bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung Microbiome Intervention Attenuates Herpesvirus-Induced Post-HCT Pulmonary Fibrosis Through PD-L1 Upregulation on Dendritic Cells
Authors: Perkins Joshua B. , Ravi Keerthikka , Guo Chunfang , Oh Gina J. , Rodriguez Bellmary G. , Gurczynski Stephen J. , Weinberg Jason B. , Huffnagle Gary B. , O’Dwyer David N. , Moore Bethany B. , Zhou Xiaofeng 
Published: July 2024

AbstractAlterations in the lung microbiome frequently accompany adverse pulmonary outcomes. Hematopoietic cell transplantation (HCT) markedly affects the lung microbiome corresponding with a high incidence of post-HCT pulmonary complications. In a preclinical mouse model of HCT, we observed a reduction inLactobacillus johnsoniiwithin the lung microbiome following transplantation. Intranasal administration of live or heat-killed (HK)L. johnsoniiat low doses reduced gammaherpesvirus-induced pulmonary fibrosis in HCT mice, in which IL-17A plays an essential role. HKL. johnsoniitreatment of HCT mice suppressed inflammatory cytokine production by lung macrophages and decreasedIl17aexpression in T helper 17 (Th17) cells. HKL. johnsoniiincreased PD-L1 expression on the surface of type II conventional dendritic cells (cDC2) in HCT mice andin vitroin bone marrow-derived dendritic cells (BMDCs). HKL. johnsonii-exposed BMDCs also inhibited IL-17A secretion from co-cultured Th17 cells in a PD-1-dependent manner. Notably, when HKL. johnsoniiwas administered to HCT mice reconstituted with bone marrow cells from PD-1 knockout (KO) mice, which lack a PD-L1 mediated response, HKL. johnsonii-mediated reduction of pulmonary fibrosis was negated. Collectively, our findings demonstrate that HKL. johnsoniimitigates herpesvirus-induced pulmonary fibrosis in HCT mice by modulating cDC2 surface expression of PD-L1, which subsequently suppressesIl17aexpression in Th17 cells, pointing towards a potential postbiotic-based strategy for immunomodulation to address pulmonary complications of HCT.
3D bioprinting of low-viscosity phase-separated food-grade bioinks byin situself-assembly
Authors: Oliveira Sara M. , DeSantis Gabriel , Pastrana Lorenzo M. 
Published: July 2024

AbstractThere is a notable gap in the scientific understanding of the cellular role in cultured cell-based foods. Unravelling the effects of the interactions between ingredient micro/nanostructure and cells and their significance on nutrition and texture is of great importance. In addition, bioprinting methods face notable limitations in animal-free formulations and scale. Herein, we introduce a proof-of-concept bioprinting method based on thein situintegration of self-assembling events, allowing printing without supporting baths. Our approach enabled a food-grade 3D bioprinted model with 8.5 mm height and a hardness of 284 mN, supporting the early differentiation of myoblasts producing embryonic myosin heavy chain, after 7 days of differentiation. Cellular protein content increased up to 18-fold per initial cell without changes in construct texture. The method provides a novel concept to produce robust, cell-dense platforms for further research on food-grade bioprinted foods.
Quantifying social roles in multi-animal videos using subject-aware deep-learning
Authors: Goss Kelly , Bueno-Junior Lezio S. , Stangis Katherine , Ardoin Théo , Carmon Hanna , Zhou Jie , Satapathy Rohan , Baker Isabelle , Jones-Tinsley Carolyn E. , Lim Miranda M. , Watson Brendon O. , Sueur Cédric , Ferrario Carrie R. , Murphy Geoffrey G. , Ye Bing , Hu Yujia 
Published: July 2024

ABSTRACTAnalyzing social behaviors is critical for many fields, including neuroscience, psychology, and ecology. While computational tools have been developed to analyze videos containing animals engaging in limited social interactions under specific experimental conditions, automated identification of the social roles of freely moving individuals in a multi-animal group remains unresolved. Here we describe a deep-learning-based system – named LabGym2 – for identifying and quantifying social roles in multi-animal groups. This system uses a subject-aware approach: it evaluates the behavioral state of every individual in a group of two or more animals while factoring in its social and environmental surroundings. We demonstrate the performance of subject-aware deep-learning in different species and assays, from partner preference in freely-moving insects to primate social interactions in the field. Our subject-aware deep learning approach provides a controllable, interpretable, and efficient framework to enable new experimental paradigms and systematic evaluation of interactive behavior in individuals identified within a group.
Characterization of eight newHydractiniai-cell markers reveals underlying heterogeneity in the adult pluripotent stem cell population
Authors: Waletich Justin , de Jong Danielle , Schnitzler Christine E. 
Published: July 2024

