bluuebunny/crossref_metadata_2025 huggingface dataset:
A Visual Framework of Meta Genomic Analysis on Variations of Whole SARS-CoV-2 Sequences
Authors: Zheng Jeffrey , Liu Jianzhong
Published: September 2020

The worldwide outbreak of the COVID-19 has become a global pandemic resulting in millions of confirmed cases and hundreds of thousands of deadths. To face such a global crisis, bioinformatics has played a key role in the diagnosis, follow-up, prognosis and treatment of COVID-19-infected patients.A novel bioinformatic tool for metagenomic analysis of whole genomes is proposed in this paper that is composed of three projections: global, clustering and genomic index. For each projection, key modules are described. Global projection provides various combinatorial distributions for a whole genome of N length, and the m-mer scheme partitions this sequence as M segments on 1D, 2D and 3D density matrices for multiple projections. Clustering projections based on distributions from global projections make special filters extract specific parts as probability eigenvalues.Genomic index projection provides comprehensive technologies under the theory of information entropy, and a list of measuring entropies are included, such as combinatorial entropy CE, integrated entropy IE, mean entropy ME and topological entropy TE. Three projections provide unified information to describe complicated functions, internal structures and refined variations for multiple groups of SARSCoV-2 on variations and other genomes in comparisons.The outputs of three projections are illustrated on variant maps to support category, clustering, classification and establishing root activities for refined quantitative operations from bottom to top strategy.
Reduction of arsenic oxoanion toxicity from contaminated water by adsorption onto iron impregnated biochar
Authors: Salmani Mohammad Hossien , Abedi Mohammad , Mozaffari Sayed Ahmad , Salmani Mohammad Javad
Published: September 2020

Several ways have systematically been employed to modify carbons for removing heavy metal from contaminated solution. In the present study, Fe impregnated pomegranate peel carbon (Fe-PPC) as a green adsorbent was prepared by addition of Fe3+ions into the pomegranate peel followed carbonization. Stability of iron on PPC was examined by releasing of Fe ions in aqueous solution at the pH range of 2–10. The effect of contact time, variable pH, and initial concentration were studied in the adsorption of arsenite and arsenate anions by Fe-PPC. Maximum removal of arsenite and arsenate anions were observed in the pH range of 5–6 and 9–11 respectively which were 76.3% and 100%. The elemental analysis and characterization of As -FePPC were performed by energy dispersive X-ray analysis (EDX) and BET. The adsorption rate (ν0) value indicated that the initial rates are suitable for arsenic anions adsorption on Fe-PPC in aqueous solution. The more than one mechanism was governed by the adsorption arsenate and was chemisorption, while the physical adsorption had the more contribution to the arsenite adsorption.
Corpus callosum in COVID-19 cytokinopathy, an update
Authors: Alambyan Vilakshan , Zhang Yan , Devenney Brooke , Prabhu Aparna , Newman George
Published: September 2020

The corpus callosum (CC) connects frontal, parietal, occipital and temporal cortices in the brain. We report a disconnection syndrome as a manifestation of coronavirus disease 2019 (COVID-19) encephalopathy. Like prior coronaviridae, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affects the brain over a spectrum of injury. Present communication is the first description of white matter involvement confined to CC’s commissural fibers in their entirety. Until case registries, longitudinal studies and animal models clarify any direct neurotropism of SARS-CoV-2; this case is consistent with recent biological evidence suggesting a cytokine mediated excitotoxic injury concomitant with the severity of infection.
Severe volcanic SO2 exposure and respiratory morbidity in the Icelandic population – a register study
Authors: Carlsen Hanne Krage , Valdimarsdóttir Unnur , Bríem Haraldur , Dominici Francesca , Finnbjornsdottir Ragnhildur Gudrun , Jóhannsson Thorsteinn , Aspelund Thor , Gislason Thorarinn , Gudnason Thorolfur
Published: September 2020

Background The Holuhraun volcanic eruption September 2014 to February 2015 emitted large amounts of sulfur dioxide (SO2). The aim of this study was to determine the association between volcanic SO2 gases on general population respiratory health some 250 km from the eruption site, in the Icelandic capital area. Methods Respiratory health outcomes were: asthma medication dispensing (AMD) from the Icelandic Medicines Register, medical doctor consultations in primary care (PCMD) and hospital emergency department visits (HED) in Reykjavík (population: 215 000) for respiratory disease from 1 January 2010 to 31 December 2014. The associations between daily counts of health events,and daily mean SO2 concentration and high SO2 levels (24-hour mean SO2>125µg/m3) were analyzed using generalized additive models. Results After the eruption began, AMD was higher than before (129.4 vs. 158.4 individuals per day, p<0.05). In regression analysis adjusted for other pollutants, SO2 was associated with estimated increases in AMD by 0.99% (95% CI 0.39 - 1.58%) per 10 µg/m3 at lag 0-2, in PCMD for respiratory causes 1.26% (95% CI 0.72 - 1.80%) per 10 µg/m3 SO2 at lag 0-2, and in HED by 1.02% (95% CI 0.02- 2.03%) per 10 µg/m3 SO2 at lag 0-2. For days over the health limit, the estimated increases were 10.9% (95% CI 2.1-19.6%), 17.2% (95% CI 10.0-24.4%) for AMD and PCMD. Dispensing of short-acting medication increased significantly by 1.09% (95% CI 0.49-1.70%%), and PCMD for respiratory infections and asthma and COPD diagnoses and increased significantly by 1.12% (95% CI 0.54-1.71%) and 2.08% (1.13-3.04%).Conclusion High levels of volcanic SO2 are associated with increases in dispensing of AMD, and health care utilization in primary and tertiary care. Individuals with prevalent respiratory disease may be particularly susceptible.
A conceptional framework of spatial epidemiological research for natural focus diseases, a perspective of disaster science
Authors: Zhao An , Li Rui
Published: September 2020

