bluuebunny/crossref_metadata_2025_split huggingface dataset:
Friends because of foes: synchronous movement within predator–prey domains
Authors: Prokopenko Christina M. , Ellington E. Hance , Robitaille Alec , Aubin Jaclyn A. , Balluffi-Fry Juliana , Laforge Michel , Webber Quinn M. R. , Zabihi-Seissan Sana , Vander Wal Eric 
Published: September 2024

For prey, movement synchrony represents a potent antipredator strategy. Prey, however, must balance the costs and benefits of using conspecifics to mediate risk. Thus, the emergent patterns of risk-driven sociality depend on variation in space and in the predators and prey themselves. We applied the concept of predator–prey habitat domain, the space in which animals acquire food resources, to test the conditions under which individuals synchronize their movements relative to predator and prey habitat domains. We tested the response of movement synchrony of prey to predator–prey domains in two populations of ungulates that vary in their gregariousness and predator community: (i) elk, which are preyed on by wolves; and (ii) caribou, which are preyed on by coyotes and black bears. Prey in both communities responded to cursorial predators by increasing synchrony during seasons of greater predation pressure. Elk moved more synchronously in the wolf habitat domain during winter and caribou moved more synchronously in the coyote habitat domains during spring. In the winter, caribou increased movement synchrony when coyote and caribou domains overlapped. By integrating habitat domains with movement ecology, we provide a compelling argument for social behaviours and collective movement as an antipredator response.
This article is part of the theme issue ‘The spatial–social interface: A theoretical and empirical integration’.
Designing a computer-assisted diagnosis system for cardiomegaly detection and radiology report generation
Authors: Zhu Tianhao , Xu Kexin , Son Wonchan , Linton-Reid Kristofer , Boubnovski-Martell Marc , Grech-Sollars Matt , Lain Antoine D. , Posma Joram M. 
Published: September 2024

AbstractChest X-ray (CXR) is a conventional diagnostic tool for cardiothoracic assessment, boasting a high degree of costeffectiveness and versatility. However, with an increasing number of scans to be evaluated by radiologists, they can suffer from fatigue which might impede diagnostic accuracy and slow down report generation. We describe a prototype computer-assisted diagnosis (CAD) pipeline employing computer vision (CV) and Natural Language Processing (NLP) trained on the publicly available MIMICCXR dataset. We perform image quality assessment, view labelling, segmentation-based cardiomegaly severity classification, and use the output of the severity classification for large language model-based report generation. Four certified radiologists assessed the output accuracy of the CAD pipeline. Across the dataset composed of 377,100 CXR images and 227,827 free-text radiology reports, our system identified 0.18% of cases with mixedsex mentions, 0.02% of poor quality images (F1=0.81), and 0.28% of wrongly labelled views (accuracy 99.4%), furthermore it assigned views for 4.18% of images which have unlabelled views. For binary cardiomegaly classification, we achieve state-of-the-art performance of 95.2% accuracy. The inter-radiologist agreement on evaluating the report’s semantics and correctness for radiologistMIMIC is 0.62 (strict agreement) and 0.85 (relaxed agreement) similar to the radiologist-CAD agreement of 0.55 (strict) and 0.93 (relaxed). Our work found and corrected several incorrect or missing metadata annotations for the MIMIC-CXR dataset, and the performance of our CAD system suggests performance on par with human radiologists. Future improvements revolve around improved text generation and the development of CV tools for other diseases.
Alpha-synuclein misfolding as a fluid biomarker for Parkinson’s disease and synucleinopathies measured with the iRS platform
Authors: Schuler Martin , Gerwert Grischa , Mann Marvin , Woitzik Nathalie , Langenhoff Lennart , Hubert Diana , Duman Deniz , Höveler Adrian , Galkowski Sandy , Simon Jonas , Denz Robin , Weber Sandrina , Kwon Eun-Hae , Wanka Robin , Kötting Carsten , Güldenhaupt Jörn , Beyer Léon , Tönges Lars , Mollenhauer Brit , Gerwert Klaus 
Published: September 2024

