bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intensification of heat transfer in chaotic modes
Authors: Podvalny S L , Vasiljev E M 
Published: January 2021

Abstract
This paper presents the results of numerical modeling and comparative studies of the effectiveness of diffusion, convective, and turbulent heat transfer modes in a liquid layer. Here the heat transfer physical model was used which is typical for reactors with an internal energy source. Conditions for the continuity of the fluid flow and the equations of heat transfer, analytical and simulation models of these modes are obtained based on the Navier-Stokes equation. Quantitative characteristics have been found using the simulation model, confirming the expected efficiency indicators ratios of these processes in the course of heat transfer. Convective and turbulent heat transfer processes properties are analyzed as control objects basing on the Comsol Multiphysics modeling system. Recommendations have been obtained concerning the multi-alternative algorithms synthesis for automatic control of these processes. In particular, it is advisable to use the heat flux density as a control action, whereas the liquid particle velocity dispersion should be used as an adjustable value. Corresponding control system model demonstrated the efficiency of the proposed algorithms.
Autonomous spheroid formation by culture plate compartmentation
Authors: Fürsatz Marian , Gerges Peter , Wolbank Susanne , Nürnberger Sylvia 
Published: January 2021

Abstract
Scaffold-free 3D cell cultures (e.g. pellet cultures) are widely used in medical science, including cartilage regeneration. Their drawbacks are high time/reagent consumption and lack of early readout parameters. While optimisation was achieved by automation or simplified spheroid generation, most culture systems remain expensive or require tedious procedures. The aim of this study was to establish a system for resource efficient spheroid generation with additional early readout parameters. This was achieved by a new approach for spheroid generation via self-assembly from monolayer via compartmentation of cell culture surfaces utilising laser engraving (grid plates). The compartmentation triggered contraction and rolling up of the cell monolayer, finishing in condensation into a spheroid in human adipose-derived stem cell (ASC/TERT1) and human articular chondrocytes (hACs)-ASC/TERT1 co-cultures, when cultivated on grid plates under chondrogenic conditions. Plates with 1 and 3 mm grid size yielded stable diameters (about 140 µm and 300 µm, respectively). ASC/TERT1 spheroids fully formed within 3 weeks while co-cultures took 1–2 weeks, forming significantly faster with increasing hAC ratio (p < 0.05 and 0.01 for 1:1 and 1:4 ASC/TERT1:hAC ratio, respectively). Co-cultures showed slightly lower spheroid diameters, due to earlier spheroid formation and incomplete monolayer formation. However, this was associated with a more homogeneous matrix distribution in the co-culture. Both showed differentiation capacity comparable to standard pellet culture in (immune-)histochemistry and RT-qPCR. To assess usability for cartilage repair, spheroids were embedded into a hydrogel (fibrin), yielding cellular outgrowth and matrix deposition, which was especially pronounced in co-cultures. The herein presented novel cell culture system is not only a promising tool for autonomous spheroid generation with the potential of experimental and clinical application in tissue engineering, but also for the generation of ‘building blocks’ for subsequential biofabrication strategies such as bioprinting.
Neohesperidin alleviated pathological damage and immunological imbalance in rat myocardial ischemia-reperfusion injury via inactivation of JNK and NF-κB p65
Authors: Li Aihua , Zhang Xin , Luo Qiuping 
Published: January 2021

ABSTRACT
Neohesperidin (NEO) exerts antiviral, antioxidant, anti-inflammation, and antitumor effects in some diseases. The purpose of this study was to investigate the effect and mechanism of NEO on myocardial ischemia-reperfusion (I/R) injury. Results indicated that NEO suppressed the levels of serum inflammatory cytokines, myocardial damage markers, and oxidative stress markers, and increased the levels of antioxidant in myocardial I/R rats. NEO also inhibited cell apoptosis. Besides, NEO also inhibited the phosphorylation of c-Jun N-terminal kinases (JNK) and nuclear factor kappa B (NF-κB) p65. Furthermore, the protective effects of NEO on myocardial tissue damage, inflammatory cytokines, myocardial injury markers, oxidative stress markers, cell apoptosis, spleen, thymus and liver indices, and phagocytic indices were reversed by JNK activator and NF-κB activator, respectively. In conclusion, NEO alleviates myocardial damage, oxidative stress, cell apoptosis, and immunological imbalance in I/R injury via the inactivation of JNK and NF-κB, making NEO a potential agent for myocardial I/R therapy.
Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2
Authors: Cheng Liang , Han Xudong , Zhu Zijun , Qi Changlu , Wang Ping , Zhang Xue 
Published: January 2021