Objective: To develop a new spatial epidemiological research framework, which would overcome the problems of multicollinearity among the independent variables and the difficulty for outcome to give an explicit explanation for disease transmission mechanism in the current spatial epidemiological methods.Methods: Comparison of schistosomiasis transmission process with disaster process; Imitation with and import of disaster risk assessment methodology into spatial epidemiological research. Results: A universal spatial epidemiological research framework was presented for the natural focal disease infection risk prediction. This new approach was expected to be extended to the risk assessment of environmental pollution-incurred public health problems. The GIS-based spatialization methods of the factors concerned in the framework were suggested as well. Conclusion: The new established spatial epidemiological framework presented has strong universality and shows many advantages in the field of public health.
Plant Electrophysiological Information Manifests the Composition and Nutrient Transport Characteristics of Membrane Protein
Authors: Zhang Cheng , Wu Yanyou , Su Yue , Xing Deke , Fang Lei
Published: September 2020

Background: Almost all life activities of plants are accompanied by electrophysiological information. Plant electrical parameters are considered to be the fastest response to environment.Results: In this study, the theoretically intrinsic relationships between the clamping force and leaf resistance (R), capacitive reactance (Xc) and inductive reactance (XL) were revealed as 3-parameter exponential decay based on bioenergetics for the first time. The intrinsic resistance (IR), intrinsic capacitive reactance (IXc) and intrinsic inductive reactance (IXL) in plant leaves were monitored via these relationships for the first time, and the nutrient transport capacity (NTC) in plant cells based on IR, IXc and IXL was first defined. The results indicate that IXc and IXL could be used to manifest the composition of surface and binding proteins in cell membrane, plant with high crude proteins and crude ash had higher NTC, and which accurately revealed the nutrient transport strategies in tested plants. Conclusions: This study highlights that plant electrophysiological information could effectively manifest the composition and nutrient transport characteristics of membrane protein in plant cells.
The role of knee arthroscopy in managing common soft-tissue complications after total knee arthroplasty: a retrospective case series study
Authors: Hou Yunfei , Gao Jiaxiang , Chen Jian , Lin Jianhao , Ni Lei , Sun Tiezheng , Jiang Jun
Published: September 2020

Background
To investigate the therapeutic efficacy of arthroscopy in 3 common soft-tissue complications, peripatellar impingement, arthrofibrosis and generalized synovitis, after total knee arthroplasty (TKA).
Methods
A retrospective review of patients undertaking arthroscopy for peripatellar impingement(PI), arthrofibrosis(AF) and generalized synovitis(GS) was conducted. Outcome measures included range of motion (ROM), and Knee Society Score (KSS). Intraoperative findings, surgical procedures and the existence of recurrence, prosthesis revision and/or complications were recorded. Paired t test, Fisher exact test, Kruskal-Wallis test and post hoc analysis with Bonferroni correction were used to for statistical evaluation.
Results
74 patients, including 35 patients peripatellar impingement, 25 with arthrofibrosis and 14 with generalized synovitis, with a mean age of 66.1 years were analyzed. The mean follow up(FU) duration was 81.3 months. Overall, patients acquired improvement on ROM from 81.7° to 96.8° (p < 0.05), on KSS knee score from 64.2 to 78.7 (p < 0.05), and on KSS function score from 61.1 to 77.3 (p < 0.05) postoperatively. Patients in all 3 groups had improvements on ROM (p < 0.05), KSS knee (p < 0.05) and KSS function score (p < 0.05). The overall recurrence rate was 22.9% (17/74) and revision rate was 14.9% (11/74). There were statistical differences on symptoms recurrence rate and the prosthesis revision rate among groups (p < 0.05). PI group had significant less symptom recurrence rate and revision rate of 11.4% and 8.6% respectively (p < 0.017), while GS group had the greatest recurrence rate (42.9%) and revision rate (35.7%) respectively (p < 0.017). There were 4 perioperative complications, including 1 acute myocardial infarction and 3 periprosthetic joint infections.
Conclusions
In the setting of symptomatic TKA, arthroscopic intervention could provide clinical improvement in most cases at an average 81.3 months follow-up. Patients with PI had the best outcome while patients with GS had the worst.
Data-Driven Treatment Pathways Mining for Early Breast Cancer Using cSPADE Algorithm and System Clustering
Authors: Yang Qing , Luo Ting , Zhang Wei , Zhong Xiaorong , He Ping , Zheng Hong
Published: September 2020

