bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stigma in the Context of COVID-19 Crisis
Authors: Khatooni Marzieh 
Published: November 2022

Background:
Stigmatizing anyone during a pandemic poses a threat to everyone and can be an obstacle to disease treatment. The stigma around COVID-19 stems from the fact that it is a life-threatening disease and a lot is unknown about it.

Aim:
This study was conducted with the aim of analyzing and clarifying the concept of stigma in the context of COVID-19; determining its psychological and socio-psychological outcomes; enhancing understanding and recognition of features, antecedents, and consequences of the concept; and proposing an adequate definition for use in clinical practice or research.

Methods:
Rodgers' evolutionary concept analysis was used.

Results/Conclusion:
Stigma in the context of COVID-19 has antecedents, which include informational and psychological issues, media performance, and some governments' policies and actions to control COVID-19 pandemic. The attributes of COVID-19 stigma are subjective and variable, perceived, and/or experienced with interrelated intrapersonal, interpersonal, and structural or institutional dimensions that can be summarized as social stigma and self-stigma. The consequences of COVID-19 stigma are social isolation and psychological burden, physical and mental violence and harassment, hiding disease, and reduced care-seeking behavior. These results will extend the body of knowledge on theory and practice and also assists future researchers in many folds.

Implications for Case Management Practice:
These findings will be a major tool for the case manager/health care team, policy makers, and other human resource planning professionals to develop plans for preventing, combating, and stopping the COVID-19–related stigma.
Distinctive Nested Glomoid Neoplasm
Authors: Papke David J. , Dickson Brendan C. , Oliveira Andre M. , Sholl Lynette M. , Fletcher Christopher D.M. 
Published: November 2022

Recently, it has been recognized that a subset of primary soft tissue neoplasms with GLI1 gene alterations exhibit nested architecture and can mimic glomus tumors or well-differentiated neuroendocrine tumors. Here, we report a series of 20 such neoplasms, which we have provisionally termed “distinctive nested glomoid neoplasm.” Eleven patients (55%) were female and 9 were male. The median age at presentation was 41.5 years (range: congenital to 74 y). The anatomic distribution was wide, with body sites including the trunk (7 tumors), lower extremity (5), tongue (4), upper extremity (3), and neck (1). Excluding tumors of the tongue, 10 tumors (62%) arose in deep soft tissue and 6 (38%) arose primarily in the subcutis. Tumor size ranged from 0.9 to 11.1 cm (median: 3 cm). Distinctive nested glomoid neoplasms are composed of nests of round-to-ovoid cells with scant, palely eosinophilic cytoplasm and monomorphic nuclei with vesicular chromatin and small nucleoli. The nests are invested by prominent capillary networks, and they are situated within large lobules separated by irregular, thick fibrous septa. Among 18 tumors for which adjacent non-neoplastic tissue could be assessed, perivascular proliferation of tumor cells was identified in 16 tumors (89%). Microcystic architecture was present at least focally in 8 tumors (40%), and myxoid stroma was identified at least focally in 5 (25%). Seven tumors (35%) showed clear cell features. By immunohistochemistry, some tumors expressed MDM2 (7/15; 47%), S100 (5 of 19; 26%), STAT6 (2 of 5; 20%), and AE1/AE3 (1/5; 20%). Tumors rarely expressed pan-keratin (1/10; 10%) or CAM5.2 (1/10), and all tumors were negative for β-catenin (12 tumors), chromogranin (12), synaptophysin (11), epithelial membrane antigen (10), desmin (10), smooth muscle actin (9), INSM1 (7), and CD34 (6). GLI1 break-apart fluorescence in situ hybridization was performed on 7 tumors, and next-generation sequencing was performed on 15 tumors (10 DNA sequencing only, 1 RNA sequencing only, 4 both DNA and RNA sequencing). Sixteen tumors, including all 15 tested by next-generation sequencing and an additional case tested by fluorescence in situ hybridization only, were found to harbor GLI1 gene alterations: 10 harbored GLI1 gene rearrangements (3 ACTB::GLI1, 2 PTCH1::GLI1, 1 HNRNPA1::GLI1, 1 NEAT1::GLI1, 1 TXNIP::GLI1, 2 undetermined fusion partners), and 6 harbored GLI1 amplification. Clinical follow-up was available for 10 patients (50%; range: 3 mo to 10 y; median: 6.4 y), including 8 with >1 year of follow-up. Three patients (30%) experienced local recurrence (at intervals of 3 mo to 10 y). None developed distant metastases or died of disease as yet. Overall, our findings support the notion that a subset of GLI1-altered soft tissue neoplasms are indolent, morphologically distinctive nested glomoid neoplasms that should not be classified as sarcomas.
MUSCLE SYNERGIES ANALYSIS SHOWS ALTERED NEURAL COMMANDS IN WOMEN WITH PATELLOFEMORAL PAIN DURING WALKING
Authors: Ferreira Cintia Lopes , Barroso Filipe O. , Torricelli Diego , Pons José L. , Politti Fabiano , Lucareli Paulo Roberto Garcia 
Published: November 2022

