bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Survey Sequencing of Common Vetch (Vicia Sativa L.) and Genetic Diversity Analysis of Chinese Germplasm with Genomic SSR Markers
Authors: ma lin , Wang Xiao , Yan Min , Liu Fang , Wang Xuemin 
Published: August 2021

Abstract
Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3,556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1,568 Mbp, 0.4345% and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.
Differences in Stem Cell Marker and Osteopontin Expression in Primary and Recurrent Glioblastoma
Authors: Polat Bülent , Wohlleben Gisela , Kosmala Rebekka , Lisowski Dominik , Mantel Frederick , Lewitzki Victor , Löhr Mario , Blum Robert , Herud Petra , Flentje Michael , Monoranu Camelia-Maria 
Published: August 2021

Abstract
Background: Despite of a multimodal approach, recurrences can hardly be prevented in glioblastoma. This may be in part due to so called glioma stem cells. However, there is no established marker to identify these stem cells. Methods: Paired samples from glioma patients were analyzed by immunohistochemistry for expression of the following stem cell markers: CD133, Musashi, Nanog, Nestin, octamer-binding transcription factor 4 (Oct4), and sex determining region Y-box 2 (Sox2). In addition, the expression of osteopontin (OPN) was investigated. The relative number of positively stained cells was determined. By means of Kaplan-Meier analysis, a possible association with overall survival by marker expression was investigated. Results: Sixty tissue samples from 30 patients (17 male, 13 female) were available for analysis. For Nestin, Musashi and OPN a significant increase was seen. There was also an increase (not significant) for CD133 and Oct4. Patients with mutated Isocitrate Dehydrogenase-1/2 (IDH-1/2) status had a reduced expression for CD133 and Nestin in their recurrent tumors. Significant correlations were seen for CD133 and Nanog between OPN in the primary and recurrent tumor and between CD133 and Nestin in recurrent tumors. By confocal imaging we could demonstrate a co-expression of CD133 and Nestin within recurrent glioma cells. Patients with high CD133 expression had a worse prognosis (22.6 vs 41.1 months, p = 0.013). A similar trend was seen for elevated Nestin levels (24.9 vs 41.1 months, p = 0.08). Conclusions: Most of the evaluated markers showed an increased expression in their recurrent tumor. CD133 and Nestin were associated with survival and are candidate markers for further clinical investigation.
Asymmetric Relationships Between Information and Communication Technology (ICT), Globalization, and Human Development in India: Evidence From Non-Linear ARDL Analysis
Authors: Behera Jayanti , Sahoo Dukhabandhu 
Published: August 2021

Abstract
The objective of the paper is to examine the asymmetric relationships between ICT, globalization, and human development in India by analyzing the annual data from 1991 to 2019 through the non-linear autoregressive distributed lag (NARDL) model. The result shows that positive and negative changes in globalization lead to a decline in human development in the long run, consistent with the literature. Further, a positive change in mobile density increases human development in the long run. A decline in internet density has a positive impact on human development in the long run, and it needs further investigation. In the short run, a positive shock in globalization with one lag has a positive impact on human development. Moreover, a previous year positive and negative shocks in internet density have a positive effect on human development while the previous two years positive and negative shocks in internet density have a negative effect on human development in the short run. It is also found that the global financial crisis 2008 has a negative impact on human development. Thus, it is suggested that India has to promote both globalization and ICT judiciously and consciously in order to improve the human development. JEL Classification: O47, F00, I32, C51
BODIPY Nanoparticles Functionalized With Lactose for Cancer-Targeted and Fluorescence Imaging-guided Photodynamic Therapy
Authors: Mai Duy Khuong , Kim Chanwoo , Lee Joomin , Vales Temmy Pegarro , Baldon Isabel Wen , Sung Cho , Yang Jaesung , Kim Ho-Joong 
Published: August 2021

