bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the origin of an insular hybrid butterfly lineage
Authors: Boman Jesper , Nolen Zachary J. , Backström Niclas 
Published: October 2024

AbstractA new species can form through hybridization between species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process has been difficult to obtain. Recent access to whole-genome sequencing data have made it more feasible to detect hybrid lineages. Here we report the discovery of a European hybrid butterfly lineage, a finding that can be considered surprising given the intense and long-term study of European butterflies. The lineage we describe is mainly inhabiting an island in the Baltic Sea and was previously designated as a subspecies (horkei) of one of the parental species (Aricia artaxerxes). By analysing whole-genome resequencing data, we determine thathorkeioriginated by hybridization between the non-sister speciesA. artaxerxesandA. agestis. This hybridization event occurred approximately 54,000 years ago, predating the last glaciation of the current distribution range.Horkeimust therefore have persisted long enough to be able to colonize its current range, despite that this area lies between the current distributions of the parental species. The hybrid origin, the maintenance of genomic integrity across times of dramatic climate change and the expression of a combination of parental traits suggest thathorkeicould be in the process of hybrid speciation.
Cannabidiol (CBD) potentiates physiological and behavioral markers of hypothalamic-pituitary-adrenal (HPA) axis responsivity in female and male mice
Authors: Jenkins Bryan W. , Spina Hayley A. , Nicholson Kate , Newman Amy E. M. , Khokhar Jibran Y. 
Published: October 2024

ABSTRACTRationaleClinical literature indicates there may be a therapeutic use of cannabidiol (CBD) for stress-related disorders. Preclinical literature remains conflicted regarding the underlying neurobehavioral mechanisms, reporting mixed effects of CBD (increased, decreased, or no effect) on anxiety- and fear-related behaviors. Preclinical data demonstrated that CBD modulates hypothalamus-pituitary-adrenal (HPA) axis gene expression; it is unknown whether CBD changes HPA axis responsivity and how this relates to altered behavior.ObjectivesWe aimed to evaluate whether acute or chronic CBD administration would alter physiological and behavioral measures of HPA axis responsivity in male or female mice.MethodsC57BL/6 mice of both sexes were injected with vehicle or CBD (30 mg/kg, i.p.) daily for 26 days. Plasma corticosterone (CORT) levels were evaluated following dexamethasone suppression and adrenocorticotropin hormone stimulation tests after acute and chronic CBD exposure. After chronic CBD, mice were tested for anxiety-like behavior using an elevated plus maze (EPM) and associative fear learning and memory using a trace fear conditioning (FC) protocol.ResultsCompared to vehicle, CBD induced a state of HPA axis hyperactivation, an effect which was significant in males; it also normalized anxiety-like behavior in female mice classified as having HPA axis hypofunction and primed all female mice for enhanced conditioned responding. Significant sex differences were also detected: females had greater plasma CORT levels and HPA axis responsivity than males, exhibited less EPM anxiety-like behavior, and were more responsive during FC.ConclusionsCBD potentiated physiological and behavioral markers of HPA axis function and normalized anxiety-like behavior in a sex-specific manner. This observation has implications for cannabinoid-based drug development targeting individuals with stress-related disorders involving HPA axis hypofunction pathology.
Evaluation of post-acute COVID-19 health outcomes (ECHOES) in England: The development of national surveillance system for long- term health outcomes following COVID-19
Authors: Allen Hester , Hassell Katie , Rawlinson Christopher , Pullen Owen , Campbell Colin , Jödicke Annika M. , Català Martí , Uribe Albert Prats , Dabrera Gavin , Prieto-Alhambra Daniel , Campos-Matos Ines 
Published: October 2024

