bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the Effectiveness of Using Magnoimmunosorbents for the Selective Concentration of Anthrax Agent Spores
Authors: Logvin F. V. , Semenova O. V. , Ryazanova A. G. , Zharnikova I. V. , Aksenova L. Yu. , Rusanova D. V. , Kurcheva S. A. , Startseva O. L. , Geogdzhayan A. S. , Kulichenko A. N. 
Published: October 2023

The aim of the study was to assess the effectiveness of the developed anthrax magnoimmunosorbents (MIS) for the selective concentration of Bacillus anthracis spores and to increase the sensitivity of anthrax agent detection techniques, including when testing soil samples.Materials and methods. We used 10 vaccine strains of B. anthracis and 30 strains of closely related bacilli of the genus Bacillus (B. cereus – 15, B. thuringiensis – 10, B. megaterium – 5) with typical species properties. The work was performed on three experimental batches of magnoimmunosorbents. DNA extraction and PCR setting was carried out in compliance with the instructions for reagent panel for B. anthracis DNA detection “ApliSens Bacillus anthracis-FRT”.Results and discussion. It is shown that when using MIS, the sensitivity of the cultural method is increased by at least 7 times (taking into account the possibility of sorption of 1–10 or more spores on a sorbent particle). The sensitivity of the PCR method is improved by 10 times and amounts to 50 B. anthracis spores per 1 ml for the samples concentrated with the help of MIS. The sensitivity of the bacteriological method using MIS increases by a factor of 7.5 when testing the artificially contaminated with B. anthracis soil samples. Hence, application of the developed MIS makes it possible to significantly enhance the sensitivity of anthrax agent detection methods and can be considered as an effective means of sample preparation for the investigation of environmental objects (soil).
Genotypic Characteristics of CTX–VPI<sup>+</sup> Clonal Complexes of <i>Vibrio cholerae</i> O1 Found in Water Bodies of the Rostov Region
Authors: Monakhova E. V. , Noskov A. K. , Kruglikov V. D. , Vodop’yanov A. S. , Selyanskaya N. A. , Men’shikova E. A. , Ezhova M. I. , Nepomnyashchaya N. B. , Shvidenko I. G. , Podoinitsyna O. A. , Pisanov R. V. 
Published: October 2023

The aim of the work was to identify genotypic features of clonal complexes formed by CTX–VPI+ strains of Vibrio cholerae isolated from water bodies of the Rostov Region in different years, based on bioinformatics analysis of their whole genome sequences (WGSs).Materials and methods. Whole genome sequencing was performed on the MiSeq (Illumina) platform; identification of genetic determinants in WGSs and bioinformatics analysis – by means of BioEdit, BLASTN, BLASTP, CARD, Vector NTI software packages.Results and discussion. The strains were almost identical in each group of 2002-, 2005-, 2007-, 2020-, 2021-, and 2022-isolates and were found at different points of water sampling over a longer or shorter periods of time (from 3 weeks to 2 months). Bioinformatics analysis of WGSs of representative strains divided them into 4 clusters, which can be considered as separate clonal complexes sharing a number of characteristic genetic markers: 1) 2002-isolates containing one SNP in regulatory rpoS gene; 2) 2007-strains carrying tandemly duplicated preCTX prophage; 3) strains isolated in 2020 in Rostov-on-Don and in 2005, during epidemiological complications in the Kamensk district of the Rostov Region, which had a “hybrid” pathogenicity island including the cluster of type 3 secretion system and the nan-nag region of the VPI-2 island, and 9 SNPs in rpoS gene; 4) 2021- and 2022-strains and a single 2018-isolate containing a 9 bp deletion in vchC collagenase gene. Despite the revealed differences, representatives of all clonal complexes possessed sufficient sets of intact determinants of pathogenicity/persistence factors to realize virulent properties and ability to survive in water bodies. Detection of clonal complexes of potentially pathogenic strains in surface water bodies indicates occasional emergence of favorable conditions for their long-term circulation, which emphasizes the importance of constant monitoring of V. cholerae in the territory of Russia.
Three-Phase Simulation of Hydrotreating of Vacuum Gas Oil
Authors: Vorobev Anatoliy , Ivashkina Elena N. , Arkenova Saniya B. , Kaliyev Toleubek A. 
Published: October 2023

