bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can transcutaneous perianal ultrasonography be the first-line diagnostic instrument for evaluating pediatric perianal fistulas?
Authors: Ding Yu-Wen , Yin Hao-Qiang , Liang Hong-Tao , Lu Jin-Gen , Wang Bo , Wang Chen 
Published: November 2022

Abstract

Background
Pediatric perianal fistula is a common disorder. It is more difficult to detect the fistula tract and internal opening (IO) in children than in adults. This study aimed to evaluate the clinical diagnostic value of transcutaneous perianal ultrasound for children with perianal fistula.

Methods
A retrospective review was conducted by analysing the preoperative transcutaneous perianal ultrasound and intraoperative exploration results of 203 consecutive patients who were &lt;3 years old and diagnosed with perianal fistula. Analyses were conducted to evaluate the accuracy and consistency of utilizing the transcutaneous perianal ultrasound in the diagnosis of the complexity and location of the IO of perianal fistulas.

Results
Compared with intraoperative exploration, the preoperative transcutaneous perianal ultrasonography has almost perfect agreement (Kappa = 0.881, P &lt; 0.001) in the diagnosis of fistula tract complexity and IO with a sensitivity of 92% and a specificity of 97%. In addition, both intraoperative exploration and transcutaneous perianal ultrasound diagnosis showed high consistency in the identification of the IO of perianal fistulas (Quadrant I Kappa = 0.831, Quadrant II Kappa = 0.773, Quadrant III Kappa = 0.735, Quadrant IV Kappa = 0.802, all P &lt; 0.01). The IOs were mainly distributed in Quadrants IV and II in both simple and complex fistulas.

Conclusions
Transcutaneous perianal ultrasound, as a non-invasive and simple imaging technique, showed high accuracy in the diagnosis and identification of the fistula classification and IO location. It could be considered a first-line diagnostic instrument for evaluating perianal fistulas among children.
Review of integrated full life cycle data management and application of the slab tracks
Authors: Ye Wenlong , Ren Juanjuan , Zhang Peng , Zhang Qi , Li Longxiang 
Published: November 2022

Abstract
The full life cycle data management and application of high-speed railway slab track has multiple benefits. While serving as the basis for scientific periodic and predictive maintenance, it is also the key to extending the service life of the track structure and improving train safety and smoothness. The paper provides a comprehensive review of the multi-source data collection methods, the integrated data management, and the multi-dimensional data applications for slab tracks from a full life cycle perspective. The data detection and monitoring methods across the design, construction, and O&M (Operation and Maintenance) phases of slab tracks are summarized, offering a potential direction for better refinement and intelligent data collection. In addition, the paper reviews the data management system at different life cycle stages of the slab track, and a integrated full life cycle data management framework is proposed. Also considered is the application of related complex mass data, in which we summarize the maintenance indexes to evaluate and predict the current and future quality of slab tracks. This study aims to lay a foundation for future scientific maintenance and repair strategies of slab tracks in high-speed railways.
High-precision magnetization vector inversion: application to magnetic data in the presence of significant remanent magnetization
Authors: Li Xiangdong , Liu Shuang , Liu Yunxiang , Ding Fufeng , Jian Xiange , Hu Xiangyun 
Published: November 2022

Abstract
Magnetization vector inversion is essential for obtaining magnetization vector information from subsurface rocks. To obtain focused inversion results that better match the true magnetization distributions, sparse constraints are considered to constrain the objective function. A compact magnetization vector inversion method is proposed that can provide accurate inversion results for magnetic data with significant remanent magnetization. Considering the sparse constraint and the correlation between the three magnetization components with different directions, the L1-norm is modified and introduced into the inversion algorithm to obtain compact results. Furthermore, to reduce the computational cost, a randomized singular value decomposition is used to replace the traditional singular value decomposition and iteratively minimize the proposed objective function. Two synthetic models with different magnetization directions are developed to verify the performance of the proposed method. The results of magnetization vectors obtained by the proposed method are focused and accurate. Finally, the proposed method is applied to igneous rocks with strong remanent magnetization in the Haba River area of northwestern China. The distributions, directions of total magnetization and remanent magnetization of the medium-base igneous rocks are revealed by the sparse magnetization vector inversion method, which provides a wealth of information about the concealed deposits in the area.
On the kinematic morphology around haloes
Authors: Luo Xiaolin , Xu Xiangling , Wang Xin 
Published: November 2022

