bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailored magnetic resonance fingerprinting of post-operative pediatric brain tumor patients
Authors: Poojar Pavan , Qian Enlin , Jin Zhezhen , Fung Maggie , Maddocks Alexis B , Geethanath Sairam 
Published: September 2022

AbstractPurposeBrain and spinal cord tumors are the second most common cancer in children and account for one out of four cancers diagnosed. However, the long acquisition times associated with acquiring both data types prohibit using quantitative MR (qMR) in pediatric imaging protocols. This study aims to demonstrate the tailored magnetic resonance fingerprinting’s (TMRF) ability to simultaneously provide quantitative maps (T1, T2) and multi-contrast qualitative images (T1weighted, T1FLAIR, T2weighted) rapidly in pediatric brain tumor patients.MethodsIn this work, we imaged five pediatric patients with brain tumors (resected/residual) using TMRF at 3T. We compared the TMRF-derived T2weighted images with those from the vendor-supplied sequence (as the gold standard, GS) for healthy and pathological tissue signal intensities. The relaxometric maps from TMRF were subjected to a region of interest (ROI) analysis to differentiate between healthy and pathological tissues. We performed the Wilcoxon rank sum test to check for significant differences between the two tissue types.ResultsWe found significant differences (P < 0.05) in both T1and T2ROI values between the two tissue types. A strong correlation was found between the TMRF-based T2weighted and GS signal intensities for the healthy (correlation coefficient, r = 0.99) and pathological tissues (r = 0.88).ConclusionThe TMRF implementation provides the two relaxometric maps and can potentially save ∼2 minutes if it replaces the T2-weighted imaging in the current protocol.
How do the activities of daily living decline in people living with rarer dementias? A systematic review
Authors: Taylor Beatrice , Mohamud Suraya , Brotherhood Emilie V , Harding Emma , Waddington Claire , Camic Paul M , Alexander Daniel C , Crutch Sebastian J , Stott Joshua , Hardy Chris , Oxtoby Neil P 
Published: September 2022

AbstractObjectiveTo study how activities of daily living (ADLs) decline over the progressive course of rarer dementias (prevalence below 10%), in a systematic review of the literature.Methods Relevant studies were identified by searching Medline, Embase, Emcare, PsycINFO and Cinahl. The databases were searched for terms relating to (rarer dementias) AND (activities of daily living) AND (longitudinal OR cross-sectional studies), using a pre-established protocol registered with the international prospective register of systematic reviews (registration: CRD42021283302).ResultsA total of 579 articles were screened for relevant content, of which 20 full-text publications were included in the analysis. Nineteen studies were about rarer dementias on the frontotemporal dementia/primary progressive aphasia spectrum, and one was about posterior cortical atrophy. Long term description of decline was limited to just seven studies following patients for longer than five years. The rate of decline, sequence of symptom onset, and symptom duration were also highlighted.ConclusionDescriptions of ADL progression were inadequately long term, covering an average of 3.5 years from symptom onset, and lacked phenotypic specificity. The literature disproportionately studied dementias on the frontotemporal dementia spectrum. To facilitate better care, more longitudinal data, quantitative analyses, and development of rarer dementia-specific ADL scales is needed. Given the low prevalence of rarer dementias, big data analyses may never be applicable and so personalised medicine approaches should be pursued, including innovative possibilities in digital biomarkers such as from wearable technology.
Commercial immunoglobulin products now contain neutralising antibodies against SARS-CoV-2 spike protein which are detectable in patient serum
Authors: Upasani Vinit , O’Sullivan Mary , Moreira Fernando , Workman Sarita , Symes Andrew , Burns Siobhan O , Tadros Susan , McCoy Laura , Lowe David M 
Published: September 2022

AbstractAntibody-deficient patients respond poorly to COVID-19 vaccination and are at risk of severe or prolonged infection. Prophylaxis with anti-SARS-CoV-2 monoclonal antibodies has been considered. We here demonstrate that many immunoglobulin preparations now contain neutralising anti-SARS-CoV-2 antibodies which are transmitted to patients in good concentrations, albeit with significant differences between products.
Wastewater surveillance of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus (RSV), rhinovirus, and seasonal coronaviruses during the COVID-19 pandemic
Authors: Boehm Alexandria B. , Hughes Bridgette , Duong Dorothea , Chan-Herur Vikram , Buchman Anna , Wolfe Marlene K. , White Bradley J. 
Published: September 2022

