bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk Factors for Developing Community-Acquired Hand Infections at a Large-Volume Urban Safety Net Hospital
Authors: Yin Raymond , Rosser Mica , Mclaughlin Matthew F. , Soroudi Daniel , Patel Alap U. , Sadjadi Ryan , Hansen Scott L. 
Published: October 2024

Background
Hand infections represent a significant burden for both health care systems and their patients. Epidemiological understanding of community-acquired hand infections is limited. This study examined a cohort of hand infection patients at a large urban safety net hospital for characteristics that were associated with protective and/or risk factors for hand infections.

Methods
We performed a retrospective chart review for all patients who required hand surgery consultation in the emergency department during a 1-year period (2021–2022). County-level population characteristics were obtained through the county-level data sources. We then performed a risk ratio (RR) analysis for demographic and socioeconomic characteristics.

Results
A total of 125 patients were included in the study cohort. Cisgender male (RR, 4.654; P < 0.001), Black (RR, 6.062; P < 0.001) and American Indian/Alaska Native (RR, 3.293; P = 0.041) patients were found to be overrepresented in our cohort when compared to county proportions, indicating an association with increased risk of hand infections. Patients between 35 and 49 years of age were also found to have an increased risk (RR, 1.679; P = 0.005). Age over 65 years, retirement, and employment were found to be protective factors (RR, 0.341 [P = 0.001]; RR, 0.397 [P = 0.043]; RR, 0.197 [P < 0.001]). In contrast, unemployment and unstable housing (unhoused or shelter) were found to have strong harmful risk for necessitating hand infection consults (RR, 7.587 [P < 0.001]; RR, 235.715 [P < 0.001]; RR, 29.990 [P < 0.001]).

Conclusions
There are clear risk factors at play for hand infection incidence. We found that housing status, employment, race, gender, and age were some of the most important contributors for incidence. This information can assist clinicians and public officials in developing more specific screening algorithms and prevention tools to reduce systematic burden. Further studies are required to elucidate specific etiologies associated with hand infection risk.
The estimated impact of mandatory front-of-pack nutrition labelling policies on adult obesity prevalence and cardiovascular mortality in England: a modelling study
Authors: Evans Rebecca , O’Flaherty Martin , Edi Putra I Gusti Ngurah , Kypridemos Chris , Robinson Eric , Colombet Zoé 
Published: October 2024

AbstractObjectivesSince 2013, industry-endorsed front-of-pack traffic light labels have been implemented voluntarily on packaged food in the UK. The UK Government is now considering alternative labelling approaches which may be more effective, such as Chile’s mandatory nutrient warning labels. The primary aim of this study was to model the likely impact of implementing mandatory front-of-pack nutrition labels in England on energy intake and consequent population-level obesity, and, secondarily, cardiovascular disease (CVD) mortality.DesignMicrosimulation modelling analysisSettingEnglandModelA microsimulation model (2024–2043) to estimate the impact of changing front-of-pack nutrition labels in England. The two main policy scenarios tested were mandatory implementation of (i) traffic light labels and (ii) nutrient warning labels. For each scenario, the impact of the policy through assumed changes in energy intake due to consumer behaviour change and reformulation was modelled.Main outcome measuresChange in obesity prevalence (%) and CVD deaths prevented or postponed.ResultsCompared to the baseline scenario (current voluntary implementation of traffic light labelling), mandatory implementation of traffic light labelling was estimated to reduce obesity prevalence in England by 2.28% (95% UI –4.06 to –0.96) and prevent or postpone 17000 (95% UI 4700 to 48000) CVD deaths. Mandatory implementation of nutrient warning labelling was estimated to have a larger impact; a 3.68% (95% UI –9.94 to –0.18) reduction in obesity prevalence and the prevention/postponement of 29000 (95% UI 1200 to 110000) CVD deaths.ConclusionsThis work offers the first modelled estimation of the impact of introducing mandatory front-of-pack nutrition labels on health outcomes in the adult population in England. Findings suggest that mandatory implementation of nutrient warning labels would reduce rates of obesity and CVD deaths, compared to current voluntary or mandatory implementation of traffic light labelling, and should therefore be considered by the UK government.FundingEuropean Research Council (Grant reference: PIDS, 8031940).
Neutrophil gelatinase-associated lipocalin and Fibrinogen-to-albumin ratio are indicators of nephropathy in adult steady state sickle cell disease patients: A multicenter case-control study in Ghana
Authors: Twumasi Stephen , Odame Anto Enoch , Obirikorang Christian , Kobina Dadzie Ephraim Richard , Sackey Benedict , Paintsil Vivian , Owusu Ansah Richard , Effah Alfred , Adofo Ayirebi Allwell , Opoku Angela , Yawson Scott Godfred , Osei Leslie , Duku Joyce , Asafo Adjei Emmanuel , Antwi Boateng Lilian 
Published: October 2024

