bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between atherosclerosis, hearing recovery, and hearing in the healthy ear in idiopathic sudden sensorineural hearing loss: a retrospective chart analysis
Authors: Tsuzuki Nobuyoshi , Wasano Koichiro , Oishi Naoki , Hentona Ko , Shimanuki Marie , Nishiyama Takanori , Hiraga Yoshihiko , Ueno Masafumi , Suzuki Narihisa , Shinden Seiichi , Ogawa Kaoru , Ozawa Hiroyuki 
Published: December 2022

AbstractAtherosclerosis is reported to be a risk factor for the severity of idiopathic sudden sensorineural hearing loss (ISSNHL). We evaluated the hypothesis that atherosclerosis affects the hearing thresholds of both the affected and healthy sides of ISSNHL patients. We conducted multivariate analyses on retrospectively collected data of patients with ISSNHL (N = 762) to evaluate the relationship between known factors linked to atherosclerosis and hearing thresholds on affected and healthy sides and whether these factors are prognostic for hearing recovery. Older ages, vertigo or dizziness, diabetes mellitus, and congestive heart failure were significantly related to higher hearing thresholds on the affected side. Older ages, male, and vascular disease were significantly related to higher hearing thresholds on the healthy side. Vertigo or dizziness, severe hearing loss and hearing loss at high frequencies on the affected side, higher hearing thresholds on the healthy side, regular anticoagulant medication, and delayed steroid treatment were significantly related to lack of recovery. Since several atherosclerosis-related factors are associated with higher hearing thresholds on both affected and healthy sides in ISSNHL and higher hearing thresholds on the healthy side predict poorer prognosis, diagnosis, and predicting prognosis of ISSNHL may benefit from rigorous evaluation of patients’ cardiovascular comorbidities and hearing levels on both the healthy and affected sides.
The historical impact of anthropogenic air-borne sulphur on the Pleistocene rock art of Sulawesi
Authors: Gagan Michael K. , Halide Halmar , Permana Raden Cecep Eka , Lebe Rustan , Dunbar Gavin B. , Kimbrough Alena K. , Scott-Gagan Heather , Zwartz Dan , Hantoro Wahyoe S. 
Published: December 2022

AbstractThe Maros-Pangkep karst in southwest Sulawesi, Indonesia, contains some of the world’s oldest rock art. However, the Pleistocene images survive only as weathered patches of pigment on exfoliated limestone surfaces. Salt efflorescence underneath the case-hardened limestone substrate causes spall-flaking, and it has been proposed that the loss of artwork has accelerated over recent decades. Here, we utilise historical photographs and superposition constraints to show that the bulk of the damage was present before 1950 CE, and describe the role of anthropogenic sulphur emissions in promoting gypsum-salt efflorescence and rock art decay. The rock art shelters have been exposed to domestic fire-use and intensive rice cultivation with post-harvest burning of straw for hundreds (if not thousands) of years, both of which release chemically reactive sulphur oxides for gypsum formation, with cumulative effects. Analysis of time-lapse photography indicates that the rate of rock art loss may be on the decline, consistent with the history of fire-use in southwest Sulawesi. At present, vandalism and sulphur emissions from diesel-powered traffic and cement-based infrastructure development constitute localised threats. Our findings indicate that there are grounds for being cautiously optimistic that targeted conservation measures will ensure the longevity of some of our oldest artistic treasures.
Altered recognition of fearful and angry facial expressions in women with fibromyalgia syndrome: an experimental case–control study
Authors: Scarpina Federica , Ghiggia Ada , Vaioli Giulia , Varallo Giorgia , Capodaglio Paolo , Arreghini Marco , Castelnuovo Gianluca , Mauro Alessandro , Castelli Lorys 
Published: December 2022

