bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Novel Coconut SSR Markers Derived From Genome-Wide Bioinformatics Prediction
Authors: Caro Reina Esther S. , Cagayan Jesmar , Gardoce Roanne R. , Manohar Anand Noel C. , Canama-Salinas Alma O. , Rivera Ramon L. , Lantican Darlon V. , Galvez Hayde F. , Reaño Consorcia E. 
Published: August 2021

Abstract
In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSR markers are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers. A total of 7,139 novel SSR markers were derived from the genome assembly of coconut ‘Catigan Green Dwarf’ (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. OligoAnalyzer-tool was also employed using the following desired parameters: %GC: 40–60%; minimum ΔG value for hairpin loop: -0.3 kcal/mol; minimum ΔG value for self-dimer: -0.9 kcal/mol; and minimum ΔG value for hetero-dimer: -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using ‘Catigan Green Dwarf’ (CATD), ‘Laguna Tall’ (LAGT), ‘West African Tall’ (WAT), and SYNVAR (LAGT x WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes. The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.
Analysis of Factors Affecting the Technical Inefficiency on Indonesian Palm Oil Plantation
Authors: Abdul Irawati , Sari Dyah Wulan , Haryanto Tri 
Published: August 2021

Abstract
This study aims to analyze the factors affecting the technical inefficiency of palm oil plantations in Indonesia by using the stochastic frontier analysis based on the translog production function. The data used in this study are taken from the Central Statistics Agency (Agricultural Business Household Income Survey) in 2013. The number of samples used was 14367 farmers. The results revealed that there is still to increase in the efficiency of palm oil plantations in Indonesia. The production function suggests that increasing the number of trees can help to increase the number of outputs. Additionally, education, age, planting system, seed quality, extension service, and plasma farmer significantly influence the technical efficiency of palm oil plantation.
Intraplate depth-dependent lithospheric stretching imaged by seismic reflection data
Authors: Dong Shuwen , Li Jianhua , Gao Rui , Cawood Peter , Thybo Hans , Zhang Yueqiao , Johnston Stephen , Wang Jinming 
Published: August 2021

Abstract
Geological and geophysical data coupled with numerical simulations have shown that lithospheric extension at passive margins may be classified into three end-member scenarios of pure shear, simple shear, and depth-dependent deformation. However, how lithospheric extension evolves in an intraplate setting remains enigmatic due to lack of reliable constraints on the deep lithospheric architecture. Here we use a seismic reflection profile across the ~800-km-wide Cretaceous intraplate extensional system of South China to illustrate depth-dependent kinematic decoupling of extension in a mechanically stratified lithosphere. The extension was initially distributed in magma-poor conditions as expressed by normal faulting in the upper crust and lower-crustal flow toward the rift axis. Necking of the crust and Moho uplift led to mantle shear-zone formation, lower-crustal flow toward the rift flanks, and deep mantle flow. We demonstrate that the extensional modes vary with decreasing mantle strength from magma-poor to magma-rich domains, as reflected in decreasing crust-mantle decoupling with increased Moho temperatures (TM), and the replacement of a two-layer (brittle vs ductile) mantle by a fully ductile mantle. These findings reveal a first-order lithospheric configuration of intraplate depth-dependent extension driven by far-field stresses attributable to slab retreat.
Identification of Biomarkers for Prognosis and Immunotherapy in Clear Cell Renal Cell Carcinoma
Authors: Yu Zuhu , Lu Bin , Gao Hong , Xiang Wuxing , Liang Rongfang , Liang Tao , Chen Wenhui , Liu Jinping 
Published: August 2021

Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the dominating subtype of renal cancer with high malignancy and poor prognosis, accounts for the majority of kidney cancer deaths. We conducted this research to identify novel potential biomarkers for the prognosis and immunotherapy of ccRCC patients. We screened out differentially expressed genes (DEGs) between ccRCC tissues and adjacent normal tissues with 4 microarray series from GEO database and took function analysis of DEGs with GO and KEGG pathway. Then, we constructed PPI network and identified target genes with prognostic value in ccRCC, performed immunological correlation analysis of the candidate genes to seek potential biomarkers of immunotherapy in ccRCC. Results: In total, 159 up-regulated genes and 223 down-regulated genes were screened out and 11 genes including TIMP1, PCK1, HMGCS2, G6PC, FBP1, ACAA1, HADH, HAO2, TGFBI, RRM2 and SUCLG1 were found to be associated with prognoses of ccRCC patients. After further screening and verification of the mRNA and protein expression, down-regulation of PCK1, HMGCS2, and up-regulation of RRM2 were significantly correlated with poorer prognoses both in overall survival and disease free survival in ccRCC. Further immunological correlation analysis showed RRM2 expression was correlated with immune infiltration and immunological checkpoint in ccRCC.Conclusion: We identified PCK1, HMGCS2 and RRM2 as potential markers for the prognosis of ccRCC patients with bioinformatic analyses. RRM2 may plays an important role in the oncogenicity of ccRCC and is a potential target for immunotherapy of ccRCC patients.
Sharp kinetic acceleration potentials during mediated redox catalysis of insulators
Authors: Cao Deqing , Shen Xiaoxiao , Wang Aiping , Yu Fengjiao , Wu Yuping , Shi Siqi , Freunberger Stefan , Chen Yuhui 
Published: August 2021

Abstract
Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li+ concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li+/e– extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.
Transcriptome Analysis of Lateral Roots Development in Aconitum Carmichaelii
Authors: Zhou Luojing , Zhong Sha , Fan Yuxin , Yin Yanpeng , Gao Jihai , Peng Cheng 
Published: August 2021

Abstract
Background: Fuzi is a processed product of the lateral root of Aconitum carmichaelii Debx, a plant of the Ranunculaceae, and has been used to treat various diseases. This study used Illumina Hiseq High-throughput platform to sequence, assemble and annotate, screen development related genes, transcription pathways and functional enrichment in true root, lateral roots and “bridge”, and analyzed their correlations with the formation and development of lateral roots of A.carmichaelii, which can reveal the process and regulation mechanism of lateral roots growth and maturation of A. carmichaelii. Results: By sequencing, a total of 66.13Gb clean data and 28,982 unigenes with function annotation were finally obtained, with N50 of 1,627 bp, and 12,833 genes were assigned to 130 specific metabolic pathways by Kyoto Encyclopedia of Genes and Genomes (KEGG), then 2,599 were significantly differentially expressed. The KEGG analysis of the DEGs revealed that it was mainly enriched in starch and sucrose metabolism, ribosome, carbon metabolism, plant hormone signal transduction which play an important role in the expansion of lateral roots. The DEGs and pathways indicated that there was little differences between true root and “bridge”, while a big difference between them and lateral roots. The DEGs of auxin, cytokinin and other pathways may be conducive to the formation of lateral roots, which explained the development mechanism of lateral roots from a molecular point of view. Conclusions: This study provides a reference for the study of cultivation and management of lateral roots of A. carmichaelii.
Unfavorable Effects of Fixatives on the Fluorescence Intensity and Biological Functions of Fluorescent Proteins in HEK293T Cells and Transgenic Mice
Authors: Tang Tao , Yuan Lan , Wang Kai , Zhao Mingwei 
Published: August 2021

Abstract
Fluorescent proteins (FPs) are commonly used probes for coding genes that enable specific protein or whole-cell labeling. Their fluorescence intensity is used for molecular quantitation and intermolecular interaction analysis. Since FPs are usually small soluble proteins, they easily cross the membranes if cell integrity is disrupted, resulting in FP signal attenuation/loss. Specimen prefixation to preserve FP localization within cells/tissues is therefore useful. However, specific fixatives can weaken or eliminate FP signals. We studied the effects of five common fixatives on FP fluorescence intensity and biological functions to determine their suitability for FP signal and FRET efficiency preservation in cells and tissues. FP (GFP, YFP, CFP and RFP)-expressing HEK293T cells with methanol, 95% ethanol, 4% PFA, acetone and glutaraldehyde, and brain tissue sections of EGFP- and tdTomato-labeled transgenic fluorescent mice was fixed with 4% PFA. The FP signals in HEK293T cells and brain tissue from transgenic fluorescent mice were weakened or even eliminated after fixation with these fixatives. The fixatives affected FP biological function, and the FP FRET efficiency significantly differed between prefixation and postfixation (all p<0.01). Thus, fixatives impair FP fluorescence to some extent, leading to attenuation/loss of signals or even biological functions. Fixatives should be applied carefully in FP-related experiments to avoid bias.
Using Text Mining Techniques to Extract Prostate Cancer Predictive Information (Gleason Score) from Semi-structured Narrative Laboratory Reports in the Gauteng Province, South Africa
Authors: Cassim Naseem , Mapundu Michael , Olago Victor , Celik Turgay , George Jaya Anna , Glencross Deborah Kim 
Published: August 2021

