bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using a health equity lens to measure patient experiences of care in diverse healthcare settings
Authors: Browne Annette J. , Varcoe Colleen , Ford-Gilboe Marilyn , Wathen C. Nadine , Wilson Erin , Bungay Vicky , Perrin Nancy 
Published: January 2024

AbstractPeople who are structurally disadvantaged and marginalized often report poor health care experiences due to intersecting forms of stigma and discrimination. There are many measures of patient experiences of care, however, few are designed to measure equity-oriented care. In alignment with ongoing calls to integrate actions in support of health equity, we report on the development and testing of patient experiences of care measures that explicitly use a health equity and intersectional lens. Our analysis focuses on two different equity-oriented health care scales. The first was piloted in a primary health care setting, where patients have an ongoing relationship with providers over time. The second was piloted in an emergency department, where care is provided on an episodic basis. Item Response Theory was used to develop the scales and evaluate their psychometric properties. The primary health care scale, tested with a cohort of 567 patients, showed that providing more equity-oriented health care predicted improvements in important patient self-report health outcomes over time. The episodic scale, tested in an emergency department setting with 284 patients, showed evidence of concurrent validity, based on a high correlation with quality of care. Both scales are brief, easy-to-administer self-report measures that can support organizations to monitor quality of care using an equity lens. The availability of both scales enhances the possibility of measuring equity-oriented health care in diverse contexts. Both scales can shed light on experiences of care using an intersectional lens and equity-oriented lens, providing a nuanced understanding of quality of care.
Self-perceived competence and its determinants among pre-intern (PRINT) doctors in Uganda
Authors: Ssewante Nelson , Wekha Godfrey , Nalunkuma Racheal , Sentongo Lawrence Katumba , Sanyu Bereta , Namusoke Moureen , Nkwanga Ayub , Ahabwe Rachel , Nantagya Vanessa Nalwoga , Kalembe Sharon Esther , Nampeera Catherine , Musoke Phillip , Byakika-Kibwika Pauline 
Published: January 2024

AbstractIntroductionUganda still survives way below the recommended doctor-patient ratio. This problem could be solved by increasing the number of doctors produced in the country annually. Attempts at this are ongoing, however, this is challenged by the absence of quality assurance programs amidst lack of a universal medical curriculum. With inadequate supervision and limited resources in health facilities, transitioning from students’ life to clinical practice is perhaps the most challenging time for an intern doctor. We used the domains of competencies provided by the General Medical Council to assess levels of self-perceived competence and its determinants among pre-intern doctors (PRINTs) in Uganda.MethodsAn online cross-sectional study was conducted using a quantitative questionnaire distributed to confirmed pre-interns in Uganda. Self-perceived competence was determined by 4 Likert scale questions and participants were dichotomized into competent and incompetent using a standardized Bloom’s cutoff criterion. Determinants of self-perceived competence were determined by the ANOVA test.ResultsWe obtained 142 entries. Of these, 68.3% were males; median age was 26 years (range: 22-49). Majority of the participants (78.9%) had no prior medical-related training and only a third (34.5%) had previous work experience. Overall scores were poor and very few participants were confident they attained a satisfactory level of competence through their medical training. Participants reported more competence in basic procedural skills (Mean score: 19.8±3.2/21), followed by Knowledge (Mean score:12.4±3.1/15), with surgical (Mean score:11.5±3.5/18) and Emergency skills (Mean score: 12.5±4.4/21) scoring least. Participants with previous work experience were more likely to report higher competence scores than their counterparts (91.7 vs 84.9, p=0.039).ConclusionThe study shows that majority of PRINTs feel deficient in knowledge and skills to start clinical practice, with less competence in surgical skills and emergency care.There is need to review the training curricula to ensure adequate clinical exposure experiences for a smooth transition to clinical practice.
Global research trends in postoperative ileus from 2011 to 2023: A Scientometric study
Authors: Zhou Yan , Yin Zi-Han , Sun Ming-Sheng , Wang Yang-Yang , Yang Chen , Li Shu-Hao , Liang Fan-Rong , Liu Fang 
Published: January 2024