ABSTRACT
In this paper, we report an interesting kinematic phenomenon around the haloes’ edge related to the ‘splashback’ radius. After the shell-crossing, cosmic flow exhibits various rotational morphologies via stream-mixing. Vorticity is generated in a particular way that coincides with the large-scale structure. Notably, one specific flow morphology, which is spiralling inward and compressing in the third direction, concentrates around haloes. A detailed examination that reveals a sharp change in the logarithmic derivative of its volume fraction coincides with the location of the splashback radius Rsp defined as the outermost caustic structure. Such a feature encodes valuable phase-space information and provides a new perspective on understanding the dynamical evolution of haloes. As a volume-weighted quantity, the profile of flow morphology is purely kinematic. And unlike other related studies, the rotational flow morphologies capture the anisotropic phase structure in the multistream region.
Comprehensive comparison of gene expression diversity among a variety of human stem cells
Authors: Yamatani Yukiyo , Nakai Kenta 
Published: November 2022

Abstract
Several factors, including tissue origins and culture conditions, affect the gene expression of undifferentiated stem cells. However, understanding the basic identity across different stem cells has not been pursued well despite its importance in stem cell biology. Thus, we aimed to rank the relative importance of multiple factors to gene expression profile among undifferentiated human stem cells by analyzing publicly available RNA-seq datasets. We first conducted batch effect correction to avoid undefined variance in the dataset as possible. Then, we highlighted the relative impact of biological and technical factors among undifferentiated stem cell types: a more influence on tissue origins in induced pluripotent stem cells than in other stem cell types; a stronger impact of culture condition in embryonic stem cells and somatic stem cell types, including mesenchymal stem cells and hematopoietic stem cells. In addition, we found that a characteristic gene module, enriched in histones, exhibits higher expression across different stem cell types that were annotated by specific culture conditions. This tendency was also observed in mouse stem cell RNA-seq data. Our findings would help to obtain general insights into stem cell quality, such as the balance of differentiation potentials that undifferentiated stem cells possess.
Glioblastoma management in a lower middle-income country: Nationwide study of compliance with standard care protocols and survival outcomes in Ukraine
Authors: Rozumenko Artem , Kliuchka Valentyn , Rozumenko Volodymir , Daschakovskiy Andriy , Fedorenko Zoja 
Published: November 2022

Abstract

Background
The effective treatment of high-grade gliomas is a complex problem that requires ubiquitous implementation of sophisticated therapy protocols. The present study aimed to perform population-based analysis of glioblastoma management in lower-middle-income countries.

Methods
The National Cancer Registry of Ukraine was screened for the records of adult patients with primary glioblastomas diagnosed in 2015–2019. Survival analysis was performed using Kaplan–Meier method and a multivariable Cox model.

Results
A total of 2973 adult patients with histologically confirmed glioblastoma were included in the study. Mean age of patients was 55.6 ± 11.4 years, males slightly prevailed—1541 (51.8%) cases. The completed clinical protocol including surgery followed by chemoradiotherapy was applied only in 658 (19.0%) patients. The minority of patients 743 (25.0%) were treated at the academic medical centers, where patients were more likely to receive combined treatment 70.1% compared with 57.9% (P  = .0001) at the community hospitals. The overall median survival was 10.6 ± 0.2 months, and the 2-year survival rate was 17%. The number of utilized treatment modalities contributed to better survival rates and was associated with lower hazard ratio: Protocol with 2 modalities — 0.62 (P = .0001), 3 modalities — 0.48 (P = .0001).

Conclusions
The management of glioblastoma in lower-middle-income countries is characterized by insufficient availability of treatment in academic medical centers and low rates of advanced therapy application. Survival analysis showed similar prognostic risk factors and outcomes compared with high-income countries.
State Neutrality and Religion in Europe: What’s the Prospect?
Authors: Evans Malcolm 
Published: November 2022

Abstract
This article examines the jurisprudence under the European Convention on Human Rights concerning the role of the state in relation to matters of religious belief. The Court’s approach to this topic has changed markedly over the last 30 years and has become increasingly focussed on the idea of ‘neutrality’. This, it is suggested, is a significant error. The article highlights the shortcomings of the approaches it has adopted and argues that the essence of neutrality under the European Convention on Human Rights does not lie in the nature of the relationship between the state and religion or belief but in the manner in which the state approaches the exercise of the substantive right itself.
Advanced sperm tests and impact on clinical male factor management
Authors: Nam Catherine S. , Mehta Akanksha 
Published: November 2022

Purpose of review
Although semen analysis remains a cornerstone of male fertility evaluation, conventional semen analysis parameters do not assess for DNA integrity or functional capacity of sperm. Sperm DNA fragmentation (SDF) and sperm aneuploidy tests have been utilized as adjunct tools to distinguish fertile and infertile men and predict pregnancy outcomes. This review serves as an update on indications and utility of advanced sperm tests, as well as associated controversies and limitations.

Recent findings
Elevated SDF is associated with prolonged time to pregnancy, lower chance of spontaneous pregnancy, and lower live birth rates. Sperm aneuploidy is more frequent in infertile men, in male partners of couples experiencing recurrent pregnancy loss, and recurrent failure of assisted reproductive technology (ART). These tests can, therefore, provide important information to guide management and counseling of infertile couples to optimize reproductive outcomes.

Summary
We evaluated data surrounding SDF and sperm aneuploidy tests, which are utilized both within and beyond the scope of AUA/ASRM guidelines. While the tests at hand require further standardization and randomized controlled studies, the current data suggest strong associations with pregnancy outcomes and can be utilized to counsel and manage infertile males.
VALPROIC ACID INHIBITS CLASSICAL MONOCYTE-DERIVED TISSUE FACTOR AND ALLEVIATES HEMORRHAGIC SHOCK-INDUCED ACUTE LUNG INJURY IN RATS
Authors: Shao Lina , Wu Bing , Liu Chang , Chong Wei 
Published: November 2022

ABSTRACT

Background: Monocytes and monocyte-derived tissue factor (TF) promote the development of sepsis-induced acute lung injury (ALI). Classical monocytes (C-Mcs) can be induced to express TF. Valproic acid (VPA) alleviates hemorrhagic shock (HS)–induced ALI (HS/ALI) and inhibits TF expression in monocytes. We hypothesized that C-Mcs and C-Mc–derived TF promoted HS/ALI and that VPA could inhibit C-Mc–derived TF expression and attenuate HS/ALI. Methods: Wistar rats and THP-1 cells were used to evaluate our hypothesis. Monocyte subtypes were analyzed by flow cytometry; mRNA expression was measured by fluorescence quantitative polymerase chain reaction; protein expression was measured by Western blotting, immunofluorescence, or immunohistology; inflammatory cytokines levels were measured by enzyme-linked immunosorbent assay; and ALI scores were used to determine the degree of ALI. Results: The blood %C-Mcs and C-Mcs/non–C-Mcs ratios, monocyte TF levels, serum and/or lung inflammatory cytokine levels, and ALI scores of HS rats were significantly increased (P < 0.05). After monocyte depletion and thrombin inhibition, the inflammatory cytokine levels and ALI scores were significantly decreased (P < 0.05). VPA reduced the %C-Mcs and C-Mc/non-C-Mc ratios, TF expression, inflammatory cytokine levels, and ALI scores during HS (P < 0.05) and inhibited HS-induced monocyte Egr-1 and p-ERK1/2 expression (P < 0.05). VPA inhibited hypoxia-induced TF expression in THP-1 cells by regulating the p-ERK1/2–Egr-1 axis. Conclusion: C-Mcs and C-Mc–derived TF accelerate the development of HS/ALI by increasing thrombin production. VPA inhibits HS-induced C-Mc production of TF by regulating the p-ERK1/2–Egr-1 axis and alleviates HS/ALI.
Potential for bias in (sero)prevalence estimates when not accounting for test sensitivity and specificity
Authors: Haile Sarah R , Kronthaler David 
Published: November 2022

