bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracking the path of predator recognition in a predator-naive population of the pond snail
Authors: Batabyal Anuradha , Lukowiak Ken 
Published: December 2022

Abstract
Organisms evolve adaptive strategies to adjust to rapidly changing environmental stressors. Predation pressure is one of the strongest selective forces and organisms respond to predatory threats via innate and learned responses. We utilized a natural, experimental set-up, where two lakes Stoney and Margo in Canada containing natural populations of the prey Lymnaea stagnalis differed in the presence and absence of an invasive, predatory Northern crayfish, Faxonius virilis. We exploited the contrast in the predation backgrounds of the snail populations from the two lakes to test, 1) predator recognition in predator-experienced snails is innate, (2) predator-naive snails learn to detect a novel invasive predator, and 3) learning about a novel predator gets transmitted to the successive generations. We quantified predator fear memory formation using a higher-order learning paradigm called configural learning. We found that 1) predator recognition in predator-experienced snails is innate, 2) predator-naive snails learned to recognize the novel predator even after a brief exposure to predator cues highlighting the role of learning in combating invasive predators and the critical time-window during development that accounts for predator recognition, and 3) the learning and predator detection mechanism in predator-naive snails are not transmitted to successive generations. The population variation observed in the predator-detection mechanism may be due to the past and current experience of predators in one population over the other. We find an interesting study system to address how fear learning occurs and prospective future directions to understand the mechanism of innate fear recognition from a learned fear recognition.
Systematic analysis of alternative splicing in time course data using Spycone
Authors: Lio Chit Tong , Grabert Gordon , Louadi Zakaria , Fenn Amit , Baumbach Jan , Kacprowski Tim , List Markus , Tsoy Olga 
Published: December 2022

Abstract

Motivation
During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing.

Results
Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection.

Availability and implementation
The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https://github.com/yollct/spycone and the documentation at https://spycone.readthedocs.io/en/latest/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Variability in Fetal Fraction Estimation: Comparing Fetal Fractions Reported by Noninvasive Prenatal Testing Providers Globally
Authors: Becking Ellis C , Linthorst Jasper , Patton Simon , Gutowska-Ding Weronika , Goodall Rebecca , Khawaja Farrah , Morgan Fiona , Deans Zandra , Chitty Lyn S , Bekker Mireille N , Scheffer Peter G , Sistermans Erik A 
Published: December 2022

AbstractBackgroundFetal fraction (FF) measurement is considered important for reliable noninvasive prenatal testing (NIPT). Using minimal FF threshold as a quality parameter is under debate. We evaluated the variability in reported FFs of individual samples between providers and laboratories and within a single laboratory.MethodsGenomic quality assessment and European Molecular Genetics Quality Network provide joint proficiency testing for NIPT. We compared reported FFs across all laboratories and stratified according to test methodologies. A single sample was sequenced repeatedly and FF estimated by 2 bioinformatics methods: Veriseq2 and SeqFF. Finally, we compared FFs by Veriseq and SeqFF in 87 351 NIPT samples.ResultsFor each proficiency test sample we observed a large variability in reported FF, SDs and CVs ranging from 1.7 to 3.6 and 17.0 to 35.8, respectively. FF measurements reported by single nucleotide polymorphism-based methods had smaller SDs (0.5 to 2.4) compared to whole genome sequencing-based methods (1.8 to 2.9). In the internal quality assessment, SDs were similar between SeqFF (SD 1.0) and Veriseq v2 (SD 0.9), but mean FF by Veriseq v2 was higher compared to SeqFF (9.0 vs 6.4, P 0.001). In patient samples, reported FFs were on average 1.12-points higher in Veriseq than in SeqFF (P 0.001).ConclusionsCurrent methods do not allow for a reliable and consistent FF estimation. Our data show estimated FF should be regarded as a laboratory-specific range, rather than a precise number. Applying strict universal minimum thresholds might result in unnecessary test failures and should be used with caution.
Communicative labor resistance practices: organizing digital news media unions and precarious work
Authors: Salamon Errol 
Published: December 2022