AbstractObjectiveTo explore the current status, trends, and frontiers of POI research from 2011 to the present based on bibliometric analysis.MethodsPublications published on POI research from 2011 to 2023 were retrieved on June 1, 2023, from the Web of Science Core Collection. CiteSpace 6.2.R2 and VOSviewer were used to conduct bibliometric visualization.ResultsIn total, 778 POI records published from 2011 to 2023 were retrieved. Over the past few decades, the annual cumulative number of related articles has linearly increased, with China and the United States of America (USA) contributing prominently. All the publications were from 59 countries and territories. China and the University of Bonn were the top contributing country and institution, respectively.Neurogastroenterology & Motilitywas the most prolific journal. The Journal ofGastrointestinal Surgeryhad the highest number of citations. Wehner Sven was the most productive author. Burst keywords (e.g., colon, prolonged ileus, acupuncture, paralytic ileus, pathophysiology, rectal cancer, gastrointestinal function, risk) and a series of reference citation bursts provided evidence for the research frontiers in recent years.ConclusionsThis study demonstrates trends in the published literature on POI and provides new insights for researchers. It emphasizes the importance of multidisciplinary cooperation in the development of this field.
Computational investigation of BMAA and its carbamate adducts as potential GluR2 modulators
Authors: Diakogiannaki Isidora , Papadourakis Michail , Spyridaki Vasileia , Cournia Zoe , Koutselos Andreas 
Published: January 2024

ABSTRACTBeta-N-methylamino-L-alanine (BMAA) is a potential neurotoxic non-protein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its L-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not been yet elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 agonists. Initially, we perform Molecular Dynamics (MD) simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding domain of the receptor. In addition, we perform alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity in the GluR2. These results provide a rationale that BMAA carbamate adducts may be in fact the modulators of GluR2 and not BMAA itself.
Mitochondrial metabolism sustains CD8+T cell migration for an efficient infiltration into solid tumors
Authors: Simula Luca , Fumagalli Mattia , Vimeux Lene , Rajnpreht Irena , Icard Philippe , An Dongjie , Pendino Frédéric , Damotte Diane , Lupo-Mansuet Audrey , Alifano Marco , Alves-Guerra Marie-Clotilde , Donnadieu Emmanuel 
Published: January 2024

AbstractThe ability of CD8+T cells to infiltrate solid tumors and reach cancer cells is associated with improved patient survival and responses to immunotherapy. Thus, identifying the factors controlling T cell migration in tumors is critical, so that strategies to intervene on these targets can be developed. Although interstitial motility is a highly energy-demanding process, the metabolic requirements of CD8+T cells migrating in a 3D environment remain unclear. Here, we demonstrate that the tricarboxylic acid (TCA) cycle is the main metabolic pathway sustaining human CD8+T cell motility in 3D collagen gels and tumor slices while glycolysis plays a much minor role. Using pharmacological and genetic approaches, we report that CD8+T cell migration depends on the mitochondrial oxidation of glucose and glutamine, but not fatty acids, and both ATP and ROS produced by mitochondria are required for T cells to migrate. Pharmacological interventions to increase mitochondrial activity improve CD8+T cells intra-tumoral migration and CAR T cell recruitment into tumor islets leading to better control of tumor growth in human xenograft models. Our study highlights the rationale of targeting mitochondrial metabolism to enhance the migration and antitumor efficacy of CAR T cells in treating solid tumors.
Individualized functional localization of the language and multiple demand network in chronic post-stroke aphasia
Authors: Clercq Pieter De , Gonsalves Alicia Ronnie , Gerrits Robin , Vandermosten Maaike 
Published: January 2024

AbstractRecent research found a distinct dissociation between brain regions supporting domain-general cognitive processes and regions supporting core language functions. The question of whether individuals with post-stroke aphasia (IWA) exhibit a comparable dissociation remains debated, particularly as previous studies overlooked individual variability in functional network organization and aphasia heterogeneity. To address this gap, we employed an individualized functional localization approach to test the involvement of the domain-general multiple demand (MD) network during language processing in chronic aphasia.We collected functional MRI data in 15 IWA and 13 age-matched controls. Participants performed a spatial working memory task, triggering MD network activation, as well as a listening and reading task, triggering language network activation. We compared both groups individualized activation patterns and investigated the link with aphasia severity. Involvement of the MD network during language processing was examined by investigating language task activity within subject-specific regions that are active during the MD task.The language and MD network each generalized well across different task modalities, but exhibited robust spatial dissociation from each other in both groups. Moreover, there was no evidence of MD network activation during language processing in either group. Additionally, the language network showed weaker activation in IWA compared to controls in left-hemispheric brain regions, with higher activation values in the left correlating with improved language performance in IWA.In conclusion, our findings suggest that the MD network does not contribute to passive, receptive language functions in chronic aphasia or healthy older adults. Instead, our results align with previous research proposing that normalized left-hemispheric language activity supports language performance in chronic aphasia.
Body-wide genetic deficiency of poly(ADP-ribose) polymerase 14 sensitizes mice to colitis
Authors: Vedantham Madhukar , Polari Lauri , Poosakkannu Anbu , Pinto Rita G. , Sakari Moona , Laine Jukka , Sipilä Petra , Määttä Jorma , Gerke Heidi , Rissanen Tiia , Rantakari Pia , Toivola Diana M. , Pulliainen Arto T. 
Published: January 2024