AbstractBackgroundRespiratory disease is a major cause of morbidity and mortality; however, current surveillance for circulating respiratory viruses is passive and biased. Seasonal circulation of respiratory viruses changed dramatically during the COVID-19 pandemic. More active methods for understanding respiratory disease dynamics are needed to better inform public health response and to guide clinical decision making. Wastewater-based epidemiology has been used to understand COVID-19, influenza A, and RSV infection rates at a community level, but has not been used to investigate other respiratory viruses.MethodsWe measured concentrations of influenza A and B, RSV A and B, human parainfluenza (1-4), rhinovirus, seasonal human coronaviruses, and human metapneumovirus RNA in wastewater solids three times per week for 17 months spanning the COVID-19 pandemic at a wastewater treatment plant in California, USA. Novel probe-based assays were developed and validated for non-influenza viral targets. We compared viral concentrations to positivity rates for viral infections from clinical specimens submitted to sentinel laboratories.FindingsWe detected RNA from all target viruses in wastewater solids. Human rhinovirus and seasonal coronaviruses were found at highest concentrations. Concentrations of viruses correlated significantly and positively with positivity rates of associated viral diseases from sentinel laboratories. Measurements from wastewater indicated limited circulation of RSV A and influenza B, and human coronavirus OC43 dominated the seasonal human coronavirus infections while human parainfluenza 1 and 4A dominated among parainfluenza infections.InterpretationWastewater-based epidemiology can be used to obtain information on circulation of respiratory viruses at a community level without the need to test many individuals because a single sample of wastewater represents the entire contributing community. Results from wastewater can be available within 24 hours of sample collection, allowing real time information to inform public health response, clinical decision making, and individual behavior modifications.
Reduction of pro-inflammatory effector functions through remodeling of fatty acid metabolism in CD8+ T-cells from Rheumatoid Arthritis patients
Authors: Kraus Franziska V. , Keck Simon , Klika Karel D. , Graf Jürgen , Carvalho Rui A. , Lorenz Hanns-Martin , Souto-Carneiro M Margarida 
Published: September 2022

AbstractObjectivesRA CD8+ T-cells (CD8) maintain their effector pro-inflammatory phenotype by changing their metabolism towards aerobic glycolysis. However, their massive energetic and biosynthetic needs may require additional substrates to furnish this high demand. Since systemic alterations in lipid metabolism have been reported in RA patients, we explored the role of fatty acid (FA) metabolism in CD8 to identify potential targets to curb their pro-inflammatory potential.MethodsThe expression of FA metabolism-related genes was analyzed for total and CD8-subsets from RA patients and healthy controls (CNT). Peripheral-blood CD8 were isolated from RA, PsA, SpA patients under different therapies (DMARD, biologicals, JAK-inhibitors) and CNT and were TCR-stimulated with or without FA metabolism inhibitors. We quantified the expression of the main FA transporters, lipid uptake, intracellular content of (un-)saturated FA, cytokine production, activation, proliferation, and capacity to inhibit tumor cell growth.ResultsThe CD8 gene expression profile of FA metabolism-related genes was significantly different between untreated RA patients and CNT. RA patients with a good clinical response after 6 months MTX therapy significantly increased the expression of FA metabolism-related genes. Cell-surface expression of FA transporters FABP4 and GPR84 and FA-uptake was higher in effector and memory CD8 of RA patients than for CNT. In vitro blockade of FA metabolism significantly impaired CD8 effector functions.ConclusionsRA CD8 present an altered FA-metabolism which can be potential therapeutic targets to control their pro-inflammatory profile, especially by targeting the transport and oxidation of free FAs which are abundant in the serum and synovial fluid of patients.
Mapping associations of polygenic scores with autism and ADHD traits in a single city region
Authors: Reed Zoe E. , Thomas Richard , Boyd Andy , Griffith Gareth J. , Morris Tim T. , Rai Dheeraj , Manley David , Smith George Davey , Davis Oliver S.P. 
Published: September 2022