AbstractBackgroundProgressive renal failure is one of the main complications in sickle cell disease. Neutrophil Gelatinase-Associated Lipocalin (NGAL) is present in gelatinase/tertiary granules of neutrophils and it is a relatively newly recognized marker of nephropathy. Fibrinogen increases and albumin decreases in inflammatoy conditions like SCD. This study investigated the diagnostic roles of NGAL and fibrinogen-to-albumin ratio in steady state adult sickle cell disease patients.MethodsIn this study, 104 sickle cell disease participants and 51 healthy subjects were analysed. Participants’ information was thoroughly documented using a structured questionnaire and patient case records. To evaluate the hematobiochemical parameters, 5ml of venous blood was drawn from each participant and a clean catch of mid-stream urine was collected from each participant. Subjects with sickle cell disease were further classified as SCD nephropathy and SCD non- nephropathy subjects based on reduced estimated Glomerular Filtration Rate (eGFR) and microalbuminuria.ResultsPrevalence of nephropathy was 32.7% among adult steady state SCD patients. Significant high levels of Urine Albumin-to-Creatinine Ratio (UACR), NGAL and fibrinogen-to-albumin ratio (FAR) were seen in SCD patients with nephropathy compared to those without nephropathy (p<0.001). NGAL levels significantly increased along with increased urine albumin-to-creatinine ratio (r=0.28,p<0.005) in both SCD with nephropathy and those without nephropathy. There was a significant negative correlation between creatinine (r=-0.90,p<0.0005), urea (r=-0.50,p<0.0005) and eGFR in SCD subjects. Similarly, a significant negative relationship existed between UACR and eGFR (r=-0.34,p<0.0005). Creatinine also had a significant positive correlation with UACR (r=0.27,p<0.005 and urea (r=0.56,p<0.0005) in SCD subjects. NGAL was found to be a good predictor of nephropathy in steady state SCD patients with AUC=0.742,p<0.0001 when compared with creatinine and urea with AUC=0.618,p=0.048 and AUC=0.531,p=0.647 respectively. However, FAR could not be used as a predictive marker since it had non-significant poor performance (AUC=0.462,p=0.536).ConclusionNGAL as independent marker, is an early predictor of kidney disease as compared to urea and creatinine. Fibrinogen-to-albumin ratio can be used to track nephropathy treatment in steady state sickle cell disease patients since it is elevated in those with sickle cell nephropathy compared to healthy individuals. These two markers can be added to the available array of test in the management of nephropathy among steady SCD patients.
Development and Validation of Automated Software for the Detection of Large Vessel Occlusion on Noncontrast CT
Authors: Tsuji Hirofumi , Ishii Akira , Abekura Yu , Nishi Hidehisa , Fuchigami Takuya , Tachibana Atsushi , Ito Hirotaka , Arakawa Yoshiki 
Published: October 2024