AbstractIntroductionElectronic health records can be used to understand the diverse presentation of post-acute and long-term health outcomes following COVID-19 infection. In England, the UK Health Security Agency in collaboration with the University of Oxford have created the ECHOES dataset to monitor how an initial SARS-CoV-2 infection episode is associated with changes in the risk of health outcomes that are recorded in routinely collected health data.MethodsThe ECHOES dataset is as a national level dataset combining national level surveillance, administrative, and healthcare data. Entity resolution and data linkages methods are used to create a cohort of individuals who have tested positive and negative for SARS-CoV-2 in England throughout the COVID-19 pandemic, alongside information on a range of health outcomes including diagnosed clinical conditions and mortality, and risk factor information.ResultsThe dataset contains comprehensive COVID-19 testing data and demographic, socio economic and health related information for 44 million individuals, who tested for SARS-CoV-2 between March 2020 and April 2022, representing 15,720,286 individuals who tested positive and 42,351,016 individuals who tested negative.DiscussionWith the application of epidemiological and statistical methods, this dataset allows a range of clinical outcomes to be investigated, including pre-specified health conditions and mortality. Furthermore, understanding of potential determinants of health outcomes can be gained, including pre-existing health conditions, acute disease characteristics, SARS-CoV-2 vaccination status and genomic variant.
Incident COVID-19 infections before Omicron in the U.S
Authors: Lobay Rachel , Srivastava Ajitesh , Tibshirani Ryan J. , McDonald Daniel J. 
Published: October 2024

AbstractThe timing and magnitude of COVID-19 infections are of interest to the public and to public health, but these are challenging to ascertain due to the volume of undetected asymptomatic cases and reporting delays. Accurate estimates of COVID-19 infections based on finalized data can improve understanding of the pandemic and provide more meaningful quantification of disease patterns and burden. Therefore, we retrospectively estimate daily incident infections for each U.S. state prior to Omicron. To this end, reported COVID-19 cases are deconvolved to their date of infection onset using delay distributions estimated from the CDC line list. Then, a novel serology-driven model is used to scale these deconvolved cases to account for the unreported infections. The resulting infections incorporate variant-specific incubation periods, reinfections, and waning antigenic immunity. They clearly demonstrate that the reported cases fail to reflect the full extent of disease burden in all states. Most notably, infections were severely underreported during the Delta wave, with an estimated reporting rate as low as 6.3% in New Jersey, 7.3% in Maryland, and 8.4% in Nevada. Moreover, in 44 states, fewer than 1/3 of infections appear as cases reports. Therefore, while reported cases offer a convenient proxy of disease burden, they fail to capture the full extent of infections, and can severely underestimate the true disease burden. This retrospective analysis also estimates other important quantities for every state, including variant-specific deconvolved cases, time-varying case ascertainment ratios, and infection-hospitalization ratios.
Functional and pangenomic exploration of Roc two-component regulatory systems identifies novel players acrossPseudomonasspecies
Authors: Simon Victor , Trouillon Julian , Attrée Ina , Elsen Sylvie 
Published: October 2024

ABSTRACTThe opportunistic pathogenPseudomonas aeruginosacounts on a large collection of two-component regulatory systems (TCSs) to sense and adapt to changing environments. Among them, the Roc (Regulationofcup) system is a one-of-a-kind network of branched TCSs, composed of two histidine kinases (HKs) (RocS1 and RocS2) interacting with three response regulators (RRs) (RocA1, RocR and RocA2), which regulate virulence, antibiotic resistance and biofilm formation. Based on extensive work on the Roc system, previous data suggested the existence of other key regulators yet to be discovered. In this work, we identified PA4080, renamed RocA3, as a fourth RR that is activated by RocS1 and RocS2 and that positively controls the expression of thecupBoperon. Comparative genomic analysis of the locus identified a gene -rocR3- adjacent torocA3in a subpopulation of strains which encodes a protein with structural and functional similarity to the c-di-GMP phosphodiesterase RocR. Furthermore, we identified a fourth branch of the Roc system consisting of the PA2583 HK, renamed RocS4, and of the Hpt protein HptA. Using a bacterial two-hybrid system, we showed that RocS4 interacts with HptA, which in turn interacts with RocA1, RocA2 and RocR3. Finally, we mapped the pangenomic RRs repertoire establishing a comprehensive view of the plasticity of such regulators among clades of the species. Overall, our work provides a comprehensive inter-species definition of the Roc system, nearly doubling the number of proteins known to be involved in this interconnected network of TCSs controlling pathogenicity inPseudomonasspecies.GRAPHICAL ABSTRACTABBREVIATED SUMMARYRoc system account for a particularly interconnected yet incomplete network of two-component regulatory system involved in the virulence ofPseudomonas aeruginosa. Our work identified the missing RocA3 regulator and propose new players of the system delineating their conservation between the clade of the species.
miR-210 locus deletion disrupts cellular homeostasis; an integrated genetic study
Authors: Preda Mihai Bogdan , Rusu-Nastase Evelyn Gabriela , Neculachi Carmen Alexandra , Zhong Xiaoling , Voellenkle Christine , Mazure Nathalie M. , Balacescu Ovidiu , Ivan Cristina , Zheng Xiao-Wei , Gherghiceanu Mihaela , Lebrigand Kevin , Simionescu Maya , Martelli Fabio , Mari Bernard , Catrina Sergiu-Bogdan , Burlacu Alexandrina , Ivan Mircea 
Published: October 2024