AbstractMisfolding and aggregation of alpha-synuclein (αSyn) plays a key role in the pathophysiology of Parkinson’s disease (PD). It induces cellular and axonal damage already in the early stages of the disease. Despite considerable advances in PD diagnostics by αSyn seed-amplification assays (SAAs), an early and differential diagnosis of PD still represents a major challenge. Here, we extended the immuno-infrared sensor (iRS) platform technology from Alzheimer’s disease (AD), in which β-amyloid misfolding was monitored as a fluid biomarker towards αSyn misfolding in PD. Using the iRS platform technology, we analyzed cerebrospinal fluid (CSF) from two independent cohorts, a discovery and a validation cohort comprising clinically diagnosed PD (n=57), atypical Parkinsonian disorders with αSyn pathology (multiple system atrophy (MSA), n= 5) or Tau pathology (corticobasal degeneration (CBD), n=5, progressive supranuclear palsy (PSP) n=9), and further disease controls (frontotemporal dementia (FTD) n=7 and other, n=51). In the discovery cohort, an AUC of 0.90, 95 %-CL 0.85 – 0.96 is obtained for the differentiation of PD/MSA vs. all controls, and in the validation cohort, an AUC of 0.86, 95 %-CL 0.80 - 0.93, respectively. In the combined dataset, the αSyn misfolding classifies PD/MSA from controls with an AUC of 0.90 (n=134, 95 %-CL 0.85 - 0.96). Using two threshold values instead of one identified people in the continuum between clearly unaffected (low misfolding group) and affected by PD/MSA (high misfolding group) with an intermediate area in between. The controls versus PD/MSA in the low vs. high misfolding group were classified with 97% sensitivity and 92% specificity.The spectral data showed misfolding in CSF from an α-helical/random-coil secondary structure of αSyn in controls to β-sheet enriched secondary structures in PD and MSA patients. In subgroups, the iRS platform implied a potential for stratifying patients with overlapping clinical symptoms. With high accuracy, the iRS αSyn misfolding platform provides a novel diagnostic tool using body fluids for differential, biological classification of the αSyn associated disorders PD and MSA. The iRS platform, indicating directly and fast all αSyn conformers, is complementary to the αSyn SAAs, which also uses αSyn misfolding as a fluid biomarker. However, monomers amplify competent misfolded conformers in SAA over time. The iRS platform opens new avenues for the stratification of PD by a body-fluid analysis and follow-ups in the continuum of healthy to clinically impaired individuals.
SARS-CoV-2 Mediated Inhibition Of Respiratory Syncytial Virus
Authors: Thornhill Elena M , Verhoeven David 
Published: September 2024

AbstractWith circulation of SARS-CoV-2, fears about coinfection with other respiratory viruses such as influenza and RSV were significant, but the opposite was observed. Distancing/barriers played a major role in reducing other viral co-infections, however, some infrequent co-infections still occurred. We investigated the relationship between SARS-CoV-2 and RSV during coinfection to understand how they might compete or synergize. We found only RSV’s replication was significantly reduced when coinfected with SARS-CoV-2. Investigation of the mechanism revealed that the SARS-CoV-2 protein Nsp1 disrupts the RSV M2-2 protein but not the upstream M2-1 protein on the same biscistronic mRNA transcript. The impact of Nsp1 on M2-2 was not dependent on M2-2 being the second ORF in a bicistronic mRNA transcript, but likely from prevention of ribosomal termination-reinitiation necessary for M2-2 production. Additional viral ORFs from influenza A, influenza B, or Sendai virus dependent on the same or other ribosomal initiation mechanisms were tested and we found only influenza B M/M2 which likely uses a similar method as M2-2 was disrupted. Various M2-2 constructs, with/without the proposed site of ribosomal termination-reinitiating, co-transfected with Nsp1 and were in agreement that disruption to M2-2 expression occurs if the site of re-initiation was present upstream. These data not only suggest Sars-CoV-2 can outcompete RSV through suppression of M2, but may also point to potential ways to interfere with RSV by targeted therapies.
Musical training does not enhance neural sound encoding at early stages of the auditory system: A large-scale multisite investigation
Authors: Whiteford Kelly L. , Baltzell Lucas S. , Chiu Matt , Cooper John K. , Faucher Stefanie , Goh Pui Yii , Hagedorn Anna , Irsik Vanessa C. , Irvine Audra , Lim Sung-Joo , Mesik Juraj , Mesquita Bruno , Oakes Breanna , Rajappa Neha , Roverud Elin , Schrlau Amy E. , Van Hedger Stephen C. , Bharadwaj Hari M. , Johnsrude Ingrid S. , Kidd Gerald , Luebke Anne E. , Maddox Ross K. , Marvin Elizabeth W. , Perrachione Tyler K. , Shinn-Cunningham Barbara G. , Oxenham Andrew J. 
Published: September 2024