Abstract
Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.
Lysosome activation in peripheral blood mononuclear cells and prognostic significance of circulating LC3B in COVID-19
Authors: Fang Shisong , Zhang Lin , Liu Yingzhi , Xu Wenye , Wu Weihua , Huang Ziheng , Wang Xin , Liu Hui , Sun Ying , Zhang Renli , Peng Bo , Liu Xiaodong , Sun Xiao , Yu Jun , Chan Francis Ka Leung , Ng Siew Chien , Wong Sunny Hei , Wang Maggie Hai Tian , Gin Tony , Joynt Gavin Matthew , Hui David Shu Cheong , Feng Tiejian , Wu William Ka Kei , Chan Matthew Tak Vai , Zou Xuan , Xia Junjie 
Published: January 2021

Abstract
Coronavirus disease 2019 (COVID-19) has spread rapidly worldwide, causing significant mortality. There is a mechanistic relationship between intracellular coronavirus replication and deregulated autophagosome–lysosome system. We performed transcriptome analysis of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients and identified the aberrant upregulation of genes in the lysosome pathway. We further determined the capability of two circulating markers, namely microtubule-associated proteins 1A/1B light chain 3B (LC3B) and (p62/SQSTM1) p62, both of which depend on lysosome for degradation, in predicting the emergence of moderate-to-severe disease in COVID-19 patients requiring hospitalization for supplemental oxygen therapy. Logistic regression analyses showed that LC3B was associated with moderate-to-severe COVID-19, independent of age, sex and clinical risk score. A decrease in LC3B concentration &lt;5.5 ng/ml increased the risk of oxygen and ventilatory requirement (adjusted odds ratio: 4.6; 95% CI: 1.1–22.0; P = 0.04). Serum concentrations of p62 in the moderate-to-severe group were significantly lower in patients aged 50 or below. In conclusion, lysosome function is deregulated in PBMCs isolated from COVID-19 patients, and the related biomarker LC3B may serve as a novel tool for stratifying patients with moderate-to-severe COVID-19 from those with asymptomatic or mild disease. COVID-19 patients with a decrease in LC3B concentration &lt;5.5 ng/ml will require early hospital admission for supplemental oxygen therapy and other respiratory support.
Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations
Authors: Yan Fang-Fang , Gao Feng 
Published: January 2021

Abstract
Temperature plays a significant role in the survival and transmission of SARS-CoV (severe acute respiratory syndrome coronavirus) and SARS-CoV-2. To reveal the binding differences of SARS-CoV and SARS-CoV-2 receptor-binding domains (RBDs) to angiotensin-converting enzyme 2 (ACE2) at different temperatures at atomic level, 20 molecular dynamics simulations were carried out for SARS-CoV and SARS-CoV-2 RBD–ACE2 complexes at five selected temperatures, i.e. 200, 250, 273, 300 and 350 K. The analyses on structural flexibility and conformational distribution indicated that the structure of the SARS-CoV-2 RBD was more stable than that of the SARS-CoV RBD at all investigated temperatures. Then, molecular mechanics Poisson–Boltzmann surface area and solvated interaction energy approaches were combined to estimate the differences in binding affinity of SARS-CoV and SARS-CoV-2 RBDs to ACE2; it is found that the binding ability of ACE2 to the SARS-CoV-2 RBD was stronger than that to the SARS-CoV RBD at five temperatures, and the main reason for promoting such binding differences is electrostatic and polar interactions between RBDs and ACE2. Finally, the hotspot residues facilitating the binding of SARS-CoV and SARS-CoV-2 RBDs to ACE2, the key differential residues contributing to the difference in binding and the interaction mechanism of differential residues that exist at all investigated temperatures were analyzed and compared in depth. The current work would provide a molecular basis for better understanding of the high infectiousness of SARS-CoV-2 and offer better theoretical guidance for the design of inhibitors targeting infectious diseases caused by SARS-CoV-2.
A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation
Authors: Rakib Ahmed , Nain Zulkar , Sami Saad Ahmed , Mahmud Shafi , Islam Ashiqul , Ahmed Shahriar , Siddiqui Adnan Bin Faisul , Babu S M Omar Faruque , Hossain Payar , Shahriar Asif , Nainu Firzan , Emran Talha Bin , Simal-Gandara Jesus 
Published: January 2021

