bluuebunny/crossref_metadata_2025_split huggingface dataset:
Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization
Authors: Morris C. Paul , Eldesouki Raghda E. , Sachithanandham Jaiprasath , Fall Amary , Norton Julie M. , Abdullah Omar , Gallagher Nicholas , Li Maggie , Pekosz Andrew , Klein Eili Y. , Mostafa Heba H. 
Published: September 2022

AbstractBackgroundThe variant of concern, Omicron, has become the sole circulating SARS-CoV-2 variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021- January 2022. In this study, we compare the clinical outcomes in patients infected with different Omicron subvariants and compare the relative viral loads, and recovery of infectious virus from upper respiratory specimens.MethodsSARS-CoV-2 positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared to infections with BA.1. Cycle threshold values (Ct) and the recovery of infectious virus on VeroTMPRSS2 cell line from clinical specimens were compared.ResultsThe BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and COVID-19 related hospitalizations at the Johns Hopkins system. After a peak in January cases fell in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct when compared to other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values less than 20.ConclusionsOmicron subvariants continue to associate with a relatively high positivity and admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves.FundingCenters for Disease Control and Prevention contract 75D30121C11061, NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, and The Modeling Infectious Diseases in Healthcare Network (MInD) under awards U01CK000589.
Associations between everyday activities and arterial spin labelling-derived cerebral blood flow: A longitudinal study in community-dwelling elderly volunteers
Authors: Sanders Anne-Marthe , Richard Geneviève , Kolskår Knut , Ulrichsen Kristine M. , Alnæs Dag , Beck Dani , Dørum Erlend S. , Engvig Andreas , Lund Martina Jonette , Nordhøy Wibeke , Pedersen Mads L. , Rokicki Jaroslav , Nordvik Jan Egil , Westlye Lars T. 
Published: September 2022

AbstractBackgroundCerebral blood flow (CBF) is critical for brain metabolism and overall function. Age-related changes in CBF have been associated with cognitive deficits and increased risk of neurocognitive disorders and vascular events such as stroke. Exercise is considered among the protective factors for age-related brain and cognitive impairment, but how different lifestyle characteristics, such as low or moderate-to-vigorous physical activity or frequency of everyday activities, relate to cross-sectional and longitudinal measures of CBF has not been established.ObjectiveWith the main aim of identifying potential targets for interventions, our objective was to examine associations between cortical and subcortical CBF and frequency of diverse everyday activities in healthy community-dwelling adults aged 65-89 years, and assess to which degree activity level at baseline is associated with longitudinal changes in CBF across a one-to-two years interval.MethodOne hundred nineteen (N = 119) adults underwent brain magnetic resonance imaging (MRI), neurocognitive, physical, and activity assessment at baseline. CBF was obtained using pseudo-continuous arterial spin labelling (ASL) MRI. Frequency of everyday activities were measured using Frenchay Activities index, while minutes of low and moderate-to-vigorous intensity physical activity were measured using a StepWatch Activity Monitor. Eighty-six participants completed a follow-up ASL MRI, on average 506 (SD = 113) days after the baseline scan.ResultsBayesian multilevel modelling revealed positive associations between baseline cortical and subcortical CBF and various everyday activities. Higher baseline accumbens, putamen and pallidum CBF was associated with more time spent on low intensity (> 0 steps/minute to < 100 steps/minute) physical activity, higher accumbens and caudate CBF with more moderate to vigorous intensity (≥ 100 steps/minute) physical activity, higher cerebral cortical CBF with more participation in social activity, higher cortical and thalamic CBF with more reading, and higher baseline pallidum CBF with more actively pursuing hobbies. We did not find evidence for an association between baseline activity level and longitudinal changes in CBF.ConclusionThe identified associations between everyday activity measures and CBF provide new knowledge on malleable lifestyle factors that may indicate or contribute to healthy brain aging. In addition to the relevance for prioritizing targets for public health guidelines, our findings contribute to disclose parts of the intricate connection between brain metabolism and everyday activities in aging.
eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species
Authors: Yang Min , Qiu Bo , He Guo-You , Zhou Jian-Yuan , Yu Hao-Jie , Zhang Yu-Ying , Li Yan-Shang , Li Tai-Song , Guo Jin-Cheng , Li Xue-Cang , Xie Jian-Jun 
Published: September 2022