Abstract
We develop a numerical model for practical simulation of hydrotreatment of vacuum gas oil in a trickle-bed reactor. The model is based on the mass balance of species; it incorporates a seven-lump chemical scheme that describes the reactions of hydrodesulphurisation and hydrodearomatisation. The novelty of the model is splitting of sulphur-containing compounds into different lumps by their reactive abilities. The splitting is supported by the chromatographic analysis of hydrocarbon mixtures that are sampled from the inlet and outlet ends of an industrial hydrotreatment unit. The analysis reveals different susceptibilities of sulphides, benzothiophene, and dibenzothiophenes to hydrotreatment. The new model is applied for simulation of the hydrotreatment at a refinery, adjusting kinetic parameters, and demonstrating that the model provides an adequate (and, at the same time, simple) description of the process, giving guidance for optimisation that is needed after each variation of the feedstock.
Anoikis-related gene signature associates with the immune infiltration and predicts the prognosis of glioma patients
Authors: Lin Jianghua , Zhao Junmiao , Wu Xinyi , Hao Leiyu , Tan Xiao , Yang Lixue , Wu Lei-lei , Zhang Xiaoling , Zhao Kaijun , Liu Yu’e 
Published: October 2023

Abstract

Glioma is the most aggressive and incurable brain tumor. Anoikis is programed apoptosis in which cells are detached from the cellular matrix and suspended to death. It plays a critical role in cancer progression. Cancer cells overcome anoikis via various methods to continue their progression and metastasis. But the role of anoikis in gliomas remains elusive. By comprehensively studying the glioma patient’s data in TCGA and other public databases, we built an anoikis-related genes risk nomogram for glioma with the combination of both LGG and GBM based on TCGA data and validate independently in CGGA data. The detailed methods and accurate R package information are listed in the “Methods” part in the text. We found the high-risk groups were enriched in the anoikis and immune-related pathways. Further analysis of high-risk score groups revealed that they had higher immune infiltration, lower IDH-mutations, higher tumor mutation burdens and higher tumor immune dysfunction and exclusion scores, indicating that there might not be successful for the high-risk score glioma patients in immunotherapy. In conclusion, we built a risk modal by applying the analysis of anoikis-related genes and immune signature genes, and this risk modal can predict glioma patients’ clinical outcomes successfully and accurately.
An Emergency Escape Strategy based on Reasonable Dynamic Constraints for Autonomous Vehicles
Authors: gao Lingfei , Yang Shichun , Sun Bin , Xu Jingyun , Lu Jiayi , Cao Yaoguang 
Published: October 2023

Abstract
Safety represents the fundamental bottleneck in the development of autonomous driving.The majority of current research focuses on driving safety in regular scenarios. However, certain actions by other vehicles may pose significant risks to the ego vehicle, rustling in emergency scenarios. In this paper, we propose an emergency escape strategy for autonomous vehicles, encompassing risk assessment, escape trajectory generation, and Model Predictive Control (MPC) based control schemes. In risk assessment module, we introduce the Fusion Time-toCollision (FTTC) concept for risk quantification. The proposed approach not only considers the maximum escape potential under extreme circumstances but also incorporates vehicle dynamics constraints during the escape process to ensure that risks such as rollover are avoided due to excessively aggressive escape trajectories.The performance of our proposed algorithm is measured in two simulation scenarios.
Identification and validation of amino acid metabolism-related genes and immunological characteristics in osteoarthritis by bioinformatics analysis
Authors: Wang Yuyan , Liu Yang , Yu Changhe , Liu Zhifeng , Wang Xiyou 
Published: October 2023

