bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Landslide Susceptibility Mapping Based on Two Machine Learning Algorithm Models
Authors: Sun Deliang , Wang Yue , Zhang Jialan , Wen Haijia , Xu Jiahui , Zhou Xinzhi 
Published: January 2022

Abstract
The purpose of this research is to develop and compare two machine learning methods, namely, artificial neural network (ANN) and random forest (RF) used for in landslide susceptibility mapping (LSM) of Wushan County. Firstly, 866 landslides were collected from extensive field investigations, historical records and satellite images from 2001 to 2016. Based on previous literature reviews and the field investigations, a geospatial database was established in geographic information system (GIS) based on topography, geological conditions, environmental conditions and human activities factors, including 22 conditioning factors. Then, based on samples of landslides and non-landslides, the 10-fold cross-validation was used to select the best training and test datasets. Finally, the LSMs of Wushan County were generated. Subsequently, susceptibility maps of the two models were divided into: very low, low, medium, high and very high class using experts’ experience method. The two models were compared with area under the receiver operating characteristic (ROC) plot values (AUC) and confusion matrix. The AUC values of the ANN and RF models’ test dataset was 0.966 and 1.000, and the accuracy were 0.953 and 1.000, respectively. According to the mean decrease Gini of RF model, the most important conditioning factors were elevation (a mean decrease accuracy of 72.38), followed by annual average rainfall (47.95) and POI kernel density (45.63). Above all, it is concluded that both ANN and RF models were satisfactory for the LSM of Wushan County at the mountainous region. The RF model had an outperformer prediction and is considerably more efficient than the ANN model.
Population Genetic Analyses Inferred a Limited Genetic Diversity in the Pvama-1 of Plasmodium Vivax Isolates from Khyber Pakhtunkhwa Regions of Pakistan
Authors: Ullah Ibrar , Afridi Sahib Gul , Israr Muhammad , Khan Hizbullah , Shams Sulaiman , Zaib Komal , Le Huong Giang , Kang Jung-Mi , Na Byoung-Kuk , Khan Asifullah 
Published: January 2022

Abstract
Background: Plasmodium vivax apical membrane antigen-1 (pvama-1) is an important vaccine candidate. Assessment of the genetic composition of pvama-1 is preliminary important to better plan the vaccine designing strategies based on the antigen.Methods: Blood samples of 84 vivax malaria patients from Khyber Pakhtunkhwa (KP) province of Pakistan were collected. The pvama-1 domain 1 (DI) region was amplified and sequenced. The QC based sequences raw data filtration was done using DNASTAR package. The downstream population genetic analyses were performed using MEGA4, DnaSP, Arlequin v3.5 and network.5.Results: The data analyses unveiled total 57 haplotypes of pvama-1 DI among 84 KP P. vivax samples with majorly prevalent H-14 and H-5haplotypes. Limited to moderate pairwise genetic distinction was observed among the samples collected from different districts of KP. Likewise, no geography-specific genetic correlation was inferred among KP samples. In context of worldwide available data, the KP samples showed major genetic differentiation against Korean samples with Fst = 0.40915 (P-value =0.0001), while low distinction observed against India and Iranian samples. An excess of low frequency polymorphism and negative Tajima’s D indicate purifying selection signatures across the pvama-1 in KP P.vivax samples. Comparison of KP pvama-1 DI with the reference pvama-1 SalI (AF063138) unveiled total 09 KP samples-specific novel non-synonymous single nucleotide polymorphisms (nsSNPs) including several trimorphic and tetramorphic substitutions. Few of these nsSNPs were mapped within the B-cell predicted epitopic motifs of the pvama-1 and, suggesting to modulate the immune response mechanisms. Conclusion: The genetic composition of the pvama-1 appeared uniform across the KP regions of Pakistan. However, the KP samples exhibited marked genetic distinction in context of worldwide samples. The information may worthy to understand genetic nature of Pakistani P. vivax and implicate in future in pvama-1 vaccine designing.
Oncoprotein CIP2A controls PKM2 dimer-tetramer transition through phosphorylation of serine 287 in non-small cell lung cancer
Authors: Liang Li-Jun , Zhang Yan-Fei , Wang Di , Wang Fu-Ying , Xie Da-Wei , Yu Hong , Wang Zheng , Sun Bei-Bei , Gao San-Hui , Guo Hua , Zhao Xin-Chao , Wang Gui-Zhen , Zhou Guang-Biao 
Published: January 2022