ABSTRACTThe role of extrachromosomal circular DNA (eccDNA) has been highlighted. More recently, eccDNA-chromosome interactions were identified, suggesting a potential role of eccDNA in transcriptional regulation. Several databases currently provide valuable resources for the study of eccDNAs. However, these databases are primarily focused on Human eccDNAs and do not provide analysis of eccDNA-chromosome interaction and eccDNA gene expression in different tissues. Herein, to further integrate available resources for eccDNA data across multiple species, we developed the eccDB database. The current version of eccDB has collected a total of 1,317,182 eccDNAs in 424 samples from four species (homo sapiens, mus musculus, saccharomyces cerevisiae, and arabidopsis thaliana). eccDB provides regulatory and epigenetic information on eccDNA, including typical enhancers, super-enhancers, transcription factors, DNA methylation positions, risk SNPs, expression quantitative trait locus, chromatin accessibility regions, and chromHMM states. In particular, eccDB provides eccDNAs intrachromosomal and interchromosomal interaction analysis to predict the transcriptional regulatory functions of eccDNA. Moreover, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of an eccDNA among different species. Overall, eccDB offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher the molecular regulatory mechanisms of eccDNA. eccDB is freely available at http://www.xiejjlab.bio/eccDB
Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes
Authors: Babajanyan Sanasar G. , Wolf Yuri I. , Khachatryan Andranik , Allahverdyan Armen , Lopez-Garcia Purificacion , Koonin Eugene V. 
Published: September 2022

AbstractThere are two fundamentally distinct but inextricably linked types of biological evolutionary units, reproducers and replicators. Reproducers are cells and organelles that reproduce via various forms of division and maintain the physical continuity of compartments and their content. Replicators are genetic elements (GE), including genomes of cellular organisms and various autonomous elements, that both cooperate with reproducers and rely on the latter for replication. All known cells and organisms comprise a union between replicators and reproducers. We explore a model in which cells emerged via symbiosis between primordial ‘metabolic’ reproducers (protocells) which evolved, on short time scales, via a primitive form of selection and random drift, and mutualist replicators. Mathematical modeling identifies the conditions, under which GE-carrying protocells can outcompete GE-less ones, taking into account that, from the earliest stages of evolution, replicators split into mutualists and parasites. Analysis of the model shows that, for the GE-containing protocells to win the competition and to be fixed in evolution, it is essential that the birth-death process of the GE is coordinated with the rate of protocell division. At the early stages of evolution, random, high-variance cell division is advantageous compared to symmetrical division because the former provides for the emergence of protocells containing only mutualists, preventing takeover by parasites. These findings illuminate the likely order of key events on the evolutionary route from protocells to cells that involved the origin of genomes, symmetrical cell division and anti-parasite defense systems.SignificanceThe origin of life, which is equivalent to the origin of cells, is arguably the greatest enigma in biology. The remarkable complexity characteristic of even the simplest extant cells could only evolve from simpler, pre-biological entities. Reconstructing that pre-cellular stage of evolution is a hard challenge. We present an evolutionary scenario in which cells evolved via symbiosis between protocells that harbored protometabolic reaction networks, could divide and were subject to selection, but lacked genomes, and primordial genetic elements. Mathematical modeling reveals conditions for the survival of such symbionts and the origin of modern-type genomes, in particular, coordination of the rates of protocell division and replication of genetic elements as well as random division of protocells.
Patch repair protects cells from the small pore-forming toxin aerolysin
Authors: Thapa Roshan , Keyel Peter A. 
Published: September 2022

AbstractSmall pore-forming toxins in the aerolysin family lyse cells by damaging the membrane, but membrane repair responses used to resist them, if any, remain controversial. Four membrane repair mechanisms have been proposed: toxin removal by caveolar endocytosis, clogging by annexins, microvesicle shedding catalyzed by MEK, and patch repair. Which of these repair mechanisms aerolysin triggers is unknown. Furthermore, Ca2+flux triggered by aerolysin is controversial, yet membrane repair responses require Ca2+. Here, we determined Ca2+influx and repair mechanisms activated by aerolysin. In contrast to cholesterol-dependent cytolysins (CDCs), removal of extracellular Ca2+protected cells from aerolysin. Aerolysin triggered sustained Ca2+influx. Since aerolysin triggered Ca2+flux, we investigated Ca2+-dependent repair pathways. Caveolar endocytosis failed to protect cells from aerolysin or CDCs. MEK-dependent repair did not protect against aerolysin. Aerolysin triggered slower annexin A6 membrane recruitment compared to CDCs. In contrast to CDCs, expression of the patch repair protein dysferlin potently protected cells from aerolysin. We propose that aerolysin triggers a Ca2+-dependent death mechanism that obscures repair responses, and the primary repair mechanism used to resist aerolysin is patch repair. We conclude that different classes of bacterial toxins trigger distinct repair mechanisms.
Millennials and the gender wage gap: do millennial women face a glass ceiling?
Authors: García Gustavo A. , Gonzales-Miranda Diego René , Gallo Óscar , Roman Calderon Juan Pablo 
Published: September 2022

