bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut microbiota in inflammatory bowel disease: a combined culturomics and metagenomics perspective
Authors: Park Hyunjoon , Yeo Soyoung , Lee Taekyu , Han Yumin , Ryu Chang Beom , Huh Chul Sung 
Published: September 2023

Abstract

Background:Gut dysbiosis has been linked to a variety of human diseases. Genome-based research has provided vast information on this topic over the past few decades, suggesting the necessity of microbial therapeutics. However, since genomic data alone are insufficient for experimental verification and clinical application of gut bacterial interactions, the need for culture-based gut microbiome research has been attracting great attention. Over the past decade, culturomics (a high-throughput cultivation and identification approach) has increased the possibility of overcoming this challenge. In our study, we explored the complementarity of culturomics and metagenomics by comparing the gut microbiota of healthy individuals with that of patients with ulcerative colitis (UC) and Crohn's disease (CD), which are subtypes of inflammatory bowel disease (IBD). Our ultimate goal was to select putative pathobionts related to each IBD subtype and probiotic candidates for microbiome-based therapeutics, which were extended from the metagenomics results.Results:We used a culturomics approach to obtain 14,131 gut bacterial isolates from UC and CD patients. They were classified into 265 species (UC, 215 and CD, 170). This IBD gut bacterial library included new species that had never been cultured. In the 16S rRNA gene amplicon sequence-based analysis, the gut dysbiosis in CD patients compared with the healthy control (HC) group was more severe than in UC patients compared with the HC group, with an increase in the abundance ofProteobacteriaand a decrease in the abundance ofActinobacteriota, which were dependent on the disease severity. Culturomics data also showed a more shifted dysbiosis in CD patients than in UC patients, with significantly decreasing species diversity, particularly anaerobes. From the two omics results, we suggested 24 taxa associated with UC or CD patients and 44 commensal species that could be used as live therapeutic candidates based on probiotic properties.Conclusions:Our study extended the understanding of gut dysbiosis in IBD patients using culturomic and metagenomic approaches. Our large-scale culture collection will be a foundation for identifying human gut bacterial diversity and strain characteristics.
The COVID-19 pandemic decreases cardiorespiratory fitness. A 3-year follow-up study in industry
Authors: Skare Øivind , Mamen Asgeir , Skogstad Marit 
Published: September 2023

Abstract
Purpose: This study aimed to determine if maximal oxygen uptake (V̇O2max), resting heart rate (RHR), and self-reported leisure- time moderate to vigorous physical activity (MVPA) changed over a 3-year follow-up (FU) among industrial workers during restrictions of outdoor movement and the concurrent closure of fitness centres due to the COVID-19 pandemic.
Methods: We assessed cardiorespiratory fitness (CRF) among workers in industry in August 2018 and in August 2021. The last 17-18 months of the 3-year FU coincided with the COVID-19 pandemic. Data from 86 participants were collected; demographics by questionnaire and cardiovascular outcomes from medical examination: V̇O2max, RHR, and fat mass (%). At both time points, workers reported on their leisure-time MVPA. To assess changes in health outcomes, we applied a linear mixed model, adjusting for baseline (BL) age, sex, pack-years, shift work, and a 5-month plant shutdown. In a second analysis, we adjusted for actual age instead of BL age.
Results: V̇O2max decreased from 39.6 ml/kg/min at BL to 34.0 at FU, a reduction of 5.6 ml/kg/min (95%CI, -7.6,-3.7). When adjusted for actual age, the corresponding figure for V̇O2max was 5.4 ml/kg/min, (95%CI, -7.4,-3.4), an annual loss of 4.6%. RHR increased from 61.3 to 64.4 beats per minute (95%CI, 0.8, 5.4). Self-reported MVPA decreased by 43.9 min/week, (95%CI, -73.5,-14.4).
Conclusion: We observed a significant decrease in V̇O2max, an increase in RHR and a decrease in self-reported MVPA over the 3-year FU among industrial workers. These changes may be attributable to physical inactivity during the COVID-19 pandemic.
ISRCTN42416837, date of registration 25.10.2018
Bioinformatics Analysis of Immune Cell Infiltration Patterns and Potential Diagnostic Markers in Atherosclerosis
Authors: Ji Haigang , Yuan Ling , Jiang Wenbo , Jiang Yinke , Jiang Mengke , Sun Xuemei , Chen Jing 
Published: September 2023

