bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and novel Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species
Authors: Rekadwad Bhagwan , Li Wen-Jun , PD Rekha 
Published: July 2021

Abstract
ObjectivesTo decipher the diversity of unique ectoine-coding housekeeping genes in the genus Halomonas.ResultsIn Halomonas, 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid has a crucial role as a stress-tolerant chaperone, a compatible solute, a cell membrane stabilizer, and a reduction in cell damage under stressful conditions. Apart from the current 16S rRNA biomarker, it serves as a blueprint for identifying Halomonas species. Halomonas elongate 1H9 was found to have 11 ectoine-coding genes. The presence of a superfamily of conserved ectoine-coding among members of the genus Halomonas was discovered after genome annotations of 93 Halomonas spp. As a result of the inclusion of 11 single copy ectoine coding genes in 32 Halomonas spp., genome-wide evaluations of ectoine coding genes indicate that 32 Halomonas spp. have a very strong association with Halomonas elongata 1H9, which has been proven evidence-based approach to elucidate phylogenetic relatedness of ectoine-coding child taxa in the genus Halomonas. Total 32 Halomonas species have a single copy number of 11 distinct ectoine-coding genes that help Halomonas spp., that produce ectoine under stressful conditions. Furthermore, the existence of the Universal stress protein (UspA) gene suggests that Halomonas species developed directly from primitive bacteria, highlighting the role of Halomonas species in evolutionary terms.
Comparison of Single and Repeated Dosing of Anti-Inflammatory Human Umbilical Cord Mesenchymal Stromal Cells in a Mouse Model of Polymicrobial Sepsis
Authors: Fazekas Barbara , Alagesan Senthilkumar , Watson Luke , Ng Olivia , Conroy Callum M. , Català Cristina , Andres Maria Velascode , Negi Neema , Gerlach Jared Q. , Lozano Francisco , Elliman Stephen J. , Griffin Matthew D. 
Published: July 2021

Abstract
Mesenchymal stromal cells (MSCs) ameliorate pre-clinical sepsis and sepsis-associated acute kidney injury (SA-AKI) but clinical trials of single-dose MSCs have not indicated robust efficacy. This study investigated immunomodulatory effects of a novel MSC product (CD362-selected human umbilical cord-derived MSCs [hUC-MSCs]) in mouse endotoxemia and polymicrobial sepsis models.Initially, mice received intra-peritoneal (i.p.) lipopolysaccharide (LPS) followed by single i.p. doses of hUC-MSCs or vehicle. Next, mice underwent cecal ligation and puncture (CLP) followed by intravenous (i.v.) doses of hUC-MSCs at 4 hours or 4 and 28 hours. Analyses included serum/plasma assays of biochemical indices, inflammatory mediators and the AKI biomarker NGAL; multi-color flow cytometry of peritoneal macrophages (LPS) and intra-renal immune cell subpopulations (CLP) and histology/immunohistochemistry of kidney (CLP).At 72 hours post-LPS injections, hUC-MSCs reduced serum inflammatory mediators and peritoneal macrophage M1/M2 ratio. Repeated, but not single, hUC-MSC doses administered at 48 hours post-CLP resulted in increased survival, lower serum concentrations of inflammatory mediators, lower plasma NGAL and reversal of sepsis-associated depletion of intra-renal T-cell and myeloid cell subpopulations. Hierarchical clustering analysis of all 48-hour serum/plasma analytes demonstrated partial co-clustering of repeated-dose hUC-MSC CLP animals with a Sham group but did not reveal a distinct signature of response to therapy. It was concluded that repeated doses of CD362-selected hUC-MSCs are required to modulate systemic and local immune/inflammatory events in polymicrobial sepsis and SA-AKI. Inter-individual variability and lack of effect of single dose MSC administration in the CLP model are consistent with observations to date from early-phase clinical trials.
A Spatial Model of a Vibrating Conveyor Taking Into Consideration The Self-Synchronisation Process of Inertial Vibrators. Analysis of The Effect of The Layout of The vibrators On The Operation of The Conveyor
Authors: Cieplok Grzegorz , Sieńko Rafał 
Published: July 2021