Background: Due to the multidimensional, multilayered, and chronological order of the cancer data in this study, it was challenging for us to extract treatment paths. Therefore, it was necessary to design a new data mining scheme to effectively extract the treatment path of breast cancer. To determine whether the cSPADE algorithm and system clustering proposed in this study can effectively identify the treatment pathways for early breast cancer. Methods: We applied data mining technology to the electronic medical records of 6891 early breast cancer patients to mine treatment pathways. We provided a method of extracting data from EMR and performed three-stage mining: determining the treatment stage through the cSPADE algorithm → system clustering for treatment plan extraction → cSPADE mining sequence pattern for treatment. The Kolmogorov-Smirnov test and correlation analysis were used to cross-validate the sequence rules of early breast cancer treatment pathways.Results: We unearthed 55 sequence rules for early breast cancer treatment, 3 preoperative neoadjuvant chemotherapy regimens, 3 postoperative chemotherapy regimens, and 2 chemotherapy regimens for patients without surgery. Through 5-fold cross-validation, Pearson and Spearman correlation tests were performed. At the significance level of P <0.05, all correlation coefficients of support, confidence and lift were greater than 0.89. Using the Kolmogorov-Smirnov test, we found no significant differences between the sequence distributions.Conclusions: The cSPADE algorithm combined with system clustering can achieve hierarchical and vertical mining of breast cancer treatment models. By uncovering the treatment pathways of early breast cancer patients by this method, the real-world breast cancer treatment behavior model can be evaluated, and it can provide a reference for the redesign and optimization of the treatment pathways.
Identification of QTL and QEI for Fiber-related Traits in Gossypium Hirsutum L. 
Authors: Sharkh Abdalla , Teng Zhonghua , Yang Peng , Ma Junrui , Athanase Nsabiyumva , Wang Wenwen , Liu Xueying , Zhang Zhengsheng
Published: September 2020

Background Cotton is one of the most important cash crops in the world, depending on fiber quality, yield, seed oil and protein content. Identifying QTL for fiber related and other agronomic traits will facilitate the genetic improvement in cotton. Results In this study, forty-seven QTL for fiber related traits were identified across four different environments and six of these QTL were detected in more than one environment, including two for lint percentage (qLP-D03-1 and qLP-D09-1), two for fiber length (qFL-A07-2 and qFL-D11-1), and two for fiber micronaire (qFM-A08-1 and qFM-D11-1), respectively. Four QTL clusters contained 12 QTL were distributed on four chromosomes including two in At subgenome and two in the Dt subgenome. Moreover, thirteen QTL by environment interactions (QEI) were recognized, including one for lint percentage, five for fiber length, three for fiber strength, two for fiber micronaire, one for fiber uniformity and one for fiber elongation, respectively. ConclusionSix QTL were detected in more than one environment and two environmentally stable QTL (qLP-D03-1 and qFM-A08-1) interacted significantly environment. The QTL detected in more than one environment could be useful for further fine-mapping and marker assisted selection in cotton.
Cross-sectional Study of the Ambulance Transport Between Healthcare Facilities With Medical Support via Telemedicine: Easy, Effective, Low-cost, and High-security Tool
Authors: Pedrotti Carlos , Accorsi Tarso A. D. , Amicis Karine De , Filho Jose R. de O. Silva , Morbeck Renata A. , Cordioli Eduardo
Published: September 2020

Background: Feasibility and safety of ambulance transport between healthcare facilities with medical support exclusively via telemedicine is unknown. Methods: This was a retrospective study with a single telemedicine center reference for satellite emergency departments of the same hospital. Study population was all critically ill patients admitted to one of the peripheral units, from November 2016 to May 2020, and who needed to be transferred to the main building. Telemedicine-assisted transportation was performed by an emergency specialist. For inclusion, the criteria demanded the patients above the age of 15 years and initial stabilization be performed at the emergency department. Unstable, intubated, ST-elevation myocardial infarction, and acute stroke patients were excluded. The primary endpoint was the number of telemedicine-guided interventions during transport. Results: 2840 patients were enrolled. The population was predominantly male (53.2%) with a median age of 60 years. Sepsis was the most prevalent diagnosis in 28% of patients, followed by acute coronary syndromes (8.5%), arrhythmia (6.7%), venous thromboembolism (6.1%), stroke (6.1%), acute abdomen (3.6%), respiratory distress (3.3%), and heart failure (2.5%). Only 22 (0.8%) patients required telemedicine-assisted support during transport. Administration of oxygen therapy and analgesics were the main remotely-oriented interventions. There were no communication problems in the telemedicine-assisted group. Conclusions: Telemedicine-assisted ambulance transportation of stabilized critically ill patients can effectively and safely substitute an onboard physician on most transfers between same-institution locations.
COVID-19 mortality risk factors in older people in a long-term care center.
Authors: Heras Eva , Garibaldi Pablo , Boix Maite , Valero Oliver , Castillo Jorge , Curbelo Yurisan , Gonzalez Elso , Mendoza Obilagilio , Anglada Maria , Miralles Joan Carles , Lllull Petra , Llovera Ricard , Pique Josep M.
Published: September 2020