AbstractMusical training has been associated with enhanced neural processing of sounds, as measured via the frequency following response (FFR), implying the potential for human subcortical neural plasticity. We conducted a large-scale multi-site preregistered study (n > 260) to replicate and extend the findings underpinning this important relationship. We failed to replicate any of the major findings published previously in smaller studies. Musical training was related neither to enhanced spectral encoding strength of a speech stimulus (/da/) in babble nor to a stronger neural-stimulus correlation. Similarly, the strength of neural tracking of a speech sound with a time-varying pitch was not related to either years of musical training or age of onset of musical training. Our findings provide no evidence for plasticity of early auditory responses based on musical training and exposure.
Contribution of GC content to differentiated region formation along a speciation continuum
Authors: Ke Fushi , Vasseur Liette 
Published: September 2024

AbstractGenome features can interact with external evolutionary processes and are involved in the formation of highly differentiated regions (i.e., genomic islands) potentially containing adaptation and speciation loci. However, GC content that can elevate both regional recombination and mutation has not been investigated in evolving lineages to test its effects on formation of heterozygous differentiation landscape. Here, we employed the genomes of 499 Asian honey bee (Apis cerana), with a widely-distributed central lineage diverged and admixed with its peripheral lineages at both population genetic and phylogenetic levels, to investigate the effects of GC content on mutation accumulation and lineage divergence along the speciation continuum. We find that genomic islands are generally with low GC content (i.e., lower-than-average), and with lower-than-average divergence (dxy) initially to higher-than-average ones at deeper divergence, corresponding to the suggested evolution models transforming from linked selection to divergent selection. When comparing with high-GC regions however, we find higher mutation load indicating inefficient natural selection in low-GC regions, which thus support the important role of low GC content instead of evolutionary process (e.g., natural selection) in genomic island formation. Finally, low-GC regions possess higher proportion of lineage-specific polymorphisms than high-GC regions due to limited recombination and admixture under the gene-flow scenario, and reconciliate discordance between mitochondrial and nuclear phylogenies inA. cerana. Our results shed light on the contribution of polymorphisms in low-GC regions to divergent region formation along the speciation continuum and their application in reconstruction of intraspecific phylogeny, especially in lineages with gene flow.
Evaluating the Impact of NHS Strikes on Patient Flow through Emergency Departments
Authors: Garner Alex , Ashcroft Quin , Kirkwood Dale , Chandrabalan Vishnu , Emsley Hedley , Mason Suzanne M , Preston Nancy , Knight Jo 
Published: September 2024

