bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil inoculation of Trichoderma asperellum M45a regulates rhizosphere microbes and triggers watermelon resistance to Fusarium wilt
Authors: Zhang Yi , Tian Cheng , Xiao Jiling , Wei Lin , Tian Yun , Liang Zhihuai
Published: July 2020

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. niveum (FON) is a soil-borne disease that seriously limits watermelon production. In the present study, the Trichoderma asperellum (T. asperellum) M45a was shown to be an effective biocontrol agent against Fusarium wilt (FW). In a pot experiment, the application of 105 cfu/g of T. asperellum M45a granules had better control effect on FW at the blooming period (up to 67.44%) from soils subjected to five years of continuous cropping with watermelon, while the average length of watermelon vine was also significantly improved(P < 0.05). Additionally, the acid phosphatase (ACP), cellulase (CL), catalase (CAT) and sucrase (SC) activities in the M45a-inoculation group were significantly higher than in the control (CK) group, and the soil nutrients (total N, NO3-N, and available P) transformation was significantly increased. Moreover, T. asperellum M45a inoculation reduced fungal diversity and increased bacterial diversity, especially enhancing the relative abundance of PGPR (plant growth promoting rhizobacteria), such as Trichoderma, Sphingomonas, Pseudomonas, Actinomadura and Rhodanobacter. Through functional prediction, the relative abundance of Ectomycorrhizal, Endophyte, Animal pathotroph and saprotroph in fungal community was determined to be significantly lower than observed in the M45a-treated soil. Correlation analysis revealed that Sphingomonas, Pseudomonas and Trichoderma had the most differences in microorganisms abundance, positively correlated with ACP, CL, CAT and SC. These findings will provide ecological fungicide advice for microecological control of FW in continuous cropping watermelon.
Investigation of Hepatitis B and Hepatitis C in the blood of hemodialysis patients from Peshawar, Pakistan.
Authors: ali Abid , Khan Gul Nabi , Salman Muhammad , Khan Muhammad Numan , Ullah Asad , Khan Abdul Haleem , Wazir Shoib , Shamim Fahad , Noureen Samra , Akbar Sher
Published: July 2020

Aim: High prevalence of Hepatitis C virus (HCV) and Hepatitis B (HBV) has reported among dialysis patients throughout the world. The aim of this study was to find out the frequency of HCV and HBV both in Hemodialysis (HD) at District Peshawar, the capital of Khyber Pakhtunkhwa Province of Pakistan.Methods: A cross-sectional study was conducted from July 2018 to March 2019. The infections were investigated through serological and molecular techniques. The polymerase chain reaction was performed for only HCV RNA detection in HD patients. The data obtained were compared with available past studies from Pakistan.Results: To evaluate the frequency of HCV, HBV, and co-infection in HD patients. 200 blood samples were collected from dialysis patients who visited Lady Reading Hospital Peshawar. Among 200, HCV infected were diagnosed in 22%, HBV in 8%. The percentages of male to female diagnosed patients with HCV were 21% and 20% respectively. Moreover, the chi-square test of association among variables based on our empirical findings, it is clear that odds of HCV positive among males is 3.467 times greater than female, with statistically significance (P= 0.012*) against 50 and above age group.. Conclusion: The percentage of HCV positive was found higher in the overall HD patient population. Only 7.5% of patients were found Negative of HBV and HCV in both males and females visited hospitals for dialysis. The high prevalence of hepatitis viruses among HD patients indicates a close relation between HD centers and hepatitis virus transmission. Therefore, preventive control measures are essential to reduce hepatitis transmission in HD centers
Improving the Prognosis of Colon Cancer Through Knowledge-Based Clinical-Molecular Integrated Analysis
Authors: Tong Danyang , Tian Yu , Ye Qiancheng , Li Jun , Ding Kefeng , Li Jingsong
Published: July 2020

BackgroundColon cancer has high morbidity and mortality rates among cancers. Existing clinical staging systems cannot accurately assess the prognostic risk of colon cancer patients. Therefore, new prognostic factors are needed. In this study, a new pathway-based prognostic factor was discovered through a knowledge-based clinical-molecular integrated analysis.MethodsA total of 374 samples from The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) dataset were used as the discovery set and 98 samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset were used as the validation set. After converting gene expression data into pathway dysregulation scores (PDS), the random survival forest and multicovariate Cox model were used to identify the best prognostic supplementary factors. Finally, a clinical prognostic model, a molecular prognostic model and a clinical-molecular integrated prognostic model were constructed to verify the supplementary effect of the discovered prognostic supplementary factor.ResultsThe PDS of 14 pathways played important roles in prognostic prediction together with clinical prognostic factors through the random survival forest. Further screening through the multicovariate Cox model revealed that the PDS of pathway hsa00532 was the best clinical prognostic supplementary factor. The clinical-molecular integrated prognostic model constructed with clinical prognostic factors and the discovered prognostic factor was superior to the clinical prognostic model and molecular prognostic model in discriminative performance (C-indexes of 0.773, 0.746, and 0.619 in the discovery set and 0.893, 0.808, and 0.810 in the validation set, respectively). The Kaplan-Meier (KM) curves of patients grouped by PDS suggested that patients with a higher PDS had poorer prognosis, and stage II patients could be distinctly distinguished.ConclusionThe PDS of pathway hsa00532 was a considerable clinical prognostic supplementary factor for colon cancer and may represent a potential prognostic marker for stage II colon cancer. The PDS calculation involves only 16 genes, which supports its potential clinical application prospects.
Chicken proventricular necrosis virus related transmissible viral proventriculitis in broiler chickens in Poland
Authors: Śmiałek Marcin , Gesek Michał , Dziwulska Daria , Samanta-Niczyporuk Jowita , Koncicki Andrzej
Published: July 2020

Background.