Abstract
This article presents a spatial model of a vibrating conveyor supported on steel-elastomer vibration isolators and vibrated by two inertial vibrators as well as the results of analyses of the effect of the layout of vibrators on the operation of the conveyor. The displacement of the line of action of the resultant of the forces of the vibrators beyond the centre of mass of the machine body manifests itself in the departure of the machine body from the desirable rectilinear motion and problems associated with the unevenness of material movement. The model presented in this article takes into account an extremely important coupling between vibrators and the body of the machine, which is responsible for the process of self-synchronisation of the vibrators and the correctness of machine operation. The results of theoretical analyses presented in this paper were verified by laboratory tests and reference to observations based on the authors’ industrial experience.
Dynamic heterogeneity in active glass-forming liquids is qualitatively different compared to its equilibrium behaviour
Authors: Paul Kallol , Nandi Saroj Kumar , Karmakar Smarajit 
Published: July 2021

Abstract
Activity driven glassy dynamics is ubiquitous in collective cell migration,intracellular transport, dynamics in bacterial and ants colonies as well as artificially driven synthetic systems such as vibrated granular materials, etc. Active glasses are hitherto assumed to be qualitatively similar to their equilibrium counterparts at a suitably defined effective temperature, ff. Combining large-scale simulations with analytical mode-coupling theory for such systems, we show that, in fact, an active glass is qualitatively different from an equilibrium glassy system. Although the relaxation dynamics can be similar to an equilibrium system at a ff, effects of activity on the dynamic heterogeneity (DH), which has emerged as a cornerstone of glassy dynamics, is quite nontrivial and complex. In particular, active glasses show dramatic growth of DH, and systems with similar relaxation time and ff can have widely varying DH. Comparison of our non-equilibrium extended mode-coupling theory for such systems with simulation results show that the theory captures the basic characteristics of such systems. Our study raises fundamental questions on the supposedly central role of DH in controlling the relaxation dynamics in a glassy system and can have important implications even for the equilibrium glassy dynamics.
P38α Deficiency in Macrophages Ameliorates Murine Experimental Colitis by Regulating Inflammation and Immune Process
Authors: Chen Wei , Liang Rui , Yi Youcai , Chen Xiaoyu , Fan Huining , Zhu Jin-Shui , Zhang Jing 
Published: July 2021

Abstract
Introduction: P38α is a mitogen-activated protein kinase (MAPK) that mediates inflammatory responses. P38α alterations have been associated with the inflammation-related diseases. However, the role of macrophages-derived p38α in dextran sulfate sodium (DSS)-induced murine experimental colitis remains unclear.Objectives: We characterized the role of macrophages-derived p38α in DSS-induced colitis.Methods: The expression of macrophage-derived p38α in human colitis and normal tissues was measured by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) analysis. Macrophage-specific p38α knockout (p38αΔMφ) and wild type (WT) mice administrated by 3% DSS were used to establish experimental colitis. The alterations in inflammatory cytokines, intestinal epithelial barrier, cell proliferation and cell apoptosis between p38αΔMφ and WT groups were determined by IHC, immunofluorescence (IF), TdT-mediated dUTP Nick-End Labeling (TUNEL) and Western blot analyses. The enriched pathways between p38αΔMφ and WT groups were identified by RNA-seq and KEGG analysis. SB203580 and BIRB796 as the p38 MAPK inhibitors were used to treat DSS-induced colitis. Results: p38α was co-localized with CD68 in the cytoplasm and their co-expression indicated an increased level in colitis tissues as compared with the normal tissues. P38α deficiency in macrophages was sufficient to suppress the exacerbated clinical symptoms and inflammation responses in experimental colitis, followed by reducing cytokine release, increasing MUC-2 and Claudin-2 secretion and promoting colonic mucosa repair. Further investigations validated that the immune process-related factors such as Lgals9, Rtp4, Ddx60, Nlrp1b, Hsh2d, Oas2 and Oas3 were upregulated in colon tissues from p38αΔMφ group as compared with the WT group. Inhibition of p38 MAPK attenuated DSS-induced colitis. Conclusion: Our findings demonstrated that p38α deficiency in macrophages ameliorated murine experimental colitis by regulating inflammation and immune process.
Supratotal Resection of Glioblastoma Allows Better Survival Outcomes than Gross Total Resection
Authors: Baik Seung Hyun , Kim So Yeon , Na Young Chul , Cho Jin Mo 
Published: July 2021

