bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgeon Factors and Their Association With Operating Room Turnover Time
Authors: Pandit Kshitij , Wang Luke , Rosenberg Joel , Goldhaber Nicole , Buckley Jill C. , Ramamoorthy Sonia , Mekeel Kristin L. , Bagrodia Aditya 
Published: September 2024

AbstractIntroductionOperating room (OR) turnover time (TT), defined as the interval between the completion of one surgery and the start of the next, is a critical measure of OR efficiency impacting healthcare costs, patient outcomes, and surgical staff well-being. Previous research has identified various contributors to TT, such as surgical team dynamics, OR preparation, and interdisciplinary workflows. However, the influence of surgeon-specific factors like gender, administrative roles, and experience on TT remains underexplored. This study aims to address this gap by examining how these individual surgeon characteristics impact OR efficiency.MethodsWe conducted a retrospective study at the UC San Diego School of Medicine, a tertiary academic medical center. We analysed 12,820 surgical case entries from January 2022 to July 2023, sourced from the electronic health record system. Surgeons were categorized by gender, ethnicity, years of experience, training at UCSD, academic rank, and administrative roles. We utilized Mann-Whitney U test for binary variables and Kruskal-Wallis H test for variables with more than two categories. Multivariable linear regression was applied, adjusting for multiple comparisons using Holm correction. A p-value of less than 0.05 was considered statistically significant. All data analysis was performed using IBM SPSS version 29.ResultsOur analysis of 12,820 surgical cases revealed that surgeons in administrative roles and those with over ten years of experience demonstrated significantly shorter turnover times (TT). Specifically, administrators demonstrated a TT of 27 minutes, compared to 35 minutes for non-administrators (p<0.001) (Table 2). Surgeons with more than ten years of experience had a TT of 31 minutes, versus 37 minutes for those with less experience (p<0.001). Multivariable linear regression confirmed these associations, with significant reductions in TT linked to administrative roles (beta: - 7.2; 95% confidence interval (CI): -8.2 to -6.2, p<0.001) and surgeon experience (beta: -4.7, 95% CI: -5.9 to -3.5, p< 0.001).ConclusionWe recommend efforts focusing on building a standardized environment for surgeons regardless of their background. This could lead to not only an equitable. OR culture but also an overall increase in the institution efficiency and patient outcomes.
Border control strategies for reducing importation risk of Clade Ib Mpox
Authors: Jin Shihui , Guan Tong , Endo Akira , Gan Gregory , Janhavi A. , Hu Gang , Ejima Keisuke , Lim Jue Tao , Dickens Borame L 
Published: September 2024

AbstractBackgroundThe Clade Ib monkeypox virus (MPXV), newly identified in the ongoing 2024 mpox outbreak, can be more transmissible through non-sexual routes compared to the previous Clade IIb strain. With imported cases sporadically reported globally, concerns have emerged about the potential of widespread transmission in the general community after importation events. Border control measures, such as screening and quarantining of arriving travellers, may help mitigate this risk and prevent localized outbreaks in the event of global spread.MethodsWe proposed nine border control strategies and evaluated their effectiveness in reducing importation risk using 10,000 microsimulations of individual infection profiles and PCR testing results under scenarios with varying disease prevalence levels (0.01%, 0.05%, and 0.1%) in the country of origin.ResultsThe proposed border-control measures would reduce missed cases by 40.1% (39.1%–41.0%), 49.8% (48.8%–50.8%), and 58.1% (57.1%–59.0%) for predeparture, on-arrival, and both tests, respectively. Replacing the on-arrival test with a seven-day quarantine and post-quarantine testing would lower the count to 21.8% (20.9%–22.6%). Quarantine-only strategies showed a linear increase in effectiveness against duration, reaching a 90.4% (89.8%–91.0%) reduction with a 28-day quarantine. Disparities in distributions of missed case counts across strategies would become more pronounced at higher prevalence levels, with stringent approaches like quarantining followed by post-quarantine screening and 28-day quarantine keeping counts below two per 10,000 travellers, even at 0.1% prevalence.ConclusionsWhen disease prevalence in the country of origin is low (0.01%), less restrictive approaches such as single on-arrival testing or a 14-day quarantine can maintain very low imported case counts of one or below. At higher prevalences, seven-day quarantining followed by post-quarantine testing, or 28-day quarantining is required to maintain similar effects. Decision makers will face balancing importation risk management and the negative impacts of such interventions to maintain safe international travel.
Learning to read transforms phonological into phonographic representations: Evidence from a Mismatch Negativity study
Authors: Pattamadilok Chotiga , Wang Shuai , Bolger Deidre , Dubarry Anne-Sophie 
Published: September 2024