Transmissible viral proventriculitis (TVP) is an infectious disease reported in all production types of chickens. TVP is manifested in decreased body weight gains, wide weight diversity of birds in the flock and poor feed conversion. Histopathological examination seems to be the most reliable method for confirming the disease. Although TVP etiology has not been explicitly defined, a novel virus identified as a member of the Birnaviridae family, named chicken proventricular necrosis virus (CPNV) has been isolated from clinical cases of TVP and it is now considered as a potential factor of a disease. The study was undertaken in order to reproduce the disease under laboratory conditions and to evaluate the etiology of first described Polish case of TVP.
Results.

Anatomopathological and histopathological evaluation reveled that we've succeeded to reproduce TVP in broiler chickens. Within 14 days after infection birds gained approximately 30,38% less body weight in comparison to Control group. In TVP infected group a seroconversion against FAdV and IBDV was recorded 14 days post infection (dpi). 14 dpi CPNV was detected in proventriculi, while FAdV in spleens and livers of infected birds.
Conclusions.

We have demonstrated that CPNV was involved in the development of the disease. We did not record the presence of IBDV in the TVP or control birds, despite our recording a strong seroconversion against IBDV in the birds from the TVP group. CPNV belongs to the same family as IBDV, which allows us to assume serological cross-reactivity between them. This possibility of CPNV infections affecting IBDV antibody levels detected by commonly available ELISAs should be taken into account under poultry field conditions and diagnosis. The role of FAdV in the development of TVP needs further evaluation.
The resilience as predictor of Quality of Life in participants with borderline personality disorder before and after of treatment
Authors: Guillén Verónica , Tormo Mireia Esplugues , Fonseca-Baeza Sara , Botella Cristina , Baños Rosa , García-Palacios Azucena , Marco Jose Heliodoro
Published: July 2020

Background
Studies suggested that psychotherapy improved QoL of participants with BPD. However, there are no studies about the differential efficacy of treatments in the QoL of participants with BPD. Moreover, the relationship between QoL and resilience has rarely been studied in participants with BPD. Objectives: a) to examine whether people with BPD have worse QoL than the non-clinical population; b) to examine whether there are statistically significant differences between DBT, STEPPS, and TAU-CBT in the improvement of QoL; c) to examine whether participants show clinically significant improvements in QoL after treatment; d) to analyse whether resilience is associated with QoL before and after the BPD treatment; e) to analyse whether the resilience is a predictor of QoL at pre-treatment and posttreatment.
Method:
The sample comprised 403 participants (n = 202 participants diagnosed with BPD, and n = 201 non-clinical). MANOVA and regression analysis were performed. Results: participants diagnosed with BPD had statistically significant lower resilience than the non-clinical population, all forms of psychotherapy improved QoL, but there was no clinical change after the treatments, resilience was associated with QoL before and after the treatment of BPD and, resilience was a predictor of QoL before and after the treatment.
Conclusion
It is necessary to assess QoL in studies of psychotherapy with BPD.
Performance Evaluation of the Combination of Medical Care and Old-age Service in Old-age Institutions in China: A Two-stage DEA Approach
Authors: Du Na , Yuan Man , Wu Peng , Li Zhiwu
Published: July 2020

Background: In the context of China’s aging population, comprehensive medical care, convenient diagnosis, comprehensive medical care and elderly care services are increasingly needed. But China's medical care and elderly care service system is still immature. This study aims to build a performance evaluation index/criteria system for the combination of medical care and elderly care services and present an empirical approach to assess them.Methods: A two-stage DEA approach is taken: 1) establish a performance evaluation index system for the combination of medical care and elderly care services, 2) adopt a two-stage DEA to evaluate the performance of 30 pension institutions in China, and 3) Determine and identify important criteria to improve the efficiency of pension institutions. Results: The results show that the two-stage DEA accounted for a relatively high affiance of medical and nursing care services, but resource allocation still needs to be further optimized. Institutions with ineffective DEA need to reduce the five factors of operations, management, fixed assets, technology and services in the input dimension. In the output dimension, the service evaluation effect and safety management effect need to be improved. The performance of combined old-age care and medical care in old-age institutions can be improved in terms of investment in fixed assets, methods of capital subsidies, supervision and management, as well as standardized operations.Conclusions: This study establish a performance evaluation index system for the combination of medical care and elderly care services and present a two-stage DEA empirical approach to evaluate the performance of 30 pension institutions in China, which provides the method supports for decision-makers and researchers in performing evaluation of pension institutions in China, outlines the suggestions in improving them.
Determinants of Successful Guideline Implementation: A National Cross-Sectional Survey
Authors: Jin Ying-hui , Tan Li-Ming , Khan Khalid S. , Deng Tong , Huang Chao , Han Fei , Zhang Jing , Huang Qiao , Huang Di , Wang Dan-qi , Wang Yu , Zeng Xian-tao , Wang Qiang , Wang Xing-huan
Published: July 2020