Abstract
A series of four lactose-modified BODIPY photosensitizers (PSs) with different substituents (-I, -H, -OCH3, and -NO2) in the para-phenyl moiety attached to the meso-position of the BODIPY core were synthesized; the photophysical properties and photodynamic anticancer activities of these sensitizers were investigated, focusing on the electronic properties of the different substituent groups. Iodine substitution (BODIPY I) enhanced the intersystem crossing (ISC) to produce singlet oxygen (1O2) due to the heavy atom effect, and maintained a high fluorescence quantum yield (ΦF) of 45.3%. Substitution with the electron-donating group (-OCH3) (BODIPY OMe) resulted in a high 1O2 generation capability and a ΦF of 49.2% while substitution with the electron-withdrawing group (-NO2) led to the PeT process. Thus, instead of assisting ISC as typically expected, this BODIPY PS induced non-radiative charge recombination, prohibiting both fluorescence emission and 1O2 generation. The BODIPY PSs formed water-soluble nanoparticles (NPs) functionalized with lactose as liver cancer-targeting ligands. BODIPY I and OMe NPs showed good fluorescence imaging and PDT activity against various tumor cells (HeLa and Huh-7 cells). Collectively, the BODIPY NPs demonstrated high 1O2 generation capability and ΦF may create a new opportunity to develop useful imaging-guided PDT agents for tumor cells.
A Personalized FEM Model for Reproducible Measurement of Anti-inflammatory Drugs in Transdermal Administration to Knee
Authors: Arpaia Pasquale , Crauso Federica , Frosolone Mirco , Mariconda Massimo , Minucci Simone , Moccaldi Nicola 
Published: August 2021

Abstract
A personalized model of the human knee for enhancing the inter-individual reproducibility of a measurement method for monitoring Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) after transdermal delivery is proposed. The model is based on the solution of Maxwell Equations in the electric-quasi-stationary limit via Finite Element Analysis. The dimensions of the custom geometry are estimated on the basis of knee circumference at the patella, body mass index, and sex of each individual. An optimization algorithm allows to find out the electrical parameters of each subject by experimental impedance spectroscopy data. Muscular tissues were characterized anisotropically, by extracting Cole-Cole equation parameters from experimental data acquired with twofold excitation, both transversal and parallel to tissue fibers. A sensitivity and optimization analysis aiming at reducing computational burden in model customization achieved a worst-case reconstruction error lower than 5%. The personalized knee model and the optimization algorithm were validated in vivo by an experimental campaign on thirty volunteers, 67% healthy and 33% affected by knee osteoarthritis (Kellgren-Lawrence grade [1,4]), with an average error of 3%.
Multivariate Data Analysis Identifies Natural Clusters of Tuberous Sclerosis Complex Associated Neuropsychiatric Disorders (TAND)
Authors: de Vries Petrus J , Leclezio Loren , Gardner-Lubbe Sugnet , Krueger Darcy , Sahin Mustafa , Sparagana Steven , De Waele Liesbeth , Jansen Anna 
Published: August 2021

Abstract
BackgroundTuberous Sclerosis Complex (TSC), a multi-system genetic disorder, is associated with a wide range of TSC-Associated Neuropsychiatric Disorders (TAND). Individuals have apparently unique TAND profiles, challenging diagnosis, psycho-education, and intervention planning. We proposed that identification of natural TAND clusters could lead to personalized identification and treatment of TAND. Two small-scale studies showed cluster and factor analysis could identify clinically meaningful natural TAND clusters. Here we set out to identify definitive natural TAND clusters in a large, international dataset.MethodCross-sectional, anonymized TAND Checklist data of 453 individuals with TSC were collected from six international sites. Data-driven methods were used to identify natural TAND clusters. Mean squared contingency coefficients were calculated to produce a correlation matrix, and various cluster analyses and exploratory factor analysis were examined. Statistical robustness of clusters was evaluated with 1000-fold bootstrapping, and internal consistency calculated with Cronbach’s alpha.ResultsWard’s method rendered seven natural TAND clusters with good robustness on bootstrapping. Cluster analysis showed significant convergence with an exploratory factor analysis solution, and, with the exception of one cluster, internal consistency of the emerging clusters was good to excellent. Clusters showed good clinical face validity.ConclusionsOur findings identified a data-driven set of natural TAND clusters from within highly variable TAND Checklist data. The seven natural TAND clusters could be used to train families and professionals and to develop tailored approaches to identification and treatment of TAND. Natural TAND clusters may also have differential aetiological underpinnings and responses to molecular and other treatments.
Estimating SARS-COV-2 Exposure Indoors in Delhi Given Outdoor Pollution Metrics Using Machine Learning
Authors: Biswas Bitan , Kaushik Ravi 
Published: August 2021