Abstract
Dimer-tetramer transition determines the pyruvate kinase activity of pyruvate kinase M2 (PKM2), the final rate-limiting enzyme in glycolysis. Several small molecules have been shown to be able to promote PKM2 confirmation change, but the role of oncoproteins including the cancerous inhibitor of protein phosphatase PP2A (CIP2A) that is overexpressed in most human malignancies, in PKM2 dimer-tetramer transition remains largely unknown. Here we reported that CIP2A inhibited glycolysis and promoted oxidative metabolism in non-small cell lung cancer (NSCLC) cells. CIP2A directly bound PKM2 and induced formation of PKM2 tetramer, whereas CIP2A depletion resulted in reduced tetrameric and increased dimeric forms of PKM2. We found that serine 287 of PKM2 was essential for PKM2 dimer-tetramer switching, whereas mutation in this residue abrogated CIP2A-induced tetramer formation and pyruvate kinase activity increment. Clinically, the expression of CIP2A was positively associated with the level of phosphorylated PKM2 S287, and CIP2Ahigh/PKM2high and PKM2high/CIP2Ahigh were associated with poor prognosis of NSCLC patients. Pharmacological inhibition of glycolysis or activation of PKM2 synergistically inhibited NSCLC cell growth when combined with CIP2A-targeting compound celastrol both in vitro and in vivo. These results demonstrated that CIP2A determines PKM2 dimer-tetramer transition and controls the metabolic reprogramming of NSCLC cells.
An Etiological and Maintenance Model of Perfectionism
Authors: Pourshahbaz Abbas , Moloodi Reza , Mohammadkhani Parvaneh , Fata Ladan , Barani Masoumeh , Egan Sarah J. , Ghaderi Ata 
Published: January 2022

Abstract
Background: The present study aimed to test a model of perfectionism investigating parenting style, early maladaptive schemas and sensitivity to reinforcement theory. Methods: A general population sample (n=384), and a clinical sample consisting of individuals with major depressive disorder (n=40), social anxiety disorder (n=35), obsessive compulsive disorder (n=39), and eating disorders (n=38) completed measures of parenting, early maladaptive schemas, perfectionism, inhibition/approach system, avoidance and overcompensation coping styles, and psychological distress.Results: The path analysis indicated that the model fits with data from both samples. Conclusion: The results inidicate that future research should further investigate a range of variables to further understand perfectionism.
A Machine Learning Approach to Identify Small Molecule Inhibitors of Secondary Nucleation in α-Synuclein Aggregation
Authors: Horne Robert , Possenti Andrea , Chia Sean , Brotzakis Z. Faidon , Staats Roxine , Nowinska Magdalena , Vendruscolo Michele 
Published: January 2022

Abstract
Drug development is an increasingly active area of application of machine learning, prompted by the need to overcome the high attrition rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where disease-modifying drugs are not widely available yet. To address this problem, we describe an approach based on a combination of machine learning with chemical kinetics to target diseases caused by protein misfolding and aggregation. We use this approach to identify specific inhibitors of the proliferation of α-synuclein aggregates through secondary nucleation, a process implicated in Parkinson’s disease. Our results demonstrate that this approach leads to the identification of novel chemical matter with an improved hit rate and potency over more traditional approaches.
Knockdown of Superoxide Dismutase 6 Inhibits Neuronal Remodelling During Metamorphosis in Tribolium Castaneum
Authors: Nishiko Maaya , Sakamoto Takuma , Mun Seulgi , Noh Mi Young , Arakane Yasuyuki , Kanost Michael , Arai Katsuhiko , Tabunoki Hiroko 
Published: January 2022

Abstract
The body form of holometabolous insects dramatically transforms from larval to adult stages during the pupal developmental stage. In motoneuron "remodelling," larval neuronal cells degenerate and reconnect to new adult muscles. However, the factor that controls location-specific neuronal remodelling has not yet been elucidated. Here, we show that an antioxidant enzyme, Tribolium castaneum superoxide dismutase 6 (TcSOD6), is secreted into the haemolymph and controls the remodelling of adult neuronal cells during metamorphosis. TcSOD6 has a unique domain architecture and is mainly expressed in the pupal developmental stage. The knockdown of TcSOD6 expression in the pupa inhibits axon formation, suggesting a need for SOD activity in neuronal remodelling. Therefore, we conclude that TcSOD6 plays a role in neuronal remodelling during metamorphosis, providing new insights into the evolution of SOD functions.
Deciphering Diversity at er Loci for Diversification of Powdery Mildew Resistance in Pea
Authors: Banyal Devender K , Dixit Himisha , Chaudhary Jaya , Malannavar Anudeep B , Thakur Nisha 
Published: January 2022