Background: CPGs are not uniformly successful in improving care and several instances of implementation failure have been reported. Performing a comprehensive assessment of the barriers and enablers is key to developing an informed implementation strategy. To investigate determinants of guideline implementation and explore associations of self-reported adherence to guidelines with characteristics of participants in China.Methods: This is a cross-sectional survey, using multi-stage stratified typical sampling based on China's economic regional divisions (the East, the Middle, the West and the Northeast). 2-5 provinces were selected from each region. 2-3 cities were selected in each province, and secondary and tertiary hospitals from each city were included. We developed a questionnaire underpinned by recommended methods for the design and conduct of self-administered surveys and based on conceptual framework of guideline use, in-depth related literature analysis, guideline development manuals, related behavior change theory. At last, multivariate analyses were performed using logistic regression to produce adjusted odds ratios (OR) and 95% confidence intervals (95%CI).Results: The questionnaire consisted of four sections: knowledge on methodology for developing guidelines; barriers to accessing guideline; barriers to guideline implementation; and methods for improving guideline implementation. There were 1732 participants (87.3% response rate) from 51 hospitals. Of these, 77.2% reported to have used guidelines frequently or very frequently. The key barriers to guideline use were lack of education or training (46.2%), and overly simplistic wording or overly broad scope of recommendations (43.8%). Level of adherence to guidelines was associated with geographical regions (the northeast P＜0.001; the west P=0.02; the middle P＜0.001 compared with the east), hospital grades(P=0.028), length of practitioners’ practice (P =0.006), education background (PhD, P=0.027; Master, P=0.002), evidence-based medicine skills acquired in work unit (P=0.012), and medical specialty of practitioner (General Practice, P=0.006; Surgery, P=0.043). Conclusion: Despite general acknowledgement of the importance of guidelines, the use of guidelines was not as frequent as might have been expected. To optimize the likelihood of adherence to guidelines, guideline implementation should follow an actively developed dissemination plan incorporating features associated with adherence in our study.
Tissue-specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum Purpureum Schum.)
Authors: Zhang Wenqing , Zhang Shengkui , Lu Xianqin , Li Can , Liu Xingwang , Dong Geyu , Xia Tao
Published: July 2020

Background:The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. Because the genome of elephant grass has not been deciphered, the study of its lignocellulose synthesis pathway and key genes is limited. Results:In this study, RNA sequencing (RNA-seq) combining with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials, were applied to reveal the genes regulating cellulose and lignin synthesis. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2 and T3. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the two most abundant metabolic pathways were phenylpropanemetabolism, starch and sucrose metabolism, which closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly correlated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. In addition, the expression of CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H, CAD and CCR at different development stages were analyzed, and found that the content of lignocellulose was correlated with the expression levels of these structural genes. Conclusions:This study not only provides new insights into the molecular mechanisms of cellulose and lignin synthesis pathways in elephant grass, but also offers a new and extensive list of candidate genes for more specialized functional studies in the future which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.
Natural Variation of Physiological Traits, Molecular Markers, and Chlorophyll Catabolic Genes Associated With Heat Tolerance in Perennial Ryegrass Accessions
Authors: Xu Bin , Zhang Jing , Li Hui , Jiang Yiwei , Li Huibin , Zhang Zhipeng , Huang Bingru
Published: July 2020

Background: Identification of genetic diversity in heat tolerance and associated traits is of great importance for improving heat tolerance in cool-season grass species. The objectives of this study were to determine genetic variations in heat tolerance associated with phenotypic and physiological traits and to identify molecular markers associated with heat tolerance in a diverse collection of perennial ryegrass (Lolium perenne L.). Results: Plants of 98 accessions were subjected to heat stress (35/30 ℃, day/night) or optimal growth temperature (25/20 ℃) for 24 d in growth chambers. Overall heattolerance of those accessions was ranked by principal component analysis (PCA) based on eight phenotypic and physiological traits. Among these traits, electrolyte leakage (EL), chlorophyll content (Chl), relative water content (RWC) had high correlation coefficients (−0.858, 0.769, and 0.764, respectively) with the PCA ranking of heat tolerance. We also found expression levels of four Chl catabolic genes (CCGs), including LpNYC1, LpNOL, LpSGR, and LpPPH, were closely related to the heat tolerance of ryegrass accessions. Furthermore, 66 pairs of simple sequence repeat (SSR) markers were used to perform association analysis based on the PCA result. The population structure of ryegrass can be grouped into three clusters, and accessions in cluster C were relatively more heat tolerant than those in cluster A and B. SSR markers significantly associated with above-mentioned traits were identified (R2>0.05, p<0.01)., including two pairs of markers located on chromosome 4 in association with Chl content and another four pairs of markers in association with EL.Conclusion:The result not only identified useful physiological parameters, including EL, Chl content, and RWC, and their associated SSR markers for heat-tolerance breeding of perennial ryegrass, but also highlighted the involvement of Chl catabolism in ryegrass heat tolerance. Such knowledge is of significance for heat-tolerance breeding and heat tolerance mechanisms in perennial ryegrass as well as in other cool-season grass species.
Early-stage predictive markers of critically ill COVID-19 cases
Authors: Zhou Zheng , Yin Shiwei , Xu Jie , Deng Yunfeng , Wang Xinfeng , Ma Xin
Published: July 2020