AbstractLearning to read changes the nature of speech representation. One possible change consists in transforming phonological representations into phonographic ones. However, evidence for such transformation remains surprisingly scarce. Here, we used a novel word learning paradigm to address this issue. During a learning phase, participants were exposed to unknown words in both spoken and written forms. Following this phase, the impact of spelling knowledge on spoken input perception was assessed at two time points through an unattended oddball paradigm, while the Mismatch Negativity component was measured by high density EEG. Immediately after the learning phase, no influence of spelling knowledge on the perception of the spoken input was found. Interestingly, one week later, this influence emerged, making similar sounding words with different spellings more distinct than similar sounding words that also share the same spelling. Our finding provides novel neurophysiological evidence of an integration of phonological and orthographic representations that occurs once newly acquired knowledge has been consolidated. These novel phonographic representations may characterize how known words are stored in literates’ mental lexicon.
Development of a competition assay to assess thein vitrofitness of dengue virus serotypes using an optimized serotype-specific qRT-PCR
Authors: Griffon Anne-Fleur , Rault Loeïza , Simon-Lorière Etienne , Dupont-Rouzeyrol Myrielle , Inizan Catherine 
Published: September 2024

AbstractBackgroundComparing thein vitrofitness of dengue virus (DENV) isolates is a pivotal approach to assess the contribution of DENV strains’ replicative fitness to epidemiological contexts, including serotype replacements. Competition assays are the gold standard to compare thein vitroreplicative fitness of viral strains. Implementing competition assays between DENV serotypes requires an experimental setup and an appropriate read-out to quantify the viral progeny of strains belonging to different serotypes.ResultsIn the current study, we optimized an existing serotyping qRT-PCR by adapting primer/probe design and multiplexing the serotype-specific qRT-PCR reactions, allowing to accurately detect and quantify all four DENV serotypes. The qRT-PCR was specific, had a limit of detection of at least 5.08×101, 5.16×101, 7.14×101and 1.36 x101genome copies/µL, an efficiency of 1.993, 1.975, 1.902, 1.898 and a linearity (R²) of 0.99975, 0.99975, 0.9985, 0.99965 for DENV-1, -2, -3 and -4 respectively. Challenge of this multiplex serotype-specific qRT-PCR on mixes of viral supernatants containing known concentrations of strains from two serotypes evidenced an accurate quantification of the amount of genome copies of each serotype. We next developed anin vitroassay to compare the replicative fitness of two DENV serotypes in the human hepatic cell line HuH7: quantification of the viral progeny of each serotype in the inoculum and the supernatant using the serotype-specific multiplex qRT-PCR unveiled an enrichment of the supernatant in DENV-1 genome copies, uncovering the enhanced replicative fitness of this DENV-1 isolate.ConclusionsThis optimized qRT-PCR combined to a relevant cellular model allowed to accurately quantify the viral progeny of two DENV strains belonging to two different serotypes in a competition assay, allowing to determine which strain had a replicative advantage. This reliable experimental setup is adaptable to the comparative study of the replicative fitness of any DENV serotypes.
Sheltered load in fungal mating-type chromosomes revealed by fitness experiments
Authors: Guyot Lou , Chahine Elizabeth , De Filippo Elsa , Lalanne Christophe , Brun Sylvain , Hartmann Fanny E. , Giraud Tatiana 
Published: September 2024

