bluuebunny/crossref_metadata_2025_split huggingface dataset:
The burden of dengue and risk factors of transmission in nine districts in Sri Lanka
Authors: Jeewandara Chandima , Karunananda Maneshka Vindesh , Fernando Suranga , Danasekara Saubhagya , Jayakody Gamini , Arulkumaran S. , Samaraweera N.Y. , Kumarawansha Sarathchandra , Sivaganesh Subramaniyam , Amarasinghe P. Geethika , Jayasinghe Chintha , Wijesekara Dilini , Marasinghe Manonath Bandara , Mambulage Udari , Wijayatilake Helanka , Senevirathne Kasun , Bandara A.D.P , Gallage C.P. , Colambage N.R. , Udayasiri A.A. Thilak , Lokumarambage Tharaka , Upasena Y. , Weerasooriya W.P.K.P. ,   seroprevalence study group, Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: April 2023

AbstractBackgroundIt is crucial to understand the differences in dengue seroprevalence rates in different regions in Sri Lanka to understand the burden of infection to plan dengue vaccination programmes.Methodsage stratified seroprevalence rates were assessed in 5208 children, aged 10 to 19 years, in nine districts representing the nine provinces in Sri Lanka. A stratified multi-stage cluster was used to select 146 schools representing each district. Probability proportionate to the size (PPS) sampling technique based on the age distribution of general population and the urbanicity in each district was used to select the number of clusters to be enrolled for the study from each district.FindingsThe overall dengue seroprevalence rates in children was 24.8%, with the highest rates reported from Trincomalee (54.3%) and the lowest rates from Badulla (14.2%), which is a high altitude estate area. There was a weak but positive correlation between the dengue antibody positivity rates and age in districts which had seroprevalence rates of >25%, while there was no increase in antibody titres with age in the other districts. While the seroprevalence rates was significantly higher in urban areas (35.8%) compared to rural (23.2%) and estate areas (9.4%), there was no association with seropositivity rates with population density (Spearmans r=-0.01, p=0.98), in each district.InterpretationThe seroprevalence rates in many districts were <25% and the rates were very different to those reported from Colombo. Therefore, it would be important to take into account these differences when rolling out dengue vaccines in Sri Lanka.FundingWe are grateful to the World Health Organization and the UK Medical Research Council for support.
FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis
Authors: Liao Xiaofeng , Ederveen Thomas H.A. , Niehues Anna , de Visser Casper , Huang Junda , Badmus Firdaws , Doornbos Cenna , Orlova Yuliia , Kulkarni Purva , van der Velde K. Joeri , Swertz Morris A. , Brandt Martin , van Gool Alain J. , ’t Hoen Peter A.C. 
Published: April 2023

AbstractMotivationWe are witnessing an enormous growth in the amount of molecular profiling (-omics) data. The integration of multi-omics data is challenging. Moreover, human multi-omics data may be privacy-sensitive and can be misused to de-anonymize and (re-)identify individuals. Hence, most biomedical data is kept in secure and protected silos. Therefore, it remains a challenge to reuse these data without infringing the privacy of the individuals from which the data were derived. Federated analysis of Findable, Accessible, Interoperable, and Reusable (FAIR) data is a privacy-preserving solution to make optimal use of these multi-omics data and transform them into actionable knowledge.ResultsThe Netherlands X-omics Initiative is a National Roadmap Large-Scale Research Infrastructure aiming for efficient integration of data generated within X-omics and external datasets. To facilitate this, we developed the FAIR Data Cube (FDCube), which adopts and applies the FAIR principles and helps researchers to create FAIR data and metadata, to facilitate re-use of their data, and to make their data analysis workflows transparent, and in the meantime ensure data security and privacy.
A Histological Assessment Tool for Breast Implant Capsules Validated in 480 Patients with and without Capsular Contracture
Authors: Larsen Andreas , Timmermann Adam M , Kring Mikela , Weltz Tim K , Ørholt Mathias , Vester-Glowinski Peter , Elberg Jens Jørgen , Trillingsgaard Jesper , Mielke Louise V , Hölmich Lisbet R , Damsgaard Tine E , Roslind Anne , Herly Mikkel 
Published: April 2023