Background: Severe cytokine storm syndrome (CSS) is considered as the cause of death among critically ill COVID-19 cases. Early identification of the high-risk severe cases is crucial to lower the fatality and healthcare costs.Methods: In this study, we retrospectively analyzed the first and second-week serum levels of IL-6, IL-8, and IL-10 of 50 COVID-19 cases. We calculated the ratios of IL-6/IL-10 and IL-8/IL-10 at 3rd, 6th, 9th, and 12th days of hospitalization. Results: We collected 50 COVID-19 cases (male 54%, mean age 51.2, range 18 - 86), including 39 mild cases (78%), 7 severe/recovered cases (14%), and 4 died cases (8%).The ratios of IL 6/IL-10 and IL-8/IL-10 among mild cases were below 27 (the highest, 26.9) along the 4 testing points of two week hospitalization, while we found that the IL-6/IL-10 and IL-8/IL-10 ratios were as high as 187.51 and 225.3 respectively in the death group on 3rd day with the highest IL-6/IL-10 ratio of 297.28 on the 6th day of hospitalization. Conclusions: Our preliminary results suggest that the ratios of IL-6/IL-10 and IL-8/IL-10 at the early stage (the first two weeks) of COVID-19 could be a predictive marker for the disease prognosis, of which the cut-off lines were suggested below 50 for a mild and recoverable severe cases.
Assessing the Immediate Impact of COVID-19 Lockdown on the Air Quality of Kolkata and Howrah, West Bengal, India
Authors: Sarkar Mohan , Das Anupam , Mukhopadhyay Sutapa
Published: July 2020

The worldwide spread of COVID-19 caused a nationwide lockdown in India from 24th March 2020 and was further extended up to 3rd May 2020 to break off the transmission of novel Coronavirus. The study is designed to assess the changes in air quality from the pre lockdown period to the during lockdown period in Kolkata and Howrah municipal corporation, West Bengal, India. GIS-based techniques include the spatial and temporal distribution of pollutants using interpolation method, on the other hand, statistical methods like Analysis of Variance (ANOVA) was applied to determine the mean differences two phases and correlation matrix helps to understand the changing association of the pollutants in pre and during-lockdown phases. Significant correlations have been found among the pollutants, ANOVA (Two-Way) has shown the significant mean difference of NAQI between the two phases, F (1,611)=465.723, p<0.0001; pairwise comparison for Ballygunj has shown the highest mean difference 108.194 at p<0.0001 significant level between lockdown and pre lockdown phase. Significant positive correlation has been found between PM2.5, PM 10 (0.99*); PM2.5, NO2 (0.81*); PM10, NO2 (0.81*); CO, NO2 (0.77*) and some negative correlations have also been found between O3, NO (-0.15); O3 and NH3 (-0.36) in the pre lockdown phase. The reduction amount of mean concentration from the pre lockdown phase to during lockdown of the main pollutants like PM 2.5, PM10 and NO2 are ~58.71%, ~57.92% and ~55.23%. Near RBU constant emission of PM2.5, 10 and NO2 have been recorded due to the nearby Cossipore thermal power station.
Prediction of Prognosis in Patients with Prostate Cancer by DNA Methylation Classification
Authors: Chen Lei , Pan Deshen , Sha Minglei , Li Deng , Xu Chaoliang , Chen Feiteng , Liu Jiayu , Zheng Danchuan , Lu Jun , Xia Shujie , Shao Yi
Published: July 2020

Background: Prostate cancer is the second most frequently diagnosed cancer and the fifth leading cause of cancer-related death. It is estimated that the incidence of prostate cancer is on the rise worldwide. Epigenetic changes in tumors play an important role in the occurrence and development of prostate cancer. DNA methylation is one of the mechanisms of tumor epigenetic regulation and may be a new biomarker that has great potential in early tumor screening, treatment guidance and prognosis prediction. The purpose of this study was to explore a classification method from the perspective of DNA methylation.Methods: The least absolute shrinkage and selection operator (LASSO) method was used to analyze DNA methylation and RNA-seq data from the Cancer Genome Atlas (TCGA). The methylation sites with small differences were eliminated, and the 21 methylation sites with the most significant differences were retained for analysis. Using their corresponding gene expression levels, a recurrence prediction model for prostate cancer patients was constructed to distinguish high-risk, medium-risk, and low-risk cases. Immune cell abundance analysis, gene enrichment analysis, Tumor burden mutation analysis and gene copy number variation analysis were then used to analyze the differences among these three subtypes and their underlying mechanisms. Results: We observed the difference in disease-free survival (DFS) of the three methylated subtypes in the test set, which was verified in the validation set. We found three subtypes have different proportions of immune cells, especially in memory B cells, M2 macrophages, Treg cells. GSVA and GSEA analysis revealed that the relevant metastasis gene sets of prostate cancer were enriched in high-risk cases. In addition, the mutation frequencies of TP53, TTN and KMT2D were the highest, and gradually increased in the three genotypes according to Tumor burden mutation (TMB) analysis. Gene copy number variation (CNV) showed that AR, LAPTM4B, and MTDH were significantly amplified, while ATP1B2 and FAM92B were significantly deleted. Finally, univariate and multivariate analysis showed that there were statistical differences among the three methylation subtypes, which can be used as an index to predict prostate cancer recurrence.Conclusions: Our study suggests that classification based on DNA methylation is an independent factor for predicting tumor recurrence in patients with prostate cancer.
Tumour-Associated Macrophage Polarisation Promotes Progression of Esophageal Carcinoma
Authors: Yuan Xin , Li Ya , Zhang An Zhi , Jiang Chen Hao , Li Fan Ping , Xie Yu Fang , Li Jiang Fen , Liang Wei Hua , Zhang Hai Jun , Liu Chun Xia , Pang Li Juan , Shen Xi Hua , Li Feng , Hu Jian Ming
Published: July 2020

