bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neo-Sagittal Suture Formation After Cranial Vault Remodeling in Sagittal Craniosynostosis
Authors: Chaisrisawadisuk Sarut , Anderson Peter J. , Moore Mark H. 
Published: September 2020

Abstract
Craniosynostosis is a condition where the cranial sutures are early fused. Sagittal suture synostosis is found to be the most prevalent. Many techniques ranging from simple suture excision to wide suturectomy have been developed for treating this condition. While repeated fusion of previously excised involved sutures is common, neosuture formation has been identified in many recent reports after craniosynostosis surgery. In this case report, the authors present a finding of the neosuture formation in a patient presented with sagittal craniosynostosis after wide suturectomy with total cranial vault remodeling so that the pathologically fused suture can be reversed.
Nocardioides flavescens sp. nov., isolated from soil of Gaoligong Mountain, PR China
Authors: Zhang Kun , Jiang Long-Qian , An De-Feng , Lang Lei , Li Gui-Ding , Jiang Ming-Guo , Li Qin-Yuan , Jiang Cheng-Lin , Jiang Yi 
Published: September 2020

A Gram-stain-positive, non-motile, aerobic, rod-shaped, golden yellow-pigmented actinobacterium, designated strain YIM 123512T, was isolated from soil sampled at Gaoligong Mountain, Yunnan Province, PR China. The strain grew at 10–40 °C (optimum, 28 °C), with 0–3.0 % (w/v) NaCl (optimum, 0–1.0 %) and at pH 5.0–11.0 (optimum, pH 7.0). The major menaquinone was MK-8(H4) and the major cellular fatty acids (>10 %) were identified as iso-C16 : 0 and C17 : 1
ω8c. Strain YIM 123512T had ll-2, 6-diaminopimelic acid as the diagnostic cell-wall diamino acid. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, two unknown phospholipids and one unknown lipid. The genomic DNA G+C content of strain YIM 123512T was 72.7 mol% based on its draft genome sequence. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 123512T appeared to be most closely related to

Nocardioides halotolerans

KCTC 19274T (97.7 % sequence similarity) and to belong to the genus

Nocardioides

. The sequence similarity values of strain YIM 123512T to other currently described type strains of the genus

Nocardioides

were less than 97.0 %. Based on the draft genome sequence, the novel strain showed an average nucleotide identity value of 80.2 % and a digital DNA–DNA hybridization value of 23.1 % with the reference strain

N. halotolerans

KCTC 19274T. The results of the polyphasic taxonomic study including phenotypic, chemotaxonomic and phylogenetic analyses show that strain YIM 123512T represents a novel species of the genus

Nocardioides

, for which the name Nocardioides flavescens sp. nov. is proposed. The type strain is YIM 123512T (=KCTC 49303T=CGMCC 4.7628T).
Improving generalization of deep learning models for diagnostic pathology by increasing variability in training data: experiments on osteosarcoma subtypes
Authors: Tang Haiming , Sun Nanfei , Shen Steven 
Published: September 2020

ABSTRACTArtificial intelligence (AI) has an emerging progress in diagnostic pathology. A large number of studies of applying deep learning models to histopathological images have been published in recent years. While many studies claim high accuracies, they may fall into the pitfalls of overfitting and lack of generalization due to the high variability of the histopathological images. We use the example of Osteosarcoma to illustrate the pitfalls and how the addition of model input variability can help improve model performance. We use the publicly available osteosarcoma dataset to retrain a previously published classification model for osteosarcoma. We partition the same set of images into the training and testing datasets differently than the original study: the test dataset consists of images from one patient while the training dataset consists images of all other patients. The performance of the model on the test set using the new partition schema declines dramatically, indicating a lack of model generalization and overfitting. We also show the influence of training data variability on model performance by collecting a minimal dataset of 10 osteosarcoma subtypes as well as benign tissues and benign bone tumors of differentiation. We show the additions of more and more subtypes into the training data step by step under the same model schema yield a series of coherent models with increasing performances. In conclusion, we bring forward data preprocessing and collection tactics for histopathological images of high variability to avoid the pitfalls of overfitting and build deep learning models of higher generalization abilities.
Surface texture limits transfer ofS. aureus, T4 Bacteriophage, Influenza B virus and Human coronavirus
Authors: Liu Qi , Brookbank Lindsey , Ho Angela , Coffey Jenna , Brennan Anthony B. , Jones Christopher J. 
Published: September 2020