AbstractBackgroundThe genetic and environmental aetiology of autistic and Attention Deficit Hyperactivity Disorder (ADHD) traits is known to vary spatially, but does this translate into variation in the association of specific common genetic variants?MethodsWe mapped associations between polygenic scores for autism and ADHD and their respective traits in the Avon Longitudinal Study of Parents and Children (N=4,255 to 6,165) across the area surrounding Bristol, UK, and compared them to maps of environments associated with the prevalence of autism and ADHD.ResultsOur maps suggest genetic associations vary spatially, with consistent patterns for autistic traits across polygenic scores constructed at different p-value thresholds. Patterns for ADHD traits were more variable across thresholds. We found that the spatial distributions often correlated with known environmental influences.ConclusionsThese findings shed light on the factors that contribute to the complex interplay between the environment and genetic influences in autism and ADHD traits.Key pointsThe prevalence of autism and ADHD vary spatially.Our study highlights that genetic influences based on PGS also vary spatially.This spatial variation correlates with spatial variation in environmental characteristics as well, which would be interesting to examine further.Our findings have implications for future research in this area examining the factors that contribute to the complex interplay between the environment and genetic influences on autistic and ADHD traits.
Large-Scale Application of Named Entity Recognition to Biomedicine and Epidemiology
Authors: Raza Shaina , Reji Deepak John , Shajan Femi , Bashir Syed Raza 
Published: September 2022

AbstractBackgroundDespite significant advancements in biomedical named entity recognition methods, the clinical application of these systems continues to face many challenges: (1) most of the methods are trained on a limited set of clinical entities; (2) these methods are heavily reliant on a large amount of data for both pretraining and prediction, making their use in production impractical; (3) they do not consider non-clinical entities, which are also related to patient’s health, such as social, economic or demographic factors.MethodsIn this paper, we develop Bio-Epidemiology-NER (https://pypi.org/project/Bio-Epidemiology-NER/) an open-source Python package for detecting biomedical named entities from the text. This approach is based on Transformer-based approach and trained on a dataset that is annotated with many named entities (medical, clinical, biomedical and epidemiological). This approach improves on previous efforts in three ways: (1) it recognizes many clinical entity types, such as medical risk factors, vital signs, drugs, and biological functions; (2) it is easily configurable, reusable and can scale up for training and inference; (3) it also considers non-clinical factors (age and gender, race and social history and so) that influence health outcomes. At a high level, it consists of the phases: preprocessing, data parsing, named entity recognition and named entities enhancement.ResultsExperimental results show that our pipeline outperforms other methods on three benchmark datasets with macro-and micro average F1 scores around 90 percent and above.ConclusionThis package is made publicly available for use by researchers, doctors, clinicians and anyone to extract biomedical named entities from unstructured biomedical texts.Author SummaryThis paper introduces and presents a python packagehttps://pypi.org/project/Bio-Epidemiology-NER/that can extract named entities from the biomedical texts. Different from previous works, this package extracts not only clinical entities, such as disease, signs, symptoms but also demographics of the patients from the texts. This package can be used with least code requirements and can be used by epidemiologists, doctors, practitioners or others in the field to see the named entities from texts. The knowledge gained from the named entities help the end users to see the statistics or spread of infectious disease in least time and while parsing a large amount of free texts.
Intestinal helminth infection impairs oral and parenteral vaccine efficacy
Authors: Hardy LaKeya C. , Kapita Camille M. , Campbell Evelyn , Hall Jason A. , Urban Joseph F. , Belkaid Yasmine , Nagler Cathryn R. , Iweala Onyinye I. 
Published: September 2022