AbstractEvidence relative to facial emotion recognition and the role played by alexithymia in fibromyalgia syndrome is rare and heterogeneous. In this work, we investigated this ability in fibromyalgia investigating the implicit behaviour in the facial emotion recognition task, focusing on fear and anger. Twenty women with fibromyalgia and twenty healthy women as controls performed a facial emotion recognition of fearful and angry expressions. Their implicit behaviour was scored in accordance with the redundant target effect. The level of alexithymic traits through a standard psychological questionnaire and its effect on behavioral performance were also assessed. Participants affected by fibromyalgia reported a lower level of accuracy in recognizing fearful and angry expressions, in comparison with the controls. Crucially, such a difference was not explained by the different levels of alexithymic traits between groups. Our results agreed with some previous evidence suggesting an altered recognition of others’ emotional facial expressions in fibromyalgia syndrome. Considering the role of emotion recognition on social cognition and psychological well-being in fibromyalgia, we underlined the crucial role of emotional difficulties in the onset and maintenance of the symptoms life-span.
Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters
Authors: Barsoum Mirna , Stenzel Alexander T. , Bochyńska Agnieszka , Kuo Chao-Chung , Tsompanidis Alexander , Sayadi-Boroujeni Roksaneh , Bussmann Philip , Lüscher-Firzlaff Juliane , Costa Ivan G. , Lüscher Bernhard 
Published: December 2022

AbstractChanges in gene expression programs are intimately linked to cell fate decisions. Post-translational modifications of core histones contribute to control gene expression. Methylation of lysine 4 of histone H3 (H3K4) correlates with active promoters and gene transcription. This modification is catalyzed by KMT2 methyltransferases, which require interaction with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, for catalytic activity. Ash2l is necessary for organismal development and for tissue homeostasis. In mouse embryo fibroblasts (MEFs), Ash2l loss results in gene repression, provoking a senescence phenotype. We now find that upon knockout of Ash2l both H3K4 mono- and tri-methylation (H3K4me1 and me3, respectively) were deregulated. In particular, loss of H3K4me3 at promoters correlated with gene repression, especially at CpG island promoters. Ash2l loss resulted in increased loading of histone H3 and reduced chromatin accessibility at promoters, accompanied by an increase of repressing and a decrease of activating histone marks. Moreover, we observed altered binding of CTCF upon Ash2l loss. Lost and gained binding was noticed at promoter-associated and intergenic sites, respectively. Thus, Ash2l loss and reduction of H3K4me3 correlate with altered chromatin accessibility and transcription factor binding. These findings contribute to a more detailed understanding of mechanistic consequences of H3K4me3 loss and associated repression of gene transcription and thus of the observed cellular consequences.
Genotypic and phenotypic profiles of EYS gene-related retinitis pigmentosa: a retrospective study
Authors: Suvannaboon Ragkit , Pawestri Aulia Rahmi , Jinda Worapoj , Tuekprakhon Aekkachai , Trinavarat Adisak , Atchaneeyasakul La-ongsri 
Published: December 2022

AbstractRetinitis pigmentosa (RP) affects 1:5000 individuals worldwide. Interestingly, variations in 271 RP-related genes are indicated to vary among populations. We aimed to evaluate the genetic prevalence and phenotypic profiles of Thai patients with RP. The clinical and whole exome sequencing data of 125 patients suggestive of inherited retinal diseases (IRD), particularly non-syndromic RP, were assessed. We found a total of 258 variants (63% of which remained unavailable in the ClinVar database) in 91 IRD-associated genes. Among the detected genes, the eyes shut homolog (EYS) gene showed the highest prevalence. We also provide insights into the genotypic, baseline, and follow-up clinical presentations of seven patients with disease-causing EYS variations. This study could provide comprehension of the prevalence of RP-related genes involved in the Asian population. It might also provide information to establish advanced and personalised therapy for RP in the Thai population.
ACE2 polymorphisms impact COVID-19 severity in obese patients
Authors: Jalaleddine Nour , Bouzid Amal , Hachim Mahmood , Sharif-Askari Narjes Saheb , Mahboub Bassam , Senok Abiola , Halwani Rabih , Hamoudi Rifat A. , Al Heialy Saba 
Published: December 2022