AbstractBackgroundReliable detection of large-vessel occlusion (LVO) via medical-image analysis has significant advantages in cases of acute ischemic stroke (AIS). In recent years, convolutional neural network (CNN)-based technologies for automated LVO detection have been developed. However, the pros and cons of CNN-based assistance in clinical practice remain poorly understood. The purpose of this study was to develop and validate a deep learning-based model to detect the hyperdense-artery sign (HAS) as a proxy for LVO and to investigate its impact on neurosurgeons’ diagnostic accuracy.MethodsWe conducted a multicenter, retrospective study of patients with LVO due to anterior-circulation AIS who underwent computed tomography angiography or magnetic resonance angiography on admission, as well as patients without LVO (patients with no indicative angiography features and patients with cerebral infarction without LVO), who were admitted from 2006 to 2022. A CNN algorithm for LVO detection was developed using data from four institutions (n=690), and model performance was validated using data from five institutions (n=129). For further investigation, five board-certified and five non-board-certified neurosurgeons performed two separate observer-performance studies with a 4-week interval, with and without the CNN for each image.ResultsThe HAS was detected in the correct location with a sensitivity and specificity of 0.79 and 0.87 by the CNN, 0.61 and 0.60 by board-certified neurosurgeons, and 0.61 and 0.66 by non-board-certified neurosurgeons, respectively. With the CNN, the mean area under the curve and figure of merit significantly increased for all readers (from 0.72 to 0.81, p<0.001, and from 0.71 to 0.77, p=0.005, respectively).ConclusionsOur deep learning-based automated LVO-detection model for non-contrast-enhanced computed tomographic images significantly improved neurosurgeons’ diagnostic performance. Further studies are needed to clarify the usefulness of the CNN in clinical practice.
Searching for Sulfotyrosines (sY) in a HA(pY)STACK
Authors: Tzvetkov Jordan , Eyers Claire E , Eyers Patrick A , Ramsbottom Kerry A , Oswald Sally O , Harris John A , Sun Zhi , Deutsch Eric W , Jones Andrew R 
Published: October 2024

AbstractProtein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is near-isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The degree to which tyrosine sulfation (sY) is misidentified as phosphorylation (pY) is thus an unresolved concern. This study explores the extent of sY misidentification within the human phosphoproteome by distinguishing between sulfation and phosphorylation based on their mass difference.Using Gaussian mixture models (GMMs), we screened ∼45M peptide-spectrum matches (PSMs) from the PeptideAtlas Human Phosphoproteome build for peptidoforms with mass error shifts indicative of sulfation. This analysis pinpointed 104 candidate sulfated peptidoforms, backed-up by Gene Ontology (GO) terms and custom terms linked to sulfation. False positive filtering by manual annotation resulted in 31 convincing peptidoforms spanning 7 known and 7 novel sY sites. Y47 in Calumenin was particularly intriguing since mass error shifts, acidic motif conservation, and MS2neutral loss patterns characteristic of sulfation provided strong evidence that this site is sulfated rather than phosphorylated.Overall, although misidentification of sulfation in phosphoproteomics datasets derived from cell and tissue intracellular extracts can occur, it appears relatively rare and should not be considered a substantive confounding factor in high-quality phosphoproteomics datasets.
Dominant contribution of Asgard archaea to eukaryogenesis
Authors: Tobiasson Victor , Luo Jacob , Wolf Yuri I , Koonin Eugene V 
Published: October 2024

AbstractOrigin of eukaryotes is one of the key problems in evolutionary biology. The demonstration that the Last Eukaryotic Common Ancestor (LECA) already contained the mitochondrion, an endosymbiotic organelle derived from an alphaproteobacterium, and the discovery of Asgard archaea, the closest archaeal relatives of eukaryotes inform and constrain evolutionary scenarios of eukaryogenesis. We undertook a comprehensive analysis of the origins of the core eukaryotic genes tracing to the LECA within a rigorous statistical framework centered around evolutionary hypotheses testing using constrained phylogenetic trees. The results reveal dominant contributions of Asgard archaea to the origin of most of the conserved eukaryotic functional systems and pathways. A limited contribution from Alphaproteobacteria was identified, primarily relating to the energy transformation systems and Fe-S cluster biogenesis, whereas ancestry from other bacterial phyla was scattered across the eukaryotic functional landscape, without consistent trends. These findings suggest a model of eukaryogenesis in which key features of eukaryotic cell organization evolved in the Asgard ancestor, followed by the capture of the Alphaproteobacterial endosymbiont, and augmented by numerous but sporadic horizontal acquisition of genes from other bacteria both before and after endosymbiosis.
Greater baseline cortical atrophy in the dorsal attention network predicts faster clinical decline in Posterior Cortical Atrophy
Authors: Katsumi Yuta , Eckbo Ryan , Chapleau Marianne , Wong Bonnie , McGinnis Scott M. , Touroutoglou Alexandra , Dickerson Bradford C. , Putcha Deepti 
Published: October 2024

