bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dependence of the severity of the course of COVID-19 on viral load in hospitalized patients
Authors: Golodyaeva M. V. , Labintсeva E. V. 
Published: September 2023

Clinical manifestations of COVID-19 vary in different patients from asymptomatic to severe multiple organ failure. The aim of this study was to analyze the severity of COVID-19 in hospitalized patients depending on the initial viral load of SARS-CoV-2. Study included 156 patients 18 years old and more. In the RT-PCR test, viral load was assessed by amplification cycle threshold Ct. The result was considered positive for Ct values < 40 and negative for Ct ≥ 40. 3 groups of 52 people each with different trajectories of the course of the disease were identified: 1 — mild, 2 — moderate, 3 — severe/fatal. The values of the median Ct cycle threshold upon admission of patients in group 3 to the hospital were significantly lower, indicating higher initial levels of viral RNA in patients with more severe disease. This pattern persisted over a 28-day period, and it was in this 3 group that higher levels of viral RNA were detected throughout the time compared to other disease trajectories. In conclusion, the effect of the initial SARS-CoV-2 viral load and its dynamics during hospitalization on the severity of COVID-19 is shown. This parameter can be a prognostic marker for assessing the clinical condition of patients during treatment.
Antimicrobial and Cytotoxic Characteristics of Antibiotic Streptofungin
Authors: Klochko Vitalii , Todosiichuk Tetiana , Lin Wu , Kobzysta Oksana , Bobyr Vitaly 
Published: September 2023

Background. Streptomycetes were and remain a source of new antimicrobial compounds of various nature. A new wave of interest in such research is associated with the possibilities of applied genomics to reveal the hidden biosynthetic potential of streptomycetes, and therefore the discovery of new practically valuable antimicrobial products. The problem of antibiotic resistance of pathogens can be solved by creating compositions of active substances of different nature to overcome the protective mechanisms of pathogens.
Objective. The purpose of the work was to establish and evaluate the antimicrobial and cytotoxic characteristics of the new antibiotic streptofungin, synthesized by Streptomyces albus 2435 (CMIM-S-668) and its mutant strains 2435/М, UN44, 4S, US101, AE6, 105, 80/5.
Methods. To establish the characteristics of streptofungin, the antagonistic activity of selected S. albus producer strains was determined (by the radial streak method), the minimum inhibitory concentration of the antibiotic (by the serial dilution method), and cytotoxicity was determined by the MTT test with resazurin.
Results. The activity of the antibiotic streptofungin against Candida fungi (C. albicans, C. utilis) is shown. Minimum inhibitory concentrations of streptofungin were determined for C. albicans ATCC 10231 (10 μg/ml), B. subtilis ATCC 6633 (200 μg/ml) and P. aeruginosa ATCC 9027 (500 μg/ml). According to the resazurin test, streptofungin does not show a cytotoxic effect in a wide range of concentrations from 2.5 to 500 μg/ml, and therefore can be considered potentially permissible for humans and animals in the studied concentrations.
Conclusions. The antagonistic activity of mutant strains of S. albus culture is due to the action of a complex of antimicrobial products that have a different antimicrobial spectrum and mechanism of action. The obtained results give reasons to consider streptofungin as a promising pharmaceutical substance with antifungal action, as well as to consider the possibility of its combination with the bacteriolytic enzyme complex of the same culture for the development of an antimicrobial agent with a wide spectrum of action.
scCircle-seq unveils the diversity and complexity of circular DNAs in single cells
Authors: Chen Jinxin Phaedo 
Published: September 2023

Abstract
Extrachromosomal circular DNAs (ecDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for genomically profiling ecDNAs and unraveling their diversity and complexity in single cells. We implemented and validated scCircle-seq in normal and cancer cell lines, demonstrating that most ecDNAs largely vary between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. ecDNAs are preferentially produced from chromatin regions enriched in H3K9me3 histone mark and are induced during replication stress conditions. Concomitant sequencing of ecDNAs and RNA from the same cell uncovered the absence of correlation between ecDNA copy number and gene expression levels, except for few oncogenes, including MYC, contained within a large ecDNA in colorectal cancer cells. Finally, we applied scCircle-seq to one prostate cancer and two breast cancer specimens, revealing different ecDNA genomic landscapes and, in one triple negative breast cancer sample, the presence of two distinct tumor subclones harboring distinct ecDNA signatures. scCircle-seq is a scalable tool that can be used to dissect the complexity of ecDNAs across different cell and tissue types, and further expands the potential of ecDNAs for cancer diagnostics.
Social determinants of late initiation of prenatal care in Taiwan: A nationwide study
Authors: Lee Yi-Chan , Liang Fu-Wen , Chen Gin-Den , Lu Tsung-Hsueh , Chiang Tung-liang 
Published: September 2023

Abstract

Objective: Late initiation of prenatal care (LIPC; i.e., initiation of the first prenatal visit after the first trimester) is a major public health concern for pregnant mothers and fetuses. This study examined the social determinants of LIPC in Taiwan, where universal health coverage has been provided since 1995.
Methods: The study population comprised 185,855 babies born in 2017 to mothers who were Taiwanese nationals. Data from several databases, namely the Birth Registration Database, Birth Certificate Application Database, Low- and Middle-Low-Income Households Database, Persons with Disabilities Database, and National Health Insurance Research Database, were retrieved to link data on social determinants to medical claims. The gradient effect of each investigated social determinant was assessed using the Cochran–Armitage trend test in SAS 9.4.
Results: The overall incidence rate of LIPC in Taiwan was 8.6% in 2017. Notably, the disparities in the initiation of prenatal care were closely associated with social disadvantages. In particular, extraordinarily high LIPC rates were identified among teenagers (40.0%), mothers with drug addiction problems (31.9%), unmarried mothers (27.6%), mothers from low income (23.0%), mothers with a high school or lower level of education (23.0%), migrants (19.2%), and mothers with disabilities (18.9%). Several social determinants had significant adverse gradient effects on LIPC, namely employment (P < .0001), education (P < .0001), socioeconomic status (P < .0001), and urbanization (P < .0001). Logistic regression revealed higher odds of LIPC among the mothers in the poorest 20% (adjusted odds ratio [aOR], 1.52; 95% confidence interval [CI], 1.43–1.61), those with a parity of >3 (aOR, 1.99; 95% CI, 1.89–2.09), unmarried mothers (aOR, 2.88; 95% CI, 2.73–3.04), mothers with drug addiction problems (aOR, 5.24; 95% CI, 4.78–5.75), mothers aged <19 years (aOR, 5.30; 95% CI, 4.84–5.81) or 20–24 years (aOR, 1.77; 95% CI, 1.67–1.89), and mothers with disabilities (aOR, 1.64; 95% CI, 1.41–1.92).
Conclusions: The findings of this study highlight the social inequalities in the initiation of prenatal care in Taiwan, indicating that the maternal and child health-care system in Taiwan should be further improved.
Abbreviated Women Empowerment in Agriculture Index and Child Nutritional Status in Hawella District, Sidama Region, Ethiopia; a Community Based Cross-sectional Study
Authors: Fentahun Selam , Jisso Meskerem , Shiferaw Yemisrach , Eshetu Betelehem , Gebretsadik Achamyelesh 
Published: September 2023

Abstract
Background
Malnutrition remains to be one of the world’s most serious and least addressed socio-economic and health problems. In Ethiopia, agriculture is of the main occupation interlinked with human nutrition where woman make up a large percentage of the workforce.
Objective
To assess the relationship between abbreviated women’s empowerment in agriculture index (A-WEAI) and nutritional status of their children in Hawella district of Sidama region, Southern Ethiopia.
Methods
A community-based cross-sectional study was conducted in Hawella district. A total 338 mothers with their children aged 6–59 months were participated in the study. The data was collected using modified, pre-tested and structured questionnaires adapted from literatures and women’s empowerment in agriculture index module A-WEAI Version. Anthropometric measurement data of children was collected using precise digital scale and stature meter. Data entry was done through Epi Data version 3.1. Woman empowerment was measured based on A-WEAI. Anthros software was used to compute height-for-age and weight-for-height and < − 2 SD was taken as cut-off points for both stunting and wasting. A statistical package for social sciences version 23.0 software was for data analysis. The statistical significance was considered at p value < 0.05.
Results
The prevalence of stunted and wasted among children were 40.5% (95% CI: 34.9, 45.6) and 12.1% (95% CI: 8.9, 16), respectively. Based on the five domains of empowerment (5DE) indicators, nearly 57% of women were empowered. The age of the mother (AOR = 2.6, 95% CI: 1.07–6.25), marital status of mothers (AOR = 6.4, 95% CI: 2.01–2.71), place of birth (AOR = 4.5, 95% CI: 2.12–9.49), and maternal educational status (AOR = 2.8 95% CI: 1.29–6.23) were factors independently associated with wasted children. Whereas, factors such as family size (AOR = 2.3, 95% CI: 1.03–5.13), overall women empowerment (AOR = 2.3 95% CI: 1.03–5.13), access to and decision on credit (AOR = 3.7, 95% CI: 1.56–7.47), and control over use of income (AOR = 9.4, 95% CI: 3.92–22.35) were associated with stunting in children.
Conclusion
this study provides evidence that intervention is needed to prevent child malnutrition through enhancing women empowerment in agriculture.
A study on the Stability of Dangerous Rock Mass under Blasting Vibration Considering Size Effect
Authors: Chen Xinggen , Qu Xinyu , Li Hongtao , Wang Xiekang , Li Cheng , Lu Gongda , Yao Qiang 
Published: September 2023

Abstract
The stability calculation of dangerous rock mass is the key for preventing and controlling dangerous rock mass collapse as a geological disaster. Indeed, it is of great practical significance to propose a scientific and relatively accurate stability computation for predicting the collapse of dangerous rock mass. Based on conventional limit equilibrium, this study proposes a new theory considering the size effect of dangerous rock mass under various blasting vibration loads to assess its stability. The approach considers dangerous rock mass shape, geometrical size, blasting vibration frequency, the initial phase of the blasting vibration wave in different directions. Based on the slice method, it establishes the stability analysis and calculation of dangerous rock mass, considering size effect under blasting vibration. The corresponding calculation program is compiled using MATLAB to carry out calculation examples. The results indicate that the calculated minimum stability coefficients of dangerous rock mass in this study are proximate to those calculated by conventional pseudo-static analysis. However, this study's calculations are slightly larger than those computed by pseudo-static analysis, with a relative difference between 5.1% and 8.2%. The method proposed in this study provides a reference for dynamic stability analysis and evaluation for dangerous rock mass.
Role of Next generation sequencing in diagnosis and management of critically ill children with suspected monogenic disorder
Authors: Puri Ratna Dua , Bhatia Sameer , Pal Swasti , Kulshrestha Samarth , Gupta Dhiren , Soni Arun , Saxena Renu , Bijarnia-Mahay Sunita , Verma Ishwar Chander 
Published: September 2023

Abstract
Next generation sequencing based diagnosis has emerged as a promising tool for evaluating critically ill neonates and children. However, there is little data on its utility in developing countries. We assessed its diagnostic rate and clinical impact on management of paediatric patients with a suspected genetic disorder requiring critical care. We analyzed 70 children with an illness requiring intensive care and obtained a precise molecular diagnosis in 32 of 70 probands (45.3 %) using diverse sequencing techniques such as clinical exome, whole exome, and whole genome. A significant change in clinical outcome was observed in 13 of 32 (40.6 %) diagnosed probands with a change in medication in 11 subjects and redirection to palliative care in two subjects. Additional benefits included specific dietary management (three cases), avoidance of a major procedure (one case) and better reproductive counselling. Dramatic therapeutic responses were observed in three cases with SCN1A, SCN2A and KCNQ2-related epileptic encephalopathy. A delayed turn-around for sequencing results was perceived as a major limiting factor in the study, as rapid and ultra-rapid sequencing was not available. Achieving a precise molecular diagnosis has great utility in managing critically ill patients with suspected genetic disorders in developing countries.
Fostering Fiscal Autonomy and Technological Innovation in China's Diverse Environmental Landscape
Authors: Ayoub Zeraibi 
Published: September 2023

Abstract
The Chinese government has made strides towards addressing environmental challenges; however, the country still faces a myriad of complex and interconnected environmental problems, such as air and water pollution, soil degradation, and climate change. This study investigates the impact of fiscal decentralization and technological development on environmental sustainability in China across its 30 provinces from 2004–2020. The findings reveal that fiscal decentralization and technological development are two crucial policy tools for promoting environmental sustainability and mitigating environmental risks. The study employs the DOLS, FMOLS, and PMG methods to examine the impact of fiscal decentralization and technological development on different environmental issues. The results indicate that the contribution of technological development varies depending on the pollutant type and its size cannot be universally applied. Technological developments directly contribute to environmental degradation by increasing the volume of COD discharge, NOX emissions, and SO2 emissions, which reflects the direct impact of technological developments on increasing industrial production. Moreover, the study shows that government expenditure decentralization contributes to increasing the volume of pollutants, revealing a competition from the bottom to the top among Chinese provinces. The EKC hypothesis test supports an inverted N-shaped EKC hypothesis, which confirms that China's economic development has come at the expense of the environment. Additionally, the D-H causation analysis reinforces this finding. The study recommends promoting environmental innovations that reduce emissions, building a strategy to support green economic growth, and establishing environmental regulations and standards to prevent competition between local governments for development at the expense of environmental sustainability in Chinese provinces.
Multicriteria evaluation of recommender systems using fuzzy analytic hierarchy process
Authors: Nedashkovskaya Nadezhda Ivanovna , Androsov Dmytro Vasyliovych 
Published: September 2023

Abstract
Offering relevant items and goods has always been a core issue for consumer-centric business. In recent years the digitalization process gave such entities a significant push towards implementing computer-aided systems for solving recommendations generation problems via applying statistical learning methods on large scale datasets of user-item interactions. Since then, there were developed a variety of algorithms for a recommender system design, based on neighborhood metrics, matrix factorization machines and deep neural networks, each of them having their application criteria and requirements on input data. The purpose of the following research is to investigate performance of graph neural networks recommender systems on two tasks – recommendation retrieval and next best offer prediction. As a result, the graph-based recommender system for solving both tasks, described above, was synthesized and benchmarked on open-source e-commerce dataset. From the conducted experiment it was gained evidence that proposed approach is feasible to solve recommendation retrieval tasks and outperform models, that are considered de-facto standard, i.e., factorization machines and recurrent neural netwoks.
Clinical phenotypes of comorbidities in end-stage knee osteoarthritis: a cluster analysis
Authors: liu ruiyu , Ma Jun , Zhang Kai , Ma Xilong , Wang Hao , Ma Chao , Zhang Yahui 
Published: September 2023

Abstract
Objectives Comorbidities, as components of these heterogeneous features, often coexist with knee osteoarthritis, and are particularly prevalent in end-stage knee osteoarthritis. Here, we attempted to identify the different clinical phenotypes of comorbidities in patients with end-stage knee osteoarthritis by cluster analysis.
Methods A total of 421 inpatients diagnosed with end-stage knee osteoarthritis who underwent inpatient surgery were included in this cross-sectional study. 23 demographic, comorbidity, inflammatory immune and evaluation scale variables were collected. Systematic clustering after factor analysis and separate two-step cluster analysis were performed for individual comorbidity variables and all variables, respectively, to objectively identify the different clinical phenotypes of the study patients.
Results Four clusters were finally identified. Cluster 1 had the largest proportion of obese patients (93.8%) and hypertension was common (71.2%). Almost all patients in cluster 2 were depressed (95.8%) and anxiety disorders (94.7%). Cluster 3 combined patients with isolated end-stage knee osteoarthritis and a few comorbidities. Cluster 4 had the highest proportion of patients with rheumatoid arthritis (58.8%).
Conclusions Patients with end-stage knee osteoarthritis may be classified into four different clinical phenotypes: "isolated end-stage knee osteoarthritis"; "obesity + hypertension"; "depression + anxiety"; and "rheumatoid arthritis", which may help guide individualized patient care and treatment strategies.
Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): Solving rare and puzzling genetic disorders is ageless.
Authors: Wallis Mathew , Bodek Simon , Munro Jacob , Rafehi Haloom , Bennett Mark F , Ye Zimeng , Schneider Amy , Gardiner Fiona , Valente Giulia , Murdoch Emma , Uebergang Eloise , Hunter Jacquie , Stutterd Chloe , Huq Aamira , Salmon Lucinda , Scheffer Ingrid , Eratne Dhamidhu , Meyn Stephen , Fong Chun Y , John Tom , Mullen Saul , White Susan M , Brown Natasha J , McGillivray George , Chen Jesse , Richmond Chris , Hughes Andrew , Krzesinski Emma , Fennell Andrew , Chambers Brian , Santoreneos Renee , LeFevre Anna , Hildebrand Michael S , Bahlo Melanie , Christodoulou John , Delatycki Martin , Berkovic Samuel 
Published: September 2023

Abstract

Background
Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes.
Methods
Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing (NGS), and/or chromosomal microarray, had already been performed were recruited. Genome sequencing (GS) and enhanced genomic analysis from the research setting were applied to aid novel gene discovery.
Results
In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance (VUS) were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP.
Conclusion
AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.
CVRmap - A Complete Cerebrovascular Reactivity Mapping Post-Porcessing BIDS Toolbox
Authors: Rovai Antonin , Lolli Valentina , Trotta Nicola , Goldman Serge , De Tiège Xavier 
Published: September 2023

Abstract
Cerebrovascular Reactivity (CVR) refers to the ability of cerebral blood vessels to dilate or constrict under the effect of vasoactive substances and can be estimated using functional Magnetic Resonance Imaging (fMRI). Computation of CVR maps is relevant in various brain diseases and requires specialized data processing. We introduce CVRmap, an opensource software that automates the computation of CVR map. The toolbox complies with the Brain Imaging Data Structure (BIDS) standards.