AbstractA strong association between obesity and COVID-19 complications and a lack of prognostic factors that explain the unpredictable severity among these patients still exist despite the various vaccination programs. The expression of angiotensin converting enzyme 2 (ACE2), the main receptor for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is enhanced in obese individuals. The occurrence of frequent genetic single nucleotide polymorphisms (SNPs) inACE2is suggested to increase COVID-19 severity. Accordingly, we hypothesize that obesity-associatedACE2polymorphisms increase the severity of COVID-19. In this study, we profiled eight frequently reportedACE2SNPs in a cohort of lean and obese COVID-19 patients (n = 82). We highlight the significant association of rs2285666, rs2048683, rs879922, and rs4240157 with increased severity in obese COVID-19 patients as compared to lean counterparts. These co-morbid-associated SNPs tend to positively correlate, hence proposing possible functional cooperation toACE2regulation. In obese COVID-19 patients, rs2285666, rs879922, and rs4240157 are significantly associated with increased blood nitrogen urea and creatinine levels. In conclusion, we highlight the contribution ofACE2SNPs in enhancing COVID-19 severity in obese individuals. The results from this study provide a basis for further investigations required to shed light on the underlying mechanisms of COVID-19 associated SNPs in COVID-19 obese patients.
Hemorrhage segmentation in mobile-phone retinal images using multiregion contrast enhancement and iterative NICK thresholding region growing
Authors: Chandhakanond Patsaphon , Aimmanee Pakinee 
Published: December 2022

AbstractHemorrhage segmentation in retinal images is challenging because the sizes and shapes vary for each hemorrhage, the intensity is close to the blood vessels and macula, and the intensity is often nonuniform, especially for large hemorrhages. Hemorrhage segmentation in mobile-phone retinal images is even more challenging because mobile-phone retinal images usually have poorer contrast, more shadows, and uneven illumination compared to those obtained from the table-top ophthalmoscope. In this work, the proposed KMMRC-INRG method enhances the hemorrhage segmentation performance with nonuniform intensity in poor lighting conditions on mobile-phone images. It improves the uneven illumination of mobile-phone retinal images using a proposed method, K-mean multiregion contrast enhancement (KMMRC). It also enhances the boundary segmentation of the hemorrhage blobs using a novel iterative NICK thresholding region growing (INRG) method before applying an SVM classifier based on hue, saturation, and brightness features. This approach can achieve as high as 80.18%, 91.26%, 85.36%, and 80.08% for recall, precision, F1-measure, and IoU, respectively. The F1-measure score improves up to 19.02% compared to a state-of-the-art method DT-HSVE tested on the same full dataset and as much as 58.88% when considering only images with large-size hemorrhages.
Experimental evidence that rill-bed morphology is governed by emergent nonlinear spatial dynamics
Authors: Morgan Savannah , Huffaker Ray , Giménez Rafael , Campo-Bescos Miguel A. , Muñoz-Carpena Rafael , Govers Gerard 
Published: December 2022

AbstractPast experimental work found that rill erosion occurs mainly during rill formation in response to feedback between rill-flow hydraulics and rill-bed roughness, and that this feedback mechanism shapes rill beds into a succession of step-pool units that self-regulates sediment transport capacity of established rills. The search for clear regularities in the spatial distribution of step-pool units has been stymied by experimental rill-bed profiles exhibiting irregular fluctuating patterns of qualitative behavior. We hypothesized that the succession of step-pool units is governed by nonlinear-deterministic dynamics, which would explain observed irregular fluctuations. We tested this hypothesis with nonlinear time series analysis to reverse-engineer (reconstruct) state-space dynamics from fifteen experimental rill-bed profiles analyzed in previous work. Our results support this hypothesis for rill-bed profiles generated both in a controlled lab (flume) setting and in an in-situ hillside setting. The results provide experimental evidence that rill morphology is shaped endogenously by internal nonlinear hydrologic and soil processes rather than stochastically forced; and set a benchmark guiding specification and testing of new theoretical framings of rill-bed roughness in soil-erosion modeling. Finally, we applied echo state neural network machine learning to simulate reconstructed rill-bed dynamics so that morphological development could be forecasted out-of-sample.
Adhesion of Rhodococcus bacteria to solid hydrocarbons and enhanced biodegradation of these compounds
Authors: Ivshina Irina B. , Krivoruchko Anastasiia V. , Kuyukina Maria S. , Peshkur Tatyana A. , Cunningham Colin J. 
Published: December 2022