Abstract
Objective: Supra-total resection (SupTR) of glioblastoma allows superior long-term disease control and increases overall survival. On the other hand, aggressive conventional approaches, including gross total resections (GTR), are limited by the impairment risk of adjacent eloquent areas, which may cause severe postoperative functional morbidity. This study aimed to analyze institutional cases with respect to the potential survival benefits of additional resection, including lobectomy, as a paradigm for SupTR in patients of glioblastoma.Methods: Between 2014 and 2018, 15 patients with glioblastoma underwent GTR and additional lobectomy at our institution. The postoperative Karnofsky performance score (KPS), progression-free survival (PFS), and overall survival (OS) were analyzed for the patients.Results: Patients with SupTR showed significantly prolonged PFS and OS. The median PFS and OS values for the entire study group were 33.5 months (95% confidence intervals [CI]: 18.5–57.3 months) and 49.1 months (95% CI: 24.7–86.6 months), respectively. Multivariate analysis revealed that O6-DNA-methylguanine methyltransferase (MGMT) promoter methylation status was the only predictor for both superior PFS (p = 0.03, OR 5.7, 95% CI 1.0–49.8) and OS (p = 0.04, OR 6.5, 95% CI 1.1–40.2). There was no significant difference between the pre- and post-operative KPS scores. Conclusions: Our results strongly suggest that SupTR with lobectomy allows superior PFS and OS without negatively affecting the patient performance.
Investigation of Jervol Water Types Properties Effects on Underwater Optical Wireless OCDMA System Performances for Different Modulation Techniques
Authors: Kandouci Chahinaz 
Published: July 2021

Abstract
In this paper, an analytical evaluation of direct detection OCDMA system using zero cross correlation codes is presented in an underwater wireless optical channel (UWOC). Performances were evaluated by varying the main simulation parameters (range,transmitted power,number of users and inclination angle) considering different modulation techniques for different water types (categorized according to Jerlov classification).
A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase
Authors: Canard Bruno , Shannon Ashleigh , Fattorini Veronique , Sama Bhawna , Selisko Barbara , Feracci Mikael , Falcou Camille , Gauffre Pierre , El-Kazzi Priscila , Decroly Etienne , Alvarez Karine , Eydoux Cecilia , Guillemot Jean-Claude , Moussa Adel , Good Steven , Colla Paolo La , Lin Kai , Sommadossi Jean-Pierre , Zhu Yingxao , Yan Xiaodong , Shi Hui , Ferron Francois , Delpal Adrien 
Published: July 2021

Abstract
A worldwide effort is ongoing to discover drugs against the Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2), which has so far caused >3.5 million fatalities (https://covid19.who.int/). The virus essential RNA-dependent RNA polymerase complex is targeted by several nucleoside/tide analogues whose mechanisms of action and clinical potential are currently evaluated. The guanosine analogue AT-527, a double prodrug of its 5'-triphosphate AT-9010, is currently in phase III clinical trials as a COVID19 treatment. Here we report the cryo-EM structure at 2.98 Å resolution of the SARS-CoV-2 nsp12-nsp7-(nsp8)2 complex with RNA showing AT-9010 bound at three sites of nsp12. At the RdRp active-site, one AT-9010 is incorporated into the RNA product. Its 2'-methyl group prevents correct alignment of a second AT-9010 occupying the incoming NTP pocket. The 2'-F, 2'-methyl 3'-OH ribose scaffold explains the non-obligate RNA chain-termination potency of this NA series for both HCV NS5 and SARS-CoV RTCs. A third AT-9010 molecule 5'-diphosphate binds to a coronavirus-specific pocket in the nsp12 N-terminus NiRAN domain, a SelO pseudo-kinase structural and functional homologue. This unique binding mode impedes NiRAN-mediated UMPylation of SARS-CoV-2 nsp8 and nsp9 proteins. Our results suggest a mechanism of action for AT-527 in line with a therapeutic use for COVID19.
Characteristics and Spatial Influencing Factors of Natural Regeneration within Aquaculture ponds in a Mangrove Forest
Authors: xin kun , Sheng Nong , Liao Baowen , Xiong Yanmei , Jiang Zhongmao , Zhang Yun 
Published: July 2021