Abstract
Background: Prostate cancer (PCa) is the leading male neoplasm in South Africa with an age-standardised incidence rate of 68.0 per 100,000 population in 2018. The Gleason score (GS) is the strongest predictive factor for PCa treatment and is embedded within semi-structured prostate biopsy narrative reports. The manual extraction of the GS is labour-intensive. The objective of our study was to explore the use of text mining techniques to automate the extraction of the GS from irregularly reported text-intensive patient reports.Methods: We used the associated Systematized Nomenclature of Medicine clinical terms morphology and topography codes to identify prostate biopsies with a PCa diagnosis for men aged >30 years between 2006 and 2016 in the Gauteng Province, South Africa. We developed a text mining algorithm to extract the GS from 1,000 biopsy reports with a PCa diagnosis from the National Health Laboratory Service database and validated the algorithm using 1,000 biopsies from the private sector. The logical steps for the algorithm were data acquisition, pre-processing, feature extraction, feature value representation, feature selection, information extraction, classification, and discovered knowledge. We evaluated the algorithm using precision, recall and F-score. The GS was manually coded by two experts for both datasets. The top five GS were reported, with the remaining scores categorised as “Other” for both datasets. The percentage of biopsies with a high-risk GS (≥8) was also reported. Results: The first output reported an F-score of 0.99 that improved to 1.00 after the algorithm was amended (the GS reported in clinical history was ignored). For the validation dataset, an F-score of 0.99 was reported. The most commonly reported GS were 5+4=9 (17.6%), 3+3= 6 (17.5%), 4+3=7 (16.4%), 3+4=7 (14.7%) and 4+4=8 (14.2%). For the validation dataset, the most commonly reported GS were: (i) 3+3=6 (37.7%), (ii) 3+4=7 (19.4%), (iii) 4+3=7 (14.9%), (iv) 4+4=8 (10.0%) and (v) 4+5=9 (7.4%). A high-risk GS was reported for 31.8% compared to 17.4% for the validation dataset. Conclusions: We demonstrated reliable extraction of information about GS from narrative text-based patient reports using an in-house developed text mining algorithm. A secondary outcome was that late presentation could be assessed.
DFT Calculation, Molecular Docking and Molecular Dynamics Simulation Study on Substituted Phenylacetamide and Benzohydrazide Derivatives
Authors: Yele Vidyasrilekha , Sigalapalli Dilep Kumar , Jupudi Srikanth , Azam Mohammed Afzal 
Published: August 2021

Abstract
The atomic and molecular properties of the title compounds were calculated by Jaguar using a basis set B3LYP/6-31G**++ with hybrid DFT in the gas phase, to determine the chemical reactivity. Analysis of Quantum chemical features such as HOMO and LUMO explained that the electronic charge transfer occurred within the system through conjugated paths of the selected compounds. The nucleophilic and electrophilic reactive sites are recognized from the molecular electrostatic potential plot. Electrophilic and nucleophilic attack-prone molecular sites were predicted by mapping ALIE and ALEA values to the molecular surface. The bond dissociation energy of the high active compound 15 (2-chloro-N-(2-(2-(2-(2-chlorobenzoyl)hydrazineyl)-2-oxoethoxy)phenyl)acetamide) was calculated to assess the probability of compounds autoxidation or degradation. Further, molecular docking, binding free energy calculations, and ADMET profile of the degradation products (DPs) of compound 15 was carried out to determine the binding affinity and toxicity profile of the formed DPs compared with the parent compound. A 150 ns molecular dynamics (MD) simulation was performed to evaluate the binding stability of the compound 15/4URL complex using Desmond. Binding free energy and binding affinity of the complex were computed for 100 trajectory frames using the MM-GBSA approach.
Individual and Community-Level Factors of Perinatal Mortality in The High Mortality Regions of Ethiopia: A Multilevel Mixed-Effect Analysis
Authors: Girma Desalegn , Abita Zinie , Fetene Gossa , Birie Bamlaku 
Published: August 2021