AbstractAdult pluripotent stem cells are found in diverse animals, including cnidarians, acoels, and planarians, and confer remarkable abilities such as whole-body regeneration. The mechanisms by which these pluripotent stem cells orchestrate the replacement of all lost cell types, however, remains poorly understood. Underlying heterogeneity within the stem cell populations of these animals is often obscured when focusing on certain tissue types or life history stages, which tend to have indistinguishable spatial expression patterns of stem cell marker genes. Here, we focus on the adult pluripotent stem cells (i-cells) ofHydractinia symbiolongicarpus, a colonial marine cnidarian with distinct polyp types and stolonal tissue. Recently, a single-cell expression atlas was generated forH. symbiolongicarpuswhich revealed two distinct clusters with i-cell signatures, potentially representing heterogeneity within this species’ stem cell population. Considering this finding, we investigated eight new putative stem cell marker genes from the atlas including five expressed in both i-cell clusters (Pcna,Nop58,Mcm4,Ubr7, andUhrf1) and three expressed in one cluster or the other (Pter, FoxQ2-like,andZcwpw1). We characterized their expression patterns in various contexts–feeding and sexual polyps, juvenile feeding polyps, stolon, and during feeding polyp head regeneration–revealing context-dependent gene expression patterns and a transcriptionally dynamic i-cell population. We uncover previously unknown differences within the i-cell population ofHydractiniaand demonstrate that its colonial nature serves as an excellent system for investigating and visualizing heterogeneity in pluripotent stem cells.
Sexually dimorphic auditory representation inAedes aegyptibrains
Authors: Ohashi Takuro S. , Xu Yifeng Y.J. , Shigaki Shunsuke , Nakamura Yukiko , Lee Tai-Ting , Loh YuMin M. , Mishiro-Sato Emi , Eberl Daniel F. , Su Matthew P. , Kamikouchi Azusa 
Published: July 2024

AbstractMale attraction to female flight sounds is a vital, reproducible component of courtship in many species of mosquitoes; however, female acoustic behaviours have proven challenging to define. To investigate sexual dimorphisms in acoustic behaviours, previous reports have largely focused on differences in mosquito peripheral ear anatomy and function. Whilst molecular investigations have recently begun on the auditory periphery, sexual dimorphisms in central processing of acoustic information have not yet been explored. Here we used a combination of neurotracing, calcium imaging and molecular analyses to examine sexual dimorphisms in auditory processing in the yellow fever mosquitoAedes aegypti. We identified shared and dimorphic neurons connecting male and female ears to the primary auditory processing centre in the brain, and defined multiple distinct neuronal clusters based on responses to auditory stimulation. We finally used transcriptomic and proteomic analyses to investigate the molecular factors underlying these differences, with motile ciliary-related terms significantly enriched in males.
A cancer immunotherapy modality based on dendritic cell reprogrammingin vivo
Authors: Ascic Ervin , Åkerström Fritiof , Sreekumar Nair Malavika , Rosa André , Kurochkin Ilia , Zimmermannova Olga , Catena Xavier , Rotankova Nadezhda , Veser Charlotte , Rudnik Michal , Ballocci Tommaso , Schärer Tiffany , Huang Xiaoli , de Rosa Torres Maria , Renaud Emilie , Velasco Santiago Marta , Met Özcan , Askmyr David , Lindstedt Malin , Greiff Lennart , Ligeon Laure-Anne , Agarkova Irina , Svane Inge Marie , Pires Cristiana F. , Rosa Fábio F. , Pereira Carlos-Filipe 
Published: July 2024