Abstract
Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic by the World Health Organization, and the situation worsens daily, associated with acute increases in case fatality rates. The main protease (Mpro) enzyme produced by SARS-CoV-2 was recently demonstrated to be responsible for not only viral reproduction but also impeding host immune responses. The element selenium (Se) plays a vital role in immune functions, both directly and indirectly. Thus, we hypothesised that Se-containing heterocyclic compounds might curb the activity of SARS-CoV-2 Mpro. We performed a molecular docking analysis and found that several of the selected selenocompounds showed potential binding affinities for SARS-CoV-2 Mpro, especially ethaselen (49), which exhibited a docking score of −6.7 kcal/mol compared with the −6.5 kcal/mol score for GC376 (positive control). Drug-likeness calculations suggested that these compounds are biologically active and possess the characteristics of ideal drug candidates. Based on the binding affinity and drug-likeness results, we selected the 16 most effective selenocompounds as potential anti-COVID-19 drug candidates. We also validated the structural integrity and stability of the drug candidate through molecular dynamics simulation. Using further in vitro and in vivo experiments, we believe that the targeted compound identified in this study (ethaselen) could pave the way for the development of prospective drugs to combat SARS-CoV-2 infections and trigger specific host immune responses.
Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations
Authors: Dérozier Sandra , Nicolas Pierre , Mäder Ulrike , Guérin Cyprien 
Published: January 2021

Abstract

Summary
Genoscapist is a tool to design web interfaces generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome datasets available for Bacillus subtilis and Staphylococcus aureus.

Availability and implementation
Websites and source code freely accessible at https://genoscapist.migale.inrae.fr
Environmentally relevant mixtures of phthalates and phthalate metabolites differentially alter the cell cycle and apoptosis in mouse neonatal ovaries†
Authors: Warner Genoa R , Meling Daryl D , De La Torre Kathy M , Wang Karen , Flaws Jodi A 
Published: January 2021

Abstract
Phthalates are a group of chemicals used as additives in various consumer products, medical equipment, and personal care products. Phthalates and their metabolites are consistently detected in humans, indicating widespread and continuous exposure to multiple phthalates. Thus, environmentally relevant mixtures of phthalates and phthalate metabolites were investigated to determine the effects of phthalates on the function of the ovary during the neonatal period of development. Neonatal ovaries from CD-1 mice were cultured with dimethyl sulphoxide (DMSO; vehicle control), phthalate mixture (0.1–100 μg/mL), or phthalate metabolite mixture (0.1–100 μg/mL). The phthalate mixture was composed of 35% diethyl phthalate, 21% di(2-ethylhexyl) phthalate, 15% dibutyl phthalate, 15% diisononyl phthalate, 8% diisobutyl phthalate, and 5% benzylbutyl phthalate. The phthalate metabolite mixture was composed of 37% monoethyl phthalate, 19% mono(2-ethylhexyl) phthalate, 15% monobutyl phthalate, 10% monoisononyl phthalate, 10% monoisobutyl phthalate, and 8% monobenzyl phthalate. After 96 h of culture, ovaries were harvested for histological analysis of folliculogenesis, gene expression analysis of cell cycle and apoptosis regulators, and immune staining for cell proliferation and apoptosis. The metabolite mixture significantly decreased the number and percentage of abnormal follicles (100 μg/mL) compared to controls. The metabolite mixture also significantly increased the expression of cell cycle inhibitors (100 μg/mL) and the antiapoptotic factor Bcl2l10 (10 μg/mL) compared to controls. The phthalate mixture did not significantly alter gene expression or follicle counts, but ovaries exposed to the phthalate mixture (0.1 μg/mL) exhibited marginally significantly increased apoptosis as revealed by DNA fragmentation staining. Overall, these data show that parent phthalates and phthalate metabolites differentially impact ovarian function.
Sequence meets function—microbiota and cardiovascular disease
Authors: Kim Myungsuk , Huda Md Nazmul , Bennett Brian J 
Published: January 2021

AbstractThe discovery that gut-microbiota plays a profound role in human health has opened a new avenue of basic and clinical research. Application of ecological approaches where the bacterial 16S rRNA gene is queried has provided a number of candidate bacteria associated with coronary artery disease and hypertension. We examine the associations between gut microbiota and a variety of cardiovascular disease (CVD) including atherosclerosis, coronary artery disease, and blood pressure. These approaches are associative in nature and there is now increasing interest in identifying the mechanisms underlying these associations. We discuss three potential mechanisms including: gut permeability and endotoxemia, increased immune system activation, and microbial derived metabolites. In addition to discussing these potential mechanisms we highlight current studies manipulating the gut microbiota or microbial metabolites to move beyond sequence-based association studies. The goal of these mechanistic studies is to determine the mode of action by which the gut microbiota may affect disease susceptibility and severity. Importantly, the gut microbiota appears to have a significant effect on host metabolism and CVD by producing metabolites entering the host circulatory system such as short-chain fatty acids and trimethylamine N-Oxide. Therefore, the intersection of metabolomics and microbiota research may yield novel targets to reduce disease susceptibility. Finally, we discuss approaches to demonstrate causality such as specific diet changes, inhibition of microbial pathways, and fecal microbiota transplant.
Distribution of Pest Wireworm (Coleoptera: Elateridae) Species in Alberta, Saskatchewan, and Manitoba (Canada)
Authors: van Herk Willem G , Vernon Robert S , Labun Ted J , Sevcik Mika H , Schwinghamer Timothy D 
Published: January 2021