Abstract
Background
This study aimed to investigate efficient diagnostic markers and molecular mechanisms of atherosclerosis and to analyze the role of immune infiltration through bioinformatics analysis.
Results
Expression profile datasets (GSE28829 and GSE43292) of patients with atherosclerosis and healthy controls were downloaded from the GEO database. Glutamine (GLN) metabolism-associated genes were obtained from the Molecular Signatures Database (MSigDB). The limma package in R was used to identify differentially expressed genes (DEGs). Significant modules were filtered using Weighted Gene Co-expression Network Analysis (WGCNA). MSigDB sets were subjected to Gene Set Enrichment Analysis and Gene Set Variation Analysis. The biological functions of DEGs were examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. STRING and Cytoscape software were used to identify hub genes and functional modules through protein–protein interaction (PPI) network analysis. The xCell software was adopted to assess the composition patterns of immune and stromal cells. Correlation analyses were performed for key genes and immune cell subtypes. We identified 308 DEGs and GLN-associated genes. Functional enrichment analysis showed that these genes were strongly enriched in muscle contract, muscle tissue development, cutile fiber, mycobacterial, and actin binding. Enriched KEGG pathways comprised dilated cardiomyopathy, Hypergraphic cardiomyopathy, and the cAMP signaling pathway. In the PPI network analysis, 27 genes were identified as hub genes. The area under the curve (AUC) values of 27 biomarkers were relatively high, indicating high diagnostic values. The atherosclerosis group exhibited a markedly higher degree of infiltration than the control group.
Conclusions
This study identified 27 GLN-associated genes as potential biomarkers for the diagnosis of atherosclerosis. It provides a new perspective on immune responses that facilitates exploration of the molecular mechanisms of atherosclerosis.
Mixed pattern study on the development of midwifery profession job satisfaction scale
Authors: DAĞLI Elif , REYHAN Feyza AKTAŞ 
Published: September 2023

Abstract

The aim of this study is to develop a measurement tool on midwifery job satisfaction. In the research, the "exploratory sequential mixed method" design was used. Case study in order to examine midwives' (n = 10) perceptions of midwifery job satisfaction in the qualitative phase of the research; Methodological research design was used to create a scale on the evaluation of factors affecting midwifery job satisfaction at the quantitative stage (n = 210). In the light of qualitative findings and literature review, a 41-item draft scale was created in line with the expert opinion created and received for the Midwifery Profession Job Satisfaction Scale. In order to test the construct validity of the scale, exploratory factor analysis was conducted using principal components method and varimax axis rotation. As a result of the analysis, a scale consisting of 40 items and a 6-factor structure with an eigenvalue above 1 and explaining 72.24% of the total variance was obtained. The confirmatory factor analysis results of the scale also show that the data fit well with the model. It was determined that the Cronbach Alpha internal consistency coefficient of the scale ranged from 0.94 and the sub-dimensions between 0.83 and 0.96. It has been determined that the developed scale is a valid and reliable measurement tool that can be used to evaluate the job satisfaction of midwives.
What are the views of Quebec and Ontario citizens on the tiebreaker criteria for prioritizing access to adult critical care in the extreme context of a COVID-19 pandemic?
Authors: Ramirez Claudia Calderon , Farmer Yanick , Frolic Andrea , Bravo Gina , Gaucher Nathalie Orr , Payot Antoine , Opatrny Lucie , Poirier Diane , Dahine Joseph , L'Espérance Audrey , Downar James , Tanuseputro Peter , Rousseau Louis-Martin , Dumez Vincent , Descôteaux Annie , Dallaire Clara , Laporte Karell , Bouthillier Marie-Eve 
Published: September 2023

