bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated group antenatal and pediatric care in Haiti: A comprehensive care accompaniment model
Authors: Jean-Baptiste Meredith C. , Julmisse Marc , Adeyemo Oluwatosin , Julmiste Thamar , Illuzzi Jessica L. 
Published: March 2024

AbstractIntroductionThe J9 Plus (J9) maternal-child accompaniment program is based on four pillars: group antenatal care (GANC), group pediatric care, psychosocial support, and community-based care. We aimed to evaluate the impact of the J9 model of care on perinatal outcomes.MethodologyWe conducted a convergent mixed methods study of maternal-newborn dyads born in 2019 at Hôpital Universitaire de Mirebalais. Quantitative data was collected retrospectively to compare dyads receiving J9 care to usual care. A secondary analysis of qualitative data described patient perspectives of J9 care.ResultsAntenatal care attendance was significantly higher among women in J9 (n=524) compared to usual care (n=523), with 490(93%) and 189(36%) having >4 visits, respectively; p <0.001, as was post-partum visit attendance [268(51%) compared to 82(16%), p<0.001] and use of post-partum family planning methods [99(19%) compared to 47(9%), p=0.003]. Incidence of severe pre-eclampsia was significantly lower in the J9 group [44(9%)] compared to the usual care group [74(14%)], p <0.001. Maternal and neonatal mortality and low birth weight did not differ across groups, but with earlier interventions, cesarean delivery [103(20%) and 82(16%), p<0.001] and preterm birth [169 (34%)] and 128 (27%), p=0.041] were higher in the J9 group compared to usual care, respectively. In the qualitative analysis, ease of access to high-quality care, meaningful social support, and maternal empowerment through education were identified as key contributors to these outcomes.ConclusionCompared to usual care, the J9 Plus maternal-child accompaniment model of care is associated with increased engagement in antenatal and postpartum care, increased utilization of post-partum family planning, and lower rates of severe pre-eclampsia, which remains a leading cause of maternal mortality in Haiti. The J9 accompaniment approach to care is an empowering model that has the potential to be replicated in similar settings to improve quality of care and outcomes globally.
Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation
Authors: Shaw Jared B. , Harvey Sophie R. , Du Chen , Xu Zhixin , Edgington Regina M. , Olmedillas Eduardo , Saphire Erica Ollmann , Wysocki Vicki H. 
Published: March 2024

ABSTRACTWe illustrate the utility of native mass spectrometry (nMS) combined with a fast, tunable gas-phase charge reduction, electron capture charge reduction (ECCR), for the characterization of protein complex topology and glycoprotein heterogeneity. ECCR efficiently reduces the charge states of tetradecameric GroEL, illustrating Orbitrapm/zmeasurements to greater than 100,000m/z. For pentameric C-reactive protein and tetradecameric GroEL, our novel device combining ECCR with surface induced dissociation (SID) reduces the charge states and yields more topologically informative fragmentation. This is the first demonstration that ECCR yields more native-like SID fragmentation. ECCR also significantly improved mass and glycan heterogeneity measurements of heavily glycosylated SARS-CoV-2 spike protein trimer and thyroglobulin dimer. Protein glycosylation is important for structural and functional properties and plays essential roles in many biological processes. The immense heterogeneity in glycosylation sites and glycan structure poses significant analytical challenges that hinder a mechanistic understanding of the biological role of glycosylation. Without ECCR, average mass determination of glycoprotein complexes is available only through charge detection mass spectrometry or mass photometry. With narrowm/zselection windows followed by ECCR, multiple glycoformm/zvalues are apparent, providing quick global glycoform profiling and providing a future path for glycan localization on individual intact glycoforms.
Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping
Authors: Joshi Saurabh , Forjaz André , Sang Han Kyu , Shen Yu , Queiroga Vasco , Xenes Daniel , Matelsk Jordan , Wester Brock , Munoz Barrutia Arrate , Kiemen Ashley L. , Wu Pei-Hsun , Wirtz Denis 
Published: March 2024

