bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmission potential of mpox in Mainland China, June-July 2023: estimating reproduction number during the initial phase of the epidemic
Authors: Akhmetzhanov Andrei R. , Wu Pei-Hsuan 
Published: September 2023

AbstractDespite reporting very few mpox cases in early 2023, Mainland China observed a surge of over 500 cases during the summer. Amid ambiguous prevention strategies and stigma surrounding mpox transmission, the epidemic silently escalated. This study aims to quantify the scale of the mpox epidemic and assess the transmission dynamics of the virus by estimating the effective reproduction number (Re) during its early phase. Publicly available data were aggregated to obtain daily mpox incidences in Mainland China, and theRewas estimated using an exponential growth model. The meanRevalue was found to be 1.76 (95% credible interval: 1.51–2.06), suggesting a case doubling time of approximately 2 weeks. This estimate was compared withRevalues from 16 other countries’ national outbreaks in 2022 that had cumulative incidences exceeding 700 symptomatic cases by the end of that year. TheReestimates for these outbreaks ranged from 1.17 for Portugal to 2.88 for Colombia. The pooled meanRewas 1.66 (95% credible interval: 1.40–1.92), which aligns closely with theRefor Mainland China. These findings underscore the need for immediate and effective control measures including targeted vaccination campaigns to mitigate the further spread and impact of the epidemic.
The Human Infertility Single-cell Testis Atlas (HISTA): An interactive molecular scRNA-Seq reference of the human testis
Authors: Mahyari Eisa , Vigh-Conrad Katinka A. , Daube Clément , Lima Ana C. , Guo Jingtao , Carrell Douglas T. , Hotaling James M. , Aston Kenneth I. , Conrad Donald F. 
Published: September 2023

ABSTRACTBackgroundThe Human Infertility Single-cell Testis Atlas (HISTA) is an interactive web tool and a reference for navigating the transcriptome of the human testis. It was developed using joint analyses of scRNA-Seq datasets derived from a dozen donors, including healthy adult controls, juveniles, and several infertility cases. HISTA is very different than other websites of testis scRNA-seq data, providing visualization and hypothesis testing tools on a batch-removed and integrated dataset of 23429 genes measured across 26093 cells using.ObjectiveThe main goal of this manuscript is to describe HISTA in detail and highlight its unique and novel features.MethodsTherefore, we used HISTA as a guide for its application and demonstrated HISTA’s translational capacity to follow up on two observations of biological relevance.ResultsOur first analytical vignette identifies novel groupings of tightly regulated long non-coding RNA (lncRNA) molecules throughout spermatogenesis, suggesting specific functional genomics of these groupings. This analysis also found highly controlled expression of pairs of sense and antisense transcripts, suggesting conjoined regulatory mechanisms. In the next investigative vignette, we examined gene patterns in undifferentiated spermatogonia (USgs). We found the NANOS family of genes function as key drivers of transcriptomic signatures involved in human spermatogonial self-renewal programming; for the first time, demonstrating the relationship of NANOS1/2/3 transcripts in humans with scRNA-seq.Discussion and ConclusionsUsing HISTA, we found new observations that contribute to unraveling the mechanisms behind transcriptional regulation and maintenance germ cells across spermatogenesis. Furthermore, our findings provide guidance on future validation studies and experimental direction. Overall, HISTA continues to be utilized in testis-related research, and thus is updated regularly with new analytical methods, visualizations, and data. We aim to have it serve as a research environment for a broad range of investigators looking to explore the testis tissue and male infertility.Availability and ImplementationHISTA is available as an interactive web tool:https://conradlab.shinyapps.io/HISTASource code and documentation for HISTA are provided on GitHub:https://github.com/eisascience/HISTA
A review of fish diversity in Mediterranean seagrass habitats, with a focus on functional traits
Authors: Lattanzi A. , Bellisario B. , Cimmaruta R. 
Published: September 2023