AbstractAdhesive activities of hydrocarbon-oxidizingRhodococcusbacteria towards solid hydrocarbons, effects of adhesion on biodegradation of these compounds by rhodococcal cells and adhesion mechanisms ofRhodococcusspp. were studied in this work. It was shown that efficiency ofRhodococcuscells’ adhesion to solidn-alkanes and polycyclic aromatic hydrocarbons (PAHs) varied from 0.0 to 10.6·106 CFU/cm2.R. erythropolisIEGM 212 andR. opacusIEGM 262 demonstrated the highest (≥ 4.3·106 CFU/cm2) adhesion. The percentage biodegradation of solid hydrocarbons (n-hexacosane and anthracene as model substrates) byRhodococcuscells was 5 to 60% at a hydrocarbon concentration of 0.2% (w/w) after 9 days and strongly depended on cell adhesive activities towards these compounds (r ≥ 0.71,p < 0.05). No strict correlation between the adhesive activities of rhodococcal cells and physicochemical properties of bacteria and hydrocarbons was detected. Roughness of the cell surface was a definitive factor ofRhodococcuscell adhesion to solid hydrocarbons. Specific appendages with high adhesion force (≥ 0.6 nN) and elastic modulus (≥ 6 MPa) were found on the surface ofRhodococcuscells with high surface roughness. We hypothesized that these appendages participated in the adhesion process.
Autoencoders for sample size estimation for fully connected neural network classifiers
Authors: Gulamali Faris F. , Sawant Ashwin S. , Kovatch Patricia , Glicksberg Benjamin , Charney Alexander , Nadkarni Girish N. , Oermann Eric 
Published: December 2022

AbstractSample size estimation is a crucial step in experimental design but is understudied in the context of deep learning. Currently, estimating the quantity of labeled data needed to train a classifier to a desired performance, is largely based on prior experience with similar models and problems or on untested heuristics. In many supervised machine learning applications, data labeling can be expensive and time-consuming and would benefit from a more rigorous means of estimating labeling requirements. Here, we study the problem of estimating the minimum sample size of labeled training data necessary for training computer vision models as an exemplar for other deep learning problems. We consider the problem of identifying the minimal number of labeled data points to achieve a generalizable representation of the data, a minimum converging sample (MCS). We use autoencoder loss to estimate the MCS for fully connected neural network classifiers. At sample sizes smaller than the MCS estimate, fully connected networks fail to distinguish classes, and at sample sizes above the MCS estimate, generalizability strongly correlates with the loss function of the autoencoder. We provide an easily accessible, code-free, and dataset-agnostic tool to estimate sample sizes for fully connected networks. Taken together, our findings suggest that MCS and convergence estimation are promising methods to guide sample size estimates for data collection and labeling prior to training deep learning models in computer vision.
Has increased telehealth access during COVID-19 led to over-utilization of primary care?
Authors: Venkatesh Kaushik P. , Raza Marium M. , Kvedar Joseph 
Published: December 2022

AbstractTelehealth use for primary care has skyrocketed since the onset of the COVID-19 pandemic. Enthusiasts have praised this new medium of delivery as a way to increase access to care while potentially reducing spending. Over two years into the pandemic, the question of whether telehealth will lead to an increase in primary care utilization and spending has been met with contradictory answers. Some evidence suggests that telehealth may be used as an addition to in-person visits. Others like Dixit et al. have found that telehealth can actually substitute for in-person care rather than contribute to overutilization. As telehealth continues to evolve, outcomes, utilization, and quality of care should be closely monitored.
Tissue registration and exploration user interfaces in support of a human reference atlas
Authors: Börner Katy , Bueckle Andreas , Herr Bruce W. , Cross Leonard E. , Quardokus Ellen M. , Record Elizabeth G. , Ju Yingnan , Silverstein Jonathan C. , Browne Kristen M. , Jain Sanjay , Wasserfall Clive H. , Jorgensen Marda L. , Spraggins Jeffrey M. , Patterson N. Heath , Weber Griffin M. 
Published: December 2022

AbstractSeventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data across 25 organs and more than 15 bulk and spatial single-cell assay types poses challenges. Here, we present software tools and user interfaces developed to spatially and semantically annotate (“register”) and explore the tissue data and the evolving HRA. A key part of these tools is a common coordinate framework, providing standard terminologies and data structures for describing specimen, biological structure, and spatial data linked to existing ontologies. As of April 22, 2022, the “registration” user interface has been used to harmonize and publish data on 5,909 tissue blocks collected by the Human Biomolecular Atlas Program (HuBMAP), the Stimulating Peripheral Activity to Relieve Conditions program (SPARC), the Human Cell Atlas (HCA), the Kidney Precision Medicine Project (KPMP), and the Genotype Tissue Expression project (GTEx). Further, 5,856 tissue sections were derived from 506 HuBMAP tissue blocks. The second “exploration” user interface enables consortia to evaluate data quality, explore tissue data spatially within the context of the HRA, and guide data acquisition. A companion website is at https://cns-iu.github.io/HRA-supporting-information/.
Common protein-coding variants influence the racing phenotype in galloping racehorse breeds
Authors: Han Haige , McGivney Beatrice A. , Allen Lucy , Bai Dongyi , Corduff Leanne R. , Davaakhuu Gantulga , Davaasambuu Jargalsaikhan , Dorjgotov Dulguun , Hall Thomas J. , Hemmings Andrew J. , Holtby Amy R. , Jambal Tuyatsetseg , Jargalsaikhan Badarch , Jargalsaikhan Uyasakh , Kadri Naveen K. , MacHugh David E. , Pausch Hubert , Readhead Carol , Warburton David , Dugarjaviin Manglai , Hill Emmeline W. 
Published: December 2022

AbstractSelection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes,G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1andSYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.
Half-millennium evidence suggests that extinction debts of global vertebrates started in the Second Industrial Revolution
Authors: Liao Ziyan , Peng Shushi , Chen Youhua 
Published: December 2022

AbstractExtinction debt describes the time-lagged process of species extinction, which usually requires dozens to hundreds of years to be paid off. However, due to the lack of long-term habitat data, it is indeterminate how strong the signal of extinction debts is at the global scale and when the debts started. Here, by compiling the geographical distributions of 6120 reptiles, 6047 amphibians, and 4278 mammals and correlating them with annual forest cover data from 1500 to 1992, we show that the beginning of the Second Industrial Revolution (the mid-19thcentury) was the earliest signal of cumulative extinction debts for global forest-dwelling vertebrate groups. More importantly, the impact of global protected areas on mitigating accumulated vertebrate extinction debt is not as immediate as that of mitigating reduced forest cover but rather suffers from pronounced time-lag effects. As the disequilibrium of vertebrate richness and forested habitat is currently taking place, preventive actions should be taken to promote a well-balanced status among forest restoration, protected areas, and biodiversity conservation to slow the accumulating debts for global forest-dwelling vertebrates.
Projective diffeomorphic mapping of molecular digital pathology with tissue MRI
Authors: Stouffer Kaitlin M. , Witter Menno P. , Tward Daniel J. , Miller Michael I. 
Published: December 2022

AbstractReconstructing dense 3D anatomical coordinates from 2D projective measurements has become a central problem in digital pathology for both animal models and human studies. Here we describe Projective Large Deformation Diffeomorphic Metric Mapping (LDDMM), a technique which projects diffeomorphic mappings of dense human magnetic resonance imaging (MRI) atlases at tissue scales onto sparse measurements at micrometre scales associated with histological and more general optical imaging modalities. We solve the problem of dense mapping surjectively onto histological sections by incorporating technologies for crossing modalities that use nonlinear scattering transforms to represent multiple radiomic-like textures at micron scales, together with a Gaussian mixture-model framework for modeling tears and distortions associated to each section. We highlight the significance of our method through incorporation of neuropathological measures and MRI, of relevance to the development of biomarkers for Alzheimer’s disease and one instance of the integration of imaging data across the scales of clinical imaging and digital pathology.