AbstractBackgroudSeveral studies suggest that the central nervous system coordinates muscle activation by modulating neural commands directed to groups of muscles combined to form muscle synergies. Individuals with patellofemoral pain (PFP) move differently from asymptomatic individuals. Understanding the neural factors involved in the execution of tasks such as walking can help comprehend how the movement is planned and better understand this clinical condition.Research questionTo compare the muscle coordination of women with and without PFP during gait.MethodsEleven women with PFP and thirteen asymptomatic women were assessed using three-dimensional kinematics and electromyography (EMG) while walking at self-selected speed. Kinematics of the trunk, pelvis and lower limbs were analyzed through the Movement Deviation Profile. Muscle synergies were extracted from the EMG signals of eight lower limb muscles collected throughout the whole gait cycle.ResultsKinematic differences between the two groups (p<0.001, z-score=3.06) were more evident during loading response, terminal stance, and pre-swing. PFP group presented a lower number of muscle synergies (p=0.037), and greater variability accounted for (VAFtotal) when using 3 (p=0.017), 4 (p=0.004), and 5 (p=0.012) synergies to reconstruct all EMG signals. The PFP group also presented higher VAFmusclefor rectus femoris (p=0.048) and gastrocnemius medialis (p=0.019) when considering 4 synergies.SignificanceOur results suggest that women with PFP show lower motor complexity and deficit in muscle coordination to execute gait, indicating that gait in PFP gait is the result of different neural commands compared to asymptomatic women.
Observational methods for COVID-19 vaccine effectiveness research: a trial emulation and empirical evaluation
Authors: Català Martí , Burn Edward , Rathod-Mistry Trishna , Xie Junqing , Delmestri Antonella , Prieto-Alhambra Daniel , Jödicke Annika M. 
Published: November 2022

AbstractDespite much research on the topic, little work has been done comparing the use of methods to control for confounding in the estimation of COVID-19 vaccine effectiveness in routinely collected medical record data. We conducted a trial emulation study to replicate the ChAdOx1 (Oxford/AstraZeneca) and BNT162b2 (BioNTech/Pfizer) COVID-19 phase 3 efficacy studies. We conducted a cohort study including individuals aged 75+ from UK CPRD AURUM (N = 916,128) in early 2021. Three different methods were assessed: Overlap weighting, inverse probability treatment weighting, and propensity score matching. All three methods successfully replicated the findings from both phase 3 trials, and overlap weighting performed best in terms of confounding, systematic error, and precision. Despite lack of trial data beyond 3 weeks, we found that even 1 dose of BNT162b2 was effective against SARS-CoV-2 infection for up to 12 weeks before a second dose was administered. These results support the UK Joint Committee on Vaccination and Immunisation modelling and related UK vaccination strategies implemented in early 2021.Key messagesReal world evidence generated using weighting (overlapping weights and inverse probability of treatment weights) and propensity score matching: all methods successfully replicate the findings of Phase 3 trials for COVID-19 vaccine effectiveness.Overlap weighting provides the least biased estimates in our study and should be considered amongst the most suitable methods for future COVID-19 vaccine effectiveness research.Despite a lack of trial data, our findings suggest that first-dose BNT162b2 provides effective protection against SARS-COV-2 infection for up to 12 weeks, in line with UK’s Joint Committee on Vaccination and Immunisation modelling and subsequent vaccination strategies.
Never let me down: new possibilities for lowering serum free cultivation media costs
Authors: Schenzle Lisa , Egger Kristina , Spangl Bernhard , Hussein Mohamed , Ebrahimian Atefeh , Kuehnel Harald , Ferreira Frederico C. , Marques Diana M. C. , Berchtold Beate , Borth Nicole , Fuchs Aleksandra , Pichler Harald 
Published: November 2022