Abstract
Background:
Osteoarthritis (OA) is a common joint disorder characterized by progressive destruction of articular cartilage and chronic inflammation. Growing evidence has implicated the roles of amino acid metabolism (AAM) and immunological factors in OA occurrence and development. However, the detailed mechanisms remain largely unknown. Therefore, identifying crucial genes and pathways related to AAM and immunology in OA using bioinformatics approaches is an important aspect to elucidate the pathogenesis of OA.
Methods:
Publicly available gene expression profiling datasets of OA were obtained from the gene expression omnibus (GEO) database. Differential expression analysis was performed to identify differentially expressed genes (DEGs) between OA and normal control samples. DEGs were intersected with amino acid metabolism related genes (AAMRGs) to obtain OA associated DEGs. Enrichment analysis including gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathways were performed on these DEGs. protein-protein interaction (PPI) network was constructed and key genes were identified by topology analysis. Immune cell infiltration was estimated by gene set enrichment analysis (GSEA) algorithm and CIBERSORT tool. receiver operating characteristic curve (ROC) curve analysis was applied to assess diagnostic performance of hub genes.
Results:
A total of 64 DEGs related to AAM were identified in OA. Enrichment analysis indicated these DEGs were mainly involved in glycine, serine and threonine metabolism. There were 8 hub genes identified from the PPI network. Immune cells analysis revealed increased infiltration of macrophages and neutrophils in OA compared to normal controls. Several hub genes such as SLC2A1 and VEGFA demonstrated high diagnostic accuracy for OA. Significant correlations were observed between AAM genes and multiple immune cells.
Conclusion
Through multi-omics analysis of osteoarthritis data, we identified AAM-related hub genes PPARG and VEGFA. Their expression associated with OA pathogenesis and immune infiltration, providing evidence for AAM involvement in the pathogenesis of OA. Further validation may facilitate their utility as OA biomarkers and therapeutic targets.
Precision determination of dipole transition matrix elements with a single trapped ion
Authors: Guan Hua 
Published: October 2023

Abstract

In the field of quantum metrology, transition matrix elements are crucial for accurately evaluating the black-body radiation shift and the parity-violating amplitude of the clock transition, and can be used as probes to test quantum electrodynamic effects, especially at the $10^{-3}$-$10^{-4}$ level. We developed a universal experimental approach to precise determination of the dipole transition matrix element with a energy level of two transition channels at various atomic species by using the quantum shelving technique. In which, the time-increased pulses were utilized to induce quantum shelving, and the resulting shelving probabilities were determined by counting the scattered photons from the excited $^{2}\!P_{1/2}$ state to the $^{2}\!S_{1/2}$ ground state. Using the scattered photons offers several advantages, including insensitivity to fluctuations in magnetic field, laser intensity, and frequency detuning. An intensity-alternating sequence to minimize detection noise and a real-time approach for background photon correction were implemented in parallel. We applied this method to single Yb$^+$ ion, and determined the $6p~^{2}\!P_{1/2}$ - $5d~^{2}\!D_{3/2}$ transition matrix element of 2.9395(21)~$ea_{0}$, which represents an order of magnitude improvement over previous determination. By combining our result with the $6p~^{2}\!P_{1/2}$ lifetime of 8.12(2)~ns, we extracted the $6s~^{2}\!S_{1/2}$ - $6p~^{2}\!P_{1/2}$ transition matrix element to be 2.4695(31)~$ea_{0}$.
Effect of acupuncture on tear proteomics in patients with VDT-related dry eye
Authors: tang na , Tang Lewei , Jiang Xiaohan , Li Yan , Xiang Shengjin , Chen Ding , Lyu Jiacheng 
Published: October 2023