Background: The immune response mediated by tumour-associated macrophages (TAMs) is vital in tumour progression in many cancers. Fibrinogen-like protein 2 (FGL2) is a critical immunosuppressive factor that regulates the tumour microenvironment. However, no study has yet reported on the relationship between FGL2, tumour-infiltrating lymphocyte recruitment, and prognosis in esophageal carcinoma (ESCA). Methods: Differentially expressed genes (DEGs) in various macrophage phenotypes were analysed using the GEO database. We identified the hub genes involved in affecting ESCA clinical prognosis using Kaplan-Meier plotter. Correlations between hub genes and immune infiltrates were analysed using the Tumour Immune Estimation Resource (TIMER) database, while correlation analysis between FGL2 and cytokine expression was assessed using cBioPortal. In vitro cell co-culture experiments were performed to examine the role of FGL2 in promoting tumorigenesis. Finally, we compared the GO terms and KEGG pathways enriched by the DEGs in M1 and M2 macrophages using DAVID.Results: High FGL2 expression was significantly associated with poorer overall survival and relapse-free survival of esophageal cancer patients. FGL2 expression was positively correlated with immune markers and infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells. In addition, FGL2 expression was strongly correlated to IL-10, MMP9, CCL5, TIM-3, IL-13, VCAM1, M-CSF and FGF-7 expression. Conclusions: M2-like TAMs may regulate the tumour microenvironment by secreting FGL2, thereby inducing the occurrence and progression of ESCA. Reversing TAM polarization may be an effective strategy that reveals new targets for immunotherapy in treating ESCA.
Phenotypic Clusters and Survival Analyses in Interstitial Pneumonia with Myositis-Specific Autoantibodies
Authors: Li Yihua , Yu Shiwen , Fan Yali , Wu Na , Wang Yiran , Ye Qiao
Published: July 2020

Background: Interstitial pneumonia (IP) is one of the common pulmonary complications of idiopathic inflammatory myopathy (IIM), among which myositis-specific autoantibodies (MSA) are specific for IIM diagnosis and prognosis. However, IP patients with MSA (MSA-IP) have not been well described. The study aimed to explore the phenotypic clusters and prognosis of MSA-IP patients.Methods: A total of 124 MSA-IP patients were prospectively enrolled for analysis. Serum MSA were detected using immunoprecipitation. Radiographic patterns of IP were determined according to the classification of idiopathic IPs. The clusters of MSA-IP patients were identified using cluster analysis. Potential risk factors of acute onset and short-term prognosis were also analyzed. Results: There were four clusters of MSA-IP patients. Cluster 1 patients were elders with chronic onset and usual interstitial pneumonia pattern on CT scan. Cluster 2 patients were all positive for anti-aminoacyl-tRNA antibodies, predominantly females and had frequent respiratory symptoms. Patients of cluster 3 showed multi-system involvements with nonspecific interstitial pneumonia pattern. Patients of cluster 4 had severe respiratory symptoms with anti-MDA5. The patients of cluster 3 (OR 6.682, 95% CI 1.560–28.622, P=0.011) or cluster 4 (OR 6.057, 95% CI 1.715–21.388, P=0.005) were susceptible to acute onset. The patients of cluster 4 were prone to disease progression (HR 2.711, 95% CI 1.128–6.519, P=0.034), which was consistent with the Kaplan–Meier curves.Conclusions: Four distinctive clusters were determined by cluster analysis suggesting the characteristics, serological antibodies and prognosis of MSA-IP.
Housing Conditions, Level of Feeding and Presence of Antibiotics in the Feed Shape Rabbit Cecal Microbiota
Authors: Velasco-Galilea María , Guivernau Miriam , Piles Miriam , Viñas Marc , Rafel Oriol , Sánchez Armand , Ramayo-Caldas Yuliaxis , González-Rodríguez Olga , Sánchez Juan P.
Published: July 2020

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes ( ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rDNA-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that the farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with the farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.
T-cell lymphoma with a granulomatous lesion of the lungs after autologous hematopoietic stem cell transplantation against Epstein–Barr virus-positive diffuse large B-cell lymphoma: a case report
Authors: Kajimoto Yusuke , Terasaki Yasuhiro , Terasaki Mika , Kunugi Shinobu , Okabe Yugo , Wakita Satoshi , Inokuchi Koiti , Shimizu Akira
Published: July 2020