Abstract
Unionization among newsworkers has increased in the U.S. since 2015. This article develops a relational theoretical framework to examine communicative labor resistance practices. It is grounded in critical organizational communication, social movement studies, sociology of work, and labor studies, responding to how newsworkers’ union resistance has been undertheorized in extant journalism and media studies research. It argues that communicative labor resistance practices should be based on three propositions: a dialectical process and continual cycle of organizing unions’ resistance and exploitative precarious work; the relationship among heterogenous alternative digital communication labor resistance practices; and a relational approach to digitally-mediated communicative material conditions and discursive forms of resistance rhetoric in social movement genres of organizational communication that mutually co-produce and constitute unions’ resistance practices and organizational self-structuring. This framework has implications for understanding precarious work, class, professional identity, and journalism’s democratic role in society, and for doing labor resistance-oriented communication research.
Sex differences in the etiology and burden of heart failure across country income level: analysis of 204 countries and territories 1990–2019
Authors: Wei Sunny , Miranda J Jamie , Mamas Mamas A , Zühlke Liesl J , Kontopantelis Evan , Thabane Lehana , Van Spall Harriette G C 
Published: December 2022

Abstract

Background
Heart failure (HF) is a global epidemic.

Objective
To assess global sex differences in HF epidemiology across country income levels.

Methods and results
Using Global Burden of Disease (GBD) data from 204 countries and territories 1990–2019, we assessed sex differences in HF prevalence, etiology, morbidity, and temporal trends across country sociodemographic index or gross national income. We derived age-standardized rates. Of 56.2 million (95% uncertainty interval [UI] 46.4–67.8 million) people with HF in 2019, 50.3% were females and 69.2% lived in low- and middle-income countries; age-standardized prevalence was greater in males and in high-income countries. Ischaemic and hypertensive heart disease were top causes of HF in males and females, respectively. There were 5.1 million (95% UI 3.3–7.3 million) years lived with disability, distributed equally between sexes. Between 1990 and 2019, there was an increase in HF cases, but a decrease in age-standardized rates per 100 000 in males (9.1%, from 864.2 to 785.7) and females (5.8%, from 686.0 to 646.1). High-income regions experienced a 16.0% decrease in age-standardized rates (from 877.5 to 736.8), while low-income regions experienced a 3.9% increase (from 612.1 to 636.0), largely consistent across sexes. There was a temporal increase in age-standardized HF from hypertensive, rheumatic, and calcific aortic valvular heart disease, and a decrease from ischaemic heart disease, with regional and sex differences.

Conclusion
Age-standardized HF rates have decreased over time, with larger decreases in males than females; and with large decreases in high-income and small increases in low-income regions. Sex and regional differences offer targets for intervention.
Same-day discharge after transvenous lead extraction: feasibility and outcomes
Authors: Atteya Gourg , Alston Michael , Sweat Austin , Saleh Moussa , Beldner Stuart , Mitra Raman , Willner Jonathan , John Roy M , Epstein Laurence M 
Published: December 2022

AbstractAimsSame-day discharge (SDD) is safe for patients undergoing electrophysiology procedures. There is no existing data regarding SDD for patients undergoing transvenous lead extraction (TLE). We report our experience with SDD for patients undergoing TLE.Methods and resultsThe study group included patients undergoing TLE between February 2020 and July 2021 without an infectious indication. A modified SDD protocol for device implants/ablations was applied to TLE patients. Patient characteristics, extraction details, outcomes, and complications were reviewed. Of 239 patients undergoing TLE, 210 were excluded (94 infections and 116 did not meet SDD criteria). Of the remaining 29 patients, seven stayed due to patient preference and 22 were discharged home the same day. The SDD group had an average age of 65.9 ± 12 (47–84), 41% female, and LVEF of 52.2 ± 18% (10–80). The indication for TLE was malfunction (20), upgrade (4), advisory lead (2), and magnetic resonance imaging compatibility (1). Extractions included four implantable cardioverter-defibrillators (ICDs), 17 pacemakers (PPM), and one cardiac resynchronization therapy (CRT)-P system. The leads were 9.6 years (1.5–21.7) old, and 1.8 leads were removed per patient (1–3); the lead extraction difficulty (LED) score was 11.6 ± 7. Twenty underwent cardiovascular implantable electronic device (CIED) re-implantation (2 ICD, 3 CRT-D, 13 PPM, and 2 CRT-P). For CIED re-implants, patients sent a remote transmission the next day, and all patients received a next-day call. There were no procedure or device-related issues, morbidities, or mortalities in the 30 days after discharge.ConclusionSame-day discharge after TLE for non-infectious aetiologies is safe and feasible in a select group of patients with early procedure completion who meet strict SDD criteria.
LMAS: evaluating metagenomic short de novo assembly methods through defined communities
Authors: Mendes Catarina Inês , Vila-Cerqueira Pedro , Motro Yair , Moran-Gilad Jacob , Carriço João André , Ramirez Mário 
Published: December 2022