AbstractSeagrass habitats are considered essential in supporting both fish diversity and fisheries’ income. Within the Mediterranean Sea most fish species are associated to seagrasses and constitute the subject of extensive literature. However, a complete synthesis of fish species observed in different seagrass habitats is still lacking at the whole-basin Mediterranean scale, so hindering a thorough understanding of the main functional traits and mechanisms involved in determining fish diversity patterns. We performed a systematic review by implementing a semi-automated, threshold-based filtering pipeline that allowed building up a dataset concerning all fish species reported in native Mediterranean seagrasses, including specific functional traits known to be involved with the potential use of seagrasses by fish. These data allowed to carry on a narrative synthesis on fish diversity in seagrass habitats. Moreover, the functional traits analysis highlighted a significant role of trophic level, size and benthic domain in determining the distribution of fish in different seagrass habitats at whole Mediterranean basin scale. Data evidenced a pattern of segregation between large piscivorous, pelagic predators and smaller benthic prey (including juveniles) with omnivorous to herbivorous feeding habit, with aggressive predators significantly associated withPosidonia oceanicaandCymodocea nodosabeds while their putative prey tend to occupy other seagrass habitats. We identified unexpected knowledge gaps on the role of habitat heterogeneity and fish life stages in determining the presence/absence of fish in different seagrasses, for which in-depth research is needed to fully understand the links between nursery habitats and the state of exploited fish stock.
Perceptual priors add sensory detail to contextual feedback processing in V1
Authors: Lazarova Yulia , Huang Yingying , Muckli Lars , Petro Lucy S. 
Published: September 2023

AbstractHow do we develop models of the world? Contextualising ambiguous information with previous experience allows us to form an enriched perception. Contextual information and prior knowledge facilitate perceptual processing, improving our recognition of even distorted or obstructed visual inputs. As a result, neuronal processing elicited by identical sensory inputs varies depending on the context in which we encounter those inputs. This modulation is in line with predictive processing accounts of vision which suggest that the brain uses internal models of the world to predict sensory inputs, with cortical feedback processing in sensory areas encoding beliefs about those inputs. As such, acquiring knowledge should enhance our internal models that we use to resolve sensory ambiguities, and feedback signals should encode more accurate estimates of sensory inputs. We used partially occluded Mooney images, ambiguous two-tone images which are difficult to recognise without prior knowledge of the image content, in behavioural and 3T fMRI experiments to measure if contextual feedback signals in early visual areas are modulated by learning. We show that perceptual priors add sensory detail to contextual feedback processing in early visual areas in response to subsequent presentations of previously ambiguous images.
Embodiment in episodic memory through premotor-hippocampal coupling
Authors: Meyer Nathalie Heidi , Gauthier Baptiste , Stampacchia Sara , Boscheron Juliette , Babo Rebelo Mariana , Potheegadoo Jevita , Herbelin Bruno , Lance Florian , Alvarez Vincent , Franc Elizabeth , Esposito Fabienne , Morais Lacerda Marilia , Blanke Olaf 
Published: September 2023

AbstractEpisodic memory (EM) allows us to remember and relieve past events and experiences, depending on cortical-hippocampal reinstatement involved during encoding. Although it has been claimed that EM is fundamental to establish a sense of self across time, this has never been shown experimentally. Here we combine immersive virtual reality and fMRI and report stronger hippocampal reinstatement for scenes encoded under preserved sense of self, reflecting later recall performance. We further link the sense of self to EM showing that hippocampal reinstatement is coupled with reinstatement in premotor cortex, a key sense of self region. We extend these findings in a severe amnesic patient (caused by bilateral hippocampal damage), whose memory and re-experiencing lacked the normal dependency on the sense of self. Premotor-hippocampal coupling in EM describes how the self at encoding is neurally reinstated during the retrieval of past episodes, enabling a sense of self across time.TeaserPremotor-hippocampal coupling reveals how the self is reinstated when retrieving past episodes.
Cortical and subcortical brain networks predict prevailing heart rate
Authors: Sentis Amy Isabella , Rasero Javier , Gianaros Peter J. , Verstynen Timothy D. 
Published: September 2023