Objectives: Despite high rates of COVID-19 infection and increased related mortality have been reported among older adults admitted in long-term care facilities, a limited amount of information is available about the natural course of this pandemic and prognostic factors in this population. In the current study, we aimed to investigate the epidemiologic, demographics, clinical, or therapeutic factors that may predict the prognosis in a cohort of COVID-19 infected elderly in a nursing home.Methods: We conducted a retrospective analysis of all COVID-19 confirmed institutionalized elderly in a nursing home transformed into a reference intermediate healthcare facility from March 15 to June 5, 2020. Epidemiological, demographic, and frailty status before infection, and clinical, laboratory, treatment, and outcome data during infection were collected. We used bivariate analysis and multivariate logistic regression to identify risk factors for mortality.Results: The analysis comprised all 100 COVID-19 confirmed cases during the study period. The median age was 85 years; 62% were female. The case fatality rate was 20%. In the bivariate analysis, male gender, fever, respiratory symptoms, severe cognitive decline, a low Barthel index, and lymphocytopenia were significantly associated with mortality. Multivariate logistic regression analysis identified male gender, low Barthel index, no pharmacological treatment, and lymphocytopenia as independent risk factors associated with mortality.Conclusions and Implications: Male gender, low Barthel index, no pharmacological treatment and lymphocytopenia are independent risk factors for COVID-19 mortality in institutionalized elderly patients in long-term care nursing homes. Treatment with hydroxychloroquine and azithromycin was associated with lower mortality in these patients.
Online single-shot pulse reconstruction for optimizing a seeded X-ray free-electron laser
Authors: Zeng Li , Gu Duan , Feng Chao , Liu Bo , Zhao Zhentang
Published: September 2020

X-ray free-electron lasers (FELs) hold promising prospects for opening up opportunities for ultra-fast sciences at the atomic and molecular system. A precise knowledge of temporal information of FEL pulses is the central issue for experiments. Here we demonstrated an online diagnostic method to determine the FEL temporal profiles at the Shanghai Soft X-ray FEL facility. This robust method, designed for seeded FELs, allows researchers to acquire real-time longitudinal profiles of FEL pulses with a resolution better than 3fs. Based on this method, for the first time, we can directly observe the generation and evolution of a seeded FEL online. This helps us to further understand the physics and realize the lasing of a stable, nearly fully coherent soft X-ray FEL through a two-stage harmonic up-shift configuration. This method also provides an intuitive way for precise detection and control of the relative timing between electron beams and external optical lasers.
Detection of Depression and Its High-Risk Group using Scanpath Comparison Based on Semantic Information
Authors: Wang Yan , Zheng Xiujuan , Huang Shen , Liu Huaqian , Zhang Yun , Liu Kai , Miao Danmin
Published: September 2020

Background: Depression is a burdensome, recurring mental health disorder with high prevalence. The traditional detection of depression relies on structured interviews and questionnaires, which is labor-intensive and time-consuming. Also, the detection results are affected by subjective factors such as the subject's honesty and the psychologists' experiences. It lacks objective and quantitative metrics.Methods: To solve the above problems, we develop a convenient and objective system to detect depression and its high-risk group using eye-tracking data. In this system, subjects are required to answer the self-rating scale, and their scanpaths are recorded as a series of gaze points and saccades by the eye-tracking technology. Then, the similarity of scanpaths are compared and quantified with the guide of semantic information. Finally, according to the similarity scores of their scanpaths, the subjects are classified into three groups: normal, high-risk group, and depression.Results: The classification accuracy based on each item of the self-rating scale is 86.79% on average, while the detection accuracy is 95.63%.Conclusion: The experimental results show that (1)There are obvious eye movement differences among normal people, high-risk groups of depression, and depression patients while answering the questionnaire. (2)The early screening system for depression provides a novel and efficient solution to detect depression and its high-risk group by integrating traditional scale assessment and quantitative scanpath comparison algorithm.
Universal adversarial attacks on deep neural networks for medical image classification
Authors: Hirano Hokuto , Minagi Akinori , Takemoto Kazuhiro
Published: September 2020

Background. Deep neural networks (DNNs) are widely investigated in medical image classification to achieve ﻿automated support for clinical diagnosis. It is necessary to evaluate the robustness of medical DNN tasks against adversarial attacks, as high-stake decision making will be made based on the diagnosis. Several previous studies have considered simple adversarial attacks. However, the vulnerability of DNNs to more realistic and higher risk attacks have not been evaluated yet, i.e., universal adversarial perturbation (UAP), which is a single perturbation that can induce DNN failure in most classification tasks.Methods. We focus on three representative DNN-based medical image classification tasks (i.e., skin cancer, referable diabetic retinopathy, and pneumonia classifications) and investigate their vulnerability of DNNs with various model architectures to UAPs.Results. We demonstrate that the DNNs are vulnerable to both nontargeted UAPs, which cause a task failure resulting in an input being assigned an incorrect class, and to targeted UAPs, which cause the DNN to classify an input into a specific class. The almost imperceptible UAPs achieved > 80% success rates for nontargeted and targeted attacks. The vulnerability to UAPs barely depended on model architecture. Moreover, we discovered that adversarial retraining, which is known to be an effective method for adversarial defenses, increased the robustness of DNNs against UAPs in only limited cases. Conclusion. Unlike previous assumptions, the results indicate that DNN-based clinical diagnosis is easier to deceive because of adversarial attacks. Adversaries can result in failed diagnoses at lower costs (e.g., without consideration of data distribution); moreover, they can affect the diagnosis. The effects of adversarial defenses may be not limited. Our findings emphasize that more careful consideration is required in developing DNNs for medical imaging and their practical applications.
Metabolomics analysis of the ameliorative effect of enhanced proline metabolism on hypoxia-induced injury in cardiomyocytes
Authors: Wang Jiacheng , Xue Zhimin , Hua Chunting , Lin Jun , Ying Hangying , Lv Qingbo , Shen Zhida , Wang Meihui , Zhou Binquan
Published: September 2020