AbstractSpread of pathogens on contaminated surfaces plays a key role in disease transmission. Surface technologies that control pathogen transfer can help control fomite transmission and are of great interest to public health. Here, we report a novel bead transfer method for evaluating fomite transmission in common laboratory settings. We show that this method meets several important criteria for quantitative test methods, including reasonableness, relevancy, resemblance, responsiveness, and repeatability, and therefore may be adaptable for standardization. In addition, this method can be applied to a wide variety of pathogens including bacteria, phage, and human viruses. Using the bead transfer method, we demonstrate that an engineered micropattern limits transfer ofStaphylococcus aureusby 97.8% and T4 bacteriophage by 93.0% on silicone surfaces. Furthermore, the micropattern significantly reduces transfer of influenza B virus and human coronavirus on silicone and polypropylene surfaces. Our results highlight the potential of using surface texture as a valuable new strategy in combating infectious diseases.ImportanceDisease transmission often occurs through contact with contaminated surfaces, called fomites. Efforts to reduce this method of fomite transmission include surface cleaning, personal hygiene, alteration of habits, and novel technologies to reduce pathogen spread. This manuscript presents a novel method for the consistent contamination of surfaces to mimic the transmission of pathogens via fomites. Using this method, we present a surface texture modeled on shark skin that significantly reduces the transfer of a variety of pathogens, includingStaphylococcus aureus, influenza B virus, and human coronavirus 229E. Utilization of novel technologies to limit pathogen spread can enhance existing methods of disease mitigation.
Novel artificial intelligence-driven software significantly shortens the time required for annotation in computer vision projects
Authors: Hansen Ulrik Stig , Landau Eric , Patel Mehul , Hayee Bu’Hussain 
Published: September 2020

AbstractThe contribution of artificial intelligence (AI) to endoscopy is rapidly expanding. Accurate labelling of source data (video frames) remains the rate-limiting step for such projects and is a painstaking, cost-inefficient, time-consuming process.A novel software platform, Cord Vision (CdV) allows automated annotation based on ‘embedded intelligence’. The user manually labels a representative proportion of frames in a section of video (typically 5%), to create ‘micro-models’ which allow accurate propagation of the label throughout the remaining video frames. This could drastically reduce the time required for annotation. We conducted a comparative study with an open-source labelling platform (CVAT) to determine speed and accuracy of labelling.Across 5 users, CdV resulted in a significant increase in labelling performance (p< 0.0005) compared to CVAT with micro-models achieving > 97% accuracy for bounding box placement. This advance represents a valuable first step in Al-image analysis projects.
Death associated with coronavirus (COVID-19) infection in individuals with severe mental disorders in Sweden during the early months of the outbreak – a exploratory cross-sectional analysis of a population-based register study
Authors: Maripuu Martin , Bendix Marie , Öhlund Louise , Widerström Micael , Werneke Ursula 
Published: September 2020