AbstractCultivated meat may be a more ethical, environmentally friendly, antibiotic-free meat alternative of the future. As of now, one of the main limiting factors for bringing cultivated meat to the market is the high cost of the cell culture media and their great dependency on serum albumins, production of which is predicted to become a major bottleneck of this industry. Here, using bovine muscle stem cells (BSC) we optimized B8/B9 medium - one of the well-established serum free, fully defined medium compositions available for purchase or for preparation in-house. We show several combinations of the growth factors/myokines/hormones, which were able to substantially increase BSCs proliferation rate, as well as treatment schemes allowing for five to ten times lower concentrations of signaling molecules for the same effect. Additionally, we identified several food grade, low-price medium stabilizers, exhibiting comparable or even superior stabilization of the B8 medium in short-term cultivations, as compared to recombinant human serum albumin (HSA). DoE aided in identifying the best cultivation conditions. Other satellite cells (porcine, chicken and fish) were grown in several final cell culture medium compositions, showing significant cell-line specific differences in performance. Also, the proliferation and yield of CHO cell line, which is relevant e.g. for the production of growth factors, was also successfully increased using our stabilization approach. We conclude that stabilizers tested here can act as versatile low-cost medium additives, partly by prolonging the half-life of growth factors. Thus, we provide an alternative to HSA, enabling up to an overall 73% reduction of medium price.
Global spatiotemporal trends and determinants of COVID-19 vaccine acceptance on Twitter: a multilingual deep learning study in 135 countries and territories
Authors: Zhou Xinyu , Zhang Xu , Larson Heidi J. , de Figueiredo Alexandre , Jit Mark , Fodeh Samah , Vermund Sten H. , Zang Sujie , Lin Leesa , Hou Zhiyuan 
Published: November 2022

ABSTRACTBackgroundCOVID-19 vaccination has faced a range of challenges from supply-side barriers such as insufficient vaccine supply and negative information environment and demand-side barriers centring on public acceptance and confidence in vaccines. This study assessed global spatiotemporal trends in demand- and supply-side barriers to vaccine uptake using COVID-19-related social media data and explored the country-level determinants of vaccine acceptance.MethodsWe accessed a total of 13,093,406 tweets sent between November 2020 and March 2022 about the COVID-19 vaccine in 90 languages from 135 countries using Meltwater™® (a social listening platform). Based on 8,125 manually-annotated tweets, we fine-tuned multilingual deep learning models to automatically annotate all 13,093,406 tweets. We present spatial and temporal trends in four key spheres: (1) COVID-19 vaccine acceptance; (2) confidence in COVID-19 vaccines; (3) the online information environment regarding the COVID-19 vaccine; and (4) perceived supply-side barriers to COVID-19 vaccination. Using univariate and multilevel regressions, we evaluated the association between COVID-19 vaccine acceptance on Twitter® and (1) country-level characteristics regarding governance, pandemic preparedness, trust, culture, social development, and population demographics; (2) country-level COVID-19 vaccine coverage; and (3) Google® search trends on adverse vaccine events.FindingsCOVID-19 vaccine acceptance was high among Twitter® users in Southeast Asian, Eastern Mediterranean, and Western Pacific countries, including India, Indonesia, and Pakistan. In contrast, acceptance was relatively low in high-income nations like South Korea, Japan, and the Netherlands. Spatial variations were correlated with country-level governance, pandemic preparedness, public trust, culture, social development, and demographic determinants. At the country level, vaccine acceptance sentiments expressed on Twitter® predicted higher vaccine coverage. We noted the declining trend of COVID-19 vaccine acceptance among global Twitter® users since March 2021, which was associated with increased searches for adverse vaccine events.InterpretationIn future pandemics, new vaccines may face the potential low-level and declining trend in acceptance, like COVID-19 vaccines, and early responses are needed. Social media mining represents a promising surveillance approach to monitor vaccine acceptance and can be validated against real-world vaccine uptake data.FundingNational Natural Science Foundation of China.
Versatile detection of diverse selective sweeps with Flex-sweep
Authors: Lauterbur M. Elise , Munch Kasper , Enard David 
Published: November 2022