Abstract
Background Acupuncture is widely used to treat dry eye disease (DED) and improved dry eye signs, but the effect has not been reported treating video display terminal (VDT)-related dry eye. Meanwhile, the mechanism of acupuncture on VDT-related dry eye remains unknown, and the treatments of DED are often associated with an altered tear protein composition.
Methods Sixty patients with VDT-related dry eye were randomly and equally allocated to the acupuncture (AC group) or the artificial tear groups (AT group). Treatment involved acupuncture or artificial tear for 4 weeks. Tear samples were collected after baseline examination of clinical parameters, including Ocular Surface Disease Index (OSDI) scores, tear film break-up time (TFBUT), and Schirmer I test (SIT) before and after treatment. Tear samples were subjected to proteomic identification and analysis by independent acquisition.
Results The OSDI scores were significantly different between the AC and AT groups at the end of the study period when performing repeated measurement analysis of before, after, and 4 weeks after treatment by repeated measurement analysis (p = 0.017), whereas the TFBUT and SIT were not significantly different between the groups. In the AC group, the OSDI scores, TFBUT, and SIT were significantly improved at 4 weeks after treatment by one-way analysis (p = 0.001, p = 0.033, p = 0.033, respectively); whereas, there was no significant improvement in the AT group at that time. A total of 7502 proteins were identified by data-independent acquisition. Proteome changes pre- and post-treatment in the AC group were associated with B cell-related immune processes, inflammation, glycolysis, and actin cytoskeleton, and, accordingly, the protein expression levels of actin-related protein 2/3 complex, subunit 3, pyruvate kinase M, gelsolin, and lactate dehydrogenase A, among others, differed significantly between the effective and ineffective patients based on the OSDI scores within the AC group. Furthermore, the proteins hexosaminidase A and mannose-binding lectin 1 could prospectively predict whether acupuncture treatment was effective, based on an inverse convolution analysis and machine learning algorithms.
Conclusions Acupuncture, relative to artificial tear, can provide greater improvement in the clinical symptoms of VDT-related dry eye. The mechanism of acupuncture in VDT-related dry eye treatment may be associated with glycolysis- and actin cytoskeleton remodeling-mediated inflammatory and immune processes. Additionally, hexosaminidase A and mannose-binding lectin 1 are biomarkers for predicting the efficacy of acupuncture for VDT-related dry eye. Key words: Acupuncture; VDT-related dry eye; Tear proteomics; Glycolysis; Actin cytoskeleton; Biomarkers.
Analysis of Agro-morphological Characters and Genetic Diversity in Some Selected Landraces of Rice During Early Drought Stress
Authors: DE ANIRNEETA , DEY AVISHEK , RAY UDAY SANKAR , RAHA SUBRATA , KAR DIPAK KUMAR 
Published: October 2023

Abstract
Drought is a major threat to rice production in many parts of the world. The red-lateritic zone of West Bengal, India, faces physiological drought each season, specifically in early growth stage due to erratic rainfall. No true-drought-tolerant variety has been developed till date due to lack of proper screening methods and undetected major Quantitative-Trait-Loci linked to drought tolerance. In this study, twenty-two landraces and check varieties were subjected to water stress at seedling stage. Root and shoot length (RL, SL), seedling-vigour-index (SVI), root fresh and dry weight (RFW, RDW), leaf rolling (LR), leaf drying (LD) were recorded. After rewatering, survivability percentage (SP), days to 50% flowering (DF), days to maturity (DM), 100 seed weight (SW), seed yield/plant (SY/P) were observed. Significant variations between the germplasms were noted. Significant positive correlation was found between SP, SW, DM, DF, RFW, SL, and SY/P whereas LD, LR were negatively correlated with SY/P. T-test between the yield of stressed and controlled conditions revealed that twelve landraces along with the positive checks did not vary significantly in SY/P. One landrace, Morogjhota outperformed the check varieties in yield. Genetic diversity analysis with 20 SSR markers divided the germplasms into two main clusters with a PIC value ranging between 0.544 – 0.907. From this study, seventeen lines were identified among which five landraces showed high Drought Resistance Index which can be used as parent material in developing climate-resilient varieties and can also be used to detect major QTLs associated with drought tolerance.
Keywords: Agro-morphological characters, Drought resistance, Landrace, Rice, SSR markers
The Anchors of Home: Understanding How Place Attachment strengthen Well-being of Sri Lanka's Migratory Fisher Communities
Authors: Koralagama D N , PVS Harshana 
Published: October 2023

Abstract

During the off-season, small-scale fishers migrate to more favourable locations to sustain their fishing activities and livelihoods. This study focuses on Sri Lanka's west coast to investigate the psychological, social, and economic motives that influence the decision making on the seasonal migration destination of these fishers. Using qualitative methods including sixty in-depth interviews and five key informant discussions, the research focuses on the overlooked aspects of well-being in fisheries literature. It introduces a holistic view of "well-being" that encompasses material gains, social motives, and functional factors, all of which are tied to the concept of place attachment. Economic drivers, such as stable income, resource access, and market opportunities, contribute to material well-being. Social factors like community ties and networking encourage migration for social benefits. Functional aspects, including emotional and cognitive factors, also play a role in migration decisions. The study concludes that the choice of migration sites is a complex blend of these economic, social, and functional motives, each linked to different facets of human well-being. The insights are extendable to other resource-dependent communities that engage in seasonal migration for livelihood and well-being, such as farmers and miners.
Cephalic Arch Stenosis : An Analysis of Outcome by Type of First Intervention
Authors: Pisano Umberto , Stevenson Karen , Kasthuri Ram , Kingsmore David 
Published: October 2023