Abstract
Background
Even though perinatal mortality has declined globally; it is still the major public health concern in sub-Saharan Africa countries. Ethiopia is one of the sub-Saharan countries which contribute the highest-burden of perinatal mortality with devastating in some of the regions. Therefore, this study aimed to identify the determinant factors of perinatal mortality in the high mortality regions of Ethiopia.
Method:
A secondary data analysis was done by using the 2016 Ethiopian Demographic and Health Survey data. A total of 4120 mothers who had been delivered at ≥ 7 months of gestational age were included. A multilevel mixed logistic regression model was fitted to identify the predictors of perinatal mortality. Finally, a statistically significant association was declared at a p-value of ≤ 0.05.
Result
The study found that birth interval < 2 years (AOR = 3.71, 95%CI:2.27, 6.07),having no antenatal care (AOR = 2.43,95%CI:1.15,5.38), Initiating breast feeding after 1hour(AOR = 4.01 ,95%CI:2.49,6.51), being distant from health institutions (AOR = 1.99, 95%CI: 1.24, 3.22), having previous terminated pregnancy (AOR = 4.68, 95%CI:2.76,7.86), being mothers not autonomous(AOR = 1.96, 95%CI:1.19,3.20),being no media exposure (AOR = 2.78, 95%CI:1.48,5.59),being households ≤ 4 family sizes (AOR = 4.12, 95%CI:2.19,7.79), having ≥ 6 parity (AOR = 2.48, 95%CI:1.21, 5.22) were associated with a high odds of perinatal mortality.
Conclusion
The study concludes that birth interval, antenatal care, time for breastfeeding initiation, distance from health institutions, previous history of a terminated pregnancy, maternal autonomy, media exposure, family size, and parity were predictors of prenatal mortality. Therefore, programmatic emphases to maternal waiting service utilization for mothers distant from health institutions and increasing media access could reduce perinatal mortality in high mortality regions of Ethiopia.
Size Effect of CeO2 Particle On Nanoscale Single-Asperity Sliding Friction
Authors: Xu Ning , Ma Jiahui , Liu Qi , Han Weizhong , Shan Zhiwei 
Published: August 2021

Abstract
The size of abrasive particle has a great impact on the fundamental friction behavior and mechanical properties of the abrasive during ultra-precision polishing performance. Here, the size effect of the tribological behavior and mechanical properties of CeO2 single abrasive were studied. Experimental results show that the size effect plays a role on coefficient of friction (COF) of each regime in single-asperity sliding friction, especially in ploughing and cutting regimes. The residual depth of the scratch and COF both decrease with the increase of the CeO2 tip radius. These results relate to the mechanical properties of CeO2 nanoparticles. We found that the effective modulus increases with the decrease of abrasive size, which corresponds to the size effect of the single-asperity sliding friction experiment.
Effects of Co-infection With Clonorchiasis Sinensis on T Cell Exhaustion Levels in Patients With Chronic Hepatitis B
Authors: Dong Huimin , Luo Minqi , Shang Mei , Wang Yang , Fu Yuechun , Hu Bo 
Published: August 2021

Abstract
BackgroundTo investigate the effects of co-infection with C. sinensis on T cell exhaustion levels in patients with chronic hepatitis BMethodsInhibitory receptors and suppressive cytokines expression in circulating CD4+ and CD8+ T cells was detected by flow cytometry. The correlations between PD-1 and TIM-3 expression and alanine aminotransaminase (ALT) levels, aspartate aminotransferase (AST) levels and HBV DNA levels were analyzed using GraphPad Prism 7.0. ResultsPD-1 and TIM-3 expression levels were significantly higher on CD4+T and CD8+T cells from co-infected patients than on those from the HBV patients. In addition, CD4+T cells and CD8+T cells function was inhibited by C. sinensis and HBV coinfection, secreting low levels of IFN-γ, IL-2 and TNF-α. Then, a significant positive correlation was found between the PD-1 and TIM-3 expression levels on T cells and the AST ,ALT levels and HBV DNA levels.Conclusions﻿Our current results suggested that C. sinensis co-infection could exacerbate T cell exhaustion in patients with chronic hepatitis B. Furthermore, it maybe one possible reason for the weaker response to antiviral therapies and the chronicity of HBV infection in co-infected patients. We must realize that the importance of C.sinensis treatment for HBV infected patients. It might provide useful information for the clinical doctors to choose the right treatment plans.
The Reinforcement Mechanisms of Graphene Oxide in Laser Directed Energy Deposition Fabricated Metal and Ceramic Matrix Composites: A Comparison Study
Authors: Li Yunze , Zhang Dongzhe , Ye Zhipeng , Ye Gaihua , He Rui , Wang Hui , Cong Weilong 
Published: August 2021