Abstract

Background
The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community.

Findings
To better compare de novo assemblers for metagenomic analysis, LMAS (Last Metagenomic Assembler Standing) was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities. Overall, in our test datasets, k-mer De Bruijn graph assemblers outperformed the alternative approaches but came with a greater computational cost. Furthermore, assemblers branded as metagenomic specific did not consistently outperform other genomic assemblers in metagenomic samples. Some assemblers still in use, such as ABySS, MetaHipmer2, minia, and VelvetOptimiser, perform relatively poorly and should be used with caution when assembling complex samples. Meaningful strain resolution at the single-nucleotide polymorphism level was not achieved, even by the best assemblers tested.

Conclusions
The choice of a de novo assembler depends on the computational resources available, the replicon of interest, and the major goals of the analysis. No single assembler appeared an ideal choice for short-read metagenomic prokaryote replicon assembly, each showing specific strengths. The choice of metagenomic assembler should be guided by user requirements and characteristics of the sample of interest, and LMAS provides an interactive evaluation platform for this purpose. LMAS is open source, and the workflow and its documentation are available at https://github.com/B-UMMI/LMAS and https://lmas.readthedocs.io/, respectively.
Evaluation of resazurin microplate method for rapid detection of vancomycin and linezolid resistance in Enterococcus faecalis and Enterococcus faecium clinical isolates
Authors: Zeng Weiliang , Han Yijia , Zheng Xiangkuo , Yao Zhuocheng , Xu Chunquan , Zhang Xiaotuan , Tang Miran , Shen Mo , Zhou Tieli 
Published: December 2022

Abstract

Background
Vancomycin and linezolid resistance among enterococci is an increasing problem due to a lack of alternative antibiotics. Early identification of vancomycin-resistant and linezolid-resistant strains can help prevent the spread of resistance to these antibiotics. Hence, early, rapid and accurate detection of vancomycin and linezolid resistance is critical.

Objectives
The resazurin microplate method (RMM) was developed for detecting vancomycin and linezolid susceptibility among Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium) clinical isolates, and its performance was further evaluated.

Methods
A total of 209 non-duplicate clinical isolates and three strains from the faeces of domestic animals, including 142 E. faecalis (71 linezolid non-susceptible and 71 linezolid susceptible) and 70 E. faecium (23 vancomycin non-susceptible, 23 vancomycin susceptible, 12 linezolid non-susceptible and 12 linezolid susceptible), were tested using RMM.

Results
The susceptibility of E. faecium to vancomycin was detected within 5 h, with high susceptibility (23/23) and specificity (23/23). The susceptibility of E. faecalis and E. faecium to linezolid was detected within 4 h, with specificities of 98.59% and 100% and susceptibilities of 94.37% and 58.33% for E. faecalis and E. faecium, respectively.