ABSTRACTThe development of novel imaging platforms has improved our ability to collect and analyze large three-dimensional (3D) biological imaging datasets. Advances in computing have led to an ability to extract complex spatial information from these data, such as the composition, morphology, and interactions of multi-cellular structures, rare events, and integration of multi-modal features combining anatomical, molecular, and transcriptomic (among other) information. Yet, the accuracy of these quantitative results is intrinsically limited by the quality of the input images, which can contain missing or damaged regions, or can be of poor resolution due to mechanical, temporal, or financial constraints. In applications ranging from intact imaging (e.g. light-sheet microscopy and magnetic resonance imaging) to sectioning based platforms (e.g. serial histology and serial section transmission electron microscopy), the quality and resolution of imaging data has become paramount.Here, we address these challenges by leveraging frame interpolation for large image motion (FILM), a generative AI model originally developed for temporal interpolation, for spatial interpolation of a range of 3D image types. Comparative analysis demonstrates the superiority of FILM over traditional linear interpolation to produce functional synthetic images, due to its ability to better preserve biological information including microanatomical features and cell counts, as well as image quality, such as contrast, variance, and luminance. FILM repairs tissue damages in images and reduces stitching artifacts. We show that FILM can decrease imaging time by synthesizing skipped images. We demonstrate the versatility of our method with a wide range of imaging modalities (histology, tissue-clearing/light-sheet microscopy, magnetic resonance imaging, serial section transmission electron microscopy), species (human, mouse), healthy and diseased tissues (pancreas, lung, brain), staining techniques (IHC, H&E), and pixel resolutions (8 nm, 2 µm, 1mm). Overall, we demonstrate the potential of generative AI in improving the resolution, throughput, and quality of biological image datasets, enabling improved 3D imaging.
Asynchronous temporal variance in learning behaviour and neural gene expression in a butterfly
Authors: Ter Yi Ting , Westerman Erica L. 
Published: March 2024

AbstractMate preference learning, including imprinting-like learning, is pervasive across animal taxa, and can affect the selection and maintenance of certain phenotypes. However, not much is known about the temporal dynamics behind imprinting-like learning, or the genetic underpinnings underlying it. To uncover the temporal dynamics of imprinting-like learning, from both a behavioural and transcriptional perspective, we conducted learning and RNA-Seq time series using the butterflyBicyclus anynana, a species where both sexes learn mate preferences. We exposed females to an unfamiliar, unpreferred male phenotype (4-spotted male) for five different exposure (training) periods, ranging from 30 minutes to three hours, and recorded their choice between the preferred, familiar male phenotype (2-spotted) and 4-spotted males in mate choice trials conducted two days after training. We also assessed differential gene expression of naïve females and females exposed to trainer males for these same five exposure periods, to identify temporal patterns in gene expression associated with learning. While we found that the longest exposure had the strongest effect on preference learning, we did not observe a linear effect of exposure time on learning. We also show that the highest peak of differentially expressed genes (DEGs) was after one hour of exposure. While a number of genes were uniquely DE at each time point, one gene, associated with transcription initiation, was differentially expressed during learning across all five time points. We observed a similar decreasing trend in both gene expression and learned response after 1.5 hours of exposure, offering new insights to possible attention and forgetting mechanisms. Therefore, our results indicate that both gene expression and learning are temporally dynamic, and not linear through time. They also highlight the role of transcription in mate preference learning and memory formation in Lepidoptera, and illustrate that imprinting-like learning may exhibit similar molecular temporal dynamics as associative learning.
A TLR7 Agonist Conjugated to a Nanofibrous Peptide Hydrogel as a Potent Vaccine Adjuvant
Authors: Euliano Erin M. , Pogostin Brett H. , Agrawal Anushka , Yu Marina H. , Baryakova Tsvetelina H. , Graf Tyler P. , Hartgerink Jeffrey D. , McHugh Kevin J. 
Published: March 2024