Abstract

Background
The prioritization protocols for accessing adult critical care in the extreme pandemic context contain tiebreaker criteria to facilitate decision-making in the allocation of resources between patients with a similar survival prognosis. Besides being controversial, little is known about the public acceptability of these tiebreaker. In order to better understand the public opinion, Quebec and Ontario’s protocols were presented to the public in a democratic deliberation during the summer of 2022.
Objectives
1) To explore the perspectives of Quebec and Ontario citizens regarding tiebreakers, identifying the most acceptable ones and their underlying values. 2) To analyze these results considering other public consultations held during the pandemic on these criteria.
Methods
This was an exploratory qualitative study. The design involved an online democratic deliberation that took place over two days, simultaneously in Quebec and Ontario. Public participants were selected from a community sample which excluded healthcare personnel. Participants were first presented the essential components of prioritization protocols and their related issues. They subsequently deliberated on the acceptability of these criteria. The deliberation was then subject to thematic content analysis. A scoping review was previously done to identify other public consultations conducted on this topic in the context of this pandemic, and to guide the analysis of our results.
Results
A total of 47 participants from the provinces of Quebec (n = 20) and Ontario (n = 27) took part in the online deliberation. A diverse audience participated excluding members of the healthcare workforce. Four themes were identified: 1) Priority to young patients - the life cycle - a preferred tiebreaker; 2) Randomization - a tiebreaker of last resort; 3) Multiplier effect of most exposed healthcare workers - a median acceptability tiebreaker, and 4) Social value – a less acceptable tiebreaker.
Conclusion
Life cycle was the preferred tiebreaker as this criterion respects intergenerational equity, which was considered relevant when allocating scarce resources to adult patients in a context of extreme pandemic. Priority to young patients is in line with other consultations conducted around the world. Additional studies are needed to further investigate the public acceptability of tiebreaker criteria.
Multivariate Motion Patterns and Applications to Rainfall Radar Data
Authors: Fischer Svenja , Oesting Marco , Schnurr Alexander 
Published: September 2023

Abstract
The classification of movement in space is one of the key tasks in environmental science. Various geospatial data such as rainfall or other weather data, data on animal movement or landslide data require a quantitative analysis of the probable movement in space to obtain information on potential risks, ecological developments or changes in future. Usually, machine-learning tools are applied for this task, as these approaches are able to classify large amounts of data. Yet, machine-learning approaches also have some drawbacks, e.g. the often required large training sets and the fact that the algorithms are often seen as black boxes. We propose a classification approach for spatial data based on ordinal patterns. Ordinal patterns have the advantage that they are easily applicable, even to small data sets, are robust in the presence of certain changes in the time series and deliver interpretative results. They therefore do not only offer an alternative to machine-learning in the case of small data sets but might also be used in pre-processing for a meaningful feature selection. In this work, we introduce the basic concept of multivariate ordinal patterns and the corresponding limit theorem. A simulation study based on bootstrap demonstrates the validity of the results. The approach is then applied to two real-life data sets, namely rainfall radar data and the movement of a leopard. Both applications emphasize the meaningfulness of the approach. Clearly, certain patterns related to the atmosphere and environment occur significantly often, indicating a strong dependence of the movement on the environment.
MSC Classification: 62M10 , 62H20 , 62F12 , 60F05 , 05A05 , 62G30
Assessment of interference scope induced by stray current in the metro depot for the corrosion risk of buried metal pipeline
Authors: Wang Chengtao , Wang Yuqiao , Xu Shaoyi , Li Wei , Wang Yifu , Xing Fangfang 
Published: September 2023

Abstract
The hazard of stray current attracts more and more attention due to the potential infrastructure failure caused by the electrochemical corrosion. In view of the poor insulation performance and lack of stray current collection system in the metro depot, stray current leakage becomes particularly evident in this area. In order to evaluate the corrosion risk of buried metal pipeline surrounding metro depot, an assessment model for interference scope induced by stray current is proposed in this paper. The distribution of stray current is calculated based on the resistive network by considering different boundary conditions in different areas of metro depot, and the interference scope is assessed by surface potential gradient for corrosion risk of corroded pipeline. Moreover, the characteristics of surface potential gradient distribution in different areas of metro depot and the influence of electrical parameters are analyzed. Finally, the proposed model is verified through CDEGS-based simulation and experimental results.
COD Removal in Organic Dyes Using Ultrasonication-Ozonation: Computational and Experimental Study
Authors: Hutagalung Sutrisno Salomo , Khotimah Khusnul , Rafryanto Ande Fudja , Suhardi Sri Harjati , Supriadi Sri , Rochman Nurul Taufiqu , Kurniadi Deddy 
Published: September 2023