ABSTRACTUnderstanding the impacts of selection pressures influencing modern-day genomic diversity is a major goal of evolutionary genomics. In particular, the contribution of selective sweeps to adaptation remains an open question, with persistent statistical limitations on the power and specificity of sweep detection methods. Sweeps with subtle genomic signals have been particularly challenging to detect. While many existing methods powerfully detect specific types of sweeps and/or those with strong signals, their power comes at the expense of versatility. We present Flex-sweep, a machine learning-based tool designed to detect sweeps with a variety of subtle signals, including those thousands of generations old. It is especially valuable for non-model organisms, for which we have neither expectations about the overall characteristics of sweeps nor outgroups with population-level sequencing to otherwise facilitate detecting very old sweeps. We show that Flex-sweep has the power to detect sweeps with subtle signals, even in the face of demographic model misspecification, recombination rate heterogeneity, and background selection. Flex-sweep detects sweeps up to 0.125 * 4Negenerations old, including those that are weak, soft, and/or incomplete; it can also detect strong, complete sweeps up to 0.25 * 4Negenerations old. We apply Flex-sweep to the 1000 Genomes Yoruba data set and, in addition to recovering previously identified sweeps, show that sweeps disproportionately occur within genic regions and close to regulatory regions. In addition, we show that virus-interacting proteins (VIPs) are strongly enriched for selective sweeps, recapitulating previous results that demonstrate the importance of viruses as a driver of adaptive evolution in humans.
Diverging trends and drivers of Arctic flower production over space and time
Authors: Becker-Scarpitta Antoine , Antão Laura H. , Martin Schmidt Niels , Blanchet F. Guillaume , Kaarlejärvi Elina , Raundrup Katrine , Roslin Tomas 
Published: November 2022

AbstractThe Arctic is warming at an alarming rate. While changes in plant community composition and phenology have been extensively reported, the effects of climate change on reproduction remain poorly understood. We quantified multidecadal changes in flower density for nine tundra plant species at a low- and a high-arctic site in Greenland. We found substantial changes in flower density over time, but the temporal trends and drivers of flower density differed both between species and sites. Total flower density increased over time at the low-arctic site, whereas the high-arctic site showed no directional change. Within and between sites, the direction and rate of change differed among species, with varying effects of summer temperature, the temperature of the previous autumn and the timing of snowmelt. Finally, all species showed a strong trade-off in flower densities between successive years, suggesting an effective cost of reproduction. Overall, our results reveal region-and taxon-specific variation in the sensitivity and responses of co-occurring species to shared climatic drivers, and a clear cost of reproductive investment among arctic plants. The ultimate effects of further changes in climate may thus be decoupled between species and across space, with critical knock-on effects on plant species dynamics, food web structure and overall ecosystem functioning.
ChromFormer: A transformer-based model for 3D genome structure prediction
Authors: Valeyre Henry , Pati Pushpak , Gossi Federico , Somnath Vignesh Ram , Martinelli Adriano , Rapsomaniki Maria Anna 
Published: November 2022

AbstractRecent research has shown that the three-dimensional (3D) genome structure is strongly linked to cell function. Modeling the 3D genome structure can not only elucidate vital biological processes, but also reveal structural disruptions linked to disease. In the absence of experimental techniques able to determine 3D chromatin structure, this task is achieved computationally by exploiting chromatin interaction frequencies as measured by high-throughput chromosome conformation capture (Hi-C) data. However, existing methods are unsupervised, and limited by underlying assumptions. In this work, we present a novel framework for 3D chromatin structure prediction from Hi-C data. The framework consists of, a novelsynthetic data generation modulethat simulates realistic structures and corresponding Hi-C matrices, and ChromFormer, a transformer-based model to predict 3D chromatin structures from standalone Hi-C data, while providing local structural-level confidence estimates. Our solution outperforms existing methods when tested on unseen synthetic data, and achieves comparable results on experimental data for a full eukaryotic genome. The code, data, and models can be accessed athttps://github.com/AI4SCR/ChromFormer.
Deciphering the maturation of tertiary lymphoid structures in cancer and inflammatory diseases of the digestive tract using imaging mass cytometry: from high-level data to a simple architectural and functional grading
Authors: Le Rochais Marion , Hémon Patrice , Ben-guigui Danivanh , Garaud Soizic , Le Dantec Christelle , Pers Jacques-Olivier , Uguen Arnaud 
Published: November 2022

ABSTRACTObjectivePersistent inflammation can promote the development of tertiary lymphoid structures (TLS) within tissues resembling the secondary lymphoid organs (SLO) as lymph nodes (LN). The composition of the TLS across different organs and diseases could be of pathophysiological and medical interest. In this work, we compared TLS to SLO and between cancer and inflammatory diseases of the digestive tract.DesignColorectal and gastric tissues with different inflammatory diseases and cancers from the department of pathology of CHU Brest were analyzed based on 39 markers using imaging mass cytometry (IMC). Unsupervised and supervised clustering analyses of IMC images were used to compare SLO and TLS.ResultsUnsupervised analyses tended to group TLS per patient but not per disease. Supervised analyses of IMC images revealed that LN had a more organized structure than TLS and non-encapsulated SLO Peyer’s patches. TLS followed a maturation spectrum with close correlations between germinal cell (GC) markers’ evolution. The correlations between organizational and functional markers made relevant the previously proposed TLS division into three stages: lymphoid-aggregates (LA) (CD20+CD21-CD23-) had neither organization nor GC functionality, non-GC TLS (CD20+CD21+CD23-) were organized but lacked GC’s functionality and GC-like TLS (CD20+CD21+CD23+) had GC’s organization and functionality. This architectural and functional maturation grading of TLS pointed to differences across diseases.ConclusionTLS architectural and functional maturation grading is accessible with few markers allowing future diagnostic, prognostic, and predictive studies on the value of TLS grading, quantification and location within pathological tissues in cancers and inflammatory diseases.KEY MESSAGES-What is already known on this topic:Tertiary lymphoid structures (TLS) arise in organs under various pathological conditions and can be of prognostic significance.-What this study adds:This study deciphers the composition of TLS in digestive cancers and inflammatory diseases using massively multiplexed (39 markers) imaging mass cytometry (IMC). Beyond the term TLS, this study points to the heterogeneity of these structures in terms of composition and maturation but also the relevance of a simple architectural and functional three-stage grading of TLS.-How this study might affect research, practice, or policy:This preliminary study paves the way for future studies evaluating the diagnostic, prognostic and theranostic values of TLS maturation grading, quantification and location within tissues as novel biomarkers in inflammatory diseases and cancers.
HeatChips: A versatile, low-cost and microscopy-compatible heating system for microfluidic devices
Authors: Aspert Théo , Charvin Gilles 
Published: November 2022

AbstractMicrofluidic systems are widely used in biology for their ability to control environmental parameters. Specifically, cell culture or chemistry in microfluidic devices requires tight control of the temperature. In addition, microfluidic devices can be made transparent to visible light and compatible with inverted microscopes. Yet, the current temperature control systems that allow high-resolution microscopy either require a set of complex secondary channels, a bulky, expensive, and microscope-dependent incubator, or fail to produce a homogenous temperature profile across the sample area. Here, we present HeatChips, a simple, cost-effective system to heat samples inside PDMS-based microfluidic devices in a homogeneous manner. It is based on a transparent heating glass in contact with the top of the microfluidic device, and a contactless, infrared temperature sensor attached to the objective that directly reads the temperature of the bottom of the chip. This portable system is compatible with most chip designs and allows imaging of the sample on inverted microscopes for extended periods of time without any optical restriction, for a cost of less than 100€.Specifications table