bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping of Qtl for Anaerobic Germination Using the Donor Ac39416a in the Genetic Background of Swarna Sub-1 (Oryza Sativa L.)
Authors: SAIMOHAN BOLLINENI , Chamundeswari N. , Haritha T. , Veronica N. 
Published: June 2021

Abstract
Background: Anaerobic germination is an important trait in particular for cultivation under direct seeding method in kharif season, as well as during nursery rising for transplant rice, as sometimes unexpected rains immediately after sowing will drastically reduce the plant population.Methods and Results: In the present investigation phenotypic screening for Anaerobic germination (AG) was carried out using 188 F2:3 population of Swarna Sub1/AC39416A at RARS (APRRI), Maruteru. The mean anaerobic germination per cent recorded after the two weeks of submergence ranged from 0% to 95% with overall mean of 47.51% whereas, for three weeks of submergence, the mean anaerobic germination per cent recorded between 0 and 95%, with overall mean of 37.66%. 134 (19.42%) out of 687 Simple Sequence Repeats (SSR) markers surveyed were polymorphic between the parents. Linkage analysis was done with 83 SSR markers showing polymorphism clearly using the integrated software called QTL IciMapping software version 4.1.0. The length of linkage map constructed across whole genome was 3600.8 cM and identified seven QTLs viz., qAG2, qAG3, qAG7-1, qAG7-2, qAG9, qAG10 and qAG12. All these seven QTLs explained phenotypic variance of about 37.47% collectively for AG trait, with their individual contributions ranging from 3.5% to 8.67% of phenotypic variation and LOD scores of 2.6 to 5.86. The LOD score and phenotypic variance is 5.86 and 8.67% respectively for qAG10 a novel QTL identified in the present study using ICIM method. Conclusion: QTL “qAG12-1” identified in this study may be considered for introgression into popular elite rice varieties otherwise susceptible for anaerobic germination after fine mapping studies.
Genetic Evidence Disapproves Coevolution between O.sinensis and Host Insects from Qing-Tibetan Plateau
Authors: Guo Zhifan , Li Xiang , Sha Tao , Li Yan 
Published: June 2021

Abstract
Host-parasite coevolution is driven by the selective pressures each partner conferring on the other to merely maintain parity with other evolving species. Ophiocordyceps sinensis represents one of excellent model host-parasite complex, allowing us to explore evolutionary relationship between host and parasite. Although previous studies have demonstrated coevolution between O.sinensis and host insects, the incongruence in phylogenetic relationship of both is incompatible. In this study, we used ITS gene of O.sinensis and COI gene of host insects to evaluate the phylogenetic relationship, estimate the divergence time, infer demographic history, analyze identity by state distance matrix, and simultaneously explore evolutionary relationship or address the evolutionary pattern. We found distinct phylogenetic topology between O.sinensis and host insects from the main distribution of China. Additionally, the branch length ratio, demographic inference, and IBS analysis consistently suggested independent evolution between O.sinensis and host insects rather than arms race coevolution. However, populations of both O. sinensis and host insects from Qinghai lake showed similar evolution rate and phylogenetic topology, which might be associated with the formation of Qinghai Lake. Together, the data presented here provided new insights into host-parasite evolutionary relationship.
Transcriptome Analysis of Clavibacter Michiganensis Subsp. Michiganensis-Infected Tomatoes: A Role Of Salicylic Acid In The Host Response
Authors: Yokotani Naoki , Hasegawa Yoshinori , Sato Masaru , Hirakawa Hideki , Kouzai Yusuke , Nishizawa Yoko , Yamamoto Eiji , Naito Yoshiki , Isobe Sachiko 
Published: June 2021

Abstract
Bacterial canker of tomato (Solanum lycopersicon) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is an economically important disease. However, the molecular events that occur are poorly understood. To understand the host defense response to C. michiganensis infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1,877 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to C. michiganensis showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of WRKYs, NACs, HSFs, and CBP60s encoding transcription factors (TFs) were upregulated, implying their involvement in defense-associated gene expression during tomato–C. michiganensis interactions. Tomato genes orthologous to Arabidopsis EDS1, EDS5/SID1, and PAD4/EDS9, which are causal genes of salicylic acid (SA)-deficient mutants, were activated, and infection drastically stimulated SA accumulation in tomatoes. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of WRKYs, suggesting that some C. michiganensis-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against C. michiganensis.
Engineering the magnetism of nanographene via co-depositing hetero precursors
Authors: Zhang Hui , Lu Jianchen , Zhang Yong , Gao Lei , Zhao Xin-Jing , Tan Yuan-Zhi , Cai Jinming 
Published: June 2021