AbstractMiR-210 is widely recognized as the quintessential hypoxia-responsive miRNA and thought to fine-tune various facets of cellular homeostasis. We hereby present an integrative appraisal of phenotypic and molecular repercussions of disrupting the corresponding locus in human and mouse cells using multiple genetic strategies. Briefly, MIR210 deletion led to decreased cellular fitness and suboptimal responses to several stress types. Transcriptomic comparisons using different profiling platforms, performed independently by members of this collaboration, revealed consistent deregulation of neighboring genes, in locus-disrupted cells. Interestingly, the anticipated enrichment in miR-210 targets failed to materialize in unbiased analyses. Our results point to the biological significance of unrecognized regulatory elements that overlap miRNA genes and should serve as note of caution for studies based for genetic disruption of such loci.
Detection and electron microscopic study of thick cross-striated linear fibrils in mammalian cell nuclei
Authors: Mosevitsky Mark I. 
Published: October 2024

SummaryUsing an electron microscope, cross-striated fibrils with an axial repeat of about 65 nm were detected in the cell nuclei of rat and calf tissues. The nuclei were purified and processed using a “complete medium” (CM) simulating the composition of salts of the intranuclear medium. These fibrils are not the filaments of the nuclear matrix described in the literature. In particular, they are thicker and not branched. The axial repeat in these fibrils is similar to that in extracellular collagen fibrils. Therefore, in this work, the main efforts were aimed at demonstrating the nuclear origin of the observed fibrils. Their presence in the material of nuclei destroyed by ultrasound, their contact with isolated nucleoli and their presence in residual nuclei are shown on samples prepared for electron microscopy in the form of “whole mounts”. The sites of attachment of chromatin and of nuclear matrix network to thick cross-striated fibrils were detected. As axial components of condensed chromosomes, thick cross-striated fibrils are preserved during mitosis. Probably, their contacts with chromatin and with elements of nuclear matrix network are also preserved providing reproduction of the internal structure of the nuclei in daughter cells. It is logical to assume that the cross-striated fibrils perform important functions attributed to the nuclear matrix.HighlightsThick cross-striated fibrils with an axial repeat of about 65 nm are present in mammalian cell nuclei.Areas of dense contact between thick cross-striated fibrils and chromatin are observed.Nucleoli are attached to thick cross-striated fibrils.Nuclear matrix network is tightly adherent to thick cross-striated fibrils.Thick cross-striated fibrils can be retained in mitosis as axial elements of chromosomes.
Greater recalled pain and movement-evoked pain are associated with longer 400-meter walk and repeat stair climb time: the Study of Muscle, Mobility and Aging
Authors: Mau Theresa , Barnes Haley N. , Simon Corey B. , Hetherington-Rauth Megan , Bauer Scott R. , Strotmeyer Elsa S. , Lane Nancy E. , Rowbotham Michael C. , Weaver Ashley A. , Blackwell Terri L. , Cai Yurun , Glynn Nancy W. , Goodpaster Bret H. , Cummings Steven R. , Newman Anne B. , Cawthon Peggy M. , Kritchevsky Stephen B. 
Published: October 2024