AbstractResting heart rate may confer risk for cardiovascular disease (CVD) and other adverse cardiovascular events. While the brainstem’s autonomic control over heart rate is well established, less is known about the regulatory role of higher-level cortical and subcortical brain regions, especially in humans. The present study sought to characterize the brain networks that predict variation in prevailing heart rate in otherwise healthy adults. We used machine learning approaches designed for complex, high-dimensional datasets, to predict variation in instantaneous heart period (the inter-heartbeat-interval) from whole brain hemodynamic signals measured by fMRI. Task-based and resting-state fMRI, as well as peripheral physiological recordings, were taken from two datasets that included extensive repeated measurements within individuals. Our models reliably predicted instantaneous heart period from whole brain fMRI data both within and across individuals, with prediction accuracies being highest when measured within-participants. We found that a network of cortical and subcortical brain regions, many linked to psychological stress, were reliable predictors of variation in heart period. This adds to evidence on brain-heart interactions and constitutes an incremental step towards developing clinically-applicable biomarkers of brain contributions to CVD risk.Impact statementUsing whole brain fMRI data, we reliably predicted instantaneous heart period within and across individuals from the activity of a network of cortical and subcortical brain regions, many linked to psychological stress. This adds to existing evidence on brain-heart interactions and constitutes a step towards developing clinically-applicable biomarkers of brain contributions to CVD risk.
Common and Rare Variant Contributions to Bradyarrhythmias from Multi-Ancestry Meta-Analyses
Authors: Weng Lu-Chen , Rämö Joel T. , Jurgens Sean J. , Khurshid Shaan , Chaffin Mark , Hall Amelia Weber , Morrill Valerie N. , Nauffal Victor , Sun Yan V. , Beer Dominik , Lee Simon , Nadkarni Girish , Duong ThuyVy , Wang Biqi , Czuba Tomasz , Austin Thomas R. , Yoneda Zachary T. , Friedman Daniel J. , Clayton Anne , Hyman Matthew C. , Judy Renae L. , Skanes Allan C. , Orland Kate M. , Treu Timothy M. , Oetjens Matthew T. , Alonso Alvaro , Soliman Elsayed Z. , Lin Honghuang , Lunetta Kathryn L. , van der Pals Jesper , Issa Tariq Z. , Nafissi Navid A. , May Heidi T. , Leong-Sit Peter , Roselli Carolina , Choi Seung Hoan ,   FinnGen, Million Veteran Program, Regeneron Genetics Center, Khan Habib R. , Knight Stacey , Linnér Richard K. , Bezzina Connie R. , Ripatti Samuli , Gaziano J. Michael , Loos Ruth , Psaty Bruce M. , Smith J. Gustav , Benjamin Emelia J. , Arking Dan E. , Rader Daniel , Shah Svati H. , Roden Dan M. , Damrauer Scott M. , Eckhardt Lee L. , Roberts Jason D. , Cutler Michael J. , Shoemaker M. Benjamin , Haggerty Christopher M. , Cho Kelly , Palotie Aarno , Wilson Peter W.F. , Ellinor Patrick T. , Lubitz Steven A. 
Published: September 2023

ABSTRACTTo broaden our understanding of bradyarrhythmias and diseases of the cardiac conduction system, we performed cross-sectional multi-ancestry genome-wide association study meta-analyses in up to 1.3 million individuals for sinus node dysfunction (SND), distal conduction disease (DCD), and pacemaker implantation (PM). We evaluated the biological relevance of bradyarrhythmia loci by analyses of transcriptomes, pleiotropy, and partitioned heritability based on cardiac single cell RNA sequencing data. Finally, we performed rare variant burden testing in 460,000 whole exome sequenced individuals from two biobanks. We identified 13, 28, and 21 common variant loci for SND, DCD, and PM, respectively. Four well-known common variant arrhythmia loci (SCN5A/SCN10A,CCDC141, TBX20, andCAMK2D)were shared for SND and DCD, while other loci were more specific for either SND or DCD. Cardiomyocyte-expressed genes were strongly enriched for contributions to DCD heritability, while SND and PM were more heterogeneous. Rare variant analyses implicatedLMNAfor all bradyarrhythmia subtypes;SMAD6andSCN5Afor DCD; andTTN,MYBPC3, andSCN5Afor PM. The genetic architectures of SND and DCD are both overlapping and distinct. Multiple genetic mechanisms involving ion channels, sarcomeric components, cellular homeostasis, and cardiac development may influence the development of bradyarrhythmias.
Maternal smoking DNA methylation risk score associated with health outcomes in offspring of European and South Asian ancestry
Authors: Deng Wei Q. , Cawte Nathan , Campbell Natalie , Azab Sandi M. , de Souza Russell J , Lamri Amel , Morrison Katherine M. , Atkinson Stephanie A. , Subbarao Padmaja , Turvey Stuart E. , Moraes Theo J. , Teo Koon K. , Mandhane Piush , Azad Meghan B. , Simons Elinor , Pare Guillaume , Anand Sonia S. 
Published: September 2023