Abstract
Regeneration is an important component of community succession and understanding regeneration dynamics is essential for forest protection and recovery management. Mangroves are distributed along coastlines and this unique habitat has resulted in very different regeneration process. This study took Dongzhaigang mangrove forest in Hainan, China as the study area, considered the 10 years regeneration process in 8 abandoned aquaculture ponds, and the spatial factors that influence the regeneration process are analyzed. The objectives were to: a) investigate the natural dynamics of the mangrove regeneration process in abandoned ponds, b) determine the main spatial factors affecting the natural regeneration process. The results showed that the number of species and individuals showed a tendency to initially rise and then decline, with the maximum occurring at 6–8 years. The results of a diversity index showed an initial rise, with stabilization then occurring over a 8 year period. Aegiceras corniculatum and Sonneratia apetala were typical pioneer mangrove species in the study area, while Bruguiera sexangula and Kandelia obovata were representative species of late regeneration period. Spatial factors, including pond area and shape, relative elevation, distance to a tidal creek and surrounding trees area played important roles in the regeneration of mangrove in ponds. Finally, the study considered the current situation regarding mangrove restoration in China and suggested that natural regeneration of mangroves is a good management option.
A High-Frequency Sound based PGC Demodulation Scheme for Fiber Optics Hydrophone
Authors: Shi Yunjie , Yin Mengke , Zhu Zijue , Wang Shun , Niu Panting , Dong Yuming , Zhang Liang 
Published: July 2021

Abstract
In the research field of fiber-optic hydrophone, the performance of demodulation scheme is crucial. In this work, a phase-generated-carrier (PGC) demodulation scheme based on high-frequency sound source is proposed. Highfrequency acoustic signal from the external sound source is applied to the fiber-optic hydrophone to achieve phase modulation of the interference signal instead of the piezo-electrical transducer (PZT) or frequency-modulated laser. It possesses the merits of low system complexity and low cost. Through the acoustic detection experiment, we achieve demodulation of acoustic signal at frequency varying from 300 Hz to 800 Hz, and the signal-to-noise ratio (SNR) is higher than 45 dB. Furthermore, the proposed scheme is successfully applied to time division multiplexing (TDM) experiment.
Bacterial and Fungal Profile, Drug Resistance Pattern and Associated Factors of Isolates Recovered From Blood Samples of Patients Referred to Ethiopian Public Health Institute: Cross-Sectional Study
Authors: Tsegaye Etsehiwot Adamu , Teklu Dejenie Shiferaw , Bonger Zelalem Tazu , Negeri Abebe Assefa , Bedada Tesfaye Legesse , Bitew Adane 
Published: July 2021

Abstract
Background
Blood stream infections are serious infections that usually induce prolongation of hospital stay, morbidity and mortality in several countries including Ethiopia. The aim of this study was to determine bacterial and fungal profile, their drug resistance patterns, and risk factors associated with blood stream infections.
Methods
A cross sectional study design was conducted from February 23 to June 23, 2020 at Ethiopian public health. A structured questionnaire was used to collect data on socio-demographic factors and clinical conditions. Blood specimens were analyzed using standard microbiological techniques. Antimicrobial susceptibility tests were performed using Kirby-Bauer disc diffusion technique and Vitek compact 2. Simple and multiple logistic regressions were used to assess the potential risk factors.
Results
A total of 175 pathogens isolated from 346 blood specimens. Of these, 60% Gram-negative bacteria, 30.86% Gram-positive bacteria and 9.14% fungal isolates were identified. Burkholderia cepacia and Coagulase negative staphylococcus were the predominant pathogen among Gram-negative and Gram-positive bacteria respectively. Among fungus, Candidia krusei (56.25%) was the most predominant isolate. The highest proportions of antibacterial resistance were observed among 3rd generation cephalosporin and penicillin. Most fungal isolates expressed resistance to fluconazole. Sex (p = 0.007), age (p < 0.001) and use of invasive medical devices (p = 0.003) were identified as risk factors for bacterial blood stream infections.
Conclusion
The study showed high prevalence of blood stream infection was due to Burkholderia cepacia and non-Candidia albicans spp. This finding alarming ongoing investigation of blood stream infection is important for recognizing future potential preventive strategies including environmental hygiene and management of comorbid medical diseases to reduce the problem.
Unconventional reconciliation path for quantum mechanics and general relativity
Authors: Yuguru Samuel 
Published: July 2021