AbstractBackground and ObjectivesPosterior Cortical Atrophy (PCA) is a clinical syndrome characterized by progressive visuospatial and visuoperceptual impairment. As the neurodegenerative disease progresses, patients lose independent functioning due to the worsening of initial symptoms and development of symptoms in other cognitive domains. The timeline of clinical progression is variable across patients, and the field currently lacks robust methods for prognostication. Here, evaluated the utility of MRI-based cortical atrophy as a predictor of longitudinal clinical decline in a sample of PCA patients.MethodsPCA patients were recruited through the Massachusetts General Hospital Frontotemporal Disorders Unit PCA Program. All patients had cortical thickness estimates from baseline MRI scans, which were used to predict longitudinal change in clinical impairment assessed by the CDR Sum-of-Boxes (CDR-SB) score. Multivariable linear regression was used to estimate the magnitude of cortical atrophy in PCA patients relative to a group of amyloid-negative cognitively unimpaired participants. Linear mixed-effects models were used to test hypotheses about the utility of baseline cortical atrophy for predicting longitudinal clinical decline.ResultsData acquired from 34 PCA patients (mean age = 65.41 ± 7.90, 71% females) and 24 controls (mean age = 67.34 ± 4.93, 50% females) were analyzed. Sixty-two percent of the PCA patients were classified as having mild cognitive impairment (CDR 0.5) at baseline, with the rest having mild dementia (CDR 1). Each patient had at least one clinical follow-up, with the mean duration of 2.78 ± 1.62 years. Relative to controls, PCA patients showed prominent baseline atrophy in the posterior cortical regions, with the largest effect size observed in the visual network of the cerebral cortex. Cortical atrophy localized to the dorsal attention network, which supports higher-order visuospatial function, selectively predicted the rate of subsequent clinical decline.DiscussionThese results demonstrate the utility of a snapshot measure of cortical atrophy of the dorsal attention network for predicting the rate of subsequent clinical decline in PCA. If replicated, this topographically-specific MRI-based biomarker could be useful as a clinical prognostication tool that facilitates personalized care planning.
Epigenetic and cognitive signatures of striatal DAT binding among healthy elderly individuals
Authors: Yaghoobi Arash , Seyedmirzaei Homa , Jamaat Marzie , Ala Moein 
Published: October 2024

AbstractBackgroundStriatal dopamine transporter (DAT) binding is a sensitive and specific endophenotype for detecting dopaminergic deficits across Parkinson’s disease (PD) spectrum. Molecular and clinical signatures of PD in asymptomatic phases help understand the earliest pathophysiological mechanisms underlying the disease. We aimed to investigate whether blood epigenetic markers are associated with inter-individual variation of striatal DAT binding among healthy elderly individuals. We also investigated whether this potential inter-individual variation can manifest as dysfunction of particular cognitive domains.MethodWe conducted a blood epigenome-wide association study of striatal DAT binding on 96 healthy individuals using the Illumina EPIC array. For functional annotation of our top results, we employed the enhancer-gene mapping strategy using a midbrain single-nucleus multimodal dataset. Finally, we conducted several investigative regression analyses on several neuropsychological tests across five cognitive domains to assess their association with striatal DAT binding among 250 healthy subjects.ResultsWe identified seven suggestive (P-value<10−5) CpG probes. Specifically, three probes were colocalized with three risk loci previously identified in PD’s largest Genome-Wide Association Study (GWAS).UCN5AandAPOEloci were identified as suggestive DMRs associated with striatal DAT binding. Functional analyses prioritized theFDFT1gene as the potential target gene in the previously reportedCTSBGWAS locus. We also showed that delayed recall memory impairment was correlated with reduced striatal DAT binding, irrespective of age.ConclusionOur study suggested epigenetic and cognitive signatures of striatal DAT binding among healthy individuals, providing valuable insights for future experimental and clinical studies of early PD.
In-Patient Repeatability and Sensitivity Study of Multi-Plane Super-Resolution Ultrasound in Breast Cancer
Authors: Morris Megan , Durie Emily , Sinnett Victoria , Toulemonde Matthieu , Roxanis Ioannis , Allen Steven , Downey Kate , Scudder Julie , Gagliardi Tanja , Scott-Mackie Pauline , Nimalasena Samantha , Yan Jipeng , Huang Biao , Hansen-Shearer Joseph , Gothard Lone , Hughes Justine , Blackledge Matthew D , Somaiah Navita , Tang Meng-Xing 
Published: October 2024