Abstract
Agricultural biotechnology aims to scrutinize the field crops which feed amongst half of the world’s population by improving their agronomic traits using various biotechnological tools. Pea- an important cash crop, rich in nutrients, but frequently infected with powdery mildew (fungal disease) that destroy the whole crop which causes the economy loss for growers. We therefore, targeted this research to find the pathogen resistant pea lines and further decipher the diversity at er locus among resistant pea lines. Screening for resistant pea lines was done with Erysiphe pisi isolates (Genebank submission: KX45 5922.1) under net house and green house conditions. Molecular studies revealed that Erysiphe resistant (er1) gene was present in 40 lines out of selected 50 pea lines and the mutational character was conferred up to 36 genotypes with 11 haplotype groups. The haplotype (gene) diversity (Hd) was found to be 0.5571±0.099 SD and the nucleotide diversity (Pi) was 0.0160±0.0042 SD Majority of resistant lines (67%) occurred in Hap-1, other remaining haplotypes (Hap 2-10) having 33% resistant lines, each showing characteristic nucleotide substitutions with respect to reference PsMLO1 gene; genotypes from these divergent haplotypes can be used in pea resistance breeding to avoid genetic homogeneity and genetic vulnerability.
Next-Generation Sequencing Analysis of Hereditary Ovarian Cancer Gene Panels in Turkish Population
Authors: TUNCER SEREF BUGRA , Celik Betul , Erciyas Seda Kılıc , Erdogan Ozge Sukruoglu , Odemis Demet Akdeniz , Gültaslar Büşra Kurt , Ghafour Arash Adamnejad , Saip Mualla Pınar , Yazici Hulya 
Published: January 2022

Abstract
Purpose: Ovarian cancer is the seventh most frequent cancer in women worldwide and the eighth leading cause of death from cancer. Approximately 5–10% of all diagnosed cancer cases are caused by hereditary cancer risk syndromes. The aim of this study was investigate the prevalence of pathogenic variants associated with hereditary ovarian cancer propensity inTurkish people. Methods:630 patients with personal or a family history of breast and/or ovarian cancer and other cancers included in the study. The Illumina NGS technology was used to enrich genomic DNA. Results:118 of the 630 tested people have pathogenic mutation (20.0%). The mutation distribution detected in a total of 130 patients was 131. 1 mutation (1,315%) in ATM , 40 different mutations (52.630%) in BRCA1, 29 different mutations in BRCA2 (38.165%), 2 different mutations (2,630) in CHEK2, 1 mutation (1,315%) in ERCC2, 1 mutation (1,315%) in MUTYH, 1 mutation (1,315%) in RAD51C, and 1 mutation (1,315%) were detected in TP53.Notably, in a patient with ovarian cancer both BRCA1 and BRCA2 mutations; BRCA1 NM_007294.3Ex1c.135-2A>Gp.?rs80358065 and BRCA2 NM_000059.3 Ex 11 c.6466_6469delTCTC p.Ser2156Asnfs*11rs879255330 were found, respectively. Conclusion: Analysis of gene panels demonstrate the clinical importance of multigene panel analysis in hereditary cancer predisposition meeting the BRCA1/2 NCCN criteria in Turkish population.
When Ankylosing Spondylitis and Takayasu Arteritis walking into a bar named Syndesmophytes
Authors: Chen Jie , Gu Liyang , Zhou Yan , Li Ting , Ye Shuang 
Published: January 2022

Abstract
ObjectivesThis study was to describe the characteristics of syndesmophytes in different inflammatory and non-inflammatory diseases aiming to reflect the aortic-vertebrae interaction.MethodsWe conducted a cross-sectional study including four group of patients, ankylosing spondylitis (AS, n=52), Takayasu's arteritis (TKA, n=31), diffuse idiopathic skeletal hyperostosis (DISH, n=30), coronary artery disease (CAD, n=100), and also age-matched healthy controls (HC, n=143). All subjects underwent a chest CT and images of the upper and lower border of seven adjacent thoracic vertebrae (T5 to T12) were captured. An ‘aorta ipsilateral ratio’ (AIR) of the syndesmophyte was calculated as the area crossed the midline toward aorta side divided by the total syndesmophyte area.ResultsThe frequency of subjects with syndesmophyte and syndesmophyte counts increased with age across the board. Frequencies of syndesmophyte in AS and TKA were much higher than age-matched HCs. The AIRs were significantly elevated in AS, TKA and CAD compared with DISH or age-matched HCs. In addition, the AIR of patients with higher CRP levels (>8mg/L) were greater than that of those with lower levels, both among AS and CAD patients.ConclusionsOur findings indicate that, in an inflammatory niche, regardless the origin or the grade of the inflammation, syndesmophyte formation will be facilitated and screwed toward aorta. There is a possible mechanistic connection between large vessel and new bone formation in the context of inflammation.
Relationship Between Blood Manganese and Bone Mineral Density and Bone Mineral Content in Adults: A Population-Based Cross-Sectional Study
Authors: Wang Chao , Zhu Yong , Long Haitao , Ou Mingning , Zhao Shushan 
Published: January 2022