ABSTRACTThe impact of endemic parasitic infection on vaccine efficacy is an important consideration for vaccine development and deployment. We have examined whether intestinal infection with the natural murine helminthHeligmosomoides polygyrus bakerialters antigen-specific antibody and cellular immune responses to oral and parenteral vaccination in mice. We found that oral vaccination of mice with a clinically relevant, live, attenuated, recombinantSalmonellavaccine that expresses chicken egg ovalbumin (Salmonella-OVA) disrupts ovalbumin-specific regulatory T cell networks in the gut associated lymphoid tissue and promotes T-effector responses to OVA. Chronic intestinal helminth infection significantly reduced Th1-skewed antibody responses to oral vaccination withSalmonella-OVA. Activated, adoptively-transferred, OVA-specific CD4+T cells accumulated in draining mesenteric lymph nodes (MLN) of vaccinated mice, irrespective of their helminth-infection status. However, helminth infection increased the frequencies of adoptively-transferred OVA-specific CD4+T cells producing IL-4 and IL-10 in the MLN. Chronic intestinal helminth infection also significantly reduced Th2-skewed antibody responses to parenteral vaccination with OVA adsorbed to alum. These findings suggest helminth-induced impairment of vaccine antibody responses may be driven by the development of IL-10-secreting CD4+T regulatory cells. They also underscore the potential need to treat parasitic infection before mass vaccination campaigns in helminth-endemic areas.
Comprehensive evaluation of harmonization on functional brain imaging for multisite data-fusion
Authors: Wang Yu-Wei , Chen Xiao , Yan Chao-Gan 
Published: September 2022

ABSTRACTTo embrace big-data neuroimaging, harmonization of site effect in resting-state functional magnetic resonance imaging (R-fMRI) data fusion is a fundamental challenge. Comprehensive evaluation of potentially effective harmonization strategies, particularly with specifically collected data has been rare, especially for R-fMRI metrics. Here, we comprehensively assess harmonization strategies from multiple perspectives, including efficiency, individual identification, test-retest reliability and replicability of group-level statistical results, on widely used R-fMRI metrics across multiple datasets including data obtained from the same participants scanned at several sites. For individual identifiability (i.e., whether the same subject could be identified across R-fMRI data scanned across different sites), we found that, while most methods decreased site effects, the Subsampling Maximum-mean-distance based distribution shift correction Algorithm (SMA) outperformed linear regression models, linear mixed models, ComBat series and invariant conditional variational auto-encoder. Test-retest reliability was better for SMA and adjusted ComBat series than alternatives, while SMA was superior to the latter in replicability, both in terms of Dice coefficient and the scale of brain areas showing sex differences reproducibly observed across datasets. Moreover, we examined test-retest datasets to identify the best target site features to optimize SMA identifiability and test-retest reliability. We noted that both sample size and distribution of the target site matter and introduced a heuristic target site selection formula. In addition to providing practical guidelines, this work can inform continuing improvements and innovations in harmonizing methodologies for big R-fMRI data.
A role for myeloid miR-155 in regulating hypoxia induced seizures in neonatal C57BL/J6 mice
Authors: Dahiya Devika , Smith Jonathan , Strickland Tammy , Morris Delphi , Reschke Cristina , Engel Tobias , Henshall David , McCoy Claire E , Dowling Jennifer K 
Published: September 2022