AbstractBackgroundIndividuals with severe mental disorder (SMD) have a higher risk of somatic comorbidity and mortality than the rest of the population. We set up a population-based study to assess whether individuals with SMD had a higher risk of death associated with a COVID-19 infection (COVID-19 associated death) than individuals without SMD.MethodsExploratory analysis with a cross-sectional design in the framework of a population-based register study covering the entire Swedish population. The Swedish Board for Health and Welfare (Socialstyrelsen) provided anonymised tabulated summary data for further analysis. We compared numbers of COVID-19 associated death in individuals with SMD (cases) and without SMD (controls). We calculated the odds ratio (OR) for the whole sample and by age group and four potential risk factors, namely diabetes, cardiovascular disease, hypertension, chronic lung disease.ResultsThe sample comprised of 7,923,859 individuals, 103,999 with SMD and 7,819,860 controls. There were 130 (0.1%) COVID-19 associated deaths in the SMD group and 4945 (0.06%) in the control group, corresponding to an OR of 1.98 (CI 1.66-2.35; p < 0.001). The odds were fourfold in the age group between 60 and 79 years. Cardiovascular diseases increased the odds by 50%. Individuals with SMD without any of the risk factors under study had three-folds odds of COVID-19 associated death.ConclusionOur preliminary results suggest that individuals with SMD are a further group at increased risk of COVID-19 associated death. The factors contributing to this increased mortality risk require clarification.
GUÍA: a digital platform to facilitate result disclosure in genetic counseling
Authors: Suckiel Sabrina A. , Odgis Jaqueline A. , Gallagher Katie M. , Rodriguez Jessica E. , Watnick Dana , Bertier Gabrielle , Sebastin Monisha , Yelton Nicole , Maria Estefany , Lopez Jessenia , Ramos Michelle , Kelly Nicole , Teitelman Nehama , Beren Faygel , Kaszemacher Tom , Davis Kojo , Laguerre Irma , Richardson Lynne D. , Diaz George A. , Pearson Nathaniel M. , Ellis Stephen B. , Stolte Christian , Robinson Mimsie , Kovatch Patricia , Horowitz Carol R. , Gelb Bruce D. , Greally John M. , Bauman Laurie J. , Zinberg Randi E. , Abul-Husn Noura , Wasserstein Melissa P. , Kenny Eimear E. 
Published: September 2020

ABSTRACTPurposeUse of genomic sequencing is increasing at a pace that requires technological solutions to effectively meet the needs of a growing patient population. We developed GUÍA, a web-based application, to enhance the delivery of genomic results and related clinical information to patients and families.MethodsGUÍA development occurred in 5 phases: formative research, content development, user interface design, stakeholder/community member input, and web application development. Development was informed by qualitative research involving parents (N=22) whose children underwent genomic testing. Participants enrolled in the NYCKidSeq pilot study (N=18) completed structured feedback interviews post-result disclosure using GUÍA. Genetic specialists, researchers, patients, and community stakeholders provided their perspectives on GUÍA’s design to ensure technical, cultural, and literacy appropriateness.ResultsNYCKidSeq participants responded positively to the use of GUÍA to deliver their children’s results. All participants (N=10) with previous experience with genetic testing felt GUÍA improved result disclosure, and 17 (94%) participants said the content was clear.ConclusionsGUÍA communicates complex genomic information in an understandable and personalized manner. Initial piloting demonstrated GUÍA’s utility for families enrolled NYCKidSeq pilot study. Findings from the NYCKidSeq clinical trial will provide insight into GUÍA’s effectiveness in communicating results among diverse, multilingual populations.
Pre-existing T cell memory as a risk factor for severe COVID-19 in the elderly
Authors: Bacher Petra , Rosati Elisa , Esser Daniela , Martini Gabriela Rios , Saggau Carina , Schiminsky Esther , Dargvainiene Justina , Schöder Ina , Wieters Imke , Khodamoradi Yascha , Eberhardt Fabian , Neb Holger , Sonntagbauer Michael , Vehreschild Maria J.G.T. , Conrad Claudio , Tran Florian , Rosenstiel Philip , Markewitz Robert , Wandinger Klaus-Peter , Rybniker Jan , Kochanek Matthias , Leypoldt Frank , Cornely Oliver A. , Koehler Philipp , Franke Andre , Scheffold Alexander 
Published: September 2020