AbstractSex chromosomes and mating-type chromosomes can carry large regions with suppressed recombination. As a result of a lower efficacy of selection, recessive deleterious mutations are expected to accumulate in these non-recombining regions. Multiple genomic analyses have indirectly inferred the presence of deleterious mutations in sex and mating-type chromosomes, but direct experimental evidence remains scarce. Here, we performed fitness assays in fungi with megabase-large and young non-recombining regions around the mating-type locus, using three Sordariales species, to test whether heterokaryons (diploid-like, heterozygous at the mating-type locus) exhibited a fitness advantage over homokaryons (haploid-like, with a single mating-type allele), in terms of spore germination dynamics or mycelium growth speed, under different conditions of light and temperature. We found a faster growth of heterokaryons compared to one of the homokaryons forPodospora anserinaat 18°C and forSchizothecium tetrasporumandSchizothecium tritetrasporumat 22°C under light. These findings suggest the presence of a sheltered load, i.e. recessive deleterious mutations at the heterozygous state in or near non-recombining regions. Genomic analyses indeed confirmed that strains in these selfing species are highly homozygous beyond the regions around the mating-type locus. We also checked that the difference in growth rates did not result from different numbers or densities of nuclei between homokaryons and heterokaryons. Leveraging the experimental assets of fungi, allowing cultivating separately haploid-like and diploid-like life stages, our experiments provided one of the rare direct experimental evidence of sheltered load around mating-compatibility loci, which is crucial for our understanding of sex-related chromosome evolution.
Ancient DNA Clarifies the Identity and Geographic Origin of the holotype of the genusCtenomys
Authors: Maestri Renan , Gonçalves Gislene Lopes , Nicolas-Colin Violaine , Bryjova Anna , Fornel Rodrigo , Coissac Eric , Taberlet Pierre , Moreira Gilson Rudinei Pires , de Freitas Thales Renato Ochotorena 
Published: September 2024

ABSTRACTCtenomysBlainville 1826 ranks among the top ten most diverse mammal genera in terms of species richness. However, the taxonomic history ofCtenomys brasiliensisBlainville,1826, the corresponding type species, has long been obscured by a dearth of information regarding the collection data of the type material, compounded by an elusive geographic origin. Here, employing ancient DNA methodology, we sequenced the complete mitogenome of the remaining type specimen and conducted an extensive historical investigation to correlate originally described locality names with present-day locales in South America. Our analysis unequivocally confirms that the type specimen corresponds to the species currently designated asCtenomys minutusNehring, 1887. This resolution lays to rest a century-old debate surrounding the provenance of the type specimen, rejecting prior hypotheses that placed its collection site in southeastern Brazil or Uruguay. Instead, our evidence suggests it was likely obtained from a third location in southernmost Brazil. Previous analyses overlooked this new location due to confusion surrounding geographic nomenclature and labeling errors, issues rectified by our combined mitogenomic and historical approach. Furthermore, quantitative morphological analyses boost our findings, demonstrating a closer affinity betweenC. brasiliensisandC. minutuswithin the same species group. Accordingly, we validateC. brasiliensisand proposeC. minutusas its junior synonym. Our study underscores the importance of robust DNA analyses in confirming the identity and geographic origins of type specimens, especially forCtenomysspecies with similar phenotypes, and specimens collected centuries ago.
Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers
Authors: Bravo Juan I. , Zhang Lucia , Benayoun Bérénice A. 
Published: September 2024

ABSTRACTLINE-1 (L1) and Alu are two families of transposable elements (TEs) occupying ∼17% and ∼11% of the human genome, respectively. Though only a small fraction of L1 copies is able to produce the machinery to mobilize autonomously, Alu and degenerate L1s can hijack their functional machinery and mobilizein trans. The expression and subsequent mobilization of L1 and Alu can exert pathological effects on their hosts. These features have made them promising focus subjects in studies of aging where they can become active. However, mechanisms regulating TE activity are incompletely characterized, especially in diverse human populations. To address these gaps, we leveraged genomic data from the 1000 Genomes Project to carry out a trans-ethnic GWAS of L1/Alu insertion singletons. These are rare, recently acquired insertions observed in only one person and which we used as proxies for variation in L1/Alu insertion numbers. Our approach identified SNVs in genomic regions containing genes with potential and known TE regulatory properties, and it enriched for SNVs in regions containing known regulators of L1 expression. Moreover, we identified reference TE copies and structural variants that associated with L1/Alu singletons, suggesting their potential contribution to TE insertion number variation. Finally, a transcriptional analysis of lymphoblastoid cells highlighted potential cell cycle alterations in a subset of samples harboring L1/Alu singletons. Collectively, our results suggest that known TE regulatory mechanisms may be active in diverse human populations, expand the list of loci implicated in TE insertion number variability, and reinforce links between TEs and disease.
The High Arctic is dominated by uncharacterized, genetically highly diverse bacteriophages
Authors: Lemieux Audrée , Poulain Alexandre J. , Aris-Brosou Stéphane 
Published: September 2024