Background

Coronary heart disease is currently the leading cause of death in humans. Its poor prognosis and high mortality are associated with myocardial ischemia, which leads to metabolic disorder-related cardiomyocyte apoptosis and reactive oxygen species (ROS) production. Previous cardiovascular metabolomics studies in humans and mice have shown that proline metabolism is severely altered after cardiomyocyte hypoxia. Proline dehydrogenase (PRODH) is an enzyme that catalyzes the first step of proline catabolism, which plays an important role in improving the cellular redox state. In vitro oxygen-glucose deprivation can mimic in vivo myocardial ischemic injury. This study aimed to investigate whether enhancing proline metabolism by overexpressing PRODH can ameliorate hypoxia-induced injury in cardiomyocytes and to reveal the related altered metabolites and mechanistic pathway via untargeted metabolomics analysis.
Results

First, through public database analysis and RT-qPCR and western blot analyses in a cardiomyocyte hypoxia model, we found that the expression of the proline-degrading enzyme PRODH was downregulated after myocardial infarction and hypoxia exposure. Second, LDH assays, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), DHE staining, flow cytometric apoptosis analysis with DCFH and Annexin V-FITC/PI, and western blot analysis were used to assess the injury level in cardiomyocytes. Enhanced proline metabolism induced by PRODH overexpression reduced the levels of reactive oxidative stress and apoptosis, whereas PRODH knockdown had the opposite effects. Third, untargeted metabolomics analysis revealed that the protective effect was associated with significant changes in metabolism linked to sphingolipid signaling pathways, unsaturated fatty acid biosynthesis, phosphocreatine, glutathione disulfide, aminoacyl-tRNA biosynthesis, and ABC transporters.
Conclusions

Our study demonstrated a protective effect of enhanced proline metabolism in cardiomyocytes under hypoxia, providing a novel strategy for exploring new treatments for coronary heart disease.
Electrical Conductive Fluidized Zones and Their Influence on the Earthquake Nucleation, Growth, and Arrest Processes of the 2016 Kumamoto Earthquake Sequence, Kyushu Island, Japan
Authors: Aizawa Koki , Takakura Shinichi , Asaue Hisafumi , Koike Katsuaki , Yoshimura Ryokei , Yamazaki Ken'ichi , Komatsu Shintaro , Utsugi Mitsuru , Inoue Hiroyuki , Tsukamoto Kaori , Uyeshima Makoto , Koyama Takao , Kanda Wataru , Yoshinaga Tohru , Matsushima Nobuo , Uchida Kazunari , Tsukashima Yuko , Matsushima Takeshi , Ichihara Hiroshi , Muramatsu Dan , Teguri Yoshiko , Shito Azusa , Matsumoto Satoshi , Shimizu Hiroshi
Published: September 2020

Crustal earthquake ruptures tend to nucleate near fluidized zones. However, it is relatively unknown whether fluidized zones can further promote or arrest these ruptures. We image the electrical resistivity structure around the focal area of the 2016 Kumamoto earthquake sequence by using 200 sites broad-band magnetotelluric data, and discuss its quantitative relationship to earthquake nucleation, growth, and arrest processes. The result shows that the earthquake hypocenters are all located within 10 km from low-resistivity fluidized zones < 30Ωm. The ruptures that nucleated along the outer edge of the low-resistivity fluidized zones tended to become large earthquakes, whereas those that initiated either distal to or within the fluidized zones did not. The ruptures were arrested by high-temperature (>400°C) fluidized zones, whereas shallower low-temperature (200°C–400°C) fluidized zones either promoted or arrested the ruptures. These results suggest that the distribution of mid-crustal fluids contributes to the nucleation, growth, and arrest of crustal earthquakes.
Gα3 subunit Thga3 positively regulates conidiation, mycoparasitism, chitinase activity, and hydrophobicity of Trichoderma harzianum
Authors: Ding Jie , Mei Jie , Huang Pei , Tian Ying , Liang Yao , Jiang Xiliang , Li Mei
Published: September 2020

Heterotrimeric G-proteins are key elements of signal transduction pathways, which participate in regulating multiple biological processes in fungi including growth, conidiation, antagonism, and mycoparasitism. Among G protein subunits, Gα3 showed diverse regulatory functions in different fungi. In this study, we cloned a Gα3 subunit coding gene thga3 from T. harzianum Th33 that can antagonize Rhizoctonia solani and some other plant pathogenic fungi. A thga3 deletion strain Δ thga3 was generated using the double-crossover homologous recombination strategy, and R thga3 was generated by transforming thga3 -expressing vector into the protoplasts of Δ thga3 by the PEG/CaCl 2 -mediated method. The biological characteristics of wild-type Th33, Δ thga3 and R thga3 were evaluated. Compared with wild-type Th33, Δ thga3 showed 15%, 94%, and 23% decrease in hyphal growth, conidia yield, and chitinase activity, respectively, and Δ thga3 showed lower antagonistic and mycoparasitism abilities, while there were no significant differences between wild-type Th33 and R thga3 . The hyphal surface hydrophobicity of Δ thga3 significantly decreased compared with those of the wild-type Th33 and R thga3 . qRT-PCR analysis revealed that transcript abundance of the hydrophobin gene (tha_09745) of Δ thga3 decreased by 80% compared with that of wild-type Th33 and R thga3 . The results showed that thga3 positively regulates the growth, conidiation, hydrophobicity, chitinase activities, and mycoparasitism of Th33 towards R. solani . We hence deduced that the expression level of Tha_09745 is correlated to the hyphal hydrophobicity of Th33 and therefore affects the other biological characteristics of Th33. The findings of this report provide a foundation for elucidating the G-protein signal regulatory mechanisms of fungi.
TREM2 Levels Are Increased in Neurodegenerative Disease Patients and in an Alzheimer's Disease Mouse Model
Authors: Zhang Xiaomin , Liu Jing , Cao Min , Yang Tingting , Wang Yaqi , Hou Yuli , Song Qiao , Cui Yuting , Wang Peichang
Published: September 2020