SummaryCoronavirus disease 2019 (COVID-19) displays high clinical variability but the parameters that determine disease severity are still unclear. Pre-existing T cell memory has been hypothesized as a protective mechanism but conclusive evidence is lacking. Here we demonstrate that all unexposed individuals harbor SARS-CoV-2-specific memory T cells with marginal cross-reactivity to common cold corona and other unrelated viruses. They display low functional avidity and broad protein target specificities and their frequencies correlate with the overall size of the CD4+ memory compartment reflecting the “immunological age” of an individual. COVID-19 patients have strongly increased SARS-CoV-2-specific inflammatory T cell responses that are correlated with severity. Strikingly however, patients with severe COVID-19 displayed lower TCR functional avidity and less clonal expansion. Our data suggest that a low avidity pre-existing T cell memory negatively impacts on the T cell response quality against neoantigens such as SARS-CoV-2, which may predispose to develop inappropriate immune reactions especially in the elderly. We propose the immunological age as an independent risk factor to develop severe COVID-19.Key points-Pre-existing SARS-CoV-2-reactive memory T cells are present in all humans, but have low functional avidity and broad target specificities-Pre-existing memory T cells show only marginal cross-reactivity to common cold corona viruses-Frequencies of pre-existing memory T cells increase with the size of the CD4+ memory compartment reflecting the “immunological age” of the individual-Low-avidity and polyclonal, but strongly enhanced SARS-CoV-2 specific T cell responses develop in severe COVID-19, suggesting their origin from pre-existing memory-The immunological age may represent a risk factor to develop severe COVID-19
Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent
Authors: Chakravorty Samya , Nallamilli Babi Ramesh Reddy , Khadilkar Satish , Singla Madhubala , Bhutada Ashish , Dastur Rashna , Gaitonde Pradnya , Rufibach Laura , Gloster Logan , Hegde Madhuri 
Published: September 2020

ABSTRACTObjectiveInherited myopathies comprise more than 200 different individually rare disease-subtypes but when combined together have a high prevalence of 1 in 6000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent.MethodsIn this cohort-study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities.ResultsClinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42%-56%) of patients with the major contributing pathogenicity in either of three genes,GNE(28%; GNE-myopathy),DYSF(25%; Dysferlinopathy) andCAPN3(19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. 78% of theDYSFpatients were homozygous for the detected pathogenic variant suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies(SGCA/B/D/G), Collagenopathy(COL6A1/2/3), Anoctaminopathy(ANO5), telethoninopathy(TCAP), Pompe-disease(GAA), Myoadenylate-deaminase-deficiency-myopathy(AMPD1), myotilinopathy(MYOT), laminopathy(LMNA), HSP40-proteinopathy(DNAJB6), Emery-Dreifuss-muscular-dystrophy(EMD), Filaminopathy(FLNC), TRIM32-proteinopathy(TRIM32), POMT1-proteinopathy(POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1(LAMA2). 13 Patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity / digenic-contribution to disease presentation and progression.ConclusionsApplication of clinically-correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically-driven molecular diagnostics.
Drug library screen identifies inhibitors of toxic astrogliosis
Authors: Masvekar Ruturaj , Kosa Peter , Barbour Christopher , Milstein Joshua , Bielekova Bibiana 
Published: September 2020

AbstractObjectiveMultiple sclerosis is a chronic neuroinflammatory disorder, in which activated immune cells directly or indirectly induce demyelination and axonal degradation. Inflammatory stimuli also change the phenotype of astrocytes, making them neurotoxic. The resulting ‘toxic astrocyte’ phenotype has been observed in animal models of neuroinflammation and in multiple sclerosis lesions. Proteins secreted by toxic astrocytes are elevated in the cerebrospinal fluid of multiple sclerosis patients and reproducibly correlate with the rates of accumulation of neurological disability and brain atrophy. This suggests a pathogenic role for neurotoxic astrocytes in multiple sclerosis.MethodsHere, we applied a commercially available library of small molecules that are either Food and Drug Administration-approved or in clinical development to an in vitro model of toxic astrogliosis to identify drugs and signaling pathways that inhibit inflammatory transformation of astrocytes to a neurotoxic phenotype.ResultsInhibitors of three pathways related to the endoplasmic reticulum stress: 1) proteasome, 2) heat shock protein 90 and 3) mammalian target of rapamycin reproducibly decreased inflammation-induced conversion of astrocytes to toxic phenotype. Dantrolene, an anti-spasticity drug that inhibits calcium release through ryanodine receptors expressed in the endoplasmic reticulum of central nervous system cells, also exerted inhibitory effect at in vivo achievable concentrations. Finally, we established cerebrospinal fluid SERPINA3 as a relevant pharmacodynamic marker for inhibiting toxic astrocytes in clinical trials.InterpretationDrug library screening provides mechanistic insight into the generation of toxic astrocytes and identifies candidates for immediate proof-of-principle clinical trial(s).
Age-specific gene signatures underlying the transcriptomes and functional connectomes of human cerebral cortex
Authors: Zhao Xingzhong , Chen Jingqi , Xiao Peipei , Feng Jianfeng , Qing Ning , Zhao Xing-Ming 
Published: September 2020