AbstractWhile the Earth’s virosphere is estimated to be in the range of 1031viral particles, the vast majority of its diversity has yet to be discovered. In recent years, metagenomics has rapidly allowed the identification of viruses, from microenvironments to extreme environments like the High Arctic. However, the High Arctic virome is largely composed of viral sequences that have few, if any, matches to classified viruses in existing databases. Here, to bypass limitations posed by similarity-based strategies, we resorted to a metagenomics approach that placed viral genes found in Lake Hazen, a High Arctic lake, in a phylogenetic context with known viruses. We show that while High Arctic viruses clustered with known bacteriophages, they have undergone unique evolutionary processes characterized by high evolutionary rates, making them distinct from and more diverse than known viruses. A better understanding of how viruses from extreme polar conditions adapt and evolve could help us gain insights on the viral response to climate change and other environmental stressors.
The transcription factor Traffic jam orchestrates the somatic piRNA pathway inDrosophilaovaries
Authors: Alizada Azad , Martins Aline , Mouniée Nolwenn , Rodriguez Suarez Julia V. , Bertin Benjamin , Gueguen Nathalie , Mirouse Vincent , Papameletiou Anna-Maria , Rivera Austin J. , Lau Nelson C. , Akkouche Abdou , Maupetit-Mehouas Stéphanie , Hannon Gregory J. , Nicholson Benjamin Czech , Brasset Emilie 
Published: September 2024

AbstractThe PIWI-interacting RNA (piRNA) pathway is essential for transposable element (TE) silencing in animal gonads. While the transcriptional regulation of piRNA pathway components in germ cells has been documented in mice and flies, their control in somatic cells ofDrosophilaovaries remains unresolved. Here, we demonstrate that Traffic jam (Tj), theDrosophilaorthologue of large Maf transcription factors in mammals, is a master regulator of the somatic piRNA pathway. Tj binds to regulatory regions of somatic piRNA factors and the major piRNA clusterflamenco, which carries a Tj-bound enhancer downstream of its promoter. Depletion of Tj in somatic follicle cells causes downregulation of piRNA factors, loss offlamexpression and de-repression ofgypsy-family TEs. We propose that the arms race between the host and TEs led to the co-evolution of promoters in piRNA pathway genes as well as TE regulatory regions that both rely on a shared transcription factor.Highlights- Traffic jam (Tj) acts as a master regulator of the somatic piRNA pathway inDrosophila.- Tj regulates a network of piRNA pathway genes, mirroring the gene-regulatory mechanism of A-MYB in the mouse testis and Ovo in fly ovaries.-Cis-regulatory elements with Tj motifs are present at the promoters of somatic piRNA pathway genes.- The expression of theflamencopiRNA cluster is directly controlled by Tj.
Cancer Interception During Treatment: Using Growth Kinetics to Create a Continuous Variable for Assessing Disease Response
Authors: Zhou Mengxi , Fojo Tito , Schwartz Larry , Bates Susan E. , Blagoev Krastan B. 
Published: September 2024