Abstract
The Global Burden of Disease journal by the Lancet(Ritchie and Roser, 2013) and states that one million deaths have occurred from 1990 to 2017 due to air pollution. In 2018, the WHO estimated a death toll of 3.8 million due to indoor pollution(WHO,2018). In these times of the pandemic, it is quintessential for countries like India, with a huge population and high levels of pollution, to take severe measures for controlling pollution. The 2020 US Policy Report in the Lancet(2020) affirmed that there is a positive correlation between the PM2.5 or PM10 particles concentration and COVID-19 infection as the virus uses the particulate matter as a piggyback. The case study here, is based on the Indian urban locality and aims to analyze and estimate the correlations between PM2.5 particles, the AQI, weather conditions and COVID-19 particles using Machine Learning models. The optimum model is also to be used for predicting the outdoor AQI and Covid-19 infection rates in the suburban localities of northwestern Delhi and the data so obtained, would aid to calculating ,and extrapolating the mortality probability due to Covid-19 infection, indoors, in the metropolitan cities of India, like Delhi.
A Study on the Heat Effect and Kinetics During Magnesiothermic Reduction of Porous SiO2
Authors: Zhang Boxia , wang Fei , Chen Jianshe , Li Binchuan , Liu Kuiren , Han Qing 
Published: August 2021

Abstract
Magnesiothermic reduction reaction (MRR) is an effective method to synthesis Si nanoparticles. In this paper, the heat effect and MRR kinetics were investigated by real-time temperature monitoring and analyzing the DSC curve of the MRR. It was found that the MRR onset temperature is about 465 °C, and the system temperature rose sharply at 535 °C. After the disappearance of the magnesium phase, the system temperature remained consistent with the set value. The exothermic peak lags and the spike decreases when adding NaCl into the system. The MRR was chemical reaction control, corresponding with the apparent activation energy was 193.456 kJ·mol-1 (without NaCl) and 191.434 kJ·mol-1 (with NaCl) in the temperature interval 465 °C −700 °C, respectively. NaCl affects the reaction mechanism by lowering the temperature of the system. Our work successfully prepared the spherical Si nanoparticles, which average grain size increased from 25 nm to 40 nm with the extended reaction duration. The conversion rate of porous SiO2 precursor was as high as 92%.
Modulatory Effects of Circadian Rhythms in the Lung Adenocarcinoma Tumor Microenvironment
Authors: Huang Qianzhun , Su Xiaoyang , Fang Ning , Huang Jian 
Published: August 2021

Abstract
Background: Dysregulated circadian dynamic balance is strongly associated with cancer development. However, biological functions of circadian rhythms in lung adenocarcinoma (LUAD) have not been elucidated. This study aimed at valuating the modulatory effects of circadian rhythms in the LUAD tumor microenvironment.Methods: Multiple open-source bioinformatics research platforms are used to comprehensively elucidate the expression level, prognosis, potential biological function, drug sensitivity, and immune microenvironment of circadian clock genes in LUAD.Results: Most circadian clock genes in LUAD are dysregulated and are strongly correlated with patient prognosis, and missense mutations at splicing sites of these genes. Besides, these genes are closely associated with some well-known cancer-related marker pathways, which are mainly involved in the inhibition of the Apoptosis, Cell cycle, and DNA Damage Response Pathway. Furthermore, functional enrichment analysis revealedthat circadian clock genes regulate transcription factor activities and circadian rhythms in LUAD tissues. As for drug sensitivity, high expression of CLOCK, CRY1, and NR1D2 as well as suppressedPER2 and CRY2 expression levels are associated with drug resistance. The expression levels of circadian clock genes in LUAD correlate with immune infiltration and are involved in the regulation of immunosuppression.Conclusions: Our multi-omics analysis provides a more comprehensive understanding of the molecular mechanisms of the circadian clock genes in LUAD and provides new insights for a more precise screening of prognostic biomarkers and immunotherapy.
Taurine Alleviates Chronic Social Defeat Stress-Induced Depression by Protecting Cortical Neurons from Dendritic Spine Loss
Authors: Zhu Yuanyuan , Wang Rui , Fan Ze , Luo Danlei , Cai Guohong , Li Xinyang , Han Jiao , Zhuo Lixia , Zhang Li , Zhang Haifeng , Li Yan , Wu Shengxi 
Published: August 2021