Background: Triggering receptor expressed on myeloid cells 2 (TREM2) is expressed on microglia, and it plays an important role in neurodegenerative diseases, especially Alzheimer’s disease (AD).This study aimed to elucidate the potential value of TREM2 as biomarker for the diagnosis of AD.Methods: Serum TREM2 levels in human subjects and mice were detected by ELISA. TREM2 mRNA and protein expressions in leukocytes and mouse brain tissues were detected using real-time quantitative PCR(RT-qPCR) and western blot analysis. The cognitive ability of patients was measured by MMSE/MoCA score. The cognitive ability of mice was evaluated by the Morris water maze (MWM) test.Results: Our results showed that the serum concentration and expression levels of TREM2 in leukocytes were increased both in neurodegenerative patients and in an AD model mice.TREM2 expression was correlated with the cognitive impairment in AD patients and APP/PS1 mice.Conclusion: This study indicates that TREM2 is a novel potential biomarker for AD diagnosis.
Carthamin yellow protected rats from cerebral ischemia–reperfusion injury by improving neuronal dendritic plasticity via antiferroptosis mediated NF-κB/NLRP3 inflammasome pathway deactivation
Authors: Guo Hui-Hui , Zhu Li-Li , Tang Ping-Ping , Chen Dong , Li Yan-Cai , Li Jian-Bing , Bao Chao
Published: September 2020

Background: Carthamin yellow (CY), a flavonoid compound extracted from safflower, has been reported to attenuate cardiac ischemia and reperfusion injury. It is unclear whether CY could ameliorate ischemic stroke. Methods: We examined the preventive effects of CY in experimental ischemic stroke using middle cerebral artery occlusion (MCAO) rats model. Neurological function, brain edema and infarct area were assessed to elucidate the effects of CY on neurological function and ischemic brain injury. MAP-2 Immunofluorescence activity, expressions in NF-κB/NLRP3 inflammasome pathway and ferroptosis were determined to reveal its underlying mechanism. Results: A 2-week CY treatment attenuated the neurological deficit score, brain water content and infarct area in MCAO rats. Meanwhile, CY intervention increased the MAP-2 Immunofluorescence activity and deactivated NF-κB/NLRP3 inflammasome pathway in the cortex. Declined serum TNF-α, IL-1β and IL-6 concentrations were detected following CY administration. Furthermore, CY treatment inhibited Fe2+ and ROS accumulation, and restored the protein expressions of ACSL4, TFR1, GPX4 and FTH1 in the brain. The levels of GSH, SOD and MDA in the serum were reversed by CY intervention. Conclusion: CY protected rats from ischemic stroke, which was associated with the improvement of neuronal dendritic plasticity through antiferroptosis mediated NF-κB/NLRP3 inflammasome pathway deactivation.
Discovery of a role for the single START-domain protein Mtsp17 in transcriptional regulation
Authors: Zhou Ying , Zhong Tianying , Wei Wenjing , Wu Zhuhua , Yang Anping , Wang Ming , Zhang Xiaoli
Published: September 2020

Background

Tuberculosis caused by the pathogen Mycobacterium tuberculosis (MTB), remains a significant threat to global health. Elucidating the mechanism of essential MTB genes will provide a theoretical basis for drug exploitation. Gene mtsp17 is essential and conserved in the Mycobacterium genus. Although the structure of Mtsp17 exhibits as a typical steroidogenic acute regulatory protein-related lipid transfer (START) family protein, its biological function is different from other START proteins. This study characterized the transcriptomes of Mycobacterium smegmatis to address the problem how suppressing mtsp17 reduces bacterial growth rate.
Results

3% down- and 1% up-regulated protein-coding genes were significantly differentiated expressed by suppressing mtsp17 gene. Among them, desA1, an essential gene involved in mycolic acid synthesis, was found to be significantly depressed (3.1-fold). Further analyses showed that mstp17 can activate desA1 to regulate the bacterial growth. In addition, the anti-anti-SigF gene was dramatically decreased (8.9-fold) and 70 of the 79 differentially expressed genes showed the same change trends in the SigF knockout strain. The data indicate that Mtsp17 regulates SigF regulon by modulating mRNA abundance of the anti-sigma factor antagonist.
Conclusions