AbstractHypoxic ischaemic injury (HIE) in the neonatal brain has significant consequences on neurodevelopment and increases the occurrence of neurological deficits in infants. HIE is also a leading cause of neonatal seizures. Therapeutic options for the treatment of HIE are very limited. Hypoxia-ischemia directly damages brain tissue in a primary-wave of injury which activates a cascade of events triggering local and systemic inflammatory responses, driven by the innate immune system, which contribute to a significant secondary-wave of injury taking place as early as 6 hours post-hypoxia-ischaemia. Levels of the well documented inflammatory microRNA, miR-155 are elevated in rodent seizure and epilepsy models. Here, we assessed the impact of, miR-155 deletion in myeloid cells, on regulating inflammation and seizure severity in a preclinical model of neonatal hypoxia-induced seizures (Hypoxia-Sz). Wildtype miR-155 (miR-155+/+LysMCre) mice were compared to a mouse line in which miR-155 was deleted in myeloid cells (miR-155fl/flLysMCre). We demonstrate significant upregulation of miR-155 target genes, brain-derived neurotrophic factor (bdnf), arginase-2 (arg-2),ship-1andsocs-1in miR-155fl/flLysMCre mice compared to controls at various time points following Hypoxia-Sz. Conversely, we report decreased mRNA levels of pro-inflammatory cytokines IL-1β and IL-6 and lower protein levels of IL-1β in miR-155fl/flLysMCre mice as compared to WTs. Myeloid miR-155 deletion significantly reduced behavioural seizure severity score, reduced electrographically (EEG) measured seizure frequency and seizure burden as compared to mice to wildtypes, suggesting miR-155 regulation of seizure occurrence in this model. Behavioural tests for motor functions at 5 weeks post Hypoxia-Sz demonstrated differences between genotypes. Excitingly this work highlights that inhibition of miR-155, specifically in myeloid cells, may hold therapeutic benefit for both seizures and comorbidities associated with hypoxic brain injury.
Validity of fecal sampling for characterizing temporal variation in threespine stickleback’s gut microbiota
Authors: Härer Andreas , Rennison Diana J. 
Published: September 2022

AbstractDiverse microbial communities associated with the guts of their hosts are crucial for many aspects of their hosts’ physiology, ecology, and evolution. The gut microbiota has been characterized for a broad range of species across the animal kingdom. Yet, for many host species we still don’t have a good understanding of whether non-lethal sampling (e.g., fecal matter) can accurately capture the diversity of gut-associated bacterial communities, as estimated from lethal sampling of intestinal tissue. We further lack knowledge on whether such non-lethal sampling methods are suitable for studying temporal gut microbiota dynamics. Here, we addressed these questions in threespine stickleback fish, a model system in evolutionary ecology, by comparing bacterial communities based on 16S rRNA gene sequencing from intestinal tissue and feces. Despite some differences in community composition between the two sample types, we show that bacterial communities of feces and intestinal tissue largely overlap. Further, we were able to detect consistent and significant changes of fecal bacterial communities associated with an experimental diet shift. These results suggest that fecal sampling represents an adequate non-lethal method to characterize the gut microbiota of threespine stickleback. This allows for studying temporal gut microbiota dynamics at the individual level, which increases opportunities for future experimental gut microbiota research.
Somatic chromosomal integration of polydnavirus during parasitism triggered their germline infiltration in multiple lepidopteran families
Authors: Heisserer Camille , Muller Héloïse , Jouan Véronique , Musset Karine , Périquet Georges , Drezen Jean-Michel , Volkoff Anne-Nathalie , Gilbert Clément 
Published: September 2022

AbstractIncreasing numbers of horizontal transfer (HT) of genes and transposable elements are reported in insects. Yet the mechanisms underlying these transfers remain unknown. Here we firs t quantify and characterize the patterns of chromosomal integration of the polydnavirus (PDV) encoded by the Campopleginae Hyposoter didymator parasitoid wasp (HdIV) in somatic cells of parasitized fall armyworm (Spodoptera frugiperda). Polydnaviruses are domesticated viruses injected by wasps together with their eggs into their hosts in order to facilitate the development of wasp larvae. We found that six HdIV DNA circles integrate into the genome of host somatic cells. Each host haploid genome suffers between 23 and 40 integration events (IEs) on average 72 hours post parasitism. Almost all IEs are mediated by DNA double strand breaks occurring in the host integration motif (HIM) of HdIV circles. We show that despite their independent evolutionary origins, PDV from both Campopleginae and Braconidae wasps use remarkably similar mechanisms for chromosomal integration. Next, our similarity search performed on 775 genomes reveals that PDVs of both Campopleginae and Braconidae wasps have recurrently colonized the germline of dozens of lepidopteran species through the same mechanisms they use to integrate into somatic host chromosomes during parasitism. We found evidence of HIM-mediated HT of PDV DNA circles in no less than 124 species belonging to 15 lepidopteran families. Thus, this mechanism underlies a major route of HT of genetic material from wasps to lepidopterans with likely important consequences on lepidopterans.