Abstract
The magnetism of carbon nanomaterials is dominated by the structure of its carbon skeleton. However, the magnetism engineering is hindered due to finite precursors. Here, we develop a new strategy to engineer the magnetism of nanographene through hetero-coupling two different precursors on Au(111) surface by using low-temperature bond-resolved scanning tunneling microscopy and scanning tunneling spectroscopy, combined with spin-polarized density functional theory calculations. Our results demonstrate that two homo-coupled products host close shell structure along with defects inducing magnetic one with the total spin number S = 1/2. Upon simultaneous depositing with another precursor, two hetero-coupled products switch to magnetic structure with the S = 1/2 and S = 1 resulting from carbon skeleton transformation. Our results provide a valid way via inducing different molecular precursors to engineer the magnetism of carbon nanomaterials, which could be extended in other magnetic materials instruction.
Uric Acid Enhances Neurogenesis in a Parkinsonian Model by Remodeling Mitochondria
Authors: Lee Ji Eun , Shin Yu Jin , Kim Ha Na , Kim Dong Yeol , Chung Seok Jong , Yoo Han Soo , Shin Jin Young , Lee Phil Hyu 
Published: June 2021

Abstract
Adult neurogenesis is the process of generating new neurons to enter neural circuits and differentiate into functional neurons. However, it is significantly reduced in Parkinson’s disease (PD). Restoring neurogenesis is suggested to be a potential disease-modifying strategy to treat PD. Uric acid (UA), a natural antioxidant, has neuroprotective properties in patients with PD. Here, we hypothesized that UA would enhance neurogenesis by modulating mitochondria, dynamic organelles and key regulators of the fate of neural stem cells. We evaluated whether elevating serum UA levels in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonian model would restore neurogenesis in the subventricular zone (SVZ). UA-elevating therapy significantly increased the number of bromodeoxyuridine (BrdU)-positive cells in the SVZ of PD animals as compared to PD mice with normal UA levels. In a cellular model, UA treatment promoted cell proliferation against 1-methyl-4-phenylpyridinium (MPP+) in primary cultured neural precursor cells (NPCs) from the SVZ. These findings demonstrate that UA enhances neurogenesis by modulating mitochondrial dynamics in the SVZ of parkinsonian models, suggesting UA elevating strategy as a potential disease-modifying therapy in treatment of parkinsonian disorders.
Genome-wide DNA Methylation and Gene Expression Patterns of Androgenetic Haploid Tiger Pufferfish (Takifugu Rubripes) Provide Insights into Haploid Syndrome
Authors: Zhou He , Wang Qian , Zhou Zi-Yu , Li Xin , Sun Yu-Qing , Shan Gu , Zheng Xin-Yi , Chen Qi , Liu Hai-Jin , Wang Wei , Shao Chang-Wei 
Published: June 2021