AbstractBackgroundSince December 2022, the NHS has experienced large-scale strikes over pay by staff. Strikes heavily impact elective care delivery. The NHS cancels approximately 12 million elective care appointments each year. One million appointments have been cancelled due to strikes between 2022 and 2024. During this time emergency care is prioritised, and in a recent opinion piece, the president of the Royal College of Emergency medicine claimed the Emergency Department ran ‘better than usual’. The aim of this paper was to investigate changes in patient flow into hospitals through the ED during the strike periods.MethodologyData from two different emergency departments (EDs) in the North West of England is analysed using Cox-regression to model time between patient arrival at the ED, and subsequent admission. Various systematic and patient-level factors are controlled for. The impact of different striking groups (nurses, junior doctors etc.) on patient time to admission is analysed.ResultsFor the Type 1 ED, hazard ratios indicate that patients are admitted through the ED more quickly on strike days where any single group of staff were striking compared to non-strike days (HRs: 1.16-1.39, all p ≤ 0.003). This increased flow was only seen for consultant strikes in the smaller ED.InterpretationThese findings for all strike types indicate that improved patient flow on strike days is likely due to the increased inpatient capacity from elective care postponement. This result may indicate that there is room for change in NHS hospital systems to improve turnaround time and reduce ED crowding.Key MessagesWhat is already known on this topicExit block is a primary issue for NHS Emergency Departments (EDs), increasing patient time spent in ED. The president of the Royal College of Emergency Medicine claimed that NHS EDs run ‘better than usual’ during strikes. There is little quantitative evidence to support this claim.What this study addsThis study identifies significant increases in flow of admitted patients into the hospital during the strikes, when accounting for differences in admission patterns.How this study might affect research, practice or policyThe improvement in flow indicates that, although strike day service is unsustainable, elements of strike preparation can have a positive impact on the running of the emergency departments - demonstrating scope to improve patient flow through NHS EDs.
Using functional near-infrared spectroscopy to explore neurocognitive function in adult survivors of childhood acute lymphoblastic leukemia
Authors: Skau Simon , Jarfelt Marianne , Glavå Gustaf , Jess Laura , Kuhn H. Georg 
Published: September 2024

ABSTRACTAcute lymphoblastic leukemia (ALL) is the most common childhood malignancy. Due to the drastic increase in survivor rate over the last 50 years, long lasting treatment effect on moods and neurocognitive function has become a present issue. Most studies of late effects of treatment of ALL survivors investigate patients in their adolescents. This pilot study aims to identify measurements for evaluating late effect of childhood ALL survivors regarding neurocognitive and mood problems in adulthood. ALL survivors who received neurotoxic treatment with high-dose methotrexate and cranial radiotherapy (Chemo+CRT) (n=10) and ALL survivors only treated with high-dose methotrexate (Chemo) (n=10), plus age and sex match controls (n=20) where recruited to the study. The study protocol involved questionnaires, neurocognitive tests and optical brain imaging with functional near infrared spectroscopy (fNIRS) over the frontal and parietal cortex. The fNIRS results indicate a reduced involvement of the parietal cortex during conflict processing for the ALL survivors compared to controls. The study protocol shows promising results for identifying subgroups that suffers from neurocognitive and mood problems and we aim to expand upon it in a larger study. As our results indicate increased challenges among female ALL survivors, especially pathological fatigue, anxiety, and information processing, it is important to explore in future investigations the interplay between the risk of hormonal interaction with chemotherapy during development and occupational and social pressure during adulthood.
Antiplatelet Therapy Following Spontaneous Coronary Artery Dissection: Systemic Review
Authors: Park Huijun Edelyn , Cho Leslie S. , Fendrikova-Mahlay Natalia , Chaudhury Pulkit , Cameron Scott J. 
Published: September 2024