AbstractToll-like receptors (TLRs) recognize pathogen- and damage-associated molecular patterns and, in turn, trigger the release of cytokines and other immunostimulatory molecules. As a result, TLR agonists are increasingly being investigated as vaccine adjuvants, though many of these agonists are small molecules that quickly diffuse away from the vaccination site, limiting their co-localization with antigens and, thus, their effect. Here, the small-molecule TLR7 agonist 1V209 is conjugated to a positively-charged multidomain peptide (MDP) hydrogel, K2, which was previously shown to act as an adjuvant promoting humoral immunity. Mixing the 1V209-conjugated K250:50 with the unfunctionalized K2produces hydrogels that retain the shear-thinning and self-healing physical properties of the original MDP, while improving the solubility of 1V209 more than 200-fold compared to the unconjugated molecule. When co-delivered with ovalbumin as a model antigen, 1V209-functionalized K2produces antigen-specific IgG titers that were statistically similar to alum, the gold standard adjuvant, and a significantly lower ratio of Th2-associated IgG1 to Th1-associated IgG2a than alum, suggesting a more balanced Th1 and Th2 response. Together, these results suggest that K2MDP hydrogels functionalized with 1V209 are a promising adjuvant for vaccines against infectious diseases, especially those benefiting from a combined Th1 and Th2 immune response.Table of ContentsActivation of toll-like receptors (TLRs) stimulates a signaling cascade to induce an immune response. A TLR7 agonist was conjugated to an injectable peptide hydrogel, which was then used to deliver a model vaccine antigen. This platform produced antibody titers similar to the gold standard adjuvant alum and demonstrated an improved balance between Th1- and Th2-mediated immunity over alum.
Conveying tactile object characteristics through customized intracortical microstimulation of the human somatosensory cortex
Authors: Verbaarschot C. , Karapetyan V. , Greenspon C.M. , Boninger M. , Bensmaia S.J. , Sorger B. , Gaunt R. A. 
Published: March 2024

AbstractMicrostimulation of the somatosensory cortex can evoke tactile percepts in people with spinal cord injury, providing a means to restore touch. While location and intensity can be reliably conveyed, two issues that prevent creating more complex naturalistic sensations are a lack of methods to effectively scan the large stimulus parameter space and difficulties with assessing percept quality. Here, we addressed both challenges with an experimental paradigm that enabled three individuals with tetraplegia to control their stimulation parameters in a blinded fashion to create sensations for different virtual objects. Participants felt they could reliably create object-specific sensations and reported vivid object-appropriate characteristics. Despite substantial overlap in stimulus parameter selections across objects, both linear classifiers and participants could match stimulus profiles with their respective objects significantly above chance without any visual cues. We conclude that while visual information contributes to the experience of artificial touch, microstimulation in the somatosensory cortex itself can evoke intuitive percepts with a variety of tactile properties. This novel self-guided stimulation approach may be used to effectively characterize percepts from future stimulation paradigms.
Integrating Step-down Care in Community-based Paediatric Palliative Services: A Realist Evaluation
Authors: Yeo Zhi Zheng , Poh Heng Chong 
Published: March 2024