Abstract
Androgenesis is an important chromosome set manipulation technique used in sex control in aquaculture. Haploid embryos exhibit haploid syndrome and show abnormalities and even die during early embryonic development. In this study, we used whole genome bisulfite sequencing (WGBS) to investigate the genome-wide DNA methylation profiles in haploid females (1n-X) and males (1n-Y), and diploid females (2n-XX) and males (2n-XY) of tiger pufferfish (Takifugu rubripes), an economically important ﬁsh in China. A total of 96.32 Gb clean data was produced. Analysis of differentially methylated regions (DMRs) showed that haploids had more hyper-methylated regions than diploids, which may be related to abnormal development and early embryonic death in haploids. There were 7,838 hyper-methylated differentially methylated genes (DMGs) and 4,755 hypo-methylated DMGs in haploid vs. diploid comparisons in both females and males. These DMGs were mainly related to genomic stability maintenance and cell cycle regulation. slf1, actr8, gas2, and pbrm1 genes were detected to validate the methylation sequencing. After combining the methylation data with the corresponding transcriptome data, we identified several genes, including guca2a, myoc, fezf2, rprml, telo2, s100a1, and marveld1, which exhibited differential expression levels modulated by DNA methylation. In conclusion, our study revealed different methylation and expression profiles between haploid and diploid T. rubripes for the first time. Several DMGs were identified between different ploidy levels, which may be related to haploid syndrome formation. The results expand the understanding of the effects of ploidy on the early development of teleosts and provide knowledge about target genes and networks to improve the survival rate of haploids.
Assessment of Genetic Diversity of Plasmodium Falciparum Circumsporozoite Protein in Sudan; The RTS,S Leading Malaria Vaccine Candidate
Authors: Mohamed Nouh Saad , AbdElbagi Hanadi , Elsadig Ahad R. , Ahmed Abdalla Elssir , Mohammed Yassir Osman , Elssir Lubna Taj , Elnour Mohammed Ahmed B , Ali Yousif , Ali Mohamed S. , Alrahman Omnia Fateh , Siddig Emmanuel Edwar , Ahmed Ayman , Omer Rihab Ali 
Published: June 2021

Abstract
The currently used malaria vaccine; the RTS,S, is designed based on the Plasmodium falciparum circumsporozoite protein (PfCSP). The PfCSP gene, besides having different polymorphic patterns, can vary between P. falciparum isolates due to geographical origin and host immune response. Such aspects are essential when considering the deployment of the RTS,S vaccine in a certain region. Therefore, in this study we assessed the genetic diversity of P. falciparum in Sudan based on the PfCSP gene by investigating the diversity at the N-terminal, central repeat, and the C-terminal regions. The results of the N-terminal region showed the presence of 2 different haplotypes with a haplotype diversity (Hapd) of 0.425 ± 0.00727. The presence of the unique insertion of NNNGDNGREGKDEDKRDGNN was reported. The KLKQP motif was conserved in all the studied isolates. At the central repeat region, 11 haplotypes were seen with a Hapd of 0.779 ± 0.00097. The analysis of the genetic diversity in the C-terminal region showed the presence of 10 haplotypes with a Hapd of 0.457 ± 0.073. In this study, the results indicated a high conservation at the PfCSP gene. This may further contribute in understanding the genetic polymorphisms of P. falciparum prior to the deployment of the RTS,S vaccine in Sudan.
Preoperative Risk Factors of Persistent Pain Following Total Knee Arthroplasty
Authors: Chodór Paweł , Kruczyński Jacek 
Published: June 2021

Abstract
Purpose

Despite good results of total knee arthroplasty (TKA) number of patients (16–33%) complain of persistent pain. It has been theorized that certain preoperative factors may increase risk of persistent pain, hence their identification should improve preoperative education regarding results of TKA.
Methods

Patients scheduled for TKA were examined one day prior to surgery. Demographics, comorbidities, pressure pain thresholds, pain intensity and duration, radiographic OA grade and range of motion were recorded. Beck Depression Inventory (BDI) and Knee injury and Osteoarthritis Outcome Score (KOOS) were collected. Study cohort was evaluated 6 months following surgery. Patients were assigned to group A if they had no pain and to group B if they complained of any pain.
Results

64 patients were included in final analysis. There were no statistically significant differences regarding preoperative factors except for duration of preoperative pain, which was shorter in group A [36 (12–180) vs 72 (24–180), p = 0,011294]. Every 12 months of preoperative pain were found to increase risk of persistent pain by 1,27 (p = 0,008779).
Conclusions

Preoperative duration of pain is a risk factor for chronic pain following TKA. Should the surgical treatment of knee arthritis be postponed, intensive and individualized pain management is highly recommended.
Genetic Diversity of Cryptosporidium Spp. in Njoro Sub County, Nakuru, Kenya
Authors: Essendi Walter Miding'a , Muleke Charles Inyagwa , Manfred Miheso , Otachi Elick Onyango 
Published: June 2021