AbstractBackgroundMusculoskeletal pain frequently accompanies the development of mobility disability and falls in old age. To better understand this, we aimed to quantify the impact of different pain measures—recalled pain and movement-evoked pain—on 400-meter walk and stair climb time in older adults participating in the Study of Muscle, Mobility and Aging (SOMMA).MethodsIn SOMMA (N=879, age=76.3 ± 5.0 years, 59% women, 84% Non-Hispanic White), participants completed usual pace 400m walk (avg=6.6 ± 1.2 min.) and repeat stair climb tests (avg=26.6 ± 7.2 sec.). Assessments of recalled pain included the Brief Pain Inventory short form (BPI-sf), total lower body pain (lower back, hips, knees, feet/ankles), stiffness (hip or knee), and Neuropathy Total Symptom Score (NTSS-6). Movement-evoked pain was assessed separately before and after the 400m walk and repeat stair climb tasks. Multivariable linear regression modeled the associations of pain with time to complete the tasks, reported as β[95%CI] expressed per SD increment of pain measure or β[95%CI] per pain categories, adjusted for age, sex, race, ethnicity, body mass index, prescription medications, and depressive symptoms.ResultsGreater degree of any pain measure was associated with longer physical performance time, though intercorrelations between recalled pain measures varied (r=0.13-0.57,p<0.05 for all). For each SD increment in lower body pain, participants had longer walk time (by 10.5 sec [6.1, 14.8]) and stair climb (by 0.6 sec [0.1, 1.1]). Compared to participants with no change in pain upon movement, walk time was longer in those with more pain upon movement (19.5 sec [10.3, 28.7]) (p<0.001) but not those with less pain upon movement; stair climb showed similar patterns.ConclusionsRecalled and movement-evoked pain measures were weakly correlated with one another but similarly associated with time to complete 400m walk and stair climb tests. Different pain assessments capture different functional domains of pain but have similar associations with physical performance in these older adults.
Distinct patterns of bioscience doctoral publication disparities by gender and race/ethnicity
Authors: Leap Katie , Payne Gregory S. , Sinsheimer Janet S. , Azurdia Diana E. 
Published: October 2024

AbstractThe ability to address the lack of diversity in the Science, Technology, Engineering and Math workforce depends on inclusive and equitable training of doctoral students to succeed in the profession. An important metric used to assess equitable training in bioscience doctoral programs is the number of publications that result from a student’s research. The purpose of this study was to investigate whether there are demographic differences in publication rates among all students in a cohort of bioscience Ph.D. programs at the University of California Los Angeles who graduated between 2011 and 2019. Using institutional data and publication database queries, we determined the number of doctoral publications parsed by authorship position, and the timing of the first publication for each student. The resulting dataset was then analyzed for the relationships between publication categories and student gender, race/ethnicity, and citizenship status. We find that female students published significantly fewer total and co-author papers compared to male students, but had the same number of first-author publications. In contrast, students from underrepresented racial/ethnic groups had fewer first-author papers compared to students from well-represented groups, but similar numbers of total and co-author publications. Publication of the first doctoral paper occurred later for female versus male, and underrepresented versus well-represented students. These results provide evidence for distinct patterns of doctoral publication disparities by gender and race/ethnicity, offering insights into a key metric of bioscience student success and informing potential strategies to achieve equitable outcomes in bioscience doctoral education.
Prevalence of subpatentPlasmodium falciparuminfections in regions with varying transmission intensities and implications for malaria elimination in Mainland Tanzania
Authors: Seth Misago D. , Popkin-Hall Zachary R. , Madebe Rashid A. , Budodo Rule , Bakari Catherine , Lyimo Beatus M. , Giesbrecht David , Moshi Ramadhani , Mbwambo Ruth B. , Francis Filbert , Pereus Dativa , Mbata Doris , Challe Daniel P. , Mandai Salehe S. , Chacha Gervas A. , Kisambale Angelina J. , Mbwambo Daniel , Aaron Sijenunu , Lusasi Abdallah , Lazaro Samwel , Mandara Celine I. , Bailey Jeffrey A. , Juliano Jonathan J. , Gutman Julie R. , Ishengoma Deus S. 
Published: October 2024