AbstractBackgroundCapsular contracture is a severe complication to breast implants, but the pathophysiology remains unclear, and consensus is lacking on how to analyze implant capsules histologically. In this study, we developed and validated a histological semiquantitative assessment tool for analyzing breast implant capsules.MethodsBiopsies of breast implant capsules from 480 patients who had undergone breast augmentation or reconstruction were collected and stained with hematoxylin and eosin. First, biopsies from 100 patients were used to select parameters for the semiquantitative assessment tool. Then, biopsies from the remaining 380 patients were used to determine intra- and interobserver agreement of two blinded observers and agreement with a pathologist. Finally, we tested the association between the parameters and capsular contracture.ResultsThe histological assessment tool consisted of ten parameters assessed on a two-, three-, or four-point scale. Intra- and interobserver agreement was almost perfect (0.83 and 0.80), and agreement with the pathologist was substantial (0.67). Inflammatory infiltration (p<0.01), thickness of the collagen layer (p<0.0001), fiber organization (p<0.01) and calcification (p<0.001) were significantly correlated with capsular contracture.ConclusionsThis is the first validated histological assessment tool for breast implant capsules that provides an objective and precise assessment of hematoxylin and eosin-stained sections of breast implant capsule biopsies which can be used in research and clinical practice.Level of evidenceNo Level Assigned
Pathways that affect anterior morphogenesis inC. elegansembryos
Authors: Boopathi Balasubramaniam , Topalidou Irini , Kelley Melissa , Meadows Sarina M. , Funk Owen , Ailion Michael , Fay David S. 
Published: April 2023

ABSTRACTDuring embryogenesis the nascentCaenorhabditis elegansepidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. We showed that two conserved proteins linked to this process, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function together in a complex. Proteomics data also suggested potential roles for FAM102A and WDR44 family proteins in intracellular trafficking, consistent with their localization patterns. Nonetheless, we found no evidence to support a clear function for SYM-3 or SYM-4 in the apical deposition of two aECM components, FBN-1 and NOAH. Surprisingly, loss of MEC-8/RBPMS2, a conserved splicing factor and regulator offbn-1, had little effect on the abundance or deposition of FBN-1 to the aECM. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. Lastly, we examined morphogenesis defects in embryos lackingmir-51microRNA family members, which display a related embryonic phenotype tomec-8; symdouble mutants. Collectively, our findings add to our knowledge of pathways controlling embryonic morphogenesis.SUMMARY STATEMENTWe identify new proteins in apical ECM biology inC. elegansand provide evidence that SYM-3/FAM102A and SYM-4/WDR44 function together in trafficking but do not regulate apical ECM protein deposition.
ElegansNet: a brief scientific report and initial experiments
Authors: Bardozzo Francesco , Terlizzi Andrea , Lió Pietro , Tagliaferri Roberto 
Published: April 2023

AbstractThis research report introduces ElegansNet, a neural network that mimics real-world neuronal network circuitry, with the goal of better understanding the interplay between connectome topology and deep learning systems. The proposed approach utilizes the powerful representational capabilities of living beings’ neuronal circuitry to design and generate improved deep learning systems with a topology similar to natural networks. The Caenorhabditis elegans connectome is used as a reference due to its completeness, reasonable size, and functional neuron classes annotations. It is demonstrated that the connectome of simple organisms exhibits specific functional relationships between neurons, and once transformed into learnable tensor networks and integrated into modern architectures, it offers bio-plausible structures that efficiently solve complex tasks. The performance of the models is demonstrated against randomly wired networks and compared to artificial networks ranked on global benchmarks. In the first case,ElegansNetoutperforms randomly wired networks. Interestingly,ElegansNetmodels show slightly similar performance with only those based on the Watts-Strogatz small-world property. When compared to state-of-the-art artificial neural networks, such as transformers or attention-based autoencoders,ElegansNetoutperforms well-known deep learning and traditional models in both supervised image classification tasks and unsupervised hand-written digits reconstruction, achieving top-1 accuracy of 99.99% on Cifar10 and 99.84% on MNIST Unsup on the validation sets.
Culture of Saos-2 cells under hypoxic conditions stimulates rapid differentiation to an osteocyte-like stage
Authors: Zelmer Anja R. , Starczak Yolandi , Solomon Lucian B. , Richter Katharina , Yang Dongqing , Atkins Gerald J. 
Published: April 2023