PurposeThis study aims to measure the gender wage gap among millennial workers in Colombia and determine if there is a marked wage difference between millennial women and men. Furthermore, this study analyzes whether millennial women face a glass ceiling, that is, whether there is a larger gender wage gap among workers earning relatively high wages.Design/methodology/approachThe study data included a sample of 2,144 millennial workers employed in 11 organizations located in the five main cities of Colombia. Oaxaca–Blinder econometric methods of wage decomposition were used to calculate both raw and adjusted gender wage gaps. The latter results in estimating the gender wage gap while controlling for observable characteristics related to individual, family, and labor. In addition, wage decompositions by education levels were carried out to approximate the extent of the glass ceiling among young workers.FindingsThe results show that millennial workers in Colombia face gender inequality in the labor market and that professional millennial women experience a distinct glass ceiling. The adjusted gender wage gap is 9.5%, and this gap increases with education level, increasing to nearly 14% among college-educated workers.Research limitations/implicationsThe empirical results are supported by a self-report survey of millennial workers. An important limitation is that the data include millennial workers employed in the formal sector and exclude the informal sector (activities not regulated or protected by the state), which represents an important part of the economy in developing countries.Originality/valueThis paper contributes to the empirical literature on gender wage inequality for younger workers. This paper is original in reviewing the gender pay gap in Colombia using a primary dataset. Most of the work in this area has been done in developed countries and this research adds to the findings that have had focused on those nations.
Why executive board membership in academic clubs helps students get interviews
Authors: Dadario Bernard , Sanner Bret 
Published: September 2022

PurposeThe paper aims to improve students' job placements, higher education institutions invest considerable resources and their students spend considerable time in academic clubs. Yet, quantitative findings on the effect of students' academic club involvement on job placements are mixed. This paper aims to help resolve ambiguity regarding the effect of academic clubs on job placements.Design/methodology/approachThe authors conducted two studies. The first developed an inductive theoretical model by interviewing recruiters and managers and extending status characteristics theory. The second study is an experiment that tested the first study's inductive model and increased the model's generalizability.FindingsThe results of both studies show that executive board membership, but not general membership, increases perceptions of applicants' emotional control and public speaking ability, and thereby increases applicants' chances of getting an interview.Practical implicationsAdministrators should consider shifting resources away from academic clubs that only benefit a few students and toward programs that help more students develop transferable skills. Students should prioritize joining clubs in which students think students can become executive board members. Academic clubs should require general members to have responsibilities that help members develop transferable skills. Industry may need to make more competitive offers to hire executive board members.Originality/valueThe two studies contribute to research on academic clubs by suggesting that the results of previous academic club membership studies are mixed, because only executive board members are more likely to get interviews. The results also highlight the importance of applying status characteristics theory to future academic club research.
The Socialocene: From Capitalocene to Transnational Waste Regimes
Authors: Gille Zsuzsa 
Published: September 2022

AbstractIn this article I will present a relational, and multiscalar, perspective on how state socialism interacted with and shaped the Capitalocene. I introduce a heuristic device, the term Socialocene, a transnational waste regime dominant through the Cold War‐era, that is, during what Will Steffen and colleagues call “the great acceleration”. When extending the concept of waste beyond contamination to include squandered resources, the Socialocene emerges as a transnational waste regime in which the modes of waste generation of Western capitalism and central planning are mutually determining. One key relation is the effect of communism on mass consumption and throwaway society in the West; the other is the use of centrally planned economies as “cheap nature”, in Jason Moore’s sense. I will demonstrate the latter through several empirical examples and, in greater detail, through a case study of an Austrian chemical company outsourcing a toxic‐waste‐intensive product to a Hungarian chemical company in the 1960s.
Genetic spectrum of Kallmann syndrome: Single‐center experience and systematic review
Authors: Patil Virendra A. , Lila Anurag Ranjan , Shah Nalini , Arya Sneha , Sarathi Vijaya , Shah Ravikumar , Jadhav Swati S. , Memon Saba Samad , Karlekar Manjiri , Bandgar Tushar 
Published: September 2022

