulphur abundance in the starless cores is at least one order of magnitude lower than the solar elemental sulphur abundance. The progressive increase in HDCS/H2CS and D2CS/H2CS with time makes these ratios powerful tools for deriving the chemical evolutionary stage of starless cores. However, they cannot be used to derive the temperature of these regions, since both ratios present a similar evolution at two different temperature ranges (7-11 K and 15-19 K). Regarding chemistry, (deuterated) thioformaldehyde is mainly formed through gas-phase reactions (double-replacement and neutral-neutral displacement reactions), while surface chemistry plays an important role as a destruction mechanism.
description: 31 pages, 26 figures
HistoLens identifies distinct patterns of podocyte injury in HIV-transgenic mice
Creators: name: Border, Samuel
name: Tomaszewski, John
name: Ginley, Brandon
name: Teruhiko Yoshida
name: Kopp, Jeffrey
name: Rosenberg, Avi
name: Pinaki Sarder
Publisher: name: F1000 Research Limited
Year: 2022

description: HIV associated nephropathy (HIVAN) is a major cause of End-Stage Renal Disease (ESRD), particularly for individuals of African descent. Histological features of HIVAN include mesangial cell proliferation, collapsing focal segmental glomerulosclerosis, and podocyte injury. Podocytes, a terminally differentiated epithelial cell typically found on outer surfaces of glomerular capillaries, fill a critical role in the filtration of proteins from the bloodstream. Assessing the extent of podocyte injury across several whole slide images (WSIs) is an exceptionally difficult task, even for experienced pathologists. Computational approaches to automate diagnosis have been developed with competitive performance with human observers. However, they are largely unable to provide meaningful interpretation of the factors that contribute to their decisions. HistoLens, a graphical user interface (GUI), enables pathologists to extract a large number of quantitative image features from annotated WSIs relating to specific biological sub-compartments. Using HistoLens, we were able to identify key underlying factors associated with podocytes in Tg26-transgenic (HIVAN) compared with Wild-Type (WT) mice including podocyte thickness, distribution, and color heterogeneity. Using these features, we were able to design a glomerular classification model that achieved an accuracy of 73% using only a subset of podocyte features.