Abstract
Physics in general is successfully governed by quantum mechanics at the microscale and principles of relativity at the macroscale. Any attempts to unify them using conventional methods have somewhat remained elusive for nearly a century up to the present stage. Here in this study, a classical gedanken experiment of electron-wave diffraction of a single slit is intuitively examined for its quantized states. A unidirectional monopole pair (MP) field as quanta of the electric field is pictorially conceptualized into 4D space-time. Its application towards quantum mechanics and general relativity appears consistent with existing knowledge in physics. This considers a multiverse of MP models at a hierarchy of scales. Einstein’s gravity is then defined to be of circular acceleration in time reversal mode to an overarching MP field precessing into forward time. Such descriptions provide a credible intuitive tool for physics applications in general. It can be further assessed using conventional methods, perhaps in incremental steps and this warrants further investigations.
A DTMEs-Based Digital Twin System Construction Method For Smart Factory
Authors: Xia Luyao , Jianfeng Lu , Zhang Hao , Xu Mengying , Li Zhaojia , Wang Sheng 
Published: July 2021

Abstract
Many enterprises have built their own digital twin factory model for physical factory planning, simulation optimization and real-time monitoring. However, the digital twin system, which has a single field, a short time cycle and unsinkable service, cannot fully reflect the interaction and integration of the physical and information world required by intelligent manufacturing. Therefore, the research on the construction method of the smart factory digital twin system with cross-domain and multi-model has an important influence on the application of smart manufacturing. In view of the above problems, this paper proposes the concept and composition of digital twin manufacturing ecosystem (DTMEs) based on the requirements and characteristics of product lifecycle, and analyzes the construction requirements of DTMEs for factory digital twin system, product digital twin system and supply chain digital twin system from the perspective of lifecycle. Finally, the smart factory digital twin system architecture is applied to the digital and intelligent upgrading of the hydraulic cylinder factory. The experimental results show that the intelligent improvement of the hydraulic factory, the reduction of Work-in-process inventory and the advance of delivery time, and prove the feasibility and effectiveness of the smart factory digital twin system.
A multi-factor trafficking site on the spliceosomal remodeling enzyme, BRR2, recruits C9ORF78 to regulate alternative splicing
Authors: Bergfort Alexandra , Preussner Marco , Kuropka Benno , Ilik İbrahim , Hilal Tarek , Weber Gert , Freund Christian , Aktas Tugce , Heyd Florian , Wahl Markus 
Published: July 2021

Abstract
The complete inventory of regulatory factors in human spliceosomes remains unknown, and many flexibly bound components are not revealed in present spliceosome structures. The intrinsically unstructured C9ORF78 protein was detected in C complex spliceosomes but is not contained in present spliceosome structures. We found a tight interaction between C9ORF78 and the key spliceosome remodeling factor, BRR2, in a large-scale yeast two-hybrid screen, validated by targeted in vitro assays. Affinity purification/mass spectrometry and RNA UV-crosslinking analyses identified several additional C9ORF78 interactors in spliceosomes. High-resolution cryogenic electron microscopy structures revealed how C9ORF78 and the spliceosomal B complex protein FBP21 wrap around the C-terminal helicase cassette of BRR2 in a mutually exclusive manner. Knock-down of C9ORF78 led to global alternative splicing changes, including a substantial usage of alternative NAGNAG 3’-splice sites, at least in part dependent on BRR2. Comparison of our structure to C* complex spliceosomes shows that C9ORF78 could contact several detected interactors from its BRR2 “home base”, in particular the RNA helicase PRPF22, a suggested 3’-splice site regulator. Together our data firmly establish C9ORF78 as a novel, late-stage splicing regulatory protein that takes advantage of a multi-factor trafficking site on BRR2, providing one explanation for the suggested, but puzzling, roles of BRR2 during splicing catalysis and alternative splicing.