AbstractBackgroundThe COVID-19 pandemic has led to many studies of seroprevalence. A number of methods exist in the statistical literature to correctly estimate disease prevalence or seroprevalence in the presence of diagnostic test misclassification, but these methods seem to be less known and not routinely used in the public health literature. We aimed to examine how widespread the problem is in recent publications, and to quantify the magnitude of bias introduced when correct methods are not used.MethodsA systematic review was performed to estimate how often public health researchers accounted for diagnostic test performance in estimates of seroprevalence. Using straightforward calculations, we estimated the amount of bias introduced when reporting the proportion of positive test results instead of using sensitivity and specificity to estimate disease prevalence.ResultsOf the seroprevalence studies sampled, 78% (95% CI 72% to 82%) failed to account for sensitivity and specificity. Expected bias is often more than is desired in practice, ranging from 1% to 12%.ConclusionsResearchers conducting studies of prevalence should correctly account for test sensitivity and specificity in their statistical analysis.
A draft genome of the ascomycotal fungal speciesPseudopithomyces maydicus(familyDidymosphaeriaceae)
Authors: Arumugam Krithika , Ho Sherilyn , Bessarab Irina , Goh Falicia Q. Y. , Haryono Mindia A. S. , Santillan Ezequiel , Wuertz Stefan , Chow Yvonne , Williams Rohan B. H. 
Published: November 2022

AbstractWe report a draft genome of the ascomycotal fungal species Pseudopithomyces maydicus (isolate name SBW1) obtained using a culture isolate from brewery wastewater. From a 22 contig assembly, we predict 13502 protein coding gene models, of which 4389 (32.5%) were annotated to KEGG Orthology and identify 39 biosynthetic gene clusters.
Single-cell Mendelian randomisation identifies cell-type specific genetic effects on human brain disease and behaviour
Authors: Haglund Alexander , Zuber Verena , Yang Yifei , Abouzeid Maya , Feleke Rahel , Ko Jeong Hun , Nott Alexi , Babtie Ann C. , Mills James D. , Muhammed Louwai , Laaniste Liisi , Gveric Djordje O. , Clode Daniel , Pagni Susanna , Bellampalli Ravishankara , Somani Alyma , McDade Karina , Anink Jasper J. , Mesarosova Lucia , Aronica Eleonora , Thom Maria , Sisodiya Sanjay M. , Srivastava Prashant K. , Malhotra Dheeraj , Bryois Julien , Bottolo Leonardo , Johnson Michael R. 
Published: November 2022

ABSTRACTTranslating genome-wide association loci to therapies requires knowledge of the causal genes, their directionality of effect and the cell-types in which they act. To infer these relationships in the human brain, we implemented Mendelian randomisation using single cell-type expression quantitative trait loci (eQTLs) as genetic anchors. Expression QTLs were mapped across 8 major cell-types in brain tissue exclusively ascertained from donors with no history of brain disease. We report evidence for a causal association between the change in expression of 118 genes and one or more of 16 brain phenotypes, revealing candidate targets for risk mitigation and opportunities for shared preventative therapeutic strategies. We highlight key causal genes for neurodegenerative and neuropsychiatric disease and for each, we report its cellular context and the therapeutic directionality required for risk mitigation. Our use of control samples establishes a new resource for the causal interpretation of GWAS risk alleles for human brain phenotypes.
CiliaMiner: an integrated database for Ciliopathy Genes and Ciliopathies
Authors: Turan Merve Gül , Orhan Mehmet Emin , Cevik Sebiha , Kaplan Oktay I. 
Published: November 2022

AbstractCilia are found in eukaryotic species ranging from single-celled organisms, such asChlamydomonas reinhardtii, to humans, but not in plants. The ability to respond to repellents and/or attractants, regulate cell proliferation and differentiation, and provide cellular mobility are just a few examples of how crucial cilia are to cells and organisms. Over 30 distinct rare disorders generally known as ciliopathy are caused by abnormalities or functional impairments in cilia and cilia-related compartments. Because of the complexity of ciliopathies and the rising number of ciliopathies and ciliopathy genes, a ciliopathy-oriented and up-to-date database is required. In addition, disorders not yet known as ciliopathy but have genes that produce cilia localizing proteins have yet to be classified. Here we present CiliaMiner, a manually curated ciliopathy database that includes ciliopathy lists collected from articles and databases. Analysis reveals that there are 55 distinct disorders likely related to ciliopathy, with over 4000 clinical manifestations. Based on comparative symptom analysis and subcellular localization data, diseases are classified as primary, secondary, or atypical ciliopathies. CiliaMiner provides easy access to all of these diseases and disease genes, as well as clinical features and gene-specific clinical features, as well as subcellular localization of each protein. Additionally, the orthologs of disease genes are also provided for mice, zebrafish, Xenopus, Drosophila, andC. elegans. CiliaMiner (https://kaplanlab.shinyapps.io/ciliaminer) aims to serve the cilia community with its comprehensive content, and highly enriched interactive heatmaps, and will be continually updated.
Targeted and Explorative Profiling of Kallikrein Proteases and Global Proteome Biology of Pancreatic Ductal Adenocarcinoma, Chronic Pancreatitis, and Normal Pancreas Highlights Disease-Specific Proteome Remodelling
Authors: Werner Janina , Bernhard Patrick , Cosenza-Contreras Miguel , Pinter Niko , Fahrner Matthias , Pallavi Prama , Eberhard Johannes , Bronsert Peter , Rückert Felix , Schilling Oliver 
Published: November 2022