AbstractThe human cerebral cortex undergoes profound structural and functional dynamic variations across the lifespan, whereas the underlying molecular mechanisms remain unclear. Here, with a novel method TCA (Transcriptome-connectome Correlation Analysis), which integrates the brain functional MR magnetic resonance images and region-specific transcriptomes, we identify age-specific cortex (ASC) gene signatures for adolescence, early adulthood, and late adulthood. The ASC gene signatures are significantly correlated with the cortical thickness (P-value <2.00e-3) and myelination (P-value <1.00e-3), two key brain structural features that vary in accordance with brain development. In addition to the molecular underpinning of age-related brain functions, the ASC gene signatures allow delineation of the molecular mechanisms of neuropsychiatric disorders, such as the regulation betweenARNT2and its target geneETF1involved in Schizophrenia. We further validate the ASC gene signatures with published gene sets associated with the adult cortex, and confirm the robustness of TCA on other brain image datasets.
Study of Distinctive Diagnostic Characteristics ofChrysomphalus dictyospermiand Closely Related Species ofChrysomphalusGenus (Insecta: Sternorryncha: Coccoidea)
Authors: Gura N.A. , Shipulin A.V. 
Published: September 2020

AbstractThe paper presents the results of microscopic study of the basic diagnostic structures of the pygidium of the Chrysomphalus dictyospermi, which allow to distinguish this species from the closely related ones of the Chrysomphalus genus.
Membrane linkage of aStreptococcus pneumoniaeWzy capsular polysaccharide occurs through an acylglycerol
Authors: Larson Thomas R. , Yother Janet 
Published: September 2020

ABSTRACTCapsular polysaccharides (capsules) protect bacteria from environmental insults and can contribute to virulence in pathogenic bacteria. Their appropriate display on the bacterial surface is critical to their functions. In Gram-positive bacteria, most capsules are synthesized by the Wzy polymerase-dependent pathway, which is also utilized in the synthesis of many capsules and O-antigens of Gram-negative bacteria. Synthesis of capsule repeat units initiates on undecaprenyl-phosphate on the inner face of the cytoplasmic membrane, with polymerization occurring on the outer face of the membrane. In Gram-positive bacteria, the capsule can be transferred to peptidoglycan, as inStreptococcus pneumoniaewhere a direct glycosidic bond to the peptidoglycanN-acetylglucosamine occurs. InS. pneumoniae, capsule can also be detected on the membrane, and this has generally been assumed to reflect polysaccharide that is linked to undecaprenyl-phosphate and in the process of synthesis. We provide evidence here, however, that final membrane linkage occurs through an acylglycerol, and essentially all of the polysaccharide is transferred from the initial undecaprenyl-phosphate acceptor to an alternate acceptor. This step allows for recycling of undecaprenyl-phosphate and represents an additional terminal step in capsule synthesis. In this regard, capsule synthesis resembles that of the wall- and lipoteichoic acids ofS. pneumoniae, wherein a common repeat unit and polymer structure are synthesized by the Wzy pathway with divergence at the terminal step that results in linkages to peptidoglycan and a membrane acylglycerol anchor.IMPORTANCELinkage of capsular polysaccharides to the bacterial cell surface is a critical step in assuring the ability of these polymers to fulfill their functions, such as the resistance to complement-mediated phagocytosis that can be essential for pathogenic organisms to survive in host environments. Knowledge of the mechanisms by which these linkages occur is incomplete. In this study, we provide evidence for linkage of anS. pneumoniaeWzy capsule to an acylglycerol, the most abundant class of lipids in the membrane. This linkage provides a terminal acceptor for capsule that occurs in addition to that of peptidoglycan. Transfer to these terminal receptors is an essential step in CPS synthesis, as failure to do so can be lethal for the cell.