Background
Post-transplant lymphoproliferative disorders (PTLDs) are serious lymphoid and/or plasmacytic proliferations that occur after undergoing solid organ or hematopoietic stem cell transplantation (HSCT). In the context of HSCT, most reported PTLDs have occurred in patients who received allogenic HSCT (AlloHSCT), but only a few cases have been reported in autologous HSCT (AHSCT) recipients. Primary pulmonary T-cell lymphoma cases are also rare and have been reported mostly in case studies.
Case presentation:
A 53-year-old female patient initially presented with enlargement of the left cervical lymph nodes and was diagnosed as Epstein–Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL). She was treated with R-CHOP, R-ACES, and autologous HSCT (AHSCT) and went into remission. Four years later, computed tomography results revealed multiple lung nodules, and abnormal infiltration and sustained and progressing hypogammaglobulinemia was observed. The pathological specimen of video-assisted thoracoscopic surgical lung biopsy demonstrated extensive invasion of lymphocytes with notable granuloma findings. Flow cytometric immunophenotyping analysis showed that lymphocytes were positive for CD3 and CD5; especially, CD3 was expressed in the cytoplasm. Southern blot analysis revealed rearrangements of the T-cell receptor Cβ1 gene. She was diagnosed with peripheral T-cell lymphoma, regarded as T-cell PTLD accompanied by granulomatous lesion.
Conclusion
Here, we report a rare case of T-cell lymphoma that mainly affected the lungs with the presentation of notable granulomatous findings following AHSCT against EBV-positive DLBCL. This uncommon presentation of rare lung lesions of granulomatous T-cell lymphoma could be related to the manifestation of a PTLD associated with sustained hypogammaglobulinemia.
Genotype Distribution of Human Papillomavirus (HPV) in Iranian Breast Cancer Patients
Authors: Mofrad Morvarid Golrokh , Sadigh Zohreh Azita , Ainechi Sanaz , Faghihloo Ebrahim
Published: July 2020

Background: the role of viruses in the aetiology of breast cancer (BC) have been significantly investigated in recent years. Human papillomavirus (HPV) has been detected in invasive breast carcinomas. Most studies have only focused on the detection of viral DNA therefore the aim of this study was to determine the genotypes of each papillomavirus.Methods: we collected and analyzed 70 blocks of Formalin Fixed Paraffin Embedded (FFPE) including 59 BC samples, and 11 noncancerous samples as control from Iranian patients using nested PCR. Real-time PCR supported nested PCR findings. Genotyping of HPV positive samples was performed, the samples were also subjected to a multiplex PCR to detect herpes simplex-1 (HSV-1), herpes simplex-2 (HSV-2), varicella zoster virus (VZV) and cytomegalovirus (CMV) in BC.Results: Papillomavirus DNA was present in 7 of 59 BC samples (11.8%); while none was detected in control samples. The most prevalent type was HPV18, followed by HPV 6, but we didn’t find HPV16 in cases. All HPV positive patients had high tumor grades (II/ III), and the age range of them were from 33 to 73 years (average was about 51). Most of HPV positive patients had low levels of education. Histologic diagnosis of all positive cases were ductal carcinoma. 5 of 59 BC specimens (8.47%), were positive for HSV-1.Conclusions: Our results suggest that high risk HPVs may play a role in breast carcinogenesis. Also we detected HPV6 and HSV1 in our BC samples, taking into account a carcinogenesis role for low risk HPVs, in addition to high risk HPVs. Further large scale studies are warranted to assess the significance of our findings.
Targeting DNA Methyltransferase 1 Limits Vesicular Stomatitis Virus Through Enhancing IRF3/IFN Signaling
Authors: Zhao Kui , Gao Fei , Lin Ye , Lin Jing , Zhang Bo , Song Deguang , Li Zi , Lan Yungang , Lu Huijun , He Wenqi , Guan Jiyu
Published: July 2020

BackgroundViruses develop strategies to escape from host anti-viral response in many aspects including hijacking host epigenetic factors. However, the relationship between host DNA methyltransferase 1 (DNMT1) and vesicular stomatitis virus (VSV) replication is largely unknown.MethodsIn the present study, we performed Western Blotting, qRT-PCR, RNA interference, Methylation-specific PCR and Cell viability assay to uncover the role of DNMT1 in the process of VSV replication.ResultsWe have observed VSV infection enhances DNMT1 protein accumulation in macrophage cell. Furthermore, DNMT1 functional blocking and gene silencing limit VSV replication. Moreover, loss of DNMT1 increases interferon responses, including Ifnb1 and IFN-stimulated genes (ISGs) upregulation. CpG islands (CGIs) of Irf3 promoter region are demethylated after DNMT1 short-term inhibition with thioguanine, which is accompanied by Irf3 transcript upregulation. Meanwhile, Irf3 silencing largely reversed DNMT1 loss-suppressed VSV replication. What is more, the basal level of endogenous retrovirus (ERV) transcripts is required for thioguanine-induced ISGs.ConclusionsDNMT1 loss-induced IRF3 enhancement leads to interferon responses and subsequent VSV suppression, which provides a potential strategy to inhibit viral replication by targeting DNMT1 with its inhibitor.
The prediction of survival and analysis of microenvironment in patients with sarcoma
Authors: Chen Jiarui , Liu Chong , Liang Tuo , Zhang Zide , Lu Zhaojun , Liao Shian , Jiang Jie , Xu Guoyong , Li Hao , Chen Tianyou , Qin Zhaojie , Liu Huijiang , Cen Jiemei , Zhan Xinli
Published: July 2020