Our findings discover the role of Mtsp17 in transcriptional regulation that was unknown before, which provides new insights into the molecular mechanisms of START family and introduces a new node to the regulatory network of mycobacteria.
TCONS_00230836 silencing restores stearic acid-induced β-cell dysfunction through alleviating endoplasmic reticulum stress via a PERK/eIF2α-dependent pathway rather than apoptosis
Authors: Guo Rui , Zhang Yunjin , Yu Yue , Su Shenghan , Zhao Qingrui , Chu Xia , Lu Huimin , Sun Changhao
Published: September 2020

Background: Chronic exposure of pancreatic β cells to high levels of stearic acid (C18:0) leads to impaired insulin secretion, which accelerates the progression of type 2 diabetes mellitus (T2DM). Recently, long noncoding RNAs (lncRNAs) were found to participate in saturated fatty acid-induced metabolism dysfunction. However, their contribution to stearic acid-induced β-cell dysfunction remains largely unknown. This study evaluated the possible role of the lncRNA TCONS_00230836 in stearic acid-stimulated lipotoxicity to β cells. Method: Using high-throughput RNA-sequencing, TCONS_00230836 was screened out as being exclusively differentially expressed in stearic acid-treated mouse β-TC6 cells. Co-expression network was constructed to reveal the potential mRNAs targeted for lncRNA TCONS_00230836. Changes in this lncRNA’s and candidate mRNAs’levels were further assessed by real-time PCR in stearic acid-treated β-TC6 cells and islets of mice fed a high-stearic-acid diet (HSD). The localization of TCONS_00230836 was detected by fluorescent in situ hybridization. The endogenous lncRNA TCONS_00230836 in β-TC6 cells was abrogated by its Smart Silencer. Results: The lncRNA TCONS_00230836 was enriched in mouse islets and mainly localized in the cytoplasm. Its expression was significantly increased in stearic acid-treated β-TC6 cells and HSD-fed mouse islets. Knockdown of TCONS_00230836 apparently restored stearic acid-impaired GSIS through alleviating endoplasmic reticulum stress via a PERK/eIF2α-dependent pathway. However, stearic acid-induced β-cell apoptosis was not obviously recovered. Conclusion: Our findings suggest the involvement of the lncRNA TCONS_00230836 in stearic acid-induced β-cell dysfunction, which provides novel insight into stearic acid-induced lipotoxicity to β cells. Anti-lncRNA TCONS_00230836 might be a new therapeutic strategy for alleviating stearic acid-induced β-cell dysfunction in the progression of T2DM.
Genome Analysis of Spiroplasma Citri Strains From Different Host Plants and Its Leafhopper Vectors
Authors: Rattner Rachel , Thapa Shree Prasad , Dang Tyler , Osman Fatima , Selvaraj Vijayanandraj , Maheshwari Yogita , Pagliaccia Deborah , Espindola Andres S. , Hajeri Subhas , Chen Jianchi , Coaker Gitta , Vidalakis Georgios , Yokomi Raymond
Published: September 2020

Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC2, C5, C189, LB319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas.Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-12 and C5; C189 and R8-A2; BR12, BLH-MB, BLH13 and LB 319. Strain GII3-3 remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. Conclusions The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1,597-2,232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3-3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.
Analysis of fuel tank collision structure based on defense point method
Authors: Liu Wenguang , Liu Haijiang , Jiang lin , Bi Shanshan
Published: September 2020

Aiming at the impact process of a fuel tank, which is a transient energy conversion process, the material absorbs energy through deformation to analyze the mechanical properties of the fuel tank during the impact process. The defense node method is adopted to simulate the dynamic response of the fuel tank during impact. The results show that it can accurately evaluate the safety of the container.
Human Osteoclasts/Osteoblasts 3D Dynamic Co-Culture System to Study the Beneficial Effects of Glucosamine on Bone Microenvironment
Authors: Penolazzi Letizia , Lambertini Elisabetta , Pandolfi Assunta , Mandatori Domitilla , Sollazzo Vincenzo , Piva Roberta
Published: September 2020

Background: Glucosamine (GlcN) functions as a building block of the cartilage matrix and its multifaceted roles in promoting joint health has been extensively investigated. On the contrary, the role of GlcN in osteogenesis and bone tissue is poorly understood, mainly due to the lack of adequate experimental models. Consequently, the benefit of GlcN in bone disorders remains controversial. In order to broaden the pharmacological relevance and potential therapeutic/nutraceutic efficacy of GlcN, we investigated the effect of GlcN on human primary osteoclasts (hOCs) and osteoblasts (hOBs) that were grown with 2D traditional methods or co-cultured in a more complex culture system one step closer to the in vivo bone microenvironment, consisting in a three-dimensional (3D) dynamic system.Methods: Osteoclasts derived from peripheral blood monocytes (hMCs) of either healthy or osteoarthritis (OA) donors, were used and kept in culture with osteoclastogenic inducers. hMCs were also combined with hOBs in a 3D dynamic co‐culture system by using RCCS-4TM bioreactor in osteogenic medium without osteoclastogenic inducers. In this condition osteoclastogenesis was supported by hOBs and sizeable self assembling aggregates were obtained. The differentiated osteoclasts were evaluated by the tartrate-resistant acid phosphatase assay, osteogenic differentiation was monitored by analyzing mineral matrix deposition through Alizarin Red staining, and expression of osteogenic markers through RT-qPCR. The cells were treated with DONA® Crystalline Glucosamine Sulfate (i.e. the original GlcN sulfate product).Results: DONA® was effective in decreasing the hOCs differentiation and function. Osteoclasts from OA donors were more sensitive than those from healthy donors. At the same time, DONA® showed anabolic effects on osteoblasts both in 2D conventional cell culture and in osteoclasts/osteoblasts 3D dynamic co-culture system.Conclusions: Here we demonstrated the effectiveness of a 3D dynamic co-culture system to provide useful information on the spectrum of action of GlcN on bone microenvironment. This can pave the way to better define the potential applications of a compound such as GlcN which is positioned between pharmaceuticals and nutraceuticals. Therefore, based on our observations, we hypothesize that GlcN could have potential benefits either in the treatment of osteopenic diseases such as osteoporosis, or in the bone health maintenance.
National implementation of in situ simulation training in Helicopter Emergency Medical Services: A multicenter study
Authors: Bredmose Per P. , Røislien Jo , Østergaard Doris , Sollid Stephen
Published: September 2020