Abstract
Carbon-based nanomaterials mainly including carbon nanotubes (CNTs), graphene, and graphene oxide (GO) have superior properties of low density, outstanding strength, and high hardness. Compared with ceramic reinforcements, a small amount of carbon-based nanomaterials can significantly improve the mechanical properties of metal matrix composites (MMCs) and ceramic matrix composites (CMCs). However, CNTs and graphite always aggregate or degrade during the fabrication with a high temperature, especially in MMCs. GO has the advantages of easier to be dispersed in other materials and better high-temperature stability. Laser directed energy deposition (DED), has been used to fabricate GO-MMCs and GO-CMCs due to the unique capabilities of coating, remanufacturing, and producing functionally graded materials. Laser DED, as a fusion manufacturing process, could fully melt the material powders, which could refine the microstructure and increase the density and mechanical properties. However, GO could react with matrix materials at high temperatures. The survival, degradation, and reactions of GO in laser DED fabricated GO-MMCs and GO-CMCs are still unknown. There is also no investigation on the reinforcement mechanisms of GO in metal matrix materials and ceramic matrix materials in the laser DED process. In this study, GO reinforced Ti (GO-Ti) and GO reinforced zirconia toughened alumina (GO-ZTA) parts were fabricated by laser DED process. Raman spectrum, XRD analysis, and EDS analysis have been applied to investigate the forms of GO in both DED fabricated GO-MMCs and GO-CMCs. The reinforcement mechanisms of GO on microhardness and compressive properties of MMCs and CMCs have been analyzed.
Results of Streamlining TAVR Procedure Towards a Minimalist Approach： A Single Center Experience in Taiwan
Authors: Ko Tsung-Yu , Kao Hsien-Li , Chen Yi-Chang , Yeh Chih-Fan , Huang Ching-Chang , Chen Ying-Hsien , Chan Chih-Yang , Lin Lung-Chun , Wang Ming-Jiuh , Chen Yih-Sharng , Lin Mao-Shin 
Published: August 2021

Abstract
Background
Trans-femoral transcatheter aortic valve replacement (TF-TAVR) performed under conscious sedation (LACS) is not yet become routine practice in Taiwan. We aimed to compared the results between patients received general anesthesia (GA) versus LACS.
Methods
Our cohort was divided into 3 groups: initial 48 patients received TF-TAVR under routine GA (GA group), subsequent 50 patients under routine LACS (LACS group 1), and recent 125 patients under LACS (LACS group 2). The baseline, procedural characteristics and all outcomes were prospectively collected and retrospectively compared.
Results
From Sep 2010 to July 2019, a total of 223 patients were included for The procedure time (157.6 ± 39.4 mins vs 131.6 ± 30.3 vs 95.2 ± 40.0, < 0.0001), contrast medium consumption (245.6 ± 92.6 ml vs 207.8 ± 77.9 vs 175.1 ± 64.6, < 0.0001), length of intensive care unit (2[1–5] days vs 2[1–3] vs 1[1–1], P = 0.0001) and hospital stay (9[7–13] days vs 8[6–11] vs 6 [5–9], P = 0.0001) decreased significantly with LACS, combined with a trend of less hospital acquired pneumonia (12.5% vs 6.0% vs 5.6%, P = 0.427). One-year survival rate were also different among 3 groups (83.3% vs 90.0% vs 93.6%, P = 0.053).
Conclusion
In our single center experience, a “minimalist” approach of TF-TAVR procedure resulted in less medical resources usage, along with more favorable clinical outcomes.