AbstractPurposeSuper-resolution ultrasound (SRUS) is a promising imaging modality for detecting early microvascular changes after cancer treatment, offering advantages over tumour-size methods to evaluate response. For clinical application, it is crucial to assess repeatability of SRUS-derived biomarkers and their sensitivity to post-treatment changes.Experimental DesignClinical data were collected from breast cancer patients undergoing radiotherapy. 24 repeatability scans were conducted, and 11 participants underwent SRUS response assessment at 2-weeks and 6-months post-radiotherapy. Ultrafast CEUS acquisitions sampled four imaging planes of each tumour, generating 2D SRUS maps of microvascular structure and dynamics. SRUS-derived quantitative parameters were extracted, with repeatability assessed using the Repeatability Coefficient (RC). Changes in quantitative parameters were analysed post-radiotherapy, and the RC defined significant changes. SRUS-derived quantitative parameters were compared to histopathological CD31 staining of biopsy samples.ResultsThe RCs of SRUS quantitative parameters improved when averaged over more imaging planes, indicating improved repeatability. Significant changes in SRUS quantitative parameters were observed at 2-weeks post-RT in 5/11 participants. In contrast, only 1/11 participants showed significant tumour size changes. By 2-weeks or 6-months post-RT, significant changes in SRUS quantitative parameter were detected in all participants, while significant changes in tumour size were observed in 6/11 participants. Among 10 participants with corresponding CD31 vessel counts, 7 showed a correlation between the direction of change in histopathological vessel count scores and SRUS vessel density.ConclusionsThis repeatability and response assessment study establishes multi-plane SRUS as a robust and sensitive tool for detecting early tumour microvascular changes in patients undergoing treatment.FundingCRUK Convergence Science Centre, Kortuc Inc., NHS, NIHR, ICiC, IAA.
Genomic characterization of a unique population ofLeishmania tropicain a new emerging focus of cutaneous leishmaniasis in Somali region of Ethiopia
Authors: Abera Adugna , Monsieurs Pieter , Pareyn Myrthe , Beyene Dereje , Tasew Geremew , Aroni-Soto Allison , Belachew Mahlet , Geleta Desalegn , Adinew Bethlehem , Gidey Bokretsion , Tadesse Henok , Gebreegziabxier Atsbeha , Abubeker Rajiha , Ali Abraham , Tafess Ketema , Rinke de Wit Tobias F. , van Griensven Johan , Dujardin Jean-Claude , Wolday Dawit , Domagalska Malgorzata Anna 
Published: October 2024

AbstractWe sequencedLeishmania tropicagenomes directly from eight human skin samples collected in a newly emerging focus of cutaneous leishmaniasis in Somali region, Ethiopia. We found a new variant with unique genomic signatures of drug resistance. Genomic homogeneity in the sampled population demonstrates the occurrence of aL. tropicaoutbreak.
Reward-driven adaptation of movements requires strong recurrent basal ganglia-cortical loops
Authors: Leblois Arthur , Boraud Thomas , Hansel David 
Published: October 2024

AbstractThe basal ganglia (BG), a set of subcortical nuclei involved in motor control, sensorimotor integration, and procedural learning, modulate movement through tonic inhibition of thalamo-cortical networks. While essential for sensorimotor integration and learning, the BG are not necessary for executing well-learned movements. During skill learning, they guide behavioral corrections via dopamine-dependent cortico-striatal plasticity, but these corrections become BG-independent as modifications occur in the motor cortex. Existing models of BG function often overlook the feedback dynamics of cortico-BG-thalamo-cortical loops, and do not address the relative role of cortex and the BG in the generation and adaptation of movement. In this work, we develop a theoretical model of this multiregional network, integrating anatomical, physiological, and behavioral evidence to explore how its dynamics shape movement execution and reward-based adaptation. We show that the BG-thalamo-cortical network influences motor output through three key factors: (i) the rich dynamics of its closed-loop architecture, (ii) attractor dynamics from recurrent cortical connections, and (iii) classical reinforcement learning via dopamine-dependent cortico-striatal plasticity. Our study highlights that efficient visuomotor adaptation requires strong feedback from the BG to the cortex. Finally, we propose a mechanism for initial movement learning through motor babbling. This model suggests the BG-cortical network shapes motor output through its intricate closed-loop dynamics and cortico-striatal dopamine-dependent plasticity.