AbstractObjectiveTo study phenotype‐genotype data of Asian−Indian Kallmann syndrome (KS) from our center and systematically review the studies analyzing multiple congenital hypogonadotropic hypogonadism (CHH) genes in KS cohorts using next‐generation sequencing.Design, Patients, MeasurementFive hundred twenty‐two KS probands (our center n = 78, published studies n = 444) were included in this systematic review. Molecular diagnosis was considered if the likely pathogenic/pathogenic variant in known CHH gene/s was reported in the appropriate allelic state. Varsome prediction tool (following American College of Medical Genetics standards) was used to analyze the variants.ResultFor our center, the molecular diagnosis was seen in 20.5% of probands and was seen more often with severe than partial reproductive phenotype (28.3% vs. 4%, p = .0013). Our center data adds eight novel variants. The molecular diagnosis was seen in 31% as per the systematic review and analysis. It ranged from 16.6% to 72.2% at different centers. The affected genes were FGFR1 (9.8%), ANOS1 (7.5%), PROKR2 (6.1%), CHD7 (5.4%), oligogenic (2.1%), and others <1% each (FGF8, SOX10, PROK2, SEMA3A, IL17RD, and GNRHR). FGFR1 and ANOS1 were the commonly affected genes globally, whereas PROKR2 was commonest in studies from China and CHD7 from Japan, South Korea and Poland.Conclusion(s)This systematic review highlights that the genetic yield is 31% in KS probands, with distinct regional variations. The association of severe reproductive phenotype with the higher genetic yield needs further validation.
Establishing UK research priorities in smell and taste disorders: A James Lind alliance priority setting partnership
Authors: Philpott Carl M. , Espehana Andreas , Garden Mairenn , Ta Ngan , Gadi Nishita , Kumaresan Kala , Maru Devina , Stafford Lorenzo D. , Bleasdale Nina , Boak Duncan 
Published: September 2022

AbstractObjectivesTo determine the top 10 research priorities in Smell and Taste Disorders (SATD).DesignAfter steering group was established, an electronic survey was disseminated to determine the list of questions. After removing out‐of‐scope responses, the remainder were consolidated to create summary questions. A literature search was conducted to remove already answered questions. A second survey was used to determine the top questions that formed the subject of final debate at a workshop attended by clinicians and patients to determine the top 10 priorities.SettingA James Lind Alliance Priority Setting Partnership (JLAPSP) was established by FifthSense to identify the top 10 research questions in SATDs in the United Kingdom.ParticipantAll stakeholders in SATDs (patients, healthcare professionals, family, carers, researchers).Main outcome measuresFinal 10 research priorities.ResultsThe 665 respondents to the initial survey provided 1698 research questions. Thirteen were out‐of‐scope and removed; remaining 1685 were then consolidated to form 147 summary questions. Following literature search and discussion with the steering group, 37 questions remained for the second survey, which 235 people responded. The top ten priorities agreed upon in the workshop covered themes of improved understanding of pathophysiologlogy, improving health services, and managing long‐term effects of smell/taste disorders. The most important research question agreed was “How can we further our understanding of the mechanism of disease in the nerve pathways that affect smell and taste disorders, including where parosmia and phantosmia exist.”ConclusionWe report the top 10 research priorities in smell and taste disorders. These priorities will now empower researchers to secure research funding and provide the basis of the FifthSense research hub.
Cytology‐histology correlation of cervical Papanicolaou smears and biopsies performed at a single institution compared to those performed at different institutions
Authors: Nikolaus Yanina , Mujumdar Vaidehi , Padgaonkar Pooja , Buchanan Edward , Goldberg Allison 
Published: September 2022

AbstractObjectiveCytology‐histology correlation (CHC) is the gold standard of quality assurance in cytology laboratories to ensure appropriate patient treatment, and as an educational tool for cytology laboratory personnel. If cervical Pap smears (CPs) and cervical biopsies (CBs) are performed at different institutions, these benefits may be lost.MethodsAll CBs performed at our institution from 1 January 2019 to 31 December 2019 with adequate CPs performed in the 6 months prior to the CB were included in this retrospective review. We compared the CHC for CPs and CBs performed at a single institution to the CHC for CPs and CBs performed at different institutions, with a focus on the proportion of overcalls on CPs, as those are the most challenging discrepant CHC to manage clinically. We used the American Society of Cytology guidelines for our discrepancy assessment grid. A Chi‐squared test was used to compare the proportions of the populations. The P‐value was set at < 0.05.ResultsOf the 305 CBs in our study population, 69 had a CP performed at our institution and 236 had a CP performed at an outside institution. The CHC for CBs and CPs performed at a single institution showed statistically significantly less disagreement than the CHC for those performed at different institutions (P < 0.05). Further, CBs and CPs performed at a single institution had statistically significantly fewer overcalls than CBs and CPs performed at different institutions (P < 0.05).ConclusionThis study further supports the use of CHC, and in light of our findings we recommend that a patient's CPs and CBs are performed at the same institution. If performing a CP and CB at the same institution is not feasible, a prospective consultation review of the CP by the institution performing the CB should be strongly considered. Further study, including an evaluation of the reason for the discrepancy in discordant cases may better elucidate the reasons for better CHC agreement when CP and CB are performed at the same institution.