IntroductionMedical simulation is used in helicopter emergency services as a tool for training the crew. Using in situ simulation we aimed to evaluate the degree of implementation, factors for successful simulation and the crew’s attitude towards this form for training.MethodsA one year prospective study on simulation at all Norwegian helicopter emergency services bases and one search and rescue base. Local facilitators were educated and conducted simulations at their own discretion.ResultsAll bases participated, but the number of simulations attempted at each base varied from 1 to 46. Busier bases had a significantly higher number of aborted simulations. Regardless of base and number of attempted simulations, participating crews scored self-evaluated satisfaction with this form of training highly. The number of local facilitators and their travel distance to work seemed to make no difference to the number of attempted simulations.DiscussionOur study reveals large differences in the number of attempted simulations between bases. Our findings suggest that the local facilitator is a key factor for successful implementation of simulation based training in helicopter emergency services.
Predictive Value of Live Birth Rate Based on Different Intrauterine Adhesion Evaluation Systems Following
Authors: Cao Mingzhu , Pan Yingying , Zhang Qingyan , You Danming , Feng Shuying , LIU Zhi
Published: September 2020

Objective: The aim of this study was to assess the predictive value of five different intrauterine adhesion (IUA) evaluation systems for live birth rate following transcervical resection of adhesion (TCRA).Method: This retrospective study included 128 women with IUA who desired for spontaneous conception after TCRA. All the patients were retrospectively scored by the American Fertility Society (AFS) classification, European Society of Gynecological Endoscopy (ESGE) classification, March’s classification (March), Nasr’s classification (Nasr) and Chinese IUA diagnosis classification criteria (Chinese). The predictive value of these evaluation systems was determined by receiver operating characteristic (ROC) curves and area under a ROC curve (AUC).Results: The correlation coefficients of AFS, ESGE, March, Nasr and Chinese classification and the live birth rate were 0.282, 0.324, 0.260, 0.418, 0.364, respectively. All five scoring systems were efficient to predict live birth rate. Among them, Nasr’s classification showed the highest AUC (0.748) with the best predictive value.Conclusion: AFS, ESGE, March, Nasr and Chinese classification were demonstrated to be capable of predicting live birth following TCRA, and Nasr’s classification showed the highest predictive value of live birth.
Influence of Seaweed Supplements on the Intestinal Bacteria in the Rabbitfish Siganus Fuscescens: Evidence for a Core Microbiome
Authors: Thepot Valentin , Slinger Joel , Rimmer Michael A , Paul Nicholas A , Campbell Alexandra H
Published: September 2020

BackgroundWe know very little about natural variation in microbiomes of marine herbivorous fish in the wild or in captivity (aquaculture). Understanding how the consumption of seaweed influences intestinal microbial communities will shed light on how such phytobiotics could enhance the health and productivity of farmed fish. Here we screened the effects of supplementing the diets of mottled rabbitfish (Siganus fuscescens), a candidate species for international aquaculture development, with 15 different species of seaweeds and functional supplements currently used in aquaculture, on the bacterial communities that colonised their hindguts. ResultsRemarkably, the second most abundant phylum and the majority (53%) of the bacterial genera were not assigned, highlighting a significant knowledge gap for the field of animal microbiomes. Dietary supplementation increased alpha diversity by up to 23% relative to the control fish. Furthermore, most supplements significantly increased the relative abundance of Firmicutes, with similar trends for Proteobacteria and consistent decreases in Bacteroides. Seaweed supplementation also had important effects at the genus level, including significant increases in Fusobacterium sp. in fish fed seaweed - especially the green Caulerpa taxifolia – and overall trends for reduced levels of Arcobacter sp., a genus that includes fish and human pathogens. When we compared microbiomes in our fish to those from two recently published studies of conspecific populations sampled many thousands of kilometres away, the populations were clearly distinct, however there were 55 ASVs that were shared across the three fish populations, of which 35 were present in 50% of all fish sampled.ConclusionThe identification of a core microbiome suggests that a host organism relies on certain microbes for key functions and our findings suggest that this candidate aquaculture species has a core microbiome in its hindgut which is robust to dietary manipulations and broad geographical and temporal variation. This insight will help guide future work investigating the functional and mechanistic bases of these relationships, as will improvements in microbial taxonomic resolution. Supplementation with seaweeds did have subtle influences on bacteria in the hindgut of Siganus fuscescens which could have important impacts on fish health and should be considered as aquaculture systems are developed for this species.