AbstractMaternal smoking has been linked to adverse health outcomes in newborns but the extent to which it impacts newborn health has not been quantified through an aggregated cord blood DNA methylation (DNAm) score. Here we examine the feasibility of using cord blood DNAm scores leveraging large external studies as discovery samples to capture the epigenetic signature of maternal smoking and its influence on newborns in White European and South Asian populations. We first examined association between individual CpGs and cigarette smoking during pregnancy, smoking exposure in two White European birth cohorts (n = 744). Several previously reported genes for maternal smoking were supported, with the strongest and most consistent signal from theGFI1gene (6 CpGs withp< 5×10-5). Leveraging established CpGs for maternal smoking, we constructed a cord blood epigenetic score of maternal smoking that was validated in one of the European-origin cohorts (n = 347). This score was then tested for association with smoking status, secondary smoking exposure during pregnancy, and health outcomes in offspring measured after birth in an independent white European (n = 397) and a South Asian birth cohort (n = 504). The epigenetic maternal smoking score was strongly associated with smoking status during pregnancy (OR=1.09 [1.07,1.10],p=5.5×10-33) and more hours of self-reported smoking exposure per week (1.93 [1.27, 2.58],p=7.8×10-9) in White Europeans, but not with self-reported exposure (p> 0.05) in South Asians. The same score was consistently associated with a smaller birth size (−0.37±0.12 cm,p=0.0023) in the South Asian cohort and a lower birth weight (−0.043±0.013kg,p=0.0011) in the combined cohorts. This cord blood epigenetic score can help identify babies exposed to maternal smoking and assess its long-term impact on growth. Notably, these results indicate a consistent association between the DNAm signature of maternal smoking and a small body size and low birthweight in newborns, in both white European mothers who exhibited some amount of smoking and in South Asian mothers who themselves were not active smokers.
Trends in AI-powered classification of thyroid neoplasms based on histopathology images, a systematic review
Authors: Kussaibi Haitham , Alsafwani Noor 
Published: September 2023

AbstractBackgroundAssessment of thyroid nodules histopathology using AI is crucial for an accurate diagnosis. This systematic review analyzes recent works employing deep learning approaches for classifying thyroid nodules based on histopathology images, evaluating their performance, and identifying limitations.MethodsEligibility criteria focused on peer-reviewed English papers published in the last five years, applying deep learning to categorize thyroid histopathology images. The PubMed database was searched using relevant keyword combinations.ResultsOut of 103 articles, 11 studies met inclusion criteria. They used convolutional neural networks to classify thyroid neoplasm. Most studies aimed at basic tumor subtyping; however, three studies targeted the prediction of tumor-associated mutation. Accuracy ranged from 77% to 100%, with most over 90%.DiscussionThe findings from our analysis reveal the effectiveness of deep learning in identifying discriminative morphological patterns from histopathology images, thus enhancing the accuracy of thyroid nodule histopathological classification. Key limitations were small sample sizes, subjective annotation, and limited dataset diversity. Further research with larger diverse datasets, model optimization, and real-world validation is essential to translate these tools into clinical practice.OtherFundingThis study did not receive any funding.RegistrationThe procedural instructions for this systematic review were officially recorded within the PROSPERO database under registration numberRD42023457854https://www.crd.york.ac.uk/Prospero/
Coping skills, depression, and anxiety in medical students
Authors: Baldassin Sergio , Zilbermann Mônica Levit , de Toledo Ferraz Alves Tania Correa , Martins-da-Silva Anderson Sousa , Castaldelli-Maia João Maurício , Nogueira-Martins Luiz Antonio 
Published: September 2023

AbstractObjectiveto describe coping strategies during medical education and their relationship with course periods, with gender, and depressive and anxiety range symptoms.Methodthe Ways of Coping Questionnaire (WCQ), the Beck Depression Inventory (BDI), and the Spielberger Trait Anxiety Inventory (STAI-T) were administered to 599 medical students from basic, intermediate and internship periods.ResultsThe response rate was 80.3% (279 females and 190 males aged 21.9 ± 2.4 years). Belong to internship or basic/intermediate levels make a significant difference in choosing coping factors. Female students reported greater use of factors indicating a need for social support and fantasy. In contrast, male students reported greater use of factors such as substance use and self-control.Twenty percent of students scored high on anxiety (STAI-T>49), whereas 7.6% scored on the depression range (>20) and 8.0% on the dysphoric range (16–20) of the BDI. Students at the normal range at the BDI and the STAI-T reported greater use of factors such as of social support and problem solving. The factor analysis of the WCQ showed that dysphoric, depressive, and high anxiety students reported greater use of factors indicating fantasy, search of relief and escape.ConclusionDysphoria, depressive, and highly anxious medical students choose similar strategies to deal with stress related to medical graduation. Women and men exhibit distinct coping strategies related to medical education and training. Support and counseling services for medical students should take into consideration these depressive and anxiety ranges, and gender differences in coping strategies, with potentially important preventive and therapeutic implications.
Trends of non-tuberculous mycobacterial disease in a low-tuberculosis prevalence setting
Authors: Mohanty Biplob Kumar , Eagan Tomas Mikal Lind , Aarli Bernt Bøgvald , Skutlaberg Dag Harald , Mustafa Tehmina 
Published: September 2023