ABSTRACTInflammatory bowel disease (IBD) is a debilitating and relapsing chronic disease of the gastrointestinal tract affecting millions of people. Here, we investigated the expression and functions of poly (ADP-ribose) polymerase 14 (Parp14), an important regulatory protein in immune cells, using a biobank IBD patient cohort as well as two mouse models of colitis, i.e., the IBD-mimicking oral dextran sulfate sodium (DSS) exposure model, and the oralSalmonellaexposure model. Parp14 was expressed in the human colon, by cells in the lamina propria, but, in particular, by the epithelial cells with a typical granular staining pattern in the cytosol. The same Parp14 staining pattern was evidenced in both colitis models. Body-wide genetic deficiency of Parp14 in C57BL/6N background sensitized mice to DSS colitis. The Parp14-deficient mice displayed increased rectal bleeding as well as stronger epithelial erosion, Goblet cell loss and immune cell infiltration. The absence of Parp14 did not affect the mouse colon bacterial microbiota based on PacBio long read sequencing. Also, the colon leukocyte populations of Parp14-deficient mice were normal based on flow cytometry. In contrast, we witnessed an altered transcriptional signature in Parp14-deficient mice with bulk tissue RNA-Seq. Gene Ontology (GO)-based classification of differentially expressed genes demonstrated that the colon transcriptional signature of Parp14-deficient mice was dominated by abnormalities in inflammation and infection responses both prior and after the 1-week DSS exposure. Overall, the data indicate that Parp14 has an important role in the maintenance of colon epithelial barrier integrity. The prognostic and predictive biomarker potential of Parp14 in IBD merits further investigation.
Modelling biological and resource fluxes in fluvial meta-ecosystems
Authors: Talluto Matthew , del Campo Rubén , Estévez Edurne , Fuß Thomas , Thuile Bistarelli Lukas , Martini Jan , Singer Gabriel A. 
Published: January 2024

AbstractMeta-ecosystem theory predicts that cross-ecosystem flows of energy, nutrients, and organisms have important implications for local community assembly and ecosystem functioning. Developments in the theory also have the potential to enhance our under-standing of biodiversity-ecosystem functioning relationships. Meta-ecosystem theory is particularly well-suited to the study of rivers, because water flow forces strong spatial interrelationships among connected ecosystems. However, models that address flows of both resources and organisms and explicitly link both are lacking. We present a model and associated R-package for cross-ecosystem flows of both resources and organisms that can be used to predict their distribution in river networks, as well as meta-ecosystem functioning. The model incorporates feedbacks between these two crucial components. To illustrate the capabilities of the model, we present an in silico experiment and analysis, as well as providing sample code.
Pervasive sublethal effects of agrochemicals as contributing factors to insect decline
Authors: Gandara Lautaro , Jacoby Richard , Laurent François , Spatuzzi Matteo , Vlachopoulos Nikolaos , Borst Noa O , Ekmen Gülina , Potel Clement M , Garrido-Rodriguez Martin , Böhmert Antonia L , Misunou Natalia , Bartmanski Bartosz J , Li Xueying C , Kutra Dominik , Hériché Jean-Karim , Tischer Christian , Zimmermann-Kogadeeva Maria , Ingham Victoria , Savitski Mikhail M , Masson Jean-Baptiste , Zimmermann Michael , Crocker Justin 
Published: January 2024

AbstractInsect biomass is declining across the globe at an alarming rate. Climate change and the widespread use of pesticides have been hypothesized as two underlying drivers. However, the lack of systematic experimental studies across chemicals and species limits our causal understanding of this problem. Here, we employed a chemical library encompassing 1024 different molecules—including insecticides, herbicides, fungicides, and plant growth inhibitors —to investigate how insect populations are affected by varying concentrations of pesticides, focusing on sublethal doses. Using a controlled laboratory pipeline forDrosophila melanogaster, we found that 57% of these chemicals affect the behavior of larvae at sublethal concentrations, and an even higher proportion compromises long-term survivability after acute exposure. Consistent with these results, we observed that exposure to chemicals at doses orders of magnitude below lethality induced widespread phosphorylation changes across the larval proteome. The effects of agrochemicals were amplified when the ambient temperature was increased by four degrees. We also tested the synergistic effects of multiple chemicals at doses found widely in nature and observed fitness-reducing changes in larval developmental time, behavior, and reproduction. Finally, we expanded our investigation to additional fly species, mosquitos, and butterflies and detected similar behavioral alterations triggered by pesticides at sublethal concentrations. Our results provide experimental evidence that strongly suggests sublethal doses of agrochemicals coupled with changes in environmental temperatures are contributing to the global decline in insect populations. We anticipate that our assays can contribute to improving chemical safety assessment, better protect the environment, secure food supplies, and safeguard animal and human health, as well as understand our rapidly changing world.
Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity
Authors: Choi Eunice , Machado Camilla R. L. , Okano Takaichi , Boyle David , Wang Wei , Firestein Gary S. 
Published: January 2024