Abstract
We present findings of a general survey of pest wireworms in Alberta, Saskatchewan, and Manitoba conducted from 2004 to 2019; the first such survey of the Canadian Prairie provinces since that published by Glen et al. (1943). Samples were collected from 571 farmland locations where crop damage from wireworms was observed or suspected, and a total of 5,704 specimens (3,548 larvae, 2,156 beetles) were identified. Most specimens (96.9%) were identified as Hypnoidus bicolor (3,278), Selatosomus aeripennis destructor (1,280), Limonius californicus (842), and Aeolus mellillus (125). This suggests that H. bicolor has replaced S. a. destructor as the predominant species and that the relative importance of L. californicus as a pest species has increased since earlier reports. Despite the relatively small number of specimens collected per location (approx. 10), H. bicolor and S. a. destructor, and S. a. destructor and L. californicus were frequently collected at or near the same location (within 1 km). We provide species records and incidence of co-occurrence at different spatial scales, discuss potential reasons for and implications of shifts in species composition, implications of species co-occurrence for managing wireworm pests in crop production, and outline pertinent research needs. A path analysis approach used to correlate incidence of the main species with various soil characteristics indicated that organic matter, cation exchange capacity, and water retention capacity all had a significant species-specific influence on wireworm presence.
Field Ecology and Food Suitability of Tarsonemus spp. (Acari: Tarsonemidae)
Authors: Gautam S G , Ouyang Y , Gu P , Grafton-Cardwell E E 
Published: January 2021

Abstract
Tarsonemus bakeri Ewing (Acari: Tarsonemidae) is a species of mite commonly associated with citrus in many countries including the United States. A short report in 1942 suggested this species is phytophagous, but it has not been reported as a pest in citrus or any other crop since then. A single survey of 78 orchards in three growing regions in California demonstrated that Tarsonemus spp. mites were only associated with leaf samples that had visible sooty mold. A seasonal population study in one citrus orchard showed that all life stages of Tarsonemus spp. were present year-round on leaves and fruit, with the population on fruit reaching a peak in December (59.7 ± 15.2 mites per fruit). Results from a food suitability study showed that the population declined sharply on both plastic and leaf substrate when the mites were not provided a supplementary food source. When supplementary food was provided in the form of Alternaria, honeydew, molasses, or combinations of these, mites survived and multiplied throughout the 29-d study, irrespective of the substrate. Tarsonemus bakeri were found on excised, decaying leaves collected from an orchard. These studies verify that Tarsonemus spp. are associated only with sooty mold in citrus orchards. T. bakeri populations cannot sustain themselves on leaf tissue alone, indicating that they are nondamaging to citrus and therefore need not be considered a phytosanitary concern by importing countries.
Risk analysis for patients with a functionally univentricular heart after systemic-to-pulmonary shunt placement
Authors: Ide Yujiro , Tachimori Hisateru , Hirata Yasutaka , Hirahara Norimichi , Ota Noritaka , Sakamoto Kisaburo , Ikeda Tadashi , Minatoya Kenji 
Published: January 2021

Abstract

OBJECTIVES
To investigate risk factors for mortality after systemic-to-pulmonary (SP) shunt procedures in patients with a functionally univentricular heart using the Japan Cardiovascular Surgery Database registry.

METHODS
Clinical data from 75 domestic institutions were collected. Overall, 812 patients with a functionally univentricular heart who underwent initial SP shunt palliation were eligible for analysis. Patients with pulmonary atresia with an intact ventricular septum and patients with a SP shunt as part of the Norwood procedure were excluded. Risk factors for 30- and 90-day mortalities were analysed using a logistic regression model.

RESULTS
Median age and body weight at SP shunt placement were 41 days and 3.6 kg, respectively. Modified Blalock–Taussig shunt, central shunt and other types of SP shunts were applied in 689 (84.9%), 94 (11.8%) and 30 (3.7%) patients, respectively. Cardiopulmonary bypass was utilized in 410 patients (51%) for 128 min (median, 19–561). There were 411 isolated SP shunt procedures. Median hospital stay was 27 days, and 742 (91.4%) patients were discharged. The 30- and 90-day mortality rates were 3.4% and 6.0%, respectively. Placement of a central shunt was identified as a risk factor for 30-day mortality, while lower body weight, preoperative ventilator support, right atrial isomerism and coexistence of major aortopulmonary collateral arteries and an unbalanced atrioventricular septal defect were identified as risk factors for 90-day mortality.

CONCLUSIONS
SP shunt carries a high mortality rate in patients with a functionally univentricular heart when it is performed in smaller patients with complex cardiac anomalies.