Abstract

Organic dye is a highly toxic, nonbiodegradable, and harmful substance that causes significant environmental contamination. The combined effort of an ultrasonication (US) method followed by ozonation (OZ) treatment for organic dye solution is described here. Using computational fluid dynamics (CFD), the optimum frequency of 26 kHz is utilised in the experiment acquired from the acceptable frequency range based on the simulation. The initial organic dye solutions in this investigation contained low-COD conditions, 40 mg L− 1 of Methylene Blue (MB), and 134 mg L− 1 of industrial effluent. The latter case exhibits that the chemical oxygen demand (COD) of industrial removal rate is 57.46%, where the lowest concentration of 57 mg L− 1 is attainable, which indicates that the combined method fulfils the acceptance range of the ZDHC International Standard of 60 mg L− 1. The sequential approaches unambiguously demonstrate a promising strategy for effective wastewater treatment for organic pollutants.
WITHDRAWN: Circular Polarization Division Multiplexing in Visible Light Communication System by Incorporating QPSK and Distortion Compensation Enabled DSP/IDSP
Authors: Pahuja Hunny , Verma Monika , Sachdeva Shippu , Kaur Simarpreet , Sindhwani Manoj , Shukla Manoj Kumar 
Published: September 2023

Abstract

Hybrid polarization division multiplexing (PDM) and Visible Light Communication (VLC) have fostered speedy data transmission in the last few years and emerged as the strong candidate that enables users to leverage the pervasive illumination/communication infrastructure. Circular PDM (CPDM) is replacing the linear PDM (LPDM) variant in wired/wireless systems due to the even scattered light distributions and elimination of polarization axis alignment requirements. In this research work, a 1.6 Tbps multi-wavelength line of sight (LoS) based VLC system is presented and data modulation is performed by employing Quadrature phase shift keying (QPSK). The conventional DSP algorithms such as Viterbi Phase Estimation (VPE), Blind Phase Search (BPS), and Constant Modulus Algorithm (CMA) algorithms are replaced with Gram-Schmidt orthogonalization procedure (GSOP), time-domain equalization algorithm (TEDA), improved Viterbi algorithm (IVA), and least mean square (LMS) algorithm in proposed IDSP. Three different systems are compared such as LPDM-VLC-DSP, CPDM-VLC-DSP, and CPDM-VLC-IDSP at different VLC link ranges, transmitter half angles (THA), incidence half angles (IHA), and optical concentrator areas (OCAs) in terms of error vector magnitude percentage (EVM%), log symbol error rate (log SER), and Q factor. After doing the extensive comprehensive literature survey, it is discerned that the presented CPDM-VLC-IDSP system has covered the longest distance i.e. 14 cm at 1.6 Tbps capacity under the acceptable bit error rate (BER) limits.
Andreev hidden spinor coordinates: Standard Model, gravity and 3He
Authors: Volovik Grigory 
Published: September 2023

Abstract
This paper is prepared for a special memorial issue of J. Low Temp. Phys. dedicated to memory of Alexander Andreev. The paper considers some ideas of Andreev on the fermion-boson transmutation, which look somewhat contradictory, but their consideration and development may lead to new physics on the more fundamental trans-Planckian level.
PACS numbers:
F1 distant hybrids between two edible lilies (Lilium brownii var. viridulum and L. davidii var. unicolor) produce more n than 2n functional eggs with more recombinant chromosomes
Authors: Liu Siyu , Sun Yanni , Peng Mingzhu , Zhang Xiaoyan , Zhou Shujun 
Published: September 2023