1.AbstractFew human osteocytein vitromodels exist and the differentiation of immature osteoblasts to an osteocyte stage typically takes at least 4-weeks of culture, making the study of this process challenging and time consuming. The osteosarcoma cell line Saos-2 has proved to be a useful model of human osteoblast differentiation through to a mature osteocyte-like stage. Culture under osteogenic conditions in a standard 5% CO2and normoxic (21% O2) atmosphere results in reproducible mineralisation and acquisition of mature osteocyte markers over the expected 28-35 day culture period. In order to expedite experimental assays, we tested whether reducing available oxygen to mimic concentrations experienced by osteocytesin vivowould increase the rate of differentiation of Saos-2 cells. Cells cultured in a 5% CO2, 1% O2atmosphere exhibited accelerated deposition of mineral, reaching near saturation by 14 days as demonstrated with the Alizarin Red and Von Kossa staining. The gene expression of the major hypoxia-induced transcription factorHIF1αand the key osteogenic transcription factorRUNX2were both elevated under 1% O2. Early (COLA1, MEPE) and mature (PHEX, DMP1andSOST) osteocyte markers were also upregulated earlier under hypoxic compared to normoxic growth conditions. Thus, culture under low oxygen accelerates key markers of osteocyte differentiation, resulting in a useful human osteocyte-likein vitrocell model within 14 days.
standR: a Bioconductor package for analysing transcriptomic Nanostring GeoMx DSP data
Authors: Liu Ning , Bhuva Dharmesh D. , Mohamed Ahmed , Bokelund Micah , Kulasinghe Arutha , Tan Chin Wee , Davis Melissa J 
Published: April 2023

ABSTRACTTo gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cellin situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here we presentstandR, a R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how application of standR enables scientists to develop in-depth insights into the biology of interest.
Reconnecting the Hand and Arm to the Brain: Efficacy of Neural Interfaces for Sensorimotor Restoration after Tetraplegia
Authors: Herring Eric Z. , Graczyk Emily L. , Memberg William D. , Adams Robert D. , Baca-Vaca Guadalupe Fernandez , Hutchison Brianna C. , Krall John T. , Alexander Benjamin J. , Conlan Emily C. , Alfaro Kenya E. , Bhat Preethi R. , Ketting-Olivier Aaron B. , Haddix Chase A. , Taylor Dawn M. , Tyler Dustin J. , Kirsch Robert F. , Ajiboye A. Bolu , Miller Jonathan P. 
Published: April 2023

ABSTRACTBackgroundParalysis after spinal cord injury involves damage to pathways that connect neurons in the brain to peripheral nerves in the limbs. Re-establishing this communication using neural interfaces has the potential to bridge the gap and restore upper extremity function to people with high tetraplegia.ObjectiveWe report a novel approach for restoring upper extremity function using selective peripheral nerve stimulation controlled by intracortical microelectrode recordings from sensorimotor networks, along with restoration of tactile sensation of the hand using intracortical microstimulation.MethodsA right-handed man with motor-complete C3-C4 tetraplegia was enrolled into the clinical trial. Six 64-channel intracortical microelectrode arrays were implanted into left hemisphere regions involved in upper extremity function, including primary motor and sensory cortices, inferior frontal gyrus, and anterior intraparietal area. Nine 16-channel extraneural peripheral nerve electrodes were implanted to allow targeted stimulation of right median, ulnar (2), radial, axillary, musculocutaneous, suprascapular, lateral pectoral, and long thoracic nerves, to produce selective muscle contractions on demand. Proof-of-concept studies were performed to demonstrate feasibility of a bidirectional brain-machine interface to restore function of the participant’s own arm and hand.ResultsMulti-unit neural activity that correlated with intended motor action was successfully recorded from intracortical arrays. Microstimulation of electrodes in somatosensory cortex produced repeatable sensory percepts of individual fingers for restoration of touch sensation. Selective electrical activation of peripheral nerves produced antigravity muscle contractions. The system was well tolerated with no operative complications.ConclusionThe combination of implanted cortical electrodes and nerve cuff electrodes has the potential to allow restoration of motor and sensory functions of the arm and hand after neurological injury.
Strategies to support substance use disorder care transitions from acute-care to community-based settings: A Scoping review and typology
Authors: Krawczyk Noa , Rivera Bianca D. , Chang Ji E. , Grivel Margaux , Chen Yu-Heng , Nagappala Suhas , Englander Honora , McNeely Jennifer 
Published: April 2023