AbstractBackgroundSpontaneous coronary artery dissection (SCAD) is an understudied cause of acute coronary syndrome (ACS), particularly in women. Heart muscle damage may result from spontaneous dissection of coronary arteries. There is no clear consensus regarding the optimum antiplatelet medication regimen and treatment duration for SCAD despite current American Heart Association (AHA) consensus guidelines recommending 12-month regimen of dual antiplatelet therapy (DAPT) consisting of a P2Y12inhibitor and aspirin for patients following myocardial infarction (MI). The objective of this study was to evaluate the safety and effectiveness of DAPT compared to using a single antiplatelet therapy (SAPT) as part of the medical armamentarium to treat SCAD.MethodsA comprehensive search of the literature was conducted to identify studies that examined SCAD outcomes including mortality, recurrence, and major adverse cardiovascular events (MACE) between 2000-2023 after antiplatelet therapy was administered. Based on the documentation in various studies, only 17 relevant studies were identified in which SAPT (primarily aspirin) and DAPT (aspirin combined with a P2Y12inhibitor) were administered. Medications used in cardiovascular medicine that did not provide comprehensive data were excluded from the studies.ResultsDAPT treatment was associated with a poorer prognosis than SAPT 12 months after patients presented with SCAD. A key observation was the prevalence of antiplatelet treatment in SCAD patients, with DAPT prescribed for the majority of cases. At the 12-month time point, DAPT demonstrated had a higher rate of mortality (P = 0.0245), MACE (P = 0.0265), and angina admission rate (P = 0.071), as well as a higher rate of recurrent SCAD (P =0.0579) (Fig. 2). An increased incidence of non-fatal myocardial infarction or emergency percutaneous coronary intervention primarily drove these adverse outcomes.ConclusionIn patients treated with antiplatelet therapy, adverse events that include unstable angina, mortality, and repeat revascularization were greater in patients with more aggressive antiplatelet therapy consisting of DAPT compared with these treated with SAPT.
Association Between Seasonal Respiratory Virus Activity and Invasive Pneumococcal Disease in Central Ontario, Canada
Authors: Simmons Alison E. , Berry Isha , Buchan Sarah A. , Tuite Ashleigh R. , Fisman David N. 
Published: September 2024

ABSTRACTBackgroundIn central Ontario, influenza, respiratory syncytial virus (RSV), and invasive pneumococcal disease (IPD) follow similar seasonal patterns, peaking in winter. We aimed to quantify the independent and joint impact of influenza A, influenza B, and RSV on IPD risk at the population level.MethodsWe used a 2:1 self-matched case-crossover study design to evaluate acute effects of respiratory virus activity on IPD risk. This design ensures that effects are not confounded by within-individual characteristics that remain constant over short periods of time. We included 3,892 IPD cases occurring between January 2000 and June 2009. Effects were measured using univariable and multivariable conditional logistic regression. Multivariable models included environmental covariates (e.g., temperature, absolute humidity, and UV index) and interaction terms between viruses.ResultsInfluenza A activity and influenza B activity were both independently associated with increased IPD risk; however, co-circulation of influenza A and B reduced the impact of both viruses. RSV activity was positively associated with increased IPD risk only in the presence of increased influenza A or influenza B activity.ConclusionsTo our knowledge this represents the first study to consider the impact of interactions between these viruses on IPD risk in Canada. Our findings suggest that the prevention of IPD should be considered as a potential health benefit of influenza and RSV vaccination programs.
Similar performance of 8 machine learning models on 71 censored medical datasets: a case for simplicity
Authors: Rebaud Louis , Capobianco Nicolò , Captier Nicolas , Escobar Thibault , Spottiswoode Bruce , Buvat Irène 
Published: September 2024

AbstractIn the analysis of medical data with censored outcomes, identifying the optimal machine learning pipeline is a challenging task, often requiring extensive preprocessing, feature selection, model testing, and tuning. To investigate the impact of the choice of pipeline on prediction performance, we evaluated 9 machine learning models on 71 medical datasets with censored targets. Only the decision tree model was consistently underperforming, while the other 8 models performed similarly across datasets, with little to no improvement from preprocessing optimization and hyperparameter tuning. Interestingly, more complex models did not outperform simpler ones, and reciprocally. ICARE, a straightforward model univariately learning only the sign of each feature instead of a weight, demonstrated similar performance to other models across most datasets while exhibiting lower overfitting, particularly in high-dimensional datasets. These findings suggest that using the ICARE model to build signatures between centers could improve reproducibility. Our findings also challenge the traditional approach of extensive model testing and tuning to improve performance.