Abstract
Background
Cephalic arch stenoses (CAS) occur in near 70% of elbow arteriovenous fistulas. Percutaneous transluminal angioplasty (PTA) remains first-line treatment despite documented stent-grafts (SG) efficacy. The study aim is to report outcomes based on CAS initial treatment on long-term follow-up.
Methods
Retrospective review of 12-year data in single tertiary centre. Outcomes included technical success, rupture rate, primary patency (PP), dialysis performance; categorical variables assessed via c2 or Fisher’s; nonparametric tests used for skewed data. Kaplan-Meier analysis used for PP and cumulative patency. Cox proportional hazard regression model to assess explanatory variables in PP.
Results
101 brachio- and radiocephalic fistulas with CAS were included. SG as first intervention had higher success than PTA (85% vs 61%, p = 0.003). Rupture occurred in 9/85 (10.6%) PTA vs 0% in SG (p = 0.046). In a subgroup with poor urea reduction rate (URR), both PTA and SG improved dialysis performance post-intervention (p = 0.002). SG demonstrated better PP than PTA (79,73,60% patency at 3, 6, 9 months; versus 71,51,47%; p = 0.195) and cumulative patency (73,61,61% at 1, 2, 3 years; versus 60,34,26%; p < 0.001). Of the variables analyzed, technical success of PTA was the only discriminating factor (coeff.-1.01; RR 35%,p = 0.035). Accesses that underwent secondary stenting performed better than primarily stented CAS (p = 0.01).
Conclusions:
SG superiority is confirmed in CAS, particularly when angioplasty is unsuccessful. While PTA has short-lived benefits, it can improve dialysis performance. Other than higher success rate, primary CAS stenting did not have advantages compared to post-PTA stenting in our study. Other factors related to inflow, outflow, conduit characteristics are presumed to be involved in access longevity.
PANI/rGO−PAM/PVA Hydrogels with Applications in Supercapacitive, Photoelectric and Strain Sensing
Authors: Li Shuo , Tao Yulun , Wu Yuannan , Zhu Shanshan , Khademi Sara , Lv Yinru , Tai Yanlong , Wang Chaoran 
Published: October 2023

Abstract
The high integration and multifunctionality in flexible electronic device play an important role in its development. In this study, we developed multifunctional hydrogels integrated with supercapacitive, photoelectric, and strain-sensing capabilities. The hydrogel composite consists of PAM/PVA matrix with polyaniline (PANI) and reduced graphene oxide (rGO) as conductive components. Two different acid dopants, citric acid (CA) and hydrochloric acid (HCl), were employed to investigate their impact on photoelectrochemical capabilities of hydrogels. Both CA-doped and HCl-doped hydrogels exhibited remarkable supercapacitive performance, achieving areal capacitances of 492 mF/cm2 and 538 mF/cm2, respectively. Furthermore, both hydrogels demonstrated photosensitivity towards shorter wavelengths such as ultraviolet (380 nm) and blue (475 nm) light. Lastly, the proposed hydrogels serving as highly sensitive strain sensors was verified through effectively sensing arm bending movements.
SparrKULee: A Speech-evoked Auditory Response Repository of the KU Leuven, containing EEG of 85 participants
Authors: Bollens Lies , Accou Bernd , Gillis Marlies , Verheijen Wendy , hamme Hugo Van , Francart Tom 
Published: October 2023

Abstract

Researchers investigating the neural mechanisms underlying speech perception often employ electroencephalography (EEG) to record brain activity while participants listen to spoken language.The high temporal resolution of EEG enables the study of neural responses to fast and dynamic speech signals.Previous studies have successfully extracted speech characteristics from EEG data and, conversely, predicted EEG activity from speech features.
Machine learning techniques are generally employed to construct encoding and decoding models, which necessitate a substantial amount of data. We present SparrKULee: A Speech-evoked Auditory Repository of EEG, measured at KU Leuven, comprising 64-channel EEG recordings from 85 young individuals with normal hearing, each of whom listened to 90-150 minutes of natural speech. This dataset is more extensive than any currently available dataset in terms of both the number of participants and the amount of data per participant. It is suitable for training larger machine learning models. We evaluate the dataset using linear and state-of-the-art non-linear models in a speech encoding/decoding and match/mismatch paradigm, providing benchmark scores for future research.