Conclusions
RMM had a good positive predictive value for the detection of vancomycin-non-susceptible E. faecium and linezolid-non-susceptible E. faecalis. It thus has the potential to become an alternative method for the rapid screening of these resistant pathogens in clinical practice.
The dangers of non-randomized, observational studies: experience from the COVID-19 epidemic
Authors: Hill Andrew , Mirchandani Manya 
Published: December 2022

Abstract
In regulatory evaluations, high-quality randomized controlled trials (RCTs) are considered the gold standard for assessing the efficacy of medical interventions. However, during the COVID-19 pandemic, the urgent need for treatment options led to regulatory approvals being made based on evidence from non-randomized, observational studies. In this study we contrast results from observational studies and RCTs of six drugs to treat COVID-19 infection. Across a range of studies evaluating hydroxychloroquine, remdesivir, ivermectin, aspirin, molnupiravir and tenofovir for COVID-19, there was statistically significant evidence of benefit from non-randomized observational studies, which was then not seen in RCTs. We propose that all observational studies need to be labelled as ‘non-randomized’ in the title. This should indicate that they are not as reliable for evaluating the efficacy of a drug and should not be used independently for regulatory approval decisions.
Detection of Cadmium and Lead in Kidney Stones. Associations with Patient Demographics, Stone Composition, and Smoking
Authors: Day Patrick L , Wermers Michelle , Pazdernik Vanessa , Jannetto Paul J , Bornhorst Joshua A 
Published: December 2022

Abstract

Background
Kidney stones are a highly prevalent disease worldwide. Additionally, both environmental and occupational exposure to Pb and Cd continue to be prevalent globally and can result in renal toxicity. The objective of this study was to examine the potential presence of Pb and Cd in kidney stones, and to assess for correlation with demographic factors including smoking, gender, age, and kidney stone matrix composition.

Methods
Patient kidney stones (n = 96) were analyzed using Fourier transform infrared spectroscopy to identify the stone constituents. Cd and Pb concentrations (µg/g) were determined by inductively coupled plasma mass spectrometry. Cd and Pb concentrations were correlated using bivariable and multivariable statistical analysis with demographic factors (age, gender, smoking status), and kidney stone composition.

Results
Kidney stone Cd (median 0.092 µg/g, range 0.014 to 2.46) and Pb concentrations (median 0.95 µg/g, range 0.060 to 15.4) were moderately correlated (r = 0.56, P &lt; 0.0001). Cd concentrations were positively associated with patient history of smoking, patient age, and calcium oxalate monohydrate levels while negatively associated with struvite and uric acid/uric acid dihydrate. Pb concentrations were positively associated with females and apatite levels while negatively associated with uric acid/uric acid dihydrate. After holding constant other stone type composition levels, smoking status, and age, both Pb and Cd were positively associated with apatite and negatively associated with uric acid/uric acid dihydrate, struvite, and calcium carbonate.

Conclusions
Cd and Pb kidney stone concentrations are associated with specific kidney stone types. Cd and Pb kidney stone concentrations are both associated with smoking.
Promoting access to justice for victims of sexual violence in Vietnam
Authors: Phan Huong Thi Lan 
Published: December 2022

Abstract
Violence against women and girls remains a critical issue in Viet Nam. Women have suffered physical or sexual violence from their husbands throughout their lifetime, but this (especially sexual violence) has not been handled effectively for many reasons including legal gaps, culture, social norms, as well as the capacity of justice system. Being a member of CEDAW from 1982 and with the aim of achieving sustainable development goals, the Vietnamese government needs to eliminate all forms of gender-based violence and enable victims to access justice to claim their rights and legitimate interests. It is essential to identify the current issues around access to justice for victims of sexual abuse and find effective ways for Vietnam to handle these issues.
Developmental thyroid hormone action on pro-opiomelanocortin-expressing cells programs hypothalamic BMPR1A depletion and brown fat activation
Authors: Wu Zhaofei , Martinez M Elena , DeMambro Victoria , Francois Marie , Hernandez Arturo 
Published: December 2022