Abstract
It has been reported that bone is the primary organ for manganese(Mn) accumulation, but the association between manganese and bone loss remains debatable. Therefore, this study aimed to evaluate the relationship between blood manganese and bone mineral density/bone mineral content (BMD/BMC) by using a representative sample from the National Health and Nutrition Examination Survey (NHANES). A total of 9732 subjects over the age of 18 with available data were enrolled in this study. The relationship between blood manganese and BMD/BMC of the total body, spine and femoral regions was evaluated using multivariate linear regression models. Subgroup analyses were also performed. We observed a negative association between blood manganese and BMD/BMC in the femoral neck and total body in the fully adjusted model, especially femoral neck BMD in women aged 50-70 years. In brief, people exposed to manganese should be aware of the increased risk of osteopenia or osteoporosis. Besides, due to the lack of available data, there are no definite values for the tolerable upper intake level (UL), average requirement (AR) and population reference intake (PRI) of manganese. The results of our study may provide some references for the establishment of AR, PRI and UL of Mn.
Differentially Expressed Genes and Key Pathways in Triple Negative Breast Cancers: A Bioinformatics Analysis
Authors: Shi Zuolin , Liu Xiyu , Zhang Na , Guan Hongna 
Published: January 2022

Abstract
Background: Triple negative breast cancer (TNBC) is usually associated with poor outcome, and is characterized by lack of estrogen and progesterone hormone receptors and lack of overexpression of HER2. The aim of this study was to identify gene signatures during TNBCs and uncover their potential mechanisms.Methods: The gene expression profiles of GDS4069 were downloaded from GEO database. The GDS4069 dataset contained 19 samples, including 5 TNBCs, and 14 non-TNBCs (Control). The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and protein–protein interaction (PPI) network of the differentially expressed genes (DEGs) was constructed by Cytoscape software. The research was conducted according to the principles of the Declaration of Helsinki.Results: In total, 603 DEGs were identified in TNBCs, including 199 up-regulated genes and 403 down-regulated genes. GO analysis results showed that up-regulated DEGs were significantly enriched in biological processes (BP), including adaptive immune response, immunological synapse, positive regulation of GTPase, positive regulation of c-Jun N-terminal kinase (JNK), and positive regulation of T cell, et al.; the down-regulated DEGs were significantly enriched in biological processes, including cilium assembly, protein transport, intracellular transport, cilium morphogenesis, anterior/posterior pattern specification, and positive regulation of cilium assembly. KEGG pathway analysis showed the up-regulated DEGs were enriched in hematopoietic cell lineage signaling pathway, cytokine-cytokine receptor interaction signaling pathway, and glycosphingolipid biosynthesis-globo series signaling pathway, while the down-regulated DEGs were enriched in peroxisome signaling pathway.Conclusions: The present study indicated that the identified DEGs and hub genes promote our understanding of the molecular mechanisms underlying the development of TNBCs, and might be used as molecular targets and diagnostic biomarkers for the treatment of TNBCs.
Comparative Transcriptome Analysis of Leaf, Stem, and Root Tissues of Semiliquidambar Cathayensis Hung T. Chang Reveals Candidate Genes Involved in Terpenoid Biosynthesis
Authors: tian xiaoming , Yan Lihong , Jiang Liyuan , Xiang Guangfeng , Li Gaofei , Wu Jia 
Published: January 2022

Abstract
Background

The roots, branches, leaves, bark, and nectar of Semiliquidambar cathayensis Hung T. Chang can treat rheumatoid arthritis, lumbar muscle strain, and other diseases. However, limited knowledge of the S. cathayensis Chang genome hampers further research on elucidating the pathways underlying active ingredient synthesis and regulation of its accumulation. In this study, we aimed to generate data to elucidate biosynthetic pathway of the active ingredient synthesis and related molecular mechanisms.
Methods

We conducted transcriptome sequencing of S. cathayensis Chang leaves, stem epidermis, stem xylem, root epidermis, and root xylem.
Results

We identified 88,582 unigenes, among which, 36,144 unigenes were annotated to the nr protein database, 21,981 to the Gene Ontology database, 11,565 to the Clusters of Orthologous Groups database, 24,209 to the Pfam database, 21,685 to the SWISS-PROT database, and 12,753 to the Kyoto Encyclopedia of Genes and Genomes (KEGG), with 5,072 unigenes common to all six databases. Of those annotated using the KEGG database, 187 unigenes were related to the terpenoid metabolism pathway, and expression analysis of the related genes indicated that the mevalonate and methylerythritol 4-phosphate pathways play different roles in terpenoid biosynthesis in different tissues of S. cathayensