bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wastewater monitoring of SARS-CoV-2 gene for COVID-19 epidemiological surveillance in Tucumán Argentina
Authors: D’Arpino María Cecilia , Sineli Pedro Eugenio , Goroso Gustavo , Watanabe William , Saavedra María Lucila , Hebert Elvira María , Martínez María Alejandra , Migliavaca Julieta , Gerstenfeld Silvina , Chahla Rossana Elena , Bellomio Augusto , Albarracín Virginia Helena 
Published: November 2023

AbstractEpidemiology based on the detection of pathogens in wastewater is extremely useful in providing information about a population’s health status. This study aimed to analyze and report the epidemiological dynamics of SARS-CoV-2 in the province of Tucumán, Argentina during the second and third surges of COVID-19 between April 2021 and March 2022. The study aimed to quantify SARS-CoV-2 RNA in wastewater, correlating it with clinically reported COVID-19 cases. Wastewater samples (n=72) were collected from 16 sampling points located in 3 cities of Tucumán (San Miguel de Tucumán, Yerba Buena y Banda del Río Salí). Detection of viral nucleocapsid markers (N1 gene) was carried out using one-step RT-qPCR. Viral loads were determined for each positive sample using a standard curve. A positive correlation (p<0.05) was observed between viral load (copies/mL) and the clinically confirmed COVID-19 cases reported during the sampling period in San Miguel de Tucumán. Our research findings provided a crucial insight into the dynamics of SARS-CoV-2 infection during epidemic outbreaks. The implementation of wastewater monitoring has proven to be an invaluable epidemiological tool, facilitating early detection of potential surges in COVID-19 cases, and enabling a comprehensive tracking of the pandemic. Our study underscores the significance of incorporating SARS-CoV-2 genome-based surveillance as a standard practice which will contribute to anticipating any future spikes in infections.
Navigational Bronchoscopy versus Computed Tomography-guided Transthoracic Needle Biopsy for the Diagnosis of Indeterminate Lung Nodules: protocol and rationale for the VERITAS multicenter randomized trial
Authors: Lentz Robert J. , Frederick-Dyer Katherine , Planz Virginia B. , Koyama Tatsuki , Aboudara Matthew C. , Swanner Briana , Roller Lance , Low See-Wei , Salmon Cristina , Avasarala Sameer K. , Hoopman Todd C. , Wahidi Momen M. , Mahmood Kamran , Cheng George Z. , Katsis James M. , Kurman Jonathan S. , D’Haese Pierre-François , Johnson Joyce , Grogan Eric L. , Walston Charla , Yarmus Lonny , Silvestri Gerard A. , Rickman Otis B. , Rahman Najib M. , Maldonado Fabien 
Published: November 2023

ABSTRACTBackgroundLung nodule incidence is increasing. Many nodules require biopsy to discriminate between benign and malignant etiologies. The gold-standard for minimally invasive biopsy, computed tomography-guided transthoracic needle biopsy (CT-TTNB), has never been directly compared to navigational bronchoscopy, a modality which has recently seen rapid technological innovation and is associated with improving diagnostic yield and lower complication rate. Current estimates of the diagnostic utility of both modalities are based largely on non-comparative data with significant risk for selection, referral, and publication biases.MethodsThe VERITAS trial (naVigationEndoscopy toReach Indeterminate lung nodules versusTransthoracic needleAspiration, a randomized controlledStudy) is a multicenter, 1:1 randomized, parallel-group trial designed to ascertain whether electromagnetic navigational bronchoscopy with integrated digital tomosynthesis is noninferior to CT-TTNB for the diagnosis of peripheral lung nodules 10-30 mm in diameter with pre-test probability of malignancy of at least 10%. The primary endpoint is diagnostic accuracy through 12 months follow-up. Secondary endpoints include diagnostic yield, complication rate, procedure duration, need for additional invasive diagnostic procedures, and radiation exposure.DiscussionThe results of this rigorously designed trial will provide high-quality data regarding the management of lung nodules, a common clinical entity which often represents the earliest and most treatable stage of lung cancer. Several design challenges are described. Notably, all nodules are centrally reviewed by an independent interventional pulmonology and radiology adjudication panel relying on pre-specified exclusions to ensure enrolled nodules are amenable to sampling by both modalities while simultaneously protecting against selection bias favoring either modality. Conservative diagnostic yield and accuracy definitions with pre-specified criteria for what non-malignant findings may be considered diagnostic were chosen to avoid inflation of estimates of diagnostic utility.Trial registrationClinicalTrials.govNCT04250194
Cardiomyopathy in patients with acute ischemic stroke and methamphetamine use: Relevance for cardioembolic stroke and outcome
Authors: Lee Sook Joung , Liu Shimeng , Blackwill Haley , Stradling Dana , Shafie Mohammad , Yu Wengui 
Published: November 2023

ABSTRACTMethamphetamine use has emerged as a major risk factor of cardiovascular and cerebrovascular disease in young adults. The aim of this study was to investigate the relevance of methamphetamine use and cardiomyopathy in patients with acute ischemic stroke.We performed a retrospective study of consecutive patients with acute ischemic stroke admitted at our medical center between 2019 and 2022. All patients were screened for methamphetamine use and cardiomyopathy defined as left ventricular ejection fraction ≤ 45%. Methamphetamine use was identified by self-reported history of use and/or positive urine drug screen. Logistic regression model was performed to analyze the relevance of methamphetamine-associated cardiomyopathy and cardioembolic stroke.Among 973 consecutive patients screened for the study, 48 (4.9%) were identified to have methamphetamine use. Compared with Non-meth group (n=892), the patients in the Meth group were significantly younger (53.2 ± 10.0 vs. 69.7 ± 15.2, p <0.001), more likely male (76.6% vs. 50.0%, p <0.001), and associated with significantly higher rate of cardiomyopathy (30.4% vs. 14.0%, p <0.01). They were also less likely to have history of atrial fibrillation (8.7% vs. 33.4%, p<0.01) or hyperlipidemia (28.3% vs. 51.7%, p <0.01). Compared with patients with cardiomyopathy without methamphetamine use, those with methamphetamine use and cardiomyopathy had better functional outcome at 3 months, likely due to younger age and fewer comorbidities. In the logistic regression model, methamphetamine-associated cardiomyopathy was found to be a significant risk factor of cardioembolic stroke (OR 2.88, 95% CI 1.81-4.58, p < 0.0001).Our results demonstrate that methamphetamine use increases the risk of cardiomyopathy and cardioembolic stroke in young adults.
Effect of outpatient cardiac rehabilitation following in-hospital stroke rehabilitation on motor function and health-related quality of life in stroke survivors
Authors: Yokota Chiaki , Kamada Masatoshi , Nakatsuka Kiyomasa , Takegami Misa , Miura Hiroyuki , Murata Makoto , Nishizono Hiroaki , Nishimura Kunihiro , Goto Yoichi 
Published: November 2023

BackgroundOutpatient cardiac rehabilitation (CR) is a promising tool for improving functional outcome in stroke survivors, however, evidence for improving emotional health is limited. We aimed to clarify the effects of outpatient CR following in-hospital stroke rehabilitation on health-related quality of life (HRQOL) and motor function.MethodsPatients with acute ischemic stroke or transient ischemic attack discharged directly home were recruited, and 128 patients (male, 92, mean age,73.5 years) who fulfilled criteria for insurance coverage of CR were divided into the CR (+) group (n=46) and CR (−) group (n=82). All patients underwent in-hospital stroke rehabilitation, and within 2 months after stroke onset, patients in the CR (+) group started a 3-month outpatient CR program of supervised outpatient sessions (1-3 times/week). Changes of motor function and HRQOL assessed by the short form-36 version 2 (SF-36) from discharge to 3 months post-discharge were compared between the two groups.ResultsTwenty-six patients in the CR (+) group completed the program and 66 patients in the CR (−) group were followed up at a 3-month examination. Least-square mean changes in 6-minute walk distance and isometric knee extension muscle strength were significantly higher in the CR (+) group than the CR (−) group (52.6 vs. 16.3 m; 10.1 vs. 3.50 kgf/kg). Improvement of HRQOL at 3 months was not observed in the CR (+) group.ConclusionsOutpatient CR followed by in-hospital stroke rehabilitation within 2 months after stroke onset improved exercise tolerance and functional strength but not HRQOL after completion of CR.
Assessing Facioscapulohumeral Muscular Dystrophy through Comparative Analysis of Bulk and Single-Cell Transcriptomes
Authors: Sayad Saed , Hiatt Mark , Mustafa Hazem 
Published: November 2023

AbstractBackgroundFacioscapulohumeral muscular dystrophy (FSHD) is a genetic disorder characterized by progressive weakening of the muscles. While the two types of FSHD (FSHD1 and FSHD2) have distinct genetic causes, they share similarities in their clinical presentations. Both result in muscle weakness, particularly in the face, shoulders, and upper arms. Genetic testing is essential for accurately diagnosing the specific type of FSHD and guiding treatment and management.MethodWe acquired bulk and single-cell gene expression data for FSHD2 from theNIH portal website. Our analysis involved an extensive array of differentially expressed genes, and pathway and gene ontology analysis. Using statistical tests, we identified the top up- and down-regulated genes, and the pathways and gene ontology terms characterizing those genes that exhibited substantial changes across both bulk and single-cell transcriptomes.ResultsThe top 10 up-regulated genes identified in the bulk gene expression analysis represent a diverse range of biological functions, but all are associated with FSHD. In contrast to the bulk down-regulated genes, the single-cell top 10 down-regulated genes are primarily linked to muscle-related functions. These genes, such asACTC1, ACTA1, MYL11, MYH3, MYL6B, MYBPH, TPM2, MYL2, MYL1, andTNNI1are integral to muscle contraction and skeletal muscle function. Moreover, all the top 10 single-cell down-regulated pathways are implicated in the pathogenesis of muscle dystrophy. Finally, the top 10 down-regulated gene ontology terms are all relevant to the pathogenesis of muscular dystrophy.ConclusionsThis study unequivocally demonstrates that single-cell transcriptomics surpasses bulk transcriptomics in elucidating the genes, pathways, biological processes, molecular functions, and cellular components associated with FSHD2. While bulk transcriptomics offers a broader perspective on gene expression, single-cell transcriptomics shines in its capacity to unveil cell-specific gene regulation, especially in the realm of muscle-related functions.
Intra-cellular accumulation of amyloid is a marker of selective neuronal vulnerability in Alzheimer’s disease
Authors: Caramello Alessia , Fancy Nurun , Tournerie Clotilde , Eklund Maxine , Chau Vicky , Adair Emily , Papageorgopoulou Marianna , Jackson Johanna , Hardy John , Matthews Paul M. 
Published: November 2023

ABSTRACTCharacterisation of vulnerable neurons that die earliest with Alzheimer’s disease (AD) could provide rationale treatment targets to slow or prevent neurodegeneration. We used imaging mass cytometry to identify the neuronal sub-types lost earliest in AD and explored associated mechanisms with paired single nuclear transcriptomics inpost-mortemmiddle temporal gyri from diseased donors. We found L5-6 RORB+and L3-6 GAD1+neurons show the greatest loss in AD. These neuronal subtypes also accumulated β-amyloids intracellularly. By contrast, pTau+tangles progressively formed in a distinct L3 RORB+GPC5+subtype that appeared resilient. Both astrocytes and microglia expressed reactive phenotype markers with AD and reactive microglia were spatially associated with vulnerable neurons. RORB+neuronal sub-types accumulating either amyloids or pTau showed increased expression of autophagy-related genes. In conclusion, we identified layer- and neuronal subtype-specific loss with AD that suggest intrinsic autophagy-related defects associated with intracellular accumulation of β-amyloids, rather than pTau, may initiate early neurodegeneration.
Care home’s resilience during the pandemic: changing to adapt
Authors: Da Silva Miguel Vasconcelos , Khan Zunera , Austbø Holteng Lise Birgitte , Gjestsen Martha Therese , Aarsland Dag , Testad Ingelin 
Published: November 2023

AbstractIntroductionThe unfolding of the pandemic in 2020 led to an unprecedented level of stress in care homes, including adjustments and changes within this pivotal service to the community in coping with the increased pressures on and need of support for the National Health Service (NHS). Care homes (CH) were crucial in providing healthcare services, but the support given to them was limited and lacked strategic information that enabled them to experience better outcomes. It was important to understand the CH’s views and strategies and how these endured during the pandemic.MethodsA total of 220 CH from the Care Home Research Network (CHRN) were invited to take part in an on-line survey, where 51 CH completed the survey. The survey comprised demographic- and open-ended questions concerning the service and adaptations/adjustments made within CH during the pandemic.ResultsCH staff reported an increase in the level of stress in their roles, including their workload, due to COVID-19, which made it difficult to cope with their tasks. CH also reported the fear of uncertainty, with some CH saying there was a lack of information. Loneliness and depression were reported as colossally increasing for residents. CH made changes to their working ways and spaces, adopting a more frequent use of technology platforms to meet residents’ needs.ConclusionCH were resilient and adaptable to highly stressful challenges, ensuring residents’ need were met. CH felt a huge pressure to support wider health services, whilst having to deal with uncertainty, staff and supply shortages as well as cope with the loss of residents. Nevertheless, CH reinvented themselves, promoted more teamwork and used supporting channels, including investment in technology to facilitate communication between residents’ and families but also with supporting services such as general practitioners (GPs). Despite these changes, loneliness and depression amongst residents was reported as high. Highlighting the need to assess the long-term impacts of this on residents includes the development of interventions or strategies that will reduce depression/loneliness.
South Asia’s unprotected poor: a systematic review of why social protection programs fail to reach their potential
Authors: Javed Warda , Mumtaz Zubia 
Published: November 2023

AbstractThe incongruity between South Asia’s economic growth and extreme poverty has led to a growing interest in social protection and the subsequent implementation of anti-poverty programs. These work to promote inclusive growth and ensure that the poor do not get left behind. However, many programs have systematically failed to achieve their full potential in reaching the poorest of the poor. We reviewed the literature to understand the determinants behind this inequity in South Asia.A search of four databases, EconLit, Global Health Database, MEDLINE, SocINDEX, supplemented by citation tracking and an external search, yielded 42 papers evaluating 23 social protection programs. All articles were assessed for quality using the GRADE and GRADE CERQual criteria. Data were analyzed using Thomas & Harding’s thematic synthesis approach to generate new higher-order interpretations.Our analysis identified five themes underscoring program processes that stop resources from reaching the poor. These include: (1) structurally flawed program theories that overlook the complexities of poverty and are instead rooted in simplistic cause-and-effect approaches overestimating the poor’s gain from participation; (2) elite capture of program resources through the direct appropriation of benefits, their powerful positioning in program implementation, and their ability to dictate the poor’s accessibility through relationships of patronage and withholding of information; (3) insufficient targeting strategies to reach the poorest and a subsequent redirection of resources toward the rich; (4) program designs that overlook gender-based restrictions, hidden costs, the poor’s lack of legal documentation, and their physical and social exclusion; (5) some of the poorest households actively choosing self-exclusion from social protection due to a desire to maintain dignity, a lack of capital, and a perception of programs as substandard.The review highlights the disconnect between social protection program designs and the ground realities of their ‘ideal’ beneficiaries: the poorest of the poor. We propose the persistence of this well-documented disconnect may stem from three sources. First, there is an unclear understanding of who the poor are in South Asia, with definitions overlooking the historical influence of the caste system. Western perceptions of poverty continue to dominate the discourse. The second challenge is effective engagement and co-production of knowledge with the poor. Lastly, despite encouragement of international collaboration, fast-paced funding calls do not allocate sufficient time to build relationships with the poor primary stakeholders. We suggest the possibility that maintenance of this disconnect is intentional, reflecting a broader power dynamic in which the global and local elite dictate the lives of the poor based on geopolitical interests and national priorities.
LST-AI: a Deep Learning Ensemble for Accurate MS Lesion Segmentation
Authors: Wiltgen Tun , McGinnis Julian , Schlaeger Sarah , Kofler Florian , Voon CuiCi , Berthele Achim , Bischl Daria , Grundl Lioba , Will Nikolaus , Metz Marie , Schinz David , Sepp Dominik , Prucker Philipp , Schmitz-Koep Benita , Zimmer Claus , Menze Bjoern , Rueckert Daniel , Hemmer Bernhard , Kirschke Jan , Mühlau Mark , Wiestler Benedikt 
Published: November 2023

AbstractAutomated segmentation of brain white matter lesions is crucial for both clinical assessment and scientific research in multiple sclerosis (MS). Over a decade ago, we introduced an engineered lesion segmentation tool, LST. While recent lesion segmentation approaches have leveraged artificial intelligence (AI), they often remain proprietary and difficult to adopt. As an open-source tool, we present LST-AI, an advanced deep learning-based extension of LST that consists of an ensemble of three 3D-UNets.LST-AI explicitly addresses the imbalance between white matter (WM) lesions and non-lesioned WM. It employs a composite loss function incorporating binary cross-entropy and Tversky loss to improve segmentation of the highly heterogeneous MS lesions. We train the network ensemble on 491 MS pairs of T1w and FLAIR images, collected in-house from a 3T MRI scanner, and expert neuroradiologists manually segmented the utilized lesion maps for training. LST-AI additionally includes a lesion location annotation tool, labeling lesion location according to the 2017 McDonald criteria (periventricular, infratentorial, juxtacortical, subcortical). We conduct evaluations on 103 test cases consisting of publicly available data using the Anima segmentation validation tools and compare LST-AI with several publicly available lesion segmentation models.Our empirical analysis shows that LST-AI achieves superior performance compared to existing methods. Its Dice and F1 scores exceeded 0.62, outperforming LST, SAMSEG (Sequence Adaptive Multimodal SEGmentation), and the popular nnUNet framework, which all scored below 0.56. Notably, LST-AI demonstrated exceptional performance on the MSSEG-1 challenge dataset, an international WM lesion segmentation challenge, with a Dice score of 0.65 and an F1 score of 0.63—surpassing all other competing models at the time of the challenge. With increasing lesion volume, the lesion detection rate rapidly increased with a detection rate of >75% for lesions with a volume between 10mm3and 100mm3.Given its higher segmentation performance, we recommend that research groups currently using LST transition to LST-AI. To facilitate broad adoption, we are releasing LST-AI as an open-source model, available as a command-line tool, dockerized container, or Python script, enabling diverse applications across multiple platforms.
Local reflects global: Life-stage dependent changes in the phenology of coastal habitat use by North Sea herring
Authors: Rademaker Mark , Peck Myron A. , van Leeuwen Anieke 
Published: November 2023

AbstractClimate warming is affecting the suitability and utilisation of coastal habitats by marine fishes around the world. Phenological changes are an important indicator of population responses to climate-induced changes but remain difficult to detect in marine fish populations. The design of large-scale monitoring surveys does not allow fine-grained temporal inference of population responses, while the responses of ecologically and economically important species groups such as small pelagic fish are particularly sensitive to temporal resolution. Here, we use the longest, highest-resolution time series of species composition and abundance of marine fishes in northern Europe to detect possible phenological shifts in the small pelagic North Sea herring. We detect a clear forward temporal shift in the phenology of nearshore habitat use by small juvenile North Sea herring. This forward shift can best be explained by changes in water temperatures in the North Sea. We find that reducing the temporal resolution of our data to reflect the resolution typical of larger surveys makes it difficult to detect phenological shifts and drastically reduces the effect sizes of environmental covariates such as seawater temperature. Our study therefore shows how local, long-term, high-resolution time series of fish catches are essential to understand the general phenological responses of marine fishes to climate warming and to define ecological indicators of system-level changes.
Cryptococcus neoformansSlu7 ensures nuclear positioning during mitotic progression through RNA splicing
Authors: Krishnan Vishnu Priya , Negi Manendra Singh , Peesapati Raghavaram , Vijayraghavan Usha 
Published: November 2023

AbstractThe position of the nucleus before it divides during mitosis is variable in different budding yeasts. Studies in the pathogenic intron-rich fungusCryptococcus neoformansreveal that the nucleus moves entirely into the daughter bud before its division. Here, we report functions of a zinc finger motif containing spliceosome proteinC. neoformansSlu7 (CnSlu7) in cell cycle progression. The budding yeast and fission yeast homologs of Slu7 have predominant roles for intron 3’ splice site definition during pre-mRNA splicing. Using a conditional knockdown strategy, we show CnSlu7 is an essential factor for viability and is required for efficient cell cycle progression with major role during mitosis. Aberrant nuclear migration, including improper positioning of the nucleus as well as the spindle, were frequently observed in cells depleted of CnSlu7. However, cell cycle delays observed due to Slu7 depletion did not activate the Mad2-dependent spindle assembly checkpoint (SAC). Mining of the global transcriptome changes in the Slu7 knockdown strain identified downregulation of transcripts encoding several cell cycle regulators and cytoskeletal factors for nuclear migration, and the splicing of specific introns of these genes was CnSlu7 dependent. To test the importance of splicing activity of CnSlu7 on nuclear migration, we complemented Slu7 knockdown cells with an intron lessPAC1minigene and demonstrated that the nuclear migration defects were significantly rescued. These findings show that CnSlu7 regulates the functions of diverse cell cycle regulators and cytoskeletal components, ensuring timely cell cycle transitions and nuclear division during mitosis.