bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulp and Papermaking Characteristics of South Sudanese Cordia Africana (Gambil) Wood
Authors: Elzaki Osman Taha , Tuphach Selim Otuk , Khider Tarig 
Published: May 2020

Abstract
The wood of an important indigenous Sudanese hardwood species, Cordia africana lam, was examined to determine its suitability for pulp and papermaking. Basic density, bark-to-wood ratio, fiber dimensions and chemical composition were studied. Pulps were evaluated and papermaking characteristics were tested. C. africana wood showed medium basic density (410 kg m-1). The average bark-to wood ratio by mass (6.82%) and volume (11.67%) were in the normal average for pulpwood and could be used for production of high grade pulp.The fibers of C. africana were long with an average fiber length of 1.13 mm, average fiber diameter was 30 µm with an average lumen diameter 20 µm and cell wall thickness of 5 µm. the wood showed high ash content (2.7%), high pentosans (25%), relatively medium lignin content (23.9%).C. africana pulped with 12-15% alkali charge as Na2O for two hours at 170 0C gave good Kappa numbers with normal and relatively high yield with very low rejects. The addition of 0.13% anthraquinone (AQ) in cooking liquor reduced the active alkali consumption by 2-2.3%, increased the pulp yield and reduced bleachable Kappa numbers. The pulp produced suitable for wrapping paper and paperboard.
SARS-CoV-2 Seroprevalence Among Parturient Women
Authors: Flannery Dustin D. , Gouma Sigrid , Dhudasia Miren B. , Mukhopadhyay Sagori , Pfeifer Madeline R. , Woodford Emily C. , Gerber Jeffrey S. , Arevalo Claudia P. , Bolton Marcus J. , Weirick Madison E. , Goodwin Eileen C. , Anderson Elizabeth M. , Greenplate Allison R. , Kim Justin , Han Nicholas , Pattekar Ajinkya , Dougherty Jeanette , Kuthuru Oliva , Mathew Divij , Baxter Amy E. , Vella Laura A. , Weaver JoEllen , Verma Anurag , Leite Rita , Morris Jeffrey S. , Rader Daniel J. , Elovitz Michal A. , Wherry E. John , Puopolo Karen M. , Hensley Scott E. 
Published: May 2020

Abstract
SARS-CoV-2 has led to a pandemic of respiratory and multisystem disease, named COVID-19.1 Limited data are available for pregnant women affected by COVID-19.2 Serological tests, particularly those that provide quantitative information, are critically important to determine exposure and immunity to SARS-CoV-2 within both individuals and populations.3 Here, we completed SARS-CoV-2 serological testing of 237 parturient women at two centers in Philadelphia from April 4 to April 15, 2020. Using an assay with a 1.0% false positive rate, we show that 14/237 (5.9%) of parturient women possessed IgG and/or IgM SARS-CoV-2-specific antibodies. We found significant racial differences, with an 11.2% seropositive rate in black women and a 1.5% seropositive rate in women of other races. Seropositive women who received nasopharyngeal (NP) SARS-CoV-2 PCR (polymerase chain reaction) testing were all found to be positive. Continued serologic surveillance among pregnant women may inform perinatal clinical practices and can potentially be used to estimate seroprevalence within the community.Authors Dustin D. Flannery and Sigrid Gouma contributed equally to this work.
Effect of Antithrombotic Therapy on Secondary Bleeding After Proctological Surgery
Authors: Maemoto Ryo , Tsujinaka Shingo , Miyakura Yasuyuki , Machida Erika , Kakizawa Nao , Takahashi Jun , Tamaki Sawako , Ishikawa Hideki , Rikiyama Toshiki 
Published: May 2020