AbstractBackgroundYoung persons with advanced life-limiting illness living at home have fluctuating and complex needs. Community paediatric palliative care (PPC) is still predominantly specialist-led. This poses a potential care vacuum as medical conditions stabilise and specialised care ceases. One home-based PPC service introduced a step-down care program (COMET) as bridge to continuous yet adaptable support. Above overall effectiveness, how different outcomes are achieved is also investigated for context.MethodsWe conducted a realist evaluation, using a mixed-methods case series design to study COMET operations and impact within the community care context (Context->Mechanism->Outcomes). Patient medical records and in-depth interviews with family caregivers and PPC professionals generated rich quantitative and qualitative data for analysis.ResultsOf 121 patients under specialist PPC homecare, 18 (14.9%) were enrolled in COMET since November 2020; 12 of these formed individual case studies. Interviews with 15 caregivers and 7 PPC clinicians produced three crucial findings: (i) Ongoing access to specialist care is required for ever evolving complexities; (ii) Continuing support at home is vital for regular management and intermittent emergencies; (iii) COMET harmonizes shifting levels of support within a single unified framework, safeguarding existing rapport and care consistency.ConclusionUntil generalist PPC expertise becomes prevalent outside the hospital setting, novel care models like COMET could plug gaps in community PPC services by offering flexible care options. Continuity of care, efficient resource management, and superior service quality are inherent benefits, if meaningful care tiering through substantive patient assessments are refined further in future iterations.
Generative AI Guidelines in Korean Medical Journals: A Survey Using Human-AI Collaboration
Authors: Ahn Sangzin 
Published: March 2024

AbstractBackgroundGenerative artificial intelligence (GAI) tools, such as large language models, have the potential to revolutionize medical research and writing, but their use also raises important ethical and practical concerns. This study examines the prevalence and content of GAI guidelines among Korean medical journals to assess the current landscape and inform future policy development.MethodsTop 100 Korean medical journals by H-index were surveyed. Author guidelines were collected and screened by a human author and AI chatbot to identify GAI-related content. Key components of GAI policies were extracted and compared across journals. Journal characteristics associated with GAI guideline adoption were also analyzed.ResultsOnly 18% of the surveyed journals had GAI guidelines, which is much lower than previously reported international journals. However, adoption rates increased over time, reaching 57.1% in the first quarter of 2024. Higher-impact journals were more likely to have GAI guidelines. All journals with GAI guidelines required authors to declare GAI use, and 94.4% prohibited AI authorship. Key policy components included emphasizing human responsibility (72.2%), discouraging AI-generated content (44.4%), and exempting basic AI tools (38.9%).ConclusionWhile GAI guideline adoption among Korean medical journals is lower than global trends, there is a clear increase in implementation over time. The key components of these guidelines align with international standards, but greater standardization and collaboration are needed to ensure responsible and ethical use of GAI in medical research and writing.Abstract Figure
Blood methylation pattern reflects epigenetic remodelling in adipose tissue after bariatric surgery
Authors: Müller Luise , Hoffmann Anne , Bernhart Stephan H. , Ghosh Adhideb , Zhong Jiawei , Hagemann Tobias , Sun Wenfei , Dong Hua , Noé Falko , Wolfrum Christian , Dietrich Arne , Stumvoll Michael , Massier Lucas , Blüher Matthias , Kovacs Peter , Chakaroun Rima , Keller Maria 
Published: March 2024

AbstractBackgroundStudies on DNA methylation following bariatric surgery have primarily focused on blood cells, while it is unclear to which extend it may reflect DNA methylation profiles in specific metabolically relevant organs such as adipose tissue (AT). Here, we investigated whether adipose tissue depots specific methylation changes after bariatric surgery are mirrored in blood.MethodsUsing Illumina 850K EPIC technology, we analysed genome-wide DNA methylation in paired blood, subcutaneous and omental visceral AT (SAT/OVAT) samples from nine individuals with severe obesity pre- and post-surgery.FindingsThe numbers and effect sizes of differentially methylated regions (DMRs) post-bariatric surgery were more pronounced in AT (SAT: 12,865 DMRs from -11.5 to 10.8%; OVAT: 14,632 DMRs from -13.7 to 12.8%) than in blood (9,267 DMRs from -8.8 to 7.7%). Cross-tissue DMRs implicated immune-related genes. Among them, 49 regions could be validated with similar methylation changes in blood from independent individuals. Fourteen DMRs correlated with differentially expressed genes in AT post bariatric surgery, including downregulation ofPIK3AP1in both SAT and OVAT. DNA methylation age acceleration was significantly higher in AT compared to blood, but remained unaffected after surgery.InterpretationConcurrent methylation pattern changes in blood and AT, particularly in immune-related genes, suggest blood DNA methylation mirrors inflammatory state of AT post-bariatric surgery.
A dynamic ensemble model for short-term forecasting in pandemic situations
Authors: Botz Jonas , Valderrama Diego , Guski Jannis , Fröhlich Holger 
Published: March 2024

AbstractDuring the COVID-19 pandemic, many hospitals reached their capacity limits and could no longer guarantee treatment of all patients. At the same time, governments endeavored to take sensible measures to stop the spread of the virus while at the same time trying to keep the economy afloat. Many models extrapolating confirmed cases and hospitalization rate over short periods of time have been proposed, including several ones coming from the field of machine learning. However, the highly dynamic nature of the pandemic with rapidly introduced interventions and new circulating variants imposed non-trivial challenges for the generalizability of such models.In the context of this paper, we propose the use of ensemble models, which are allowed to change in their composition or weighting of base models over time and can thus adapt to highly dynamic pandemic or epidemic situations. In that regard, we also explored the use of secondary metadata - Google searches - to inform the ensemble model. We tested our approach using surveillance data from COVID-19, Influenza, and hospital syndromic surveillance of severe acute respiratory infections (SARI). In general, we found ensembles to be more robust than the individual models. Altogether we see our work as a contribution to enhance the preparedness for future pandemic situations.
Enhancing gout management by creating a register using automated queries in electronic health records
Authors: Bürgisser Nils , Mongin Denis , Mehouachi Samia , Buclin Clement P. , Guemara Romain , Darbellay Farhoumand Pauline , Braillard Olivia , Lauper Kim , Courvoisier Delphine S. 
Published: March 2024

AbstractObjectiveTo develop an automatic gout register to improve gout management.MethodsWe analysed the electronic health records (EHR) of all patients >18 years old from a tertiary academic hospital (2013-2022) based on six criteria: International Classification of Diseases 10 (ICD-10) gout diagnosis, urate-lowering therapy (ULT) prescription, uric acid crystal in joint aspiration and gout-related terms in problem lists, clinical or imaging reports. We assessed the positive and negative predictive value (PPV and NPV) of the query by chart reviews.ResultsOf 2,110,902 out- and inpatients, 10,289 had at least one criterion for gout. The combination of joint aspiration OR diagnostic in the problem list OR ≥ 2 other criteria created a register of 5,138 patients, with a PPV of 92.4% (95%CI: 88.5 to 95.0), and an NPV of 94.3% (95%CI: 91.9 to 96.0). PPV and NPV were similar amongst outpatients and inpatients. Incidence was 2.9 per 1000 person-year and dropped by 30% from the COVID-19 pandemic onward. Patients with gout were on average 71.2 years old (SD 14.9), mainly male (76.5%), overweight (69.5%) and polymorbid (mean number of comorbidities of 3, IQR 1-5). More than half (57.4%) had received a urate lowering treatment, 6.7% had a gout that led to a hospitalisation or ≥2 flares within a year, and 32.9% received a rheumatology consultation.ConclusionAn automatic EHR-based gout register is feasible, valid and could be used to evaluate and improve gout management. Interestingly, the register uncovered a marked underdiagnosis or underreporting of gout since the COVID-19 pandemic.Key messagesWhat is already known on this topic?-Gout is the most prevalent inflammatory arthritis, but it remains undertreated despite affordable and effective treatment options.-Quantifying this undertreatment and detecting its causes and risk factors to pilot quality improvement initiative requires an extensive register of gout patients.What this study adds?-This is the first automatic EHR-based gout register, allowing frequent, inexpensive, and sustainable updates.-The automated queries show high positive and negative predictive values to identify gout patients.How this study might affect research, practice or policy?-This register can facilitate the assessment of the adequacy of gout management and the monitoring of quality indicators following improvement projects, or change in policies-It provides an easy platform for cohort studies or adaptive trials-Its methodology is reproducible, facilitating the establishment of gout or other disease registers within different EHR systems