AbstractImmunotherapy leads to long-term survival of cancer patients, yet generalized success has been hampered by insufficient antigen presentation and exclusion of immunogenic cells from the tumor microenvironment. Here, we developed an approach to reprogram tumor cellsin vivoby adenoviral delivery of the transcription factors PU.1, IRF8, and BATF3, which enabled them to present antigens as type 1 conventional dendritic cells. Reprogrammed tumor cells remodeled their tumor microenvironment, recruited, and expanded polyclonal cytotoxic T cells, induced complete tumor regressions, and established long-term systemic immunity in different mouse melanoma models. In human tumor spheroids and xenografts, reprogramming to immunogenic dendritic-like cells progressed independently of immunosuppression, which usually limits immunotherapy. Our study paves the way for first-in-human trials and other applications of immune cell reprogrammingin vivo.One-Sentence SummaryReprogramming of tumor cells to cDC1-like cellsin vivoelicits systemic and long-term antitumor immunity.
Unveiling Clonal Cell Fate and Differentiation Dynamics: A Hybrid NeuralODE-Gillespie Approach
Authors: Gao Mingze , Barile Melania , Chabra Shirom , Haltalli Myriam , Calderbank Emily F. , Chao Yiming , Laurenti Elisa , Gottgens Bertie , Huang Yuanhua 
Published: July 2024

AbstractRecent lineage tracing single-cell techniques (LT-scSeq), e.g., the Lineage And RNA RecoverY (LARRY) barcoding system, have enabled clonally resolved interpretation of differentiation trajectories. However, the heterogeneity of clone-specific kinetics remains understudied, both quantitatively and in terms of interpretability, thus limiting the power of bar-coding systems to unravel how heterogeneous stem cell clones drive overall cell population dynamics. Here, we present CLADES, a NeuralODE-based framework to faithfully estimate clone-specific kinetics of cell states from newly generated and publicly available human cord blood LARRY LT-scSeq data. By incorporating a stochastic simulation algorithm (SSA) and differential expression gene (DEGs) analysis, CLADES yields cell division dynamics across differentiation timecourses and fate bias predictions for the early progenitor cells. Moreover, clone-level quantitative behaviours can be grouped into characteristic types by pooling individual clones into meta-clones. By benchmarking with CoSpar, we found that CLADES improves fate bias prediction accuracy at the meta-clone level. In conclusion, we report a broadly applicable approach to robustly quantify differentiation kinetics using meta-clones while providing valuable insights into the fate bias of cellular populations for any organ system maintained by a pool of heterogeneous stem and progenitor cells.
QuickFit: A high-throughput RT-qPCR-based assay to quantify viral growth and fitnessin vitro
Authors: Galvez Nicolas M.S. , Sheehan Maegan L. , Lin Allen Z. , Cao Yi , Lam Evan C. , Jackson Abigail M. , Balazs Alejandro B. 
Published: July 2024

ABSTRACTThe quantification of viral growth rates is key to understanding evolutionary dynamics and the potential for mutants to escape antiviral drugs. Defining evolutionary escape paths and their impact on viral fitness allows for the development of drugs that are resistant to escape. In the case of HIV, combination antiretroviral therapy can successfully prevent or treat infection, but it relies on strict adherence to prevent escape. Here, we present a method that enables the quantification of viral fitness termed QuickFit, which employs large numbers of parallel viral cultures to accurately measure growth rates. QuickFit consistently recapitulated HIV growth measurements obtained by traditional approaches but with significantly higher throughput and lower error. This method represents a promising tool for rapid and consistent evaluation of viral fitness.
The Role of the Clinical Pharmacist in Addressing Drug-Related Problems in Stroke Patients in a Tertiary Care Centre
Authors: Philip Susan , George Jeesa , Kumar A Pramod , Begum Foujia , Divya Bharathi K 
Published: July 2024

ABSTRACTThe morbidity, mortality, and diminished quality of life of patients are all impacted by drug-related problems. Stroke is one of the leading causes of disability and death in India and since the stroke patients are at an increased risk of DRPs (Drug Related Problems), early identification, prevention and resolution of the same is important for improving the quality of life of stroke patients. The aim of the study was to assess the incidence of DRPs in stroke patients by using Hepler-strand classification and the acceptance rate by the multidisciplinary team. The relevant information were documented using a predefined data collection form and was analyzed for drug related problems and categorized according to Hepler–Strand classification. A total of 510 DRPs from 130 participants with an average incidence of 3.92 DRPs per patient. Drug-drug interaction was found to be 23.53% and ADRs accounted for 12.55 % of total DRPs. The study found a high acceptance rate of recommendations by healthcare professionals at 97.36%, with changes in therapy being made 68.13% of the time. Early detection and resolution of DRP by clinical pharmacist may improve the therapeutic outcomes in stroke patients. This also helps in preventing complications and unnecessary hospitalization, high cost of treatment and deaths among stroke patients.
Psychometric characteristics of ADHD-T-5 in its Dari version among public primary school students in Kabul City, Afghanistan
Authors: Azimi Ziauddin , Wang Seok Mui , Khan Jesmine , Ismail Zaliha , Isa Mohamad Rodi 
Published: July 2024

AbstractIntroductionOne of the key instruments used to assess attention-deficit/hyperactivity disorder (ADHD) in children and adolescents is the ADHD Rating Scale-5. This study aimed to test the psychometric characteristics of the ADHD Rating Scale-5 teacher version (ADHD-T) in Dari among school-aged children in Kabul City.MethodsFace and content validity, explanatory factor analysis (EFA), confirmatory factor analysis (CFA) and reliability of the questionnaire were conducted. The structure, validity, and reliability of the scales were evaluated using the translated versions of the ADHD-T questionnaires for the assessment of ADHD in children. Teachers completed the ADHD-T-Dari on behalf of three hundred and fifty-eight public primary school students.ResultsFace validity, content quality, and internal consistency of the ADHD-T-Dari were excellent. Significant collinearity was found between the items of the inattention and/or hyperactivity-impulsivity domains of the ADHD-T-Dari. The Kaiser-Meyer-Olkin index was 0.913 and was satisfactory. The two-factor model of the scale showed a better fit with an RMSEA of 0.065, a CMIN/dfof 20.501, and a CFI of 905 compared to the one- and three-factor models of ADHD-T-Dari. The Cronbach’s alpha for the total ADHD-T-Dari scale with 18 items was 0.898, while it was 0.851 and 0.847 for the inattention and/or hyperactivity-impulsivity subscales with 9 items each.ConclusionThe exploratory and CFA showed that the psychometric qualities have strong concept validity and very good psychometric properties with good reliability. Therefore, the ADHD-T-Dari is valid, reliable, and suitable for the assessment of ADHD symptoms in Afghan school children and adolescents.
Self-Supervised Data-Driven Approach Defines Pathological High-Frequency Oscillations in Human
Authors: Zhang Yipeng , Daida Atsuro , Liu Lawrence , Kuroda Naoto , Ding Yuanyi , Oana Shingo , Kanai Sotaro , Monsoor Tonmoy , Duan Chenda , Hussain Shaun A. , Qiao Joe X , Salamon Noriko , Fallah Aria , Sim Myung Shin , Sankar Raman , Staba Richard J. , Engel Jerome , Asano Eishi , Roychowdhury Vwani , Nariai Hiroki 
Published: July 2024

ABSTRACTObjectiveInterictal high-frequency oscillations (HFOs) are a promising neurophysiological biomarker of the epileptogenic zone (EZ). However, objective criteria for distinguishing pathological from physiological HFOs remain elusive, hindering clinical application. We investigated whether the distinct mechanisms underlying pathological and physiological HFOs are encapsulated in their signal morphology in intracranial EEG (iEEG) recordings and whether this mechanism-driven distinction could be simulated by a deep generative model.MethodsIn a retrospective cohort of 185 epilepsy patients who underwent iEEG monitoring, we analyzed 686,410 HFOs across 18,265 brain contacts. To learn morphological characteristics, each event was transformed into a time-frequency plot and input into a variational autoencoder. We characterized latent space clusters containing morphologically defined putative pathological HFOs (mpHFOs) using interpretability analysis, including latent space disentanglement and time-domain perturbation.ResultsmpHFOs showed strong associations with expert-defined spikes and were predominantly located within the seizure onset zone (SOZ). Discovered novel pathological features included high power in the gamma (30–80 Hz) and ripple (>80 Hz) bands centered on the event. These characteristics were consistent across multiple variables, including institution, electrode type, and patient demographics. Predicting 12-month postoperative seizure outcomes using the resection ratio of mpHFOs outperformed unclassified HFOs (F1=0.72 vs. 0.68) and matched current clinical standards using SOZ resection (F1=0.74). Combining mpHFO data with demographic and SOZ resection status further improved prediction accuracy (F1=0.83).InterpretationOur data-driven approach yielded a novel, explainable definition of pathological HFOs, which has the potential to further enhance the clinical use of HFOs for EZ delineation.
Gasdermin D-Mediated Neutrophil Pyroptosis drives Inflammation in Psoriasis
Authors: Liu Jian , Jiang YuYing , Diao ZiYue , Chen DanDan , Xia RuiYuan , Wang BingWei , Yang Shuo , Yin ZhiQiang 
Published: July 2024