AbstractBackgroundAcute-care interventions that identify patients with substance use disorders (SUDs), initiate treatment, and link patients to community-based services, have proliferated in recent years. Yet, much is unknown about the specific strategies being used to support continuity of care from emergency department (ED) or inpatient hospital settings to community-based SUD treatment. In this scoping review, we synthesize the existing literature on patient transition interventions, and form an initial typology of reported strategies.MethodsWe searched Pubmed, Embase, CINAHL and PsychINFO for peer-reviewed articles published between 2000-2021 that studied interventions linking SUD patients from ED or inpatient hospital settings to community-based SUD services. Eligible articles measured at least one post-discharge treatment outcome and included a description of the strategy used to promote linkage to community care. Detailed information was extracted on the components of the transition strategies and a thematic coding process was used to categorize strategies into a typology based on shared characteristics. Facilitators and barriers to transitions of care were synthesized using the Consolidated Framework for Implementation Research.ResultsForty-five articles met inclusion criteria. 62% included ED interventions and 44% inpatient interventions. The majority focused on patients with opioid (71%) followed by alcohol (31%) use disorder. The transition strategies reported across studies were heterogeneous and often not well described. An initial typology of ten transition strategies, including five pre- and five post-discharge transition strategies is proposed. The most common strategy was scheduling an appointment with a community-based treatment provider prior to discharge. A range of facilitators and barriers were described, which can inform efforts to improve hospital-to-community transitions of care.ConclusionsStrategies to support transitions from acute-care to community-based SUD services, although critical for ensuring continuity of care, vary greatly across interventions and are inconsistently measured and described. More research is needed to classify SUD care transition strategies, understand their components, and explore which lead to the best patient outcomes.
A Compressed Language Model Embedding Dataset of ICD 10 CM Descriptions
Authors: Kane Michael J. , King Casey , Esserman Denise , Latham Nancy K. , Greene Erich J. , Ganz David A. 
Published: April 2023

AbstractThis paper presents novel datasets providing numerical representations of ICD-10-CM codes by generating description embeddings using a large language model followed by a dimension reduction via autoencoder. The embeddings serve as informative input features for machine learning models by capturing relationships among categories and preserving inherent context information. The model generating the data was validated in two ways. First, the dimension reduction was validated using an autoencoder, and secondly, a supervised model was created to estimate the ICD-10-CM hierarchical categories. Results show that the dimension of the data can be reduced to as few as 10 dimensions while maintaining the ability to reproduce the original embeddings, with the fidelity decreasing as the reduced-dimension representation decreases. Multiple compression levels are provided, allowing users to choose as per their requirements. The readily available datasets of ICD-10-CM codes are anticipated to be highly valuable for researchers in biomedical informatics, enabling more advanced analyses in the field. This approach has the potential to significantly improve the utility of ICD-10-CM codes in the biomedical domain.
Variability in excess deaths across countries with different vulnerability during 2020-2023
Authors: Ioannidis John P.A. , Zonta Francesco , Levitt Michael 
Published: April 2023

AbstractExcess deaths provide total impact estimates of major crises, such as the COVID-19 pandemic. We evaluated excess death’s trajectories during 2020-2023 across countries with accurate death registration and population age structure data; and assessed relationships with economic indicators of vulnerability. Using the Human Mortality Database on 34 countries, excess deaths were calculated for 2020-2023 (to week 29, 2023) using 2017-2019 as reference, with weekly expected death calculations and adjustment for 5 age strata. Countries were divided into less and more vulnerable; the latter had per capita nominal GDP<$30,000, Gini>0.35 for income inequality and/or at least 2.5% of their population living in poverty. Excess deaths (as proportion of expected deaths, p%) were inversely correlated with per capita GDP (r=-0.60), correlated with proportion living in poverty (r=0.66) and modestly correlated with income inequality (r=0.45). Incidence rate ratio for deaths was 1.06 (95% confidence interval, 1.04-1.08) in the more versus less vulnerable countries. Excess deaths started deviating in the two groups after the first wave. Between-country heterogeneity diminished over time within each of the two groups. Less vulnerable countries had mean p%=-0.8% and 0.4% in 0-64 and >65 year-old strata while more vulnerable countries had mean p%=7.0% and 7.2%, respectively. Usually lower death rates were seen in children 0-14 years old during 2020-2023 versus pre-pandemic years. While the pandemic hit some countries earlier than others, country vulnerability dominated eventually the cumulative impact. Half of the analyzed countries witnessed no substantial excess deaths versus pre-pandemic levels, while the other half suffered major death tolls.Significance StatementExcess deaths during 2020-2023 reflect the direct and indirect effects of the COVID-19 pandemic and of the measures taken. Data from 34 countries with detailed death registration and allowing to adjust for changes in the age structure of the population over time show two groups, each with very different excess death outcomes. The 17 more vulnerable countries (those with per capita nominal GDP<$30,000, Gini>0.35 for income inequality and/or at least 2.5% of their population living in poverty) had very high excess deaths compared with 2017-2019, while the other 17 less vulnerable countries had deaths during 2020-2023 that were comparable to 2017-2019. Continuous monitoring of excess deaths helps understand how country vulnerability shapes long-term impacts.