Abstract
Abnormal amino acid metabolism in neural cells is involved in the occurrence and development of major depressive disorder. Taurine is an important amino acid required for brain development. Here, microdialysis combined with metabonomics analysis showed that the level of taurine in the extracellular fluid of the cerebral medial prefrontal cortex (mPFC) was significantly reduced in mice with chronic social defeat stress (CSDS)-induced depression. Therefore, taurine supplementation may be an intervention for depression. We found that taurine supplementation could effectively rescue the decreased preference for sucrose consumption and the increased immobility time during a tail suspension assay and improve social avoidance behaviors in CSDS mice. Moreover, taurine treatment protected the CSDS mice from impairments of dendrite complexity, spine density, and spine ratios. The expression of N-methyl D-aspartate receptor subunit 2A (NR2A), an important synaptic receptor, was largely restored in the mPFC after taurine supplementation. These results demonstrated that taurine exhibited an antidepressive effect by protecting cortical neurons from dendritic spine loss and synaptic protein deficits.
The adenoviral E1B-55k protein present in HEK293 cells mediates abnormal accumulation of key WNT signaling proteins in large cytoplasmic aggregates
Authors: Olsen Petter Angell , Krauss Stefan 
Published: August 2021

Abstract
HEK293 cells are one of the most widely used cell lines in research and HEK293 cells are frequently used as an in vitro model for studying the WNT signaling pathway. The HEK293 cell line was originally established by transfection of human embryonic kidney cells with sheared adenovirus 5 DNA and it is known that that HEK293 cells stably express the adenoviral E1A and E1B-55k proteins. Here we show that HEK293 cells display an unexpected distribution of key components of the WNT/β-catenin signaling pathway where AXIN1, APC, DVL2 and tankyrase are all co-localized in large spherical cytoplasmic aggregates. The cytoplasmic aggregates are enclosed by a narrow layer of the adenoviral E1B-55k protein. Reduction of E1B-55k protein levels leads to disappearance of the cytoplasmic aggregates thus corroborating an essential role of the E1B-55k protein in mediating the formation of the aggregates. Furthermore, HEK293 cells with reduced E1B-55k protein levels display reduced levels of transcriptional activation of WNT/β-catenin signaling upon stimulation by the Wnt3A agonist. The demonstrated influence of the E1B-55k protein on the cellular localization of WNT/β-catenin signaling components and on transcriptional regulation of WNT/β-catenin signaling asks for caution in the interpretation of data derived from the HEK293 cell line.
Clitorin, a Flavonoid Compound of Papaya, Ameliorates Non-Alcoholic Fatty Liver Disease in Western Diet- induced Mice and Oleic Acid-induced HepG2 Cells
Authors: Cominguez Divina C. , Park Yea-Jin , Kang Yun-Mi , Nugroho Agung , Kim Suhyun , An Hyo-Jin 
Published: August 2021

Abstract
Nonalcoholic fatty liver disease (NAFLD) is usually correlated with metabolic diseases, such as obesity, insulin resistance, and hyperglycemia. Herein, we investigated the inhibitory effects and underlying governing mechanism of clitorin in a western diet (WD)-induced mouse model, and in oleic acid-induced HepG2 cells. Male C57BL/6 mice were fed a normal diet, WD, WD + 10 or 20 mg/kg orlistat, and WD + 10 or 20 mg/kg clitorin. HepG2 cells were treated with 1 mM oleic acid to induce lipid accumulation with or without clitorin. Clitorin administration reduced body weight gain and hepatic steatosis symptoms in WD-induced mice. Additionally, clitorin administration decreased the expression of sterol regulatory element-binding protein 1 (SREBP1), peroxisome proliferator-activated receptor γ (PPARγ), and CCAAT/enhancer binding protein α (C/EBPα) in WD-induced mice. Moreover, clitorin administration significantly decreased the mRNA levels of liver X receptor (LXR) and acetyl-CoA carboxylase (ACC); additionally, it enhanced the mRNA levels of peroxisome proliferator-activated receptor α (PPARα) and carnitine palmitoyltranserase-1 (CTP-1), as well as adenosine monophosphate-activated protein kinase (AMPK) mRNA levels, in the liver of WD-induced mice. Furthermore, clitorin treatment significantly impeded lipid accumulation in oleic acid-induced HepG2 cells. Our findings demonstrated that clitorin is a potentially efficacious candidate for NAFLD treatment.
Role of NRF2 cascade in determining the differential response of cervical cancer cells to anticancer drugs- an in vitro study
Authors: Ramesh Pushkal Sinduvadi , Raja Sharanya , Udayakumar Shwethambari Harave , Chandrashekar Shruthi , Nataraj Suma M , Devegowda Devananda 
Published: August 2021