The authors have requested that this preprint be removed from Research Square.
Comparison of the effectiveness of the XEN microstent in the treatment of different types of glaucoma
Authors: Schargus Marc , Teilig Therese , Rehak Matus , Busch Catharina , Bormann Caroline , Unterlauft Jan Darius
Published: July 2020

PurposeThe aim of this study was to compare the efficacy and safety profile of the XEN-microstent in different types of primary and secondary open angle glaucoma. MethodsThe XEN microstent was implanted in patients with primary open-angle glaucoma (POAG), normal-tension glaucoma (NTG), pseudoexfoliation glaucoma (PEX) and secondary glaucoma (Sec.Gl). The intraocular pressure (IOP), the active substances of the applied IOP-lowering drugs, the best corrected visual acuity (BCVA) and the mean deviation (MD) of the perimetry were measured at baseline and at regular follow-ups, scheduled at 2 days and 1, 3, 6 and 12 months after surgery. Results153 eyes were included in this analysis. 113 eyes were affected by POAG (74%), 5 eyes by NTG (3%), 22 eyes by PEX (14%) and 13 eyes by Sec.Gl (9%). Mean IOP decreased in all treatment groups during the 12 months of follow-up (complete group: 23.9±7.4 to 15.4±5.1 mmHg (p<0.01); POAG: 22.8±6.5 to 15.1±4.6 mmHg (p<0.01); NTG: 16.6±3.4 to 11.6±2.2 mmHg (p<0.05); PEX: 28.0±7.9 to 17.1±6.6 mmHg (p<0.01); Sec.Gl: 28.9±13.9 to 15.5±6.9 mmHg (p<0.05)). In the 153 eyes the average number of IOP-lowering drugs applied decreased from 2.6±1.2 to 0.8±1.3 12 months after surgery (p<0.01). BCVA and mean deviation of automated standard perimetry remained stable in all groups during follow-up. ConclusionAs in eyes suffering from POAG, IOP and number of IOP-lowering drugs applied can be effectively reduced by XEN implantation in eyes suffering from NTG, PEX and secondary glaucoma while leaving BCVA and visual field unchanged. Trial registrationTrial was registered at DRKS (registration number: DRKS00020800, Registered 25.February 2020 - Retrospectively registered, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00020800)
A Severe Case of Tafro Syndrome With myocardial and Skeletal Muscle calcification Despite Hypocalcemia: A Case Report
Authors: Minomo Shogo , Fujiwara Yu , Sakashita Shota , Takamura Akito , Nagata Kaoru
Published: July 2020

Background TAFRO (thrombocytopenia, anasarca, fever, renal insufficiency or reticulin fibrosis, and organomegaly) syndromeis a recently recognized disease with a variety of presentation of variable severity. In acute settings, this disease also involves organ dysfunction because of the associated systemic inflammation. However, cases of TAFRO syndrome with myocardial and/or skeletal muscle calcification have never been reported.Case presentation A 24-year-old healthy young man was admitted with intermittent epigastric pain and fever for two weeks. Computed tomography revealed pleural effusion, ascites and systemic lymphadenopathy. Laboratory tests showed thrombocytopenia, elevated C-reactive protein, hypoalbuminemia, anemia and renal dysfunction. Based on these findings and bone marrow biopsy, we diagnosed his disease as TAFRO syndrome and commenced hemodialysis for the renal dysfunction.However, he developed refractory hypocalcemia with unstable vital signs, for which we administered calcium gluconate hydrate. Thereafter, myocardial and skeletal musclecalcification was revealed radiologically, with the myocardial calcification causing sick sinus syndrome. He was treated with tocilizumab and finally discharged in an ambulatory condition after prolonged hospitalization with residual lesions of calcification.Conclusion This is the first TAFRO syndromereport with the complication of organ calcification. The etiology of calcification in this case is not clear.Systemic inflammation with possible hypercytokinemia might have been involved in the unexpected complication of systemic calcification.It is important to handle general management of TAFRO syndrome carefully because of various complications.
Quality Validation of Platelets Obtained From the Haemonetics and Trima Accelautomated Blood-collection Systems
Authors: Wang Hsuan-Hui , Liao Li-Na , Lin Chi-Ling , Yen Ling-Ling , Hsiao Yi-Min , Ko Jiunn-Liang
Published: July 2020