AbstractBackgroundLimited data are available regarding factors associated with initiation of treatment and treatment outcomes after diagnosis of non-tuberculous mycobacteria (NTM) pulmonary infection and disease.ObjectiveTo investigate trends of NTM pulmonary infections, patient characteristics and factors associated with initiation of treatment and treatment outcomes in patients with NTM pulmonary infection and disease.MethodsWe evaluated 154 patients with NTM pulmonary infection, identified by having at least one record coded with ICD-10 A31.0 at Haukeland University Hospital in Bergen, Norway, from 2000 to 2021. A univariate and multivariate binary logistic regression was carried out to find the odds of factors associated with the initiation of treatment and treatment outcomes.Results70% of the patients were older than 65 years. 49 % of patients had pulmonary comorbidity and the three most common symptoms were cough, dyspnoea, and weight loss. The most frequently observed mycobacterial species wasM. avium complex(MAC), followed byM. malmoense, andM. abscessus. There was a decreasing trend in NTM pulmonary infection and NTM pulmonary disease from the year 2000 to 2014, while an increase was observedfrom 2015 to 2019. A total of 72 (47%) patients received antibiotic treatment. Patients with high symptom scores, those below the age of 65, and those with MAC infection had more than three times the odds of receiving antibiotic treatment (P = 0.006, P = 0.006, and P = .005 respectively). Of 72 patients who received treatment, 53 (74%) had a favourable response and culture conversion. 17 (32%) of them had a relapse. Out of 82 patients who did not receive treatment, 45 (55%) had spontaneous culture conversion. 8 (18%) of them had a relapse. No factor was identified to be significantly associated with a favourable treatment response including the time taken to start treatment or presence of pulmonary cavities.ConclusionFavourable response to treatment was seen in 74% patients whereas spontaneous culture conversion was seen in 55% of non-treated patients. Factors associated with favourable treatment response were not found.
Identification of Metabolic Pathways Altered in Thyroid Cancer Progression and Metastasis
Authors: de Oliveira Andrade Luís Jesuino , Matos de Oliveira Luisa Correia , Matos de Oliveira Gabriela Correia , Vinhaes Bittencourt Alcina Maria , Peixoto Silva Catharina , Matos de Oliveira Luís 
Published: September 2023

ABSTRACTIntroductionThyroid cancer is a common endocrine malignancy with a rising incidence. However, to improve patient outcomes, it is essential to understand the molecular mechanisms driving its progression and metastasis, and the metabolomics can unveil alterations in metabolic pathways that contribute to thyroid cancer.ObjectiveTo identify the metabolic pathways altered in thyroid cancer progression and metastasis.MethodsMultiple bioinformatics tools were employed in the research. Gene expression data was obtained from the Gene Expression Omnibus and The Cancer Genome Atlas. Functional assessment of the expressed genes in thyroid cancer was performed using gene set enrichment analysis. The Kyoto Encyclopedia of Genes and Genomes database was utilized to identify the metabolic pathway involved in thyroid cancer progression and metastasis. A computational algorithm was developed to estimate the activity levels of the identified metabolic pathways and construct a signaling pathway.ResultsThe altered metabolic pathways in thyroid cancer progression and metastasis were identified based on the following algorithm: activation of growth factor signaling, activation of multiple signaling pathways, regulation by transcription factors, dysregulation of downstream signaling cascades, changes in cellular metabolism, tumor progression, invasion and metastasis, and feedback regulation.ConclusionBy applying a comprehensive algorithm, we were able to uncover key molecular events driving the aggressive behavior of thyroid cancer. These findings provide insights into the underlying mechanisms of thyroid cancer progression and metastasis.