Abstract
Cryptosporidium spp. cause Cryptosporidiosis in humans through zoonotic and anthroponotic transmission. Previous studies have illustrated the significance of domestic animals as reservoirs of this parasite. However, there is no information on the Cryptosporidium spp. and genotypes circulating in Njoro Sub County. A total of 2174 samples from humans, cattle, chicken, sheep and goats were assessed for presence of Cryptosporidium spp. Thirty-three positive samples were successfully sequenced. The sequences obtained were compared to Cryptosporidium sequences in the GenBank using NCBI’s (National Center for Biotechnology Information) online BLAST (Basic Local Alignment Search Tool) algorithmic program. Sequence alignment was done using the Clustal W program and phylogenetic analysis was executed in MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The Cryptosporidium spp. present in the watershed showed great genetic diversity with nine (9) Cryptosporidium spp. namely: C. parvum, C. hominis, C. ubiquitum, C. meleagridis, C. andersoni, C. baileyi, C. muris, C. xiaoi and C. viatorum. Cattle were the biggest reservoirs of zoonotic Cryptosporidium spp. hence a potential source of zoonosis in humans while goats had the least species. This is the first study that reported presence of C. viatorum in Kenya.
The importance of future urban development in hourly extreme rainfall projections- comparing global warming and urbanization forcing over the Pearl River Delta region
Authors: Hu Chenxi , Tam Chi-Yung , Li Xinwei , Huang Kangning , Ren Chao , Fung Kwun Yip , Wang Ziqian 
Published: June 2021

Abstract
The impacts of future urban development and global warming forcing on hourly extreme rainfall over the Pearl River Delta (PRD) area have been investigated, by dynamically downscaling General Circulation Model (GCM) outputs using the Weather Research and Forecasting Model (WRF) at convection-permitting resolution, coupled with an Urban Canopy Model (UCM). Three downscaling experiments corresponding to different urban land cover (1999 and projected 2030) and climate (1951-to-2000 and 2001-to-2050 GCM simulations) were designed. Near-future climate change (up to 2050) and 1999-to-2030 urban development effects on PRD extreme precipitation were then examined. Results show that climate change and rapid urban development forcing have comparable positive effects on the intensity as well as heavy hourly rainfall probability over the PRD megacity. Global warming tends to increase heavy rainfall probability (from 40 to 60mm/hr) by about 1.3 to 1.8 times, but suppresses the frequency of light rainfall. Urban development increases urban rainfall probability within the whole range of intensity, with frequency for very heavy rainfall (> 90mm/hr) almost doubled. Overall, forcing due to rapid urban development plays an important role for projecting rainfall characteristic over the highly urbanized coastal PRD megacity, with impacts that can be comparable to global warming in the near future.
Seroprevalence of COVID-19 among health workers in the Kathmandu valley, Nepal (SEVID-KaV): a longitudinal cohort study
Authors: Pandey Kiran Raj , Bhattarai Aseem , Pant Suman , Barakoti Rimmy , Pandey Janaki , Subedee Anup , Adhikari Prabhat , Aryal Diptesh , Pokharel Prakash Jyoti , Shrestha Gentle Sunder , Pandit Kamal , Timalsina Narendra , Thapa Sameer , Gyanwali Pradip 
Published: June 2021

Abstract
Coronavirus Disease 2019 (COVID-19) burden is often underestimated when relying on case-based incidence reports. Seroprevalence studies accurately estimate infectious disease burden by estimating the population that has developed antibodies following an infection. Sero-Epidemiology of COVID-19 in the Kathmandu valley (SEVID-KaV) is a longitudinal survey of hospital-based health workers in the Kathmandu valley. Between December 3-25, we sampled 800 health workers from 20 hospitals and administered a questionnaire eliciting COVID-19 related history and tested for COVID-19 IgG antibodies. We then used a probabilistic multilevel regression model with post-stratification to correct for test accuracy, the effect of hospital-based clustering, and to establish representativeness. 522 (65.2%) of the participants were female, 372 (46%) were between ages 18-29, and 7 (0.9%) were 60 or above. 287 (36%) of the participants were nurses. About 23% of the participants previously had a PCR positive infection. 321 (40.13%) individuals tested positive for COVID-19 antibodies. Adjusted for test accuracy and weighted by age, gender and occupation category, the seroprevalence was 38.17% (95% Credible Interval (CrI) 29.26%–47.82%). Posterior predictive hospital-wise seroprevalence ranged between 38.1% (95% CrI 30.7.0%– 44.1%) and 40.5% (95% CrI 34.7%–47.0%).
Gender Disparities of Heart Disease and the Association with Smoking and Alcohol Drinking Behavior Among the Middle-Aged and Older Population in the US and China, a Cross-Sectional Study of CHARLS and HRS Data
Authors: Li Yifei , Lu Yuanan , Hurwitz Eric L. , Wu Yanyan 
Published: June 2021