Abstract
The prognosis of cervical cancer patients with metastasis remains unfavorable due to the fact that most of the cervical carcinomas are either resistant to anticancer drugs or show signs of relapse after initial treatment. Therefore, it is important to control the chemoresistance as it is the key to develop effective treatment options. NRF2 (nuclear factor erythroid-2-related factor 2), a transcription factor whose aberrant expression is known to induce chemoresistance in various cancers was assessed in the study. It was evaluated whether the differences in the expression profiles of antioxidant genes regulated by NRF2 led to the variations in the sensitivities of the cervical cancer cells to cisplatin and oxaliplatin treatment. The variations in the ROS profile as well as the addition of exogenous drugs to manipulate the intracellular ROS and its effect on NRF2 pathway genes was also investigated. HeLa and SiHa cells which had significantly lower NRF2 gene levels, NQO1 enzyme activity and basal GSH levels than C33A cells were more sensitive to treatment. Levels of ROS induced were higher in HeLa than C33A cells. Overall, the differences in the cellular levels of antioxidant regulatory genes led to the differential response of cervical cancer cells to anti-cancer drugs.
First reported case of acute megakaryoblastic leukemia successfully treated with decitabine and venetoclax combined with imatinib
Authors: Xie Wanzhuo 
Published: August 2021

Abstract
Acute megakaryocytic leukemia (AMKL) is a rare type of acute myeloid leukemia (AML), which is characterized by its effect on megakaryocytes in bone marrow. Despite standard doses of anthracycline plus cytarabine based regimen, AMKL is notorious for its poor prognosis. With the continuous development of targeted drugs, the choice of chemotherapy regimens for AML patients has been gradually enriched. However, as far as we known, there is little data with this regimen in AMKL with decitabine and Bcl-2 inhibitor combined with imatinib. Herein, we reported the first case of adult AMKL with BCR-ABL positive successfully treated with decitabine and venetoclax combined with imatinib.
Determination of representative elementary volume (REV) for jointed rock masses exhibiting scale-dependent behavior: A numerical investigation
Authors: Sari Mehmet 
Published: August 2021

Abstract
Representative elementary volume (REV) is defined as the usual size of a rock mass structure beyond which its mechanical properties are homogenous and isotropic, and its behavior can be modeled using the equivalent continuum approach. Determination of REV is a complex problem in rock engineering due to its definition ambiguity and application area. This study is one of the first attempts to define a REV for jointed rock masses using the equivalent continuum approach. It is aimed to numerically search a ratio between the characteristic size of an engineering structure and pre-existing joint spacing, which are the two most important contributing elements in assessing REV. For this purpose, four hypothetical engineering cases were investigated using the RS2 (Phase2 v. 9.0) finite element (FE) analysis program. An underground circular opening with a constant diameter, an open-pit mine with varying bench heights, a single bench with a constant height, and an underground powerhouse cavern with a known dimension were executed for possible changes in the safety factor and total displacement measurements under several joint spacing values. Different cut-off REVs were calculated for FE models depending on the type of excavation and measurement method. An average REV size of 19.0, ranging between a minimum of 2 for tunnels and a maximum of 48 for slopes, was found in numerical analysis. The calculated sizes of REV were significantly larger than the range of values (5 to 10) commonly reported in the relevant geotechnical literature.