AbstractBackgroundSubpatentPlasmodium falciparuminfections, defined as infections with parasitaemia density below the detection limit of routine malaria diagnostic tests, contribute to infectious reservoirs, sustain transmission, and cause the failure of elimination strategies in target areas. This study assessed the prevalence of and factors associated with subpatentP. falciparuminfections in 14 regions of Mainland Tanzania with varying endemicity.MethodsThe study used samples randomly selected from RDT-negative dried blood spots (DBS) (n = 2,685/10,121) collected in 2021 at 100 health facilities across 10 regions of Mainland Tanzania, and four communities in four additional regions. The regions were selected from four transmission strata; high (five regions), moderate (three), low (three), and very low (three regions). DNA was extracted by Tween-Chelex method, and thePf18SrRNA gene was amplified by quantitative polymerase chain reaction (qPCR). Logistic regression analysis was used to assess the associations between age groups, sex, fever status, and transmission strata with of subpatent infections status, while linear regression analysis was used to assess the association between these factors and subpatent parasite density.ResultsOf the selected samples, 525/2,685 (19.6%) were positive by qPCR forP. falciparum, and the positivity rates varied across different regions (range: 4.8 to 39.6%). Under-fives (aOR: 1.4, 95% CI 1.04-1.88; p<0.05) from health facilities had higher odds of subpatent infections compared to other groups, while those from community surveys (aOR: 0.33, 95% CI 0.15-0.72; p = 0.005) had lower odds. Participants from very low transmission stratum had significantly lower odds of subpatent infection compared to those from high transmission straum (aOR=0.53, 95% CI=0.37-0.78; p < 0.01). The log-transformed median parasite density (interquartile range) was 6.9 (5.8 - 8.5) parasites/µL, with significantly higher parasitaemia in the low transmission stratum compared to very low (11.4 vs 7.0 parasites/µL, p<0.001).ConclusionEven in very low transmission settings, the prevalence of subpatent infections was 13%, and in low transmission settings it was even higher at 29.4%, suggesting a substantial reservoir which is likely to be missed by routine malaria case management strategies. Thus, control and elimination programmes may benefit from adoption of more sensitive detection methods to ensure that a higher proportion of subpatent infections are detected.
Statistical Relationship Between Wastewater Data and Case Notifications for COVID-19 Surveillance in the United States, 2020-2023: A Bayesian Hierarchical Model
Authors: Haraguchi Masahiko , Klaassen Fayette , Cohen Ted , Salomon Joshua A. , Menzies Nicolas A. 
Published: October 2024

AbstractDuring the COVID-19 pandemic a number of jurisdictions in the United States began to regularly report levels of SARS-CoV-2 in wastewater for use as a proxy for SARS-CoV-2 incidence. Despite the promise of this approach for improving situational awareness, the degree to which viral levels in wastewater track with other outcome data has varied, and better evidence is needed to understand the situations in which wastewater surveillance tracks closely with traditional surveillance data. In this study, we quantified the relationship between wastewater data and traditional case-based surveillance data for multiple jurisdictions. To do so, we collated data on wastewater SARS-CoV-2 RNA levels and COVID-19 case reports from July 2020 to March 2023, and employed Bayesian hierarchical regression modeling to estimate the statistical relationship between wastewater data and reported cases, allowing for variation in this relationship across counties. We compared different model structural approaches and assessed how the strength of the estimated relationships varied between settings and over time. These analyses revealed a strong positive relationship between wastewater data and COVID-19 cases for the majority of locations, with a median correlation coefficient between observed and predicted cases of 0.904 (interquartile range 0.823 – 0.943). Across locations, the COVID-19 case rate associated with a given level of wastewater SARS-CoV-2 RNA concentration declined over the study period. Counties with higher population size and of higher levels of urbanicity had stronger concordance between wastewater data and COVID-19 cases. Ideally, use of wastewater data for decision-making should be based on an understanding of their local historical performance.