Abstract
Background: The purpose of this study was to identify the incidence and severity of secondary bleeding after proctological surgery for patients with or without antithrombotic therapy.Methods: We retrospectively identified 113 patients who underwent proctological surgery in our hospital from March 2009 to February 2019. In general, antiplatelet drugs were continued and anticoagulant drugs were either substituted or withdrawn prior to the surgery. The severity of secondary bleeding was classified as mild, moderate, severe.Results: Eighteen patients underwent antiplatelet therapy (A group) and 95 patients did not undergo antithrombotic therapy (N group). Secondary bleeding was observed in nine patients (8.0%) and patients in the A group exhibited significantly higher rate of secondary bleeding rate than patients in the N group (39% vs. 2.4%, P < 0.01). The median interval from surgery to the onset of secondary bleeding was 5 (range: 0-11days). The severity of bleeding was the highest in patients administered direct oral anticoagulants (DOAC) and was the lowest in those administered aspirin. There was no mortality or cardiovascular event.Conclusions: Antithrombotic therapy is associated with high risk of secondary bleeding after proctological surgery, particularly in patients who undergo anticoagulant therapy. Delaying of postoperative resumption of anticoagulants may be considered in balancing the individual risk of postoperative thromboembolic complications against the risk of secondary bleeding. Future prospective studies with larger number of patients are needed to determine the appropriate timing of resuming antithrombotic therapy.
Point-of-care serological assays for SARS-CoV-2 in a UK hospital population: potential for enhanced case finding
Authors: Pallett Scott , Denny Sarah , Patel Aatish , Charani Esmita , Mughal Nabeela , Stebbing Justin , Davies Gary , Moore Luke 
Published: May 2020

Abstract
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic. Case identification is currently made by real-time polymerase chain reaction (PCR) during the acute phase and largely restricted to healthcare laboratories. Serological assays are emerging but independent validation is urgently required to assess their utility.We evaluated five different point-of-care (POC) SARS-CoV-2 antibody test kits against PCR, finding concordance across the assays (n=15). We subsequently tested 200 patients using the OrientGene COVID-19 IgG/IgM Rapid Test Cassette and find a sensitivity of 74% in the early infection period (day 5-9 post symptom onset), with 100% sensitivity not seen until day 13. Specificity was 96%, but in validating the serological tests uncovered potential false-negatives from PCR testing late-presenting cases. A positive predictive value (PPV) of 37% in the general population precludes any use for general screening. Where a case definition is applied however, the PPV is substantially improved (95·4%), supporting use of serology testing in carefully targeted populations. Larger studies in specific patient cohorts, including those with mild infection are urgently required to inform on the applicability of POC serological assays to help control the spread of SARS-CoV-2 and improve case finding of patients that may experience late complications.
EPDR1 correlates with immune cell infiltration in hepatocellular carcinoma and can be used as a prognostic biomarker
Authors: Chen Ruochan , Zhang Yiya 
Published: May 2020

Abstract
Background: Hepatocellular carcinoma (HCC) has high mortality rate and is a serious disease burden globally. Hence, identification and characterization of novel biomarkers for the diagnosis and prognosis of HCC are critically important. The protein EPDR1 (ependymin related 1) is a member of piscine brain glycoproteins and is involved in cell adhesion. This is the first study to report the expression of EPDR1 and its prognostic significance, pathological role, and association with cancer immunity in HCC.Methods: The gene expression, prognostic, and clinicopathological analyses were performed based on the data obtained from multiple transcriptome databases. Protein expression of EPDR1 in HCC was verified using human protein atlas and CPTAC databases. Co-expression network analysis using the LinkedOmics database was performed to identify genes co-expressed with EPDR1 expression. Functional analysis of the co-expressed genes, including gene set enrichment analysis was performed to identify the functional role of EPDR1. The statistical analysis was conducted in R, and the relationship between EPDR1 expression and immune cell infiltration was analyzed using TIMER and CIBERSORT resources. Results: The expression of EPDR1 was found to be significantly higher in HCC tissues than in the normal tissues and is an independent prognostic factor for the overall survival of HCC patients. Further, a high level of EPDR1 was shown to be correlated with advanced stage of HCC. Functional analysis revealed that EPDR1 is associated with multiple signaling pathways as well as pathways related to cancer and apoptosis. Notably, EPDR1 expression significantly correlated with purity and the infiltration levels of B cells, CD8+ and CD4+ T cells, macrophages, neutrophils, and dendritic cells in HCC. Further, the EPDR1 expression significantly correlated with the expression of immune signatures, such as KIR2DL4, ITGAM, GATA3, STAT6, STAT5A, BCL6, STAT3, and HAVCR2.Conclusions: Our study identified EPDR1 as a novel prognostic biomarker in HCC. The expression of EPDR1 was shown to be associated with immune cell infiltration as well as the signature molecules that potentially regulate these processes during the carcinogenesis of HCC. With better understanding of its biological function, EPDR1 could become an effective target for HCC diagnosis and treatment in the future.
To procrastinate or not to procrastinate: the optimal timing of containing the global COVID-19 pandemic spread
Authors: Li Jun , Zhou Yimin , Ye Lingjian , Zhang Joy Y , Chen Zhuo 
Published: May 2020

Abstract
As global public health is under threat by the 2019-nCoV, an urgent question to ask is what the optimal strategy of epidemic prevention and control (P&C) measures would be, especially in terms of the timing of enforcing aggressive policy response so as to maximise health efficacy and to contain pandemic spread. Here, we developed a logistic probability function configured SEIR model to analyse the COVID-19 outbreak and estimate its transmission pattern under different “anticipate- or delay-to-activate” policy response scenarios in containing the pandemic. We wound that the potential positive effects of stringent P&C measures would be cancelled out in case of significantly delayed action, whereas a partially procastinatory wait-and-see control policy may still be able to contribute to containing the degree of epidemic spread although its effectiveness may be significantly compromised compared to a scenario of early intervention coupled with stringent P&C measures. A laissez faire policy adopted by the government and health authority to tackling the uncertainly of COVID19-type pandemic development during the early stage of the outbreak turns out to be a very bad strategy from optimal control perspective, as significant damages would be produced in that case. Authors Jun Li and Yimin Zhou contributed equally to this work.
Drug repurposing: Dipeptidyl peptidase IV (DPP4) inhibitors as potential agents to treat SARS-CoV-2 (2019-nCov) infection
Authors: Rao Praveen P. N. , Pham Amy Trinh , Shakeri Arash , Shatshat Amna El , Zhao Yusheng , Karuturi Rahul C. , Hefny Ahmed A. 
Published: May 2020

Abstract

The current outbreak of severe acute respiratory distress syndrome (SARS) or nCOVID-19 pandemic, caused by the coronavirus-2 (CoV-2), continues to wreak havoc globally. Unfortunately, there are no concrete treatment options available which has severely hampered the pharmacotherapy of this devastating infection. This calls for an urgent need to consider alternative strategies which can be employed quickly, as discovering new drugs for SARS-CoV-2 infections is a time consuming and expensive proposition. In this regard, drug repurposing is an appealing approach which can provide rapid access to therapeutics with proven record of safety and efficacy. Accordingly, we investigated the drug repurposing potential of a library of dipeptidyl peptidase 4 (DPP4) inhibitors which are currently marketed for type-2 diabetes, to treat SARS-CoV-2 infections. Computational studies were conducted in the crystal structure of the substrate binding site of viral protease, the SARS-CoV-2 Mpro dimer, which led to the identification of three marketed DPP4 inhibitors; gemigliptin, linagliptin and evogliptin exhibiting favorable binding, in the SARS-CoV-2 Mpro dimer, viral protease. These studies support the repurposing of DPP4 class of inhibitors in treating SARS-CoV-2 infections, especially in elderly patients with type-2 diabetes, who are at a greater risk of suffering from increased disease severity and mortality.
Analysis of the full genome sequences of SARS-CoV-2 isolates to determine antigenic proteins and epitopes to be used for the development of a vaccine or a diagnostic approach for COVID-19
Authors: Can Hüseyin , Köseoğlu Ahmet Efe , Alak Sedef Erkunt , Güvendi Mervenur , Döşkaya Mert , Karakavuk Muhammet , Gürüz Adnan Yüksel , Ün Cemal 
Published: May 2020