SUMMARYBackgroundWe applied 11 mathematical models of tumor growth to clinical trial data available from public and private sources. We have previously described the remarkable capacity for a simple biexponential model of tumor growth to fit thousands of datasets, and to correlate with overall survival. The goal of this study was to extend our analysis to additional tumor types and to evaluate whether alternate growth models could describe the time course of disease burden in the small subset of patients in whom the biexponential model failed.MethodsFor this analysis, we obtained data for tumor burden from 17,140 patients with six different tumor types. Imaging data and serum levels of tumor markers were available for 3,346 and 13,794 patients, respectively. Data from patients were first analyzed using the biexponential model to determine rates of tumor growth (g) and regression (d); for those whose data could not be described by this model, fit of their data was assessed using seven alternative models. The model that minimized the Akaike Information Criterion was selected as the best fit. Using the model that best fit an individual patient’s data, we estimated the rates of growth (g) and regression (d) of disease burden over time. The rates of tumor growth (g) were examined for association with a traditional endpoint (overall survival).FindingsFor each model, the number of patient datasets that fit the model were obtained. As we have previously reported, data from most patients fit a simple model of exponential growth and exponential regression (86%). Data from another 7% of patients fit an alternative model, including 3% fitting to a model of constant or linear regression and exponential growth of tumor on the surface and 3% fitting to model of exponential decay on tumor surface with asymmetric growth. As previously reported, we found that growth rate correlates well with overall survival, remarkably even when data from various histologies are considered together. For patients with multiple timepoints of tumor measurement, the growth rate could often be estimated even during the phase when only net regression of tumor quantity could be discerned.InterpretationThe validation of a simple mathematical model across different cancers and its application to existing clinical data allowed estimation of the rate of growth of a treatment resistant subpopulation of cancer cells. The quantification of available clinical data using the growth rate of tumors in individual patients and its strong correlation with overall survival makes the growth rate an excellent marker of the efficacy of therapy specific to the individual patient.
Exploring the Phaeosphere: characterizing the microbiomes ofPhaeocystis antarcticacolonies from the coastal Southern Ocean and laboratory culture
Authors: Brisbin Margaret Mars , Acord McCaela , Davitt Rachel , Bent Shavonna , Van Mooy Benjamin A.S. , Flaum Eliott , Norlin Andreas , Turner Jessica , Krinos Arianna , Alexander Harriet , Saito Mak 
Published: September 2024

AbstractInteractions between phytoplankton and bacteria play critical roles in shaping marine ecosystems. However, the intricate relationships within these communities—particularly in extreme and rapidly changing environments like the coastal Southern Ocean—remain poorly understood. Here, we apply targeted methods to directly characterize the microbiomes of individual colonies ofPhaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, for the first time. We show that colony microbiomes are consistent in distinct geographic locations at approximately the same time, but shift significantly after a year of laboratory culture. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated the microbiomes of all field-collected colonies, whereas Caulobacterales, Cellvibrionales, and Rhodobacterales dominated colony microbiomes after culturing. Notably, the most abundant genera in field-collected colony microbiomes, the psychrophilesParaglaciecolaandColwellia,were lost in culture. The shift in microbiome structure emphasizes the importance of field-based studies to capture the complexity of microbial interactions, especially for species from polar environments that are difficult to replicate in laboratory conditions. Furthermore, the relative abundances of bacterial taxa comprising the majority of field-collected colony microbiomes—e.g.,Paraglaciecola sp.(Alteromonadales) and Nitrincolaceae (Oceanospirillales)—were strongly associated withPhaeocystisabundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. This research provides valuable insights into the ecological significance of prokaryotic interactions with a key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.
EPOP Restricts PRC2.1 Targeting to Chromatin by Directly Modulating Enzyme Complex Dimerization
Authors: Gong Lihu , Liu Xiuli , Yang Xin , Yu Ze , Chen Siming , Xing Chao , Liu Xin 
Published: September 2024

ABSTRACTPolycomb repressive complex 2 (PRC2) mediates developmental gene repression as two classes of holocomplexes, PRC2.1 and PRC2.2. EPOP is an accessory subunit specific to PRC2.1, which also contains PCL proteins. Unlike other accessory subunits that collectively facilitate PRC2 targeting, EPOP was implicated in an enigmatic inhibitory role, together with its interactor Elongin BC. We report an unusual molecular mechanism whereby EPOP regulates PRC2.1 by directly modulating its oligomerization state. EPOP disrupts the PRC2.1 dimer and weakens its chromatin association, likely by disabling the avidity effect conferred by the dimeric complex. Congruently, an EPOP mutant specifically defective in PRC2 binding enhances genome-wide enrichments of MTF2 and H3K27me3 in mouse epiblast-like cells. Elongin BC is largely dispensable for the EPOP-mediated inhibition of PRC2.1. EPOP defines a distinct subclass of PRC2.1, which uniquely maintains an epigenetic program by preventing the over-repression of key gene regulators along the continuum of early differentiation.