AbstractThyroid hormone excess secondary to global type 3 deiodinase (DIO3) deficiency leads to increased locomotor activity and reduced adiposity, but also to concurrent alterations in parameters of the leptin–melanocortin system that would predict obesity. To distinguish the underlying contributions to the energy balance phenotype of DIO3 deficiency, we generated mice with thyroid hormone excess targeted to pro-opiomelanocortin (POMC)-expressing cells via cell-specific DIO3 inactivation. These mice exhibit a male-specific phenotype of reduced hypothalamic Pomc expression, hyperphagia, and increased activity in brown adipose tissue, with adiposity and serum levels of leptin and thyroid hormones remained normal. These male mice also manifest a marked and widespread hypothalamic reduction in the expression of bone morphogenetic receptor 1a (BMPR1A), which has been shown to cause similar phenotypes when inactivated in POMC-expressing cells. Our results indicate that developmental overexposure to thyroid hormone in POMC-expressing cells programs energy balance mechanisms in a sexually dimorphic manner by suppressing adult hypothalamic BMPR1A expression.
Three-dimensional electron tomography and recent expansion of its applications in materials science
Authors: Baba Norio , Hata Satoshi , Saito Hikaru , Kaneko Kenji 
Published: December 2022

AbstractElectron tomography (ET) is a powerful tool for elucidating the properties and functionalities of materials. The innovative development of aberration-corrected electron microscopy in the early 21st century and the remarkable progress in the development of detectors, equipment and devices related to ET have resulted in substantial improvements in resolution. However, not only advances in hardware but also remarkable developments in reconstruction algorithms and related three-dimensional (3D) analysis methods have contributed to the resolution improvements. ET has its own problems, including the missing-wedge problem due to the limited tilt-angle range and the need to acquire numerous specimen-tilt images, the latter of which is time-consuming and can potentially damage the specimen. This review paper aims to (i) describe the established basic theories and definitions regarding 3D resolution of ET and practical 3D resolution measurement methods, (ii) discuss various reconstruction algorithms that effectively overcome the aforementioned problems and (iii) describe recent progress in the core of ET applications in materials science with respect to atomic ET, analytical ET and in-situ ET. The aforementioned ET problems have been addressed with each method developed in each field of application. Notably, in terms of aim (ii), recently developed reconstruction algorithms can reduce the number of projection images (specimen-tilt images) needed to attain a certain resolution without violating the Nyquist criterion. This approach is interpreted as a novel non-linear sampling theorem.
Generating a sentiment dictionary in R and dictionary-based sentiment analysis in Turkish texts
Authors: Alkan Bilal Barış , Karakus Leyla , Direkci Bekir 
Published: December 2022

Abstract
Dictionary-based sentiment analysis is a text mining application that allows comments about the sentimental states of the text or documents through the sentimental poles of the words. In recent years, it has become quite popular in many disciplines such as trade, health, education, usage for various purposes. It is applied in many languages depending on the sentiment dictionaries, which are the main component, are created. Unlike inflectional languages such as English and German, the number of dictionary-based sentiment analysis studies using the Turkish language, which is a sequencing language, is very limited. When the literature of sentiment analysis is examined separately in terms of the material used; it is seen that the number of studies on long-format literary texts, which have been functioning as sentiment transmission throughout history, is also quite limited. In the light of these knowledges, a comprehensive method of creating a domain-specific sentiment dictionary and applying dictionary-based sentiment analysis on Turkish texts is proposed in the R software.
Problematising diversity: The change that international lawyers (do not) want for international courts
Authors: de Carvalho Juliana Santos , Uriburu Justina 
Published: December 2022

Abstract
Scholars working on international courts and tribunals (ICTs) have recently seized the agenda of the diversity of the international judiciary and international institutions more broadly. Focusing, above all, on the lack of women in the different international benches around the world, they have criticised and proposed reforms to the composition of ICTs. This paper argues that the burgeoning literature on the diversity in ICTs expresses a particular politics of inclusion for the composition of the international judiciary. We begin by explaining the importance of looking into knowledge production in international legal scholarship as a site of (re)production of the field’s boundaries and situating the literature under study within the broader universe of the scholarship on ICTs. We then lay out this paper’s main contribution: a reconstruction and critical analysis of the normative commitments of the politics of inclusion underlying the literature on diversity in ICTs.