bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low Field Magnetic Resonance Imaging to Detect Acute Kidney Injury
Authors: Kishimoto Shun , Horie Kazumasa , Devasahayam Nallathamby , Yamashita Kota , Gadisetti Chandramouli , Yamamoto Kazutoshi , Brender Jeffrey R. , Mitchell James B. , Krishna Murali C. , Linehan W. Marston , Crooks Daniel R. 
Published: January 2025

AbstractRenal oxygenation is essential for maintaining kidney function. Disruptions in oxygen delivery can lead to renal hypoxia, which can exacerbate kidney injury through multiple pathways, including inflammation, oxidative stress, and ischemia-reperfusion injury. Despite the recognized importance of oxygenation in renal pathology, non-invasive and reliable methods for assessing kidney oxygen levels are limited. Current techniques either lack sensitivity or involve invasive procedures, restricting their use in routine monitoring. Therefore, there is a pressing need for innovative approaches to assess renal oxygenation, particularly in kidney injury. This study evaluated Electron Paramagnetic Resonance (EPR)-based oxygen imaging using the paramagnetic tracer Ox071 to assess kidney oxygen levels in mice with cyclophosphamide-induced kidney injury. Urine pO2 was also assessed as a potential surrogate marker. EPR oximetry accurately measured kidney oxygen distribution, revealing a temporary increase in pO2 post-injury. Urine oximetry, however, did not reliably reflect changes in kidney oxygenation. Furthermore, EPR oximetry provided high-resolution spatial mapping of oxygen levels within the kidney, allowing for a detailed understanding of the impact of hypoxia on renal tissue. EPR oximetry is a promising, non-invasive tool for monitoring renal oxygenation, offering high-resolution mapping and longitudinal assessment. Its ability to provide detailed information about oxygen distribution within the kidney makes it a valuable tool for studying the pathophysiology of renal diseases and for developing novel therapeutic strategies.Translational Statement: Quantitative spatially resolved measurement of renal oxygenation has the potential to guide clinical decision making in renal disorders such as acute kidney injury. In this study we demonstrate the utility of electron paramagnetic resonance imaging to provide non-invasive and quantitative high-resolution mapping of kidney oxygen concentrations.
Spatially explicit capture–recapture models for relative density
Authors: Efford M. G. 
Published: January 2025

AbstractSpatially explicit capture–recapture (SECR) methods are used widely to estimate animal population density and related parameters. Maximum likelihood has been applied to two flavors of SECR model - a full model that includes absolute density as a spatially varying parameter, and a model conditional on the number of detected individuals that assumes uniform density. We show how the conditional model may be extended to estimate relative density as a function of habitat and other spatial variables. The conditional model has the major advantage of seamlessly including individual covariates of detection. It is also faster to fit than the full model and more robust with an ‘identity’ link. The spatial absolute density surface may be derived from the conditional model fit. We demonstrate this with a spline surface fitted to data on American black bears (Ursus americanus). The relative density formulation also allows an adjustment for spatially selective prior marking. The problem arises when fish are caught and implanted with transponders, such as acoustic tags, and later monitored intensively with passive recorders. The confounding spatial effect of undocumented initial sampling may be removed from spatial analyses of the monitoring data by including an offset proportional to the smoothed sampling effort.
Plasmid copy number variation impacts pathogenicity and quantification ofCurtobacterium flaccumfacienspv.flaccumfaciensinfecting mung bean
Authors: Saad Ahmed , Vaghefi Niloofar , Poudel Barsha , Young Anthony J. , Kelly Lisa A. , Knight Noel L. 
Published: January 2025

ABSTRACTIn bacteria, plasmids can confer the ability to cause disease. Although they can potentially vary in copy number, little has been reported on the dynamics of plasmids in plant pathogenic bacteria. Pathogenicity of the bacteriumCurtobacterium flaccumfacienspv.flaccumfaciens(Cff), which causes foliar disease on leguminous crops, including mung bean (Vigna radiata), has previously been linked to a plasmid. This study explored the variation in plasmid copy number among a genetically diverse collection of 25Cffisolates using purposely designed quantitative PCR assays for chromosomal and plasmid DNA targets. Pathogenicity and virulence of sixCffisolates, including one plasmid-free isolate, were assessed on the susceptible mung bean cultivar Opal-AU using visual symptoms, trifoliate dry weights andCffDNA quantities following stem inoculation. Plasmid copy numbers varied significantly (p<0.001) among plasmid-carrying isolates, ranging from 1.37 to 2.74. For subsequent quantificationin planta, the single-copy chromosomal PCR target gene, gyrase b, was selected. Mung beans inoculated with plasmid-carrying isolates exhibited significant variation in visual symptoms (p<0.001), while trifoliate dry weights andCffDNA quantities did not significantly differ. The treatment using a plasmid-free isolate was not significantly different from the negative control for each of the disease traits. Knowledge of plasmid dynamics inCffpopulations lays a foundation for improved understanding of the inheritance and impact of plasmid-related traits. The quantification assays will be useful for monitoringCffpopulations and the demonstrated variation in pathogenicity and virulence can assist efforts to breed host plant germplasm with reduced susceptibility toCff.
SMTdb: A comprehensive spatial meta-transcriptome resource in cancer
Authors: Zhou Weiwei , Yang Qingyi , Guo Jiyu , Li Si , Su Minghai , Leng Feng , Rong Tingyu , Shi Jingyi , Gao Yueying , Jiang Tiantongfei , Xu Juan , Li Yongsheng 
Published: January 2025

ABSTRACTMicrobes have been found in various tumors and the research of tumor microbiome has been garnering increased attention. However, it remains challenge to investigate the microbiome in cancer at spatial resolution. The rapid advent of spatially resolved transcriptomics techniques has given rise to map transcripts at single-cell resolution in various types of cancer. Here, we constructed a comprehensive spatial meta-transcriptome resource by manually curating 203 fresh frozen (FF) slices from 20 cancers encompassing 334,253 spots and 1,908,646 cells. SMTdb (http://bio-bigdata.hrbmu.edu.cn/SMTdb/) was constructed to provide comprehensive insights into the abundance, distribution and enriched TME regions of 1218 microbiota in spatial tissue slices. SMTdb enables vast interactive data exploration of spatial distribution and expression of microbiota, host gene modules associated with certain microbiota and co-occurrence between microbiota and immune cells within tumor microenvironment. The atlas resource serves as a one-stop and time-effective platform to investigate the interactions among microbial ecosystems and hosts in cancer.
Shared molecular regulation of quiescence in neural and glioma stem cells reveals therapeutic vulnerabilities
Authors: Choudhury Chandra , Singleton Matthew , Brauer Stephanie , Friess Dana , Hart Jessica , Skarne Niclas , Pullela Karthik , Mao Likai , Day Bryan W , Harris Lachlan 
Published: January 2025

SUMMARYQuiescence, a reversible state of cell-cycle arrest, is an adaptive feature of many adult tissue stem cells, including those in the adult brain. In gliomas, brain tumour stem cells that reside in a quiescent state preferentially survive chemotherapy and radiotherapy, highlighting their critical role in therapy resistance and disease progression. To date, it remains unclear whether the molecular programs governing these states are functionally conserved between neural stem cells and brain tumour stem cells. Here, we establish novelin vitromodels to study quiescence and find that glioma stem cells are markedly more resistant to entering quiescence than neural stem cells, suggesting that glioma stem cell quiescence more closely resembles a slow-cycling phenotype or shallow quiescence. Nonetheless, direct comparison of quiescent neural stem cells and quiescent/slow-cycling glioma stem cells, as they transition towards proliferation, reveals conserved gene expression trajectories, indicating shared molecular mechanisms. Furthermore, we find that pathways influencing quiescence in neural stem cells exert similar effects in glioma stem cells, underscoring the functional parallels between these populations. Finally, we identify that inhibition of TGF-β signalling might provide an avenue to improve current standard-of-care treatments by targeting quiescent glioma stem cells.
How immigration affects the burden of tuberculosis among foreign-born Canadians: estimates with dynamic models
Authors: Chiu Jeremy , Ruth William , Rutherford Alexander , Wijaya Kezia , Lee Timothy , Williams JF , Wong Albert 
Published: January 2025

AbstractDespite only comprising about a quarter of the total population of Canada, foreign-born individuals bear about three-quarters of the burden of active tuberculosis (TB) cases. New immigrants arriving in Canada are screened for active TB, but generally not latent TB infection (LTBI); thus the burden of LTBI among foreign-born Canadians is not well understood.To investigate the impact of immigration on the burden of TB among foreign-born Canadians, we develop an SEIR-compartment model that distinguishes between actively infected, latently infected, and uninfected individuals. Unknown parameters are calibrated to reports on the incidence and prevalence of active TB in Canada. We validate our model by comparing model computed quantities to other reports of tuberculosis burden among foreign-born Canadians, such as our estimate of the prevalence of LTBI among immigrants entering Canada.If the profile and number of immigrants arriving into Canada in the next decade is similar to the past decade, our model predicts that Canada will not meet the End TB 2035 goal of reducing incidence by 90% compared to 2015. Even if Canada were to limit immigration only to the WHO geographic region with the lowest incidence (Americas), we would still fail to meet the target.Author summaryOur model examines how immigration affects the burden of tuberculosis among foreign-born Canadians. We fit a compartment model to calibration data, then find a feasible parameter set based on validation data. We forecast the incidence of TB in 2035 and demonstrate that if the number of immigrants entering Canada in the next decade is similar to the past decade, regardless of which WHO geographic region they originate from, Canada will fail to meet the WHO End TB’s 2035 incidence goal (90% less than 2015).
Current status and expectations of medical interns in the advanced phase of the DES (specialized medical studies) in medical gynecology regarding medical theses
Authors: Poisson Aurelie , Jochum Floriane , Gougis Paul , Savarino Raphaelle , Coussy Florence , Sonigo Charlotte , Laas Enora , Roux Damien , Reyal Fabien , Rousset-Jablonski Christine , Hamy Anne-Sophie 
Published: January 2025

SummaryIntroductionIn France, Writing and defending a medical thesis are mandatory components of medical education curriculum to obtain the degree of Doctor of Medicine. The expectations of medical interns in medical gynecology regarding their medical thesis have not been evaluated.MethodsA 10-question form was distributed during the national teaching of the advanced phase of the specialized medical studies (DES) in medical gynecology (corresponding to the 2ndand 3rdyear of internship). Responses were collected using the Wooclap* software.ResultsA total of 131 interns participated in the survey out of 170 interns solicited. Approximately two-thirds of the surveyed students had a medical thesis topic at the time of the survey. Among students with a thesis topic, thesis supervisors were most often university practitioners (MCU-PH/PH-U/PU-PH, 37.4%), followed by hospital practitioners (22.8%). The quality of supervision by the thesis supervisor was rated at 6.9/10, and the quality of supervision by the university was rated at 3.3/10. Overall, 53.4% of students wished to leverage their work through scientific publication. Nearly all students (94%) wished for guidance on at least one of the following topics: writing scientific articles (83%), basic statistics (83%), basic data collection (75%), training in the use of Pubmed (68%), Excel (65%), Zotero (63%), project management (53%), Word (15%).ConclusionSupport for medical interns in medical gynecology for their medical thesis could be improved, particularly through modules on scientific publication, bibliography, and office automation.
Partial loss ofFITM2function causes hereditary spastic paraplegia
Authors: Salazar-Villacorta Ainara , Bond Laura M. , Kim Leehyeon , Anagnostopoulou Katherine , Scardamaglia Annarita , Filippakopoulou Eugenia , Ververi Athina , Efthymiou Stephanie , Dinopoulos Argirios , Murphy David , Karadima Georgia , Koutsis Georgios , Kaliakatsos Marios , Houlden Henry , Walther Tobias C. , Farese Robert V. 
Published: January 2025

AbstractFITM2encodes fat-storage inducing transmembrane protein 2 (FIT2), a lipid diphosphatase in the ER that cleaves acyl-CoAs and is crucial for ER homeostasis. In humans, homozygous null mutations inFITM2are associated with a syndrome characterized by deafness and dystonia. Here, we report two families with hereditary spastic paraplegia (HSP) in whom exome sequencing revealed compound heterozygosity forFITM2mutations. In each family, the affected probands carry one putative null allele and one G100R missense allele. Functional analyses demonstrated that the G100R allele is hypomorphic, with FIT2 protein levels reduced to 20% of wild type, leading to proportionately decreased enzyme activity. The occurrence of similar HSP disease phenotypes and the same hypomorphic mutation in these families suggests that the G100R mutation and its associated reduced enzyme activity represent a newly recognized clinical manifestation ofFITM2mutations, expanding the spectrum of conditions associated with this gene.
Accuracy of rapid antigen testing for COVID-19 in shelter settings
Authors: Garad Yasmin , Manea Andreea A. , Pak Negin , Barker Bronwyn , Kasperavicius Danielle , Danok Lames , Baral Stefan , Orkin Aaron M. , Siddiqui Amna , Straus Sharon E. , Fahim Christine 
Published: January 2025

AbstractBackgroundThe COVID-19 pandemic disproportionally affected congregate living settings, including shelters. COVID-19 transmission can have more adverse outcomes in these settings due to the vulnerability of residents. Point of care rapid antigen testing (RAT) represents a strategy with potential benefits for COVID-19 detection in shelters, including rapid results, ease of use, cost-effectiveness, and early detection.ObjectivesOur primary objective was to assess the real-world test accuracy of RAT for COVID-19 using the Quidel Sofia 2 Flu + SARS Antigen fluorescent immunoassay (Sofia RAT) compared to polymerase chain reaction (PCR) testing among shelter residents in Ontario, Canada.Study DesignA consecutive sample of 102 residents across six shelters who were symptomatic for, or exposed to COVID-19 were included. The RAT and PCR samples were taken on the same day for each participant. Results from the Sofia RAT were compared to PCR test results to determine test accuracy. Participant demographic data could not be collected due to workforce constraints.ResultsWe reported our methods and findings using the QUality Assessment tool of Diagnostic Accuracy Studies (QUADAS-2) guidelines. Sofia 2 RAT specificity was 97.9% (95% CI: 92.7% to 99.7%) for COVID-19 compared to PCR. Due to a lack of true positive cases, sensitivity could not accurately be calculated (0.00% (95% CI: 0.00% to 52.2%)).ConclusionThese data suggest that the Sofia RAT is a highly specific test for COVID-19.
Multi-Night Home testing with portable EEG shows Improvement in Sleep Quality after Starting CPAP for Obstructive Sleep Apnoea
Authors: Lee Kieran O. , Bekinschtein Tristan A. , Smith Ian E. 
Published: January 2025

AbstractObstructive sleep apnoea (OSA) impacts sleep quality and has considerable night to night variability. This study explored the use of low-density EEG headbands to evaluate changes in sleep architecture and sleep features in the patients’ own homes over multiple nights both Pre and Post treatment with continuous positive airway pressure (CPAP). Seven participants recorded 144 high-quality EEG sessions (84 Pre-CPAP, 60 Post-CPAP). Comparing Pre and Post-CPAP there were significant reductions in N1 (P < 0.0001) and N2 (P < 0.0001) sleep, increases in N3 (P < 0.0001) and REM (P < 0.0001) sleep and fewer sleep stage shifts (P < 0.0001), micro-arousals (P < 0.0001) and awakenings (P < 0.0001). Total sleep time did not change. Strength testing identified that one participant (who had the most severe OSA, and produced the most EEG recordings), was a major driver of the effects, however, improvements in REM, shifts, and micro arousals remained when this participant was excluded. These results suggest low-density EEG devices can be used for multi-night monitoring, potentially advancing OSA research and personalised care.Statement of SignificanceOSA is a highly prevalent condition, with increasing global demand for care resources. Current OSA diagnostic and follow-up methods face two significant limitations: they do not capture night-to-night variability in sleep quality, and polysomnography, the current gold-standard measurement of sleep quality, requires substantial resources and is usually performed in a laboratory, which will not always reflect sleep quality achieved at home. This study collected 144 high-quality sleep recordings from seven participants using low-density EEG headbands in a community setting, both Pre and Post-CPAP. Results showed significant improvements in multiple measures of sleep quality after initiating CPAP. These findings demonstrate the feasibility of portable EEG headbands for OSA and suggest potential for enhancing clinical monitoring and advancing research through multi-night frameworks.
Real-world smartphone data predicts mood after cerebrovascular symptoms and may constitute digital endpoints
Authors: Zawada Stephanie , Acosta Jestrii , Collins Caden , Dumitrascu Oana , Harahsheh Ehab , Hagen Clint , Ganjizadeh Ali , Mahmoudi Elham , Erickson Bradley , Demaerschalk Bart 
Published: January 2025

AbstractThough depression is prevalent in patients with cerebrovascular dysfunction, screening for symptoms is not routine and is often limited via subjective patient-reported surveys. Using smartphone sensors, we sought to evaluate the performance of objective behavior measures and self-report surveys at predicting depression severity in patients with cerebrovascular syndromes. Among enrolled participants (n = 54), 35 patients with ischemic stroke or transient ischemic attack symptoms were monitored in real-world settings using the Beiwe app for 8 or more weeks with adequate compliance. Depression symptoms were tracked via weekly Patient Health Questionnaire-8 (PHQ-8) surveys, monthly personnel-administered Montgomery-Asberg Depression Rating Scale (MADRS) assessments, and passive smartphone sensors. Across weeks, several passive measures were significantly associated with PHQ-8 scores. Personnel-assessed depression severity moderately correlated with self-reported scores. To estimate MADRS, we applied linear mixed models using passive data and PHQ-8 scores. Using antecedent PHQ-8 scores and demographic data, average root-mean-squared error (RMSE) for depression severity prediction across models was 1.54 with accelerometer data, 1.40 also including global position system (GPS) data, and 1.33 also including PHQ-8 open survey duration. Though future research should validate this decentralized approach in a larger cohort, real-world monitoring with active and passive data may triage cerebrovascular patients for efficient depression screening and provide novel mobility and response time outcome measures.
Intracranial Photobiomodulation In De Novo Parkinson’s Patients: preliminary data of an ongoing randomized controlled trial
Authors: Chabardès Stéphan , Thobois Stéphane , Mitrofanis John , Beaudoin-Gobert Maude , Anglade Daniel , Aubert Nicolas , Auboiroux Vincent , Bleuet Pierre , Costecalde Thomas , De Schlichting Emmanuel , Faivre Olivier , Mastrosimone Marine , Molet Jenny , Poizat Adrien , Renault Sarah , Torres Napoleon , Chabrol Claude , Moro Cecile , Benabid Alim Louis 
Published: January 2025

ABSTRACTParkinson’s disease (PD) is a progressive neurodegenerative disorder and current treatment options only tackle symptoms. We aimed to evaluate the effect of intracranial photobiomodulation (iPBM) on dopaminergic neurons and its consequences on motor symptoms in de novo PD patients.This randomised open label study included 6 de novo PD patients, 3 served as control and 3 were treated by chronic iPBM during 2 years. Researcher analysing the PET data was unaware of patients’ iPBM status but clinical examinator was aware of it. Data analysis was performed on June 2024.De novo PD patients were recruited and randomized (1:1) to receive iPBM or medical treatment alone for 4 years. PD diagnosis was < 2 years, and no medication was allowed at inclusion. PET scan was performed at baseline and at 1 yearPrimary outcome was safety. The secondary outcome measure was the evolution at 2 years of motor scales using the MDS-UPDRS part III and the evolution of PET scan (using the [11C]-PE2I ligand) at 1 year.Six patients (1f, 5m) were recruited with a mean age (SD) of 55.3 years (7.6). We showed that iPBM was feasible and safe on the first 3 operated patients. The first novelty of the study was that iPBM improved motor scores in average at 2 years whereas the control group followed the natural clinical decline. Mean (SD) clinical outcome with iPBM was -6.2% (32.9%) improvement on the MDS-UPDRS (part III) compared to baseline versus +130% (143%) for control group. The second novelty was that in the iPBM group, [11C]-PE2I PET scans showed an unusual mean increase in tracer binding within the caudate +21.3%(15.9), nucleus accumbens +22.2%(23.7%), pallidum +89.7% (94.8%) and putamen +26.1%(34%). in the control group, as expected, tracer binding was decreased (SD) on average in the caudate - 16.9%(−16.3%), nucleus accumbens -27.5%(−28.4%), and putamen -19.5%(−11.4%), but slightly increased in the pallidum +10.7%(+39.6%). Because of the small number of patients, no statistical test was performed at this stage.ConclusionsiPBM was feasible and safe in this small group of patients. It showed an unusual improvement of motor scores at 2 years that was associated with striking increase of dopamine transporter in the basal ganglia observed on the [11C]-PE2I PET. These preliminary data suggest a possible modifying disease effect related to iBPM. A larger number of patients with longer follow up is mandatory to validate our preliminary results.Trial Registrationthe EvNIR study is registered atClinicalTrials.gov(NCT04261569).