Background: Platelet transfusion is required to treat haemo-oncology or trauma patients. Platelet apheresis (PPH) performed with apheresis equipment has increased rapidly in recent years. Leucocyte-reduced platelet apheresis (LRPH) can reduce the risk of platelet refractoriness and febrile nonhemolytic transfusion reactions (FNHTRs) for transfusion. Accordingly, this study aimed to investigate and compare the platelet metabolic and functional responses between PPH performed with Haemonetics and LRPH performed with Trima Accel cell separator.Methods: The qualities of platelets collected through PPH and LRPH were evaluated in terms of visual appearance, morphology, platelet-aggregation changes, metabolic activities, and bacterium-screening test during 5-day storage. Statistical analyses included two-sample t-test and generalised estimating equation(GEE) method.Results: During 5-day storage in LRPH, residual leucocytes were all <1.0×106, and the parameters of platelet function were as follows: platelet aggregated to agonists such as adenosine 5′-diphosphate (ADP) and collagen, and the extent of shape change and pO2 showed no statistically significant difference between PPH and LRPH. The hypotonic shock reaction (HSR) on days 0, 1, and 3 were significantly higher in LRPH than in PPH (71.78±6.92 vs. 64.10±7.42; p=0.002; 71.53±8.98 vs. 62.96±9.84; p=0.007; 68.05±7.28 vs. 57.76±6.80; p<0.0001, respectively). Values of mean platelet volume (MPV) were statistically larger in PPH than in LRPH on days 0, 1, and 3. On day 5, the swirling score was higher in LRPH than in PPH. The mean lactate levels had no statistically significant difference between PPH and LRPH. Moreover, no growth was observed through bacterium-screening test conducted on 40 samples.Conclusion: Comparison of LRPH and PPH products collected from the Trima Accel and Haemonetics automated blood-collection systems, respectively, revealed that both products possessed good platelet qualities even though additional processes are needed to reduce leucocytes. Furthermore, investigating the outcomes of other apheresis instruments with focus on the safety of donors, products, and recipients is necessary.
Malnutrition and Associated Factors with Nutritional Status Among Orphan Children: An Evidence-Based Study From Nepal
Authors: Acharya Shiva Raj , Adhikari Shiksha , Moon Deog Hwan , Pahari Sandip , Shin Yong Chul
Published: July 2020

Background: Malnutrition is common public health problem among children in low- and middle-income countries. Orphan’s children are vulnerable and neglected group in the society and are more prone to malnutrition. The study aims to identify prevalence of underweight, stunting and thinness of children residing in slum area with its associated factors. Method: Quantitative method & analytical cross-sectional research design were used to assess the nutritional status and its associated factors among orphan children in Pokhara, Nepal. The sample size of 160 children were obtained by simple random technique. Semi-structured questionnaire, digital bathroom scale, stadiometer was used as data collection technique. Data management and analysis was done from Epi-info, SPSS 25 version & WHO Anthro plus. Result: Out of 160 children, majority 80% were malnourished & 55.1% were stunted whereas 13.8% were thinness & 6.9% were found to be overweight. Our study revealed a significant association between sex, age, ethnicity, duration of stay in children’s home and education of caregiver (p <0.05). Conclusion: Malnutrition is highly prevalent in orphan children and need to be addressed. Nutritional status should be monitored regularly for early identification & timely intervention of malnutrition to promote the nutrition health status of children.
COVID 19 Antibody Detection using Lateral Flow Assay Tests in a Cohort of Convalescent Plasma Donors
Authors: Ragnesola Brett , Jin Daniel , Lamb Chris C. , Shaz Beth H. , Hillyer Christopher D. , Luchsinger Larry L.
Published: July 2020

Objective: COVID19 has caused a global and ongoing pandemic. The need for population seroconversion data is apparent to monitor and respond to the pandemic. Using a lateral flow assay (LFA) testing platform, the seropositivity in 63 New York Blood Center (NYBC)Convelescent Plasma (CP) donor samples were evaluated for the presence of COVID19 specific IgG and IgM.Results: CP donors showed diverse antibody result.Convalescent donor plasma contains SARS-CoV-2 specific antibodies. Weak antibody bands may identify low titer CP donors.LFA tests can identify antibody positive individuals that have recovered from COVID19. Confirming suspected cases using antibody detection could help inform the patient and the community as to the relative risk to future exposure and a better understanding of disease exposure.
Focal brain ischemia in mice does not cause electrophysiological signs of critical illness neuropathy
Authors: Huehnchen Petra , Toyka Klaus Viktor , Gertz Karen , Endres Matthias , Boehmerle Wolfgang
Published: July 2020

Objective
Critical illness polyneuropathy (CIP) is a common complication of severe systemic illness treated in intensive care medicine. Ischemic stroke leads to an acute critical injury of the brain with hemiparesis, immunosuppression and subsequent infections, all of which require extended medical treatment. Stroke-induced sarcopenia further contributes to poor rehabilitation and is characterized by muscle wasting and denervation in the paralytic, but also the unaffected limbs. Therefore, we asked whether stroke leads to an additional CIP-like neurodegeneration.
Results
Focal brain ischemia was induced in adult mice by 60-minute middle cerebral artery occlusion (MCAo) following reperfusion and led to functional deficits and marked hemispheric brain atrophy. Nerve conduction function and muscle potentials were measured in the ipsilateral sciatic nerve and gastrocnemius and quadriceps muscle with electroneurography/-myography on days 10, 22, 44 after stroke. An additional crush-injury to the sciatic nerve was included in two sham mice as positive control (sham+). We found no differences in nerve conduction function nor spontaneous electromyographic activity between MCAo and sham animals. Sham + mice developed marked reduction of the motor action potential amplitudes and conduction velocities with pathologic spontaneous activity.