Abstract
Background

Heart disease remains the leading cause of death globally with substantial variabilities in mortalities by gender and region. Smoking and alcohol drinking are known modifiable health behaviors associated with heart disease. This study aims to estimate the prevalence of heart disease and to examine the association with smoking and drinking behavior for men and women in the United States (US) and China.
Methods

This study utilized the Harmonized data from the US Health and Retirement Study (HRS) and the China Health and Retirement Longitudinal Study (CHARLS), which are sister surveys as part of the Gateway to Global Aging Data (https://g2aging.org/). We performed cross-sectional comparisons using the 2016 wave HRS and 2015 wave CHARLS data. Age was categorized into four groups (50–59, 60–69, 70–79, and 80 years or older) and smoking and drinking behavior were combined to neither, smoking only, drinking only and both behaviors. Weighted analyses were conducted to estimate the prevalence and prevalence ratios (PRs) of heart disease accounting for complex survey design.
Results

The overall prevalence of heart disease was higher in men (24.5%) than in women (20.6%) in the US. In contrast, women had higher prevalence (22.9%) than men (16.1%) in China. The prevalence of heart disease increased by age with increasing gender gap in the US, while in China, the highest prevalence was observed in the 70–79 age group and gender difference were more apparent before 80 years of age. Adjusting for socio-demographic variables and health conditions, smoking only was associated with a higher prevalence of heart disease in both countries and the associations were stronger among women (US: PR = 1.39, 95%CI: 1.26 to 1.54; China: PR = 1.49, 95%CI: 1.30 to 1.72) than among men (US: PR = 1.20, 95%CI: 1.04 to 1.38; China: PR = 1.37, 95%CI: 0.94 to 1.98).
Conclusions

Findings from this study will improve present understanding of heart disease etiology and provide essential insights for future prevention, treatment, and control. Better management of smoking behaviors by gender might be beneficial for reducing the burden of heart disease in both countries and worldwide.
Integrated Analysis of Diffrentially Expressed Genes and Epigenetics Biomarkers in HCV-cirrhosis
Authors: Cheng Junxiong , Zuo Guoqing , Cao Wenfu 
Published: June 2021

Abstract
PurposeTo identify the key genes and epigenetics biomarkers in HCV-cirrhosis based on informatics analysis of 4 GEO datasets.MethodsAfter downloaded GEO datasets from NCBI, two GEO datasets (GSE6764 and GSE14323) were used to screen for the differentially expressed genes (DEGs) by limma package in R. Then DEGs were applied for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis by clusterProfiler package in R. Protein-protein interaction network was constructed by cytoscape to identify the hub genes of HCV-cirrhosis. DNA methylation dataset GSE60753 was analyzed by ChAMP package in R to identify the differentially methylated genes (DMGs). Cross-analysis of DEGs and DMGs were performed to identify the genes differentially expression and methylation, and further more indicated the methylation of them. Results357 DEGs and 8830 DMGs were identified in HCV-cirrhosis. Functional analysis of DEGs obtained pathways that may involved in the pathgenesis of HCV-cirrhosis, including focal adhesion, influenza A, ECM-receptor interaction, protein digestion and absorption, etc. Cross-analysis of DEGs and DMGs identified 212 genes that changed in mRNA level and methylation status, and most of them were methylated in genebodies, but not CpG island. PPI construction in cytoscape revealed 25 hub genes in GEGs, and 5 of which were further analyzed for their probability as markers of HCV-cirrhosis by ROC curve and validation in another GEO dataset.Conclusions﻿Our study identified the key genes in HCV-cirrhosis patient, which may provide new approach for clarifying the mechanism and new therapy of HCV-cirrhosis.