Abstract
In genome of SARS-CoV-2, the 5’-terminus encodes a polyprotein (pp1ab), which is further cleaved into 15 non-structural proteins (nsp-1 to nsp-10 and nsp-12 to nsp-16) whereas the 3’ terminus encodes four structural proteins (spike, envelope, membrane, and nucleocapsid) and eight accessory proteins (3a, 3b, p6, 7a, 7b, 8b, 9b, and orf14). Among these 27 proteins, the present study aimed to discover likely antigenic proteins and epitopes to be used for during the development of a vaccine or serodiagnostic assay using a reverse vaccinology in silico approach. For this purpose, after the full genome analyses of SARS-CoV-2 isolates, viral surface proteins including spike, envelope and membrane proteins as well as proteins with predicted signal peptide were determined as probable vaccine candidates whereas the remaining were considered as possible antigens to be used during development of serodiagnostic assays. According to results, the phylogenetic analysis of SARS-CoV-2 isolates from 31 different countries showed two significant clusters in which one was clustered with China-Wuhan and the other one with China-Yunnan isolates. During the analyses, 105 SNPs were identified that resulted in change in 70 amino acid positions. Among the 27 proteins, 26 of them were predicted as probable antigen, except nsp-16. In 26 proteins, spike protein was selected as the best vaccine candidate because of having a signal peptide, negative grand average of hydropathicity value, one transmembrane helix, moderate aliphatic index, a big molecular weight, a long-estimated half-life, beta wrap motifs as well as having a stable, soluble and non-allergic features. In addition, orf7a, orf8 and nsp-10 proteins were considered as potential vaccine candidates because of having signal peptides. Nucleocapsid protein and a highly antigenic GGDGKMKD epitope of nucleocapsid protein were identified as ideal antigens to be used in development of serodiagnostic assays. Moreover, considering MHC-I alleles, highly antigenic KLNDLCFTNV and ITLCFTLKRK epitopes belonging to spike and orf7a proteins can be used to develop an epitope-based peptide vaccine or used as antigen for development of serodiagnostic assay.
Complete Genome Analysis of A Virulent Vibrio Scophthalmi Strain VSc190401 Isolated form Diseased Marine Fish Half-Smooth Tongue Sole, Cynoglossus Semilaevis
Authors: Zhang Zheng , Yu Yong-xiang , Wang Yin-geng , Liu Xiao , Wang Lifang , Zhang Hao , Liao Mei-jie , Li Bin 
Published: May 2020

Abstract
Background: Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in marine environment. Earlier studies have suggested that it is a normal microorganism in turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanism.Results: In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3,185 coding genes. Among these genes, 2,648, 2,298 and 1,915 genes could be found through annotation information in COG, Blast2GO and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI database showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance.Conclusions: Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism might be complicated.
A Rice Promoter Protein Binding Microarray for Cis-Acting Elements for Rice Transcription Factors
Authors: KIM JOUNG SUG , Chae SongHwa , Jun Kyong Mi , Lee Gang-Seob , Jeon Jong-Seong , Kim Kyungdo , Kim Yeon-Ki 
Published: May 2020

Abstract
BackgroundTranscription factors (TFs) regulate the expression of genes at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas for the functional analysis of TFs in the postgenomic era. Although many methods have been developed for this challenge, there are still many TFs with unknown DNA-binding motifs.FindingsIn this paper, we designed an rice (Oryza sativa)-specific protein binding microarray (RPBM), and its probes are 40 bp long with 20 bp of overlap; there are 49 probes spanning the 1 kb promoter region before the translation start site of each gene. To confirm the efficiency of RPBM technology, we selected two TFs, OsWOX13 and OsSMF1. We identified the ATTGATTG DNA-binding sequence and 635 putative target genes of OsWOX13. OsSMF1 bound to GCTGACTCA and GGATGCC sequences and bound especially strongly to CCACGTCA. A total of 932 putative target genes were identified for OsSMF1.ConclusionsRPBM can be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in extended natural promoter regions. The analysis can also be applicable to TFs that have single or multiple binding motifs. The technology might even be expanded for application to TFs that are heterodimers or form higher-order complexes.
Construction of a Prognostic Value Model in Papillary Renal Cell Carcinoma by Immune-Related Genes
Authors: Wang Leilei , Gu Weile , Ni Huijun 
Published: May 2020

Abstract
Papillary renal cell carcinoma (PRCC) is the second most common type of renal carcinoma following clear cell renal cell carcinoma, and the role of immune-related genes (IRGs) in tumorigenesis and metastasis is evident; its prognostic value in PRCC remains unclear. In this study, we downloaded the gene expression profiles and clinical data of patients with PRCC from The Cancer Genome Atlas (TCGA) database and obtained IRGs from the ImmPort database. A total of 371 differentially expressed IRGs (DEIRGs) were discovered between PRCC and normal kidney tissues. Prognostic DEIRGs (PDEIRGs) were identified by univariate Cox regression analysis. Then, we screened the four most representative PDEIRGs (IL13RA2, CCL19, BIRC5, and INHBE) and used them to construct a risk model to predict the prognosis of patients with PRCC. This model precisely stratified survival outcome and accurately identified mutation burden in PRCC. Thus, our results suggest that these four PDEIRGs are available prognostic predictors for PRCC. They could be used to assess the prognosis and to guide individualized treatments for patients with PRCC.
Quality of life, Social Support and Self-Efficacy in Women After A Miscarriage
Authors: Iwanowicz-Palus Grażyna , Mróz Mariola , Bień Agnieszka 
Published: May 2020

Abstract
Background Pregnancy loss is typically experienced as a traumatic, critical event, which may lead to secondary psychological health disorders. Its burden involves both the experience of loss and related medical issues, which are associated with pain, hospitalization, limitation in one’s social roles, decreased sense of security, and changes in one’s perceived quality of life. The purpose of the present study was to evaluate levels of quality of life (QoL), social support and self-efficacy among women who had suffered a miscarriage.Methods The study was performed using a diagnostic survey method with questionnaires administered to 610 patients hospitalized due to spontaneous pregnancy loss in hospitals in Lublin (Poland). The instruments used were: the Berlin Social Support Scales (BSSS), the Generalized Self-Efficacy Scale (GSES), the WHOQoL–BREF questionnaire, and a standardized interview questionnaire.Results Respondents rated their overall QoL (3.90 points) higher than their overall perceived health (3.66). In terms of social support, the highest scores were noted for perceived available instrumental support (M = 3.78), perceived available emotional support (M = 3.68) and actually received support (M = 3.60). The mean generalized self-efficacy score among the women after pregnancy loss was 30.29. Respondents’ QoL was significantly correlated with multiple social support subscales and self-efficacy (p < 0.05). Conclusions Women after a miscarriage perceive their overall QoL as better than their overall health, while reporting the poorest QoL in the psychological domain. They also have a high level of self-efficacy. Regarding the types of social support, perceived available support, both instrumental and emotional, and actually received support was rated highly. Social support and self-efficacy contributed to better perceived QoL among the respondents.
Human health risk assessment through the comparative analysis of diverse irrigation regimes for Luffa (Luffa cylindrica (L.) Roem.)
Authors: Khan Zafar Iqbal , Ugulu Ilker , Sahira Shagufta , Mehmood Naunain , Ahmad Kafeel , Bashir Humayun , Dogan Yunus 
Published: May 2020

Abstract
In the present study, the effects of untreated wastewater and associated health risks were assessed in an abundantly consumed vegetable, Luffa cylindrica. In this direction, trace metal accumulations in L. cylindrica samples irrigated with three different water regimes (municipal wastewater, groundwater, and canal water) were determined. The metal levels were defined by atomic absorption spectrophotometer equipped with a graphite furnace and D2 corrector. Trace metal concentrations in L. cylindrica samples were in the range of 7.91–9.01, 3.78–4.22, 0.54–0.63, 39.18–43.27, 15.76–20.82, 29.04–42.49, 6.96–8.24, 5.85–7.72, 4.06–4.39 and 0.18–0.42 mg/kg for Mo, As, Se, Fe, Cu, Zn, Ni, Pb, Cd and Co, respectively. The health risk index values of As, Cd, Pb, Mo, Ni, Se and Co; and pollution load index values of As, Mo, Ni, Cu, Cd and Pb were high, indicating possible phytotoxicity. As had the highest value for the pollution load index suggesting high-risk levels. High levels of some metals could be an alarm call for consumers as the vegetable is irrigated with untreated wastewater.