Abstract
Lilium brownii var. viridulum (BB) and L. davidii var. unicolor (AdAd) are grown for edible in China, but their breeding lags far more than other ornamental lily breeding. To improve the situation, F1 BA hybrids were used as seed parents to cross with AdAd and other diploid Asiatic lilies (AA). The results showed that the F1 BA hybrids could produce BC1 progenies. The average seedlings obtained from the combinations per fruits were very variable from 1.7 to 22.5, indicating that their compatibilities are different depending on their males. Among the 18 progenies with genomic in situ hybridization (GISH), ten of them were diploid (2n = 2x = 24), two are aneuploid - near diploid (2n = 2x ± 1), and other six were allotriploid (2n = 3x = 36); and all of them contain much more recombinant chromosomes and breakpoints than other distant lily hybrids. We concluded that F1 LA hybrids produced much more n functional egg cells than 2n functional egg cells and this would pay a new way to realize lily ingression breeding at diploid ploidy level.
The effects of Curcumin and Crocin on the inflammatory phase of thyroid eye disease: a randomized controlled clinical trial
Authors: Yazd Mohammadreza Akhondian , Kiarudi Mohammad Yaser , Bakhtiari Elham , Saber-moghaddam Niloufar , Avan Amir , Shariati Mehrdad Motamed , Sabermoghaddam Aliakbar 
Published: September 2023

Abstract
Objective
A randomized, triple-blinded study was designed to assess the influences of curcumin and crocin on clinical findings and serologic markers, including IL-6 and TNF-α, of the inflammatory phase of thyroid eye disease (TED).
Methods
The curcumin and crocin were added to the traditional care of the patients after randomizing to placebo, curcumin, and crocin groups. Before interventions, CAS was evaluated and a blood sample (to measure the serum levels of IL-6 and TNF-α) was taken. The CAS was reassessed in the first and second months and the blood sampling was repeated in the second month afterward.
Results
A total of 46 TED cases (22 to 64 years old) were enrolled, 16 patients in the Placebo group, 17 patients in the Curcumin group, and 13 patients in the Crocin group. CAS, TNF-α, and IL-6 significantly reduced in all patients, regardless of their group and received drugs. No statistically significant difference was observed in the reduction of CAS score and TNF-α level in a two-month follow-up between the study groups.
Conclusion
Daily consumption of 30 milligrams (mg) of crocin or 80 mg of curcumin in addition to standard care could be effective in decreasing CAS in TED patients.
A Quantum Optimization Case Study for a Transport Robot Scheduling Problem
Authors: Leib Dominik , Seidel Tobias , Jäger Sven , Heese Raoul , Jones Caitlin Isobel , Awasthi Abhishek , Niederle Astrid Elisa , Bortz Michael 
Published: September 2023

Abstract
We present a comprehensive case study comparing the performance of D-Waves' quantum-classical hybrid framework, Fujitsu's quantum-inspired digital annealer, and Gurobi's state-of-the-art classical solver in solving a transport robot scheduling problem. This problem originates from an industrially relevant real-world scenario. We provide three different models for our problem following different design philosophies. In our benchmark, we focus on the solution quality and end-to-end runtime of different model and solver combinations. We find promising results for the digital annealer and some opportunities for the hybrid quantum annealer in direct comparison with Gurobi. Our study provides insights into the workflow for solving an application-oriented optimization problem with different strategies, and can be useful for evaluating the strengths and weaknesses of different approaches.
A Benchmark of Existing Tools for Outlier Detection and Cleaning in Trajectories
Authors: Duarte Mariana Machado Garcez , Sakr Mahmoud 
Published: September 2023

Abstract
Outlier detection and cleaning is an essential step in data preprocessing to ensure the integrity and validity of data analyses. This paper focuses on outlier points within a individual trajectories, i.e., points that deviate significantly inside a single trajectory. We benchmark ten open-source libraries to comprehensively evaluate available tools, comparing their efficiency and accuracy in identifying and cleaning outliers. This benchmarking considers the libraries as they are offered to end users, with real-world applicability. We compare existing outlier detection libraries, introduce a method for establishing ground-truth, and aim to guide users in choosing the most appropriate tool for their specific outlier detection needs. Furthermore, we survey the state-of-the-art algorithms for outlier detection and classify them into seven types: Statistic-based methods, Sliding window algorithms, Clustering-based methods, Graph-based methods, Ensemble-based methods, Learning-based methods, and Heuristic-based methods. Our research provides insights into these libraries' performance and contributes to developing data preprocessing and outlier detection methodologies.