AbstractPancreatic ductal adenocarcinoma (PDAC) represents one of the most aggressive and lethal malignancies worldwide with an urgent need for new diagnostic and therapeutic strategies. One major risk factor for PDAC is the pre-indication of chronic pancreatitis (CP), which represents highly inflammatory pancreatic tissue. Kallikreins (KLKs) are secreted serine proteases that play an important role in various cancers as components of the tumor microenvironment. Previous studies of KLKs in solid tumors largely relied on either transcriptomics or immunodetection. We present one of the first targeted mass spectrometry profiling of kallikrein proteases in PDAC, CP, and normal pancreas. We show that KLK6 and KLK10 are significantly upregulated in PDAC (n=14) but not in CP (n=7) when compared to normal pancreas (n=21), highlighting their specific intertwining with malignancy. Additional explorative proteome profiling identified 5936 proteins in our pancreatic cohort and observed disease-specific proteome rearrangements in PDAC and CP. As such, PDAC features an enriched proteome motif for extracellular matrix (ECM) and cell adhesion while there is depletion of mitochondrial energy metabolism proteins, reminiscent of the Warburg effect. Although often regarded as a PDAC hallmark, the ECM fingerprint was also observed in CP, alongside with a prototypical inflammatory proteome motif as well as with an increased wound healing process and proteolytic activity, thereby possibly illustrating tissue autolysis. Proteogenomic analysis based on publicly accessible data sources identified 112 PDAC-specific and 32 CP-specific single amino acid variants, which among others affect KRAS and ANKHD1. Our study emphasizes the diagnostic potential of kallikreins and provides novel insights into proteomic characteristics of PDAC and CP.
Highly potent antisense oligonucleotides (ASOs) targeting the SARS-CoV-2 RNA genome
Authors: Dauksaite V. , Tas A. , Wachowius F. , Spruit A. , van Hemert M.J. , Snijder E.J. , van der Veer E.P. , van Zonneveld A.J. 
Published: November 2022

AbstractCurrently the world is dealing with the third outbreak of the human-infecting coronavirus with potential lethal outcome, cause by a member of the Nidovirus family, the SARS-CoV-2. The severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused the last worldwide pandemic. Successful development of vaccines highly contributed to reduce the severeness of the COVID-19 disease. To establish a control over the current and newly emerging coronaviruses of epidemic concern requires development of substances able to cure severely infected individuals and to prevent virus transmission. Here we present a therapeutic strategy targeting the SARS-CoV-2 RNA using antisense oligonucleotides (ASOs) and identify locked nucleic acid gapmers (LNA gapmers) potent to reduce by up to 96% the intracellular viral loadin vitro. Our results strongly suggest promise of our preselected ASOs for further development as therapeutic or prophylactic anti-viral agents.One sentence summaryASOs (LNA gapmers) targeting the SARS-CoV-2 RNA genome have been effective in viral RNA (load) reductionin vitro.
Fast protein structure searching using structure graph embeddings
Authors: Greener Joe G , Jamali Kiarash 
Published: November 2022

AbstractComparing and searching protein structures independent of primary sequence has proved useful for remote homology detection, function annotation and protein classification. Fast and accurate methods to search with structures will be essential to make use of the vast databases that have recently become available, in the same way that fast protein sequence searching underpins much of bioinformatics. We train a simple graph neural network using supervised contrastive learning to learn a low-dimensional embedding of protein structure. The method, called Progres, is available as software athttps://github.com/greener-group/progresand as a web server athttps://progres.mrc-lmb.cam.ac.uk. It has accuracy comparable to the best current methods and can search the AlphaFold database TED domains in a tenth of a second per query on CPU.