AbstractThe mechanisms responsible for the distribution and severity of joint involvement in rheumatoid arthritis (RA) are not known. To explore whether site-specific FLS biology might be associated with location-specific synovitis and explain the predilection for hand (wrist/metacarpal phalangeal joints) involvement in RA, we generated transcriptomic and chromatin accessibility data from FLS to identify the transcription factors (TFs) and pathways. Networks were constructed by integration of chromatin accessibility and gene expression data. Analysis revealed joint-specific patterns of FLS phenotype, with proliferative, migratory, proinflammatory, and matrix-degrading characteristics observed in resting FLS derived from the hand joints compared with hip or knee. TNF-stimulation amplified these differences, with greater enrichment of proinflammatory and proliferative genes in hand FLS compared with hip and knee FLS. Hand FLS also had the greatest expression of markers associated with an ‘activated’ state relative to the ‘resting’ state, with the greatest cytokine and MMP expression in TNF-stimulated hand FLS. Predicted differences in proliferation and migration were biologically validated with hand FLS exhibiting greater migration and cell growth than hip or knee FLS. Distinctive joint-specific FLS biology associated with a more aggressive inflammatory response might contribute to the distribution and severity of joint involvement in RA.
SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data
Authors: Yu Hongyu , Wu Daiqing , Shen Guning , Hu Ming , Li Yun 
Published: January 2024

ABSTRACTChromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available athttps://github.com/hyuyu104/SnapFISH-IMPUTE.
Identification, characterization and transcriptional analysis of the long non-coding RNA landscape in the familyCucurbitaceae
Authors: Villalba-Bermell Pascual , Marquez-Molins Joan , Gomez Gustavo 
Published: January 2024

AbstractLong non-coding RNAs (lncRNAs) constitute a fascinating class of regulatory RNAs, widely distributed in eukaryotes. In plants, they exhibit features such as tissue-specific expression, spatiotemporal regulation, and responsiveness to stress, suggesting their involvement in specific biological processes. Although an increasing number of studies support the regulatory role of lncRNAs in model plants, our knowledge about these transcripts in relevant crops is limited. In this study we employ a custom pipeline on a dataset of over 1,000 RNA-seq studies across nine representative species of the familyCucurbitaceaeto predict 91,209 non-redundant lncRNAs. LncRNAs were predicted according to three confidence levels and classified into intergenic, natural antisense, intronic, and sense overlapping. Predicted lncRNAs have lower expression levels compared to protein-coding genes but a more specific behavior when considering plant tissues, developmental stages, and response to stress, emphasizing their potential roles in regulating various aspects of plant-biology. The evolutionary analysis indicates higher positional conservation than sequence conservation, which may be linked to the presence of conserved modular motifs within syntenic lncRNAs. In short, this research provides a comprehensive map of lncRNAs in the agriculturally relevantCucurbitaceaefamily, offering a valuable resource for future investigations in crop improvement.
Fine-Grained Forecasting of COVID-19 Trends at the County Level in the United States
Authors: Song Tzu-Hsi , Clemente Leonardo , Pan Xiang , Jang Junbong , Santillana Mauricio , Lee Kwonmoo 
Published: January 2024

AbstractThe novel coronavirus (COVID-19) pandemic, first identified in Wuhan China in December 2019, has profoundly impacted various aspects of daily life, society, healthcare systems, and global health policies. There have been more than half a billion human infections and more than 6 million deaths globally attributable to COVID-19. Although treatments and vaccines to protect against COVID-19 are now available, people continue being hospitalized and dying due to COVID-19 infections. Real-time surveillance of population-level infections, hospitalizations, and deaths has helped public health officials better allocate healthcare resources and deploy mitigation strategies. However, producing reliable, real-time, short-term disease activity forecasts (one or two weeks into the future) remains a practical challenge. The recent emergence of robust time-series forecasting methodologies based on deep learning approaches has led to clear improvements in multiple research fields. We propose a recurrent neural network model named Fine-Grained Infection Forecast Network (FIGI-Net), which utilizes a stacked bidirectional LSTM structure designed to leverage fine-grained county-level data, to produce daily forecasts of COVID-19 infection trends up to two weeks in advance. We show that FIGI-Net improves existing COVID-19 forecasting approaches and delivers accurate county-level COVID-19 disease estimates. Specifically, FIGI-Net is capable of anticipating upcoming sudden changes in disease trends such as the onset of a new outbreak or the peak of an ongoing outbreak, a skill that multiple existing state-of-the-art models fail to achieve. This improved performance is observed across locations and periods. Our enhanced forecasting methodologies may help protect human populations against future disease outbreaks.