AbstractPsoriasis is a multifactorial immune-mediated inflammatory disease. Its pathogenesis involves abnormal accumulation of neutrophils and T-cell related abnormalities. Pyroptosis is a type of regulated cell death associated with innate immunity, but its role in psoriasis is unclear. In this study, we found thatgasdermin D (Gsdmd)is higher in human psoriatic skin than that in normal skin, and in imiquimod-induced psoriasis-like mouse skin, the expression ofGsdmdwas most significantly altered in neutrophils andIl1bwas also mainly expressed in neutrophils. Immunohistochemical staining of serial sections of skin lesions from psoriasis patients and healthy control also showed that GSDMD expression is higher in psoriasis lesion, especially in neutrophils.Gsdmddeficiency mitigates psoriasis-like inflammation in mice. GSDMD in neutrophils contributes to psoriasis-like inflammation, whileGsdmddepletion in neutrophils attenuates the development of skin inflammation in psoriasis and reduces the release of the inflammatory cytokines. We found that neutrophil pyroptosis is involved in and contributes to psoriasis inflammation, which provides new insights into the treatment of psoriasis by targeting neutrophil pyroptosis.
CAF to the rescue! Potential and challenges of combination antifungal therapy for reducing morbidity and mortality in hospitalized patients with serious fungal infections
Authors: Jacobs Samantha E. , Chaturvedi Vishnu 
Published: July 2024

AbstractThe global burden of invasive fungal disease (IFD) is substantial and escalating. Combination antifungal therapy (CAF) may improve patient outcomes by reducing development of resistance, improving drug penetration and rate of fungal clearance, and allowing for lower, less toxic antifungal drug doses; yet, increased cost, antagonism, drug-drug interactions, and toxicity are concerns. Clinical practice guidelines recommend antifungal monotherapy, rather than CAF, for most IFDs due to a lack of comparative randomized clinical trials. An examination of the existing body of CAF research should frame new hypotheses and determine priorities for future CAF clinical trials. We performed a systematic review of CAF clinical studies for invasive candidiasis, cryptococcosis, invasive aspergillosis, and mucormycosis. Additionally, we summarize findings from animal models of CAF and assess laboratory methods available to evaluate CAF efficacy. Future CAF trials should be prioritized according to animal models showing improved survival and observational clinical data supporting efficacy and safety.
Silence in physician clinical practice: a scoping review protocol
Authors: Kelly Martina Ann , Rivera Stefanie , McClurg Caitlin , Sweeney Catherine , Mosca Stephen , McLeod Ellen , Bennett Deirdre , Brown Megan 
Published: July 2024

AbstractObjectiveThe objective of this review is to map, describe and conceptualize how silence is discussed within literature on interactions between physicians and patients, in clinical settings.MethodsWe will use the methodological framework of Arksey & O’Malley, adapted by Levac et al and Joanna Briggs Institute. Empirical studies including quantitative, qualitative, mixed methods, observational studies and reviews will be included. Commentaries, editorials, and grey literature will also be examined. The databases MEDLINE, Cumulative Index to Nursing and Allied Health Literature, PsycINFO, Scopus and Web of Science will be searched. A two-part study selection strategy will be applied. First, reviewers will follow inclusion and exclusion criteria based on ‘Population-Concept-Context’ framework to independently screen titles and abstracts. Next, full texts will be screened. Data will be extracted, collated, and charted to summarize methods, outcomes and key findings from the articles included.Expected results and implicationsThis scoping review will provide an extensive description of how physicians engage with silence in clinical settings. Findings will identify how silence is perceived in physician patient interactions, the roles it plays, what factors influence use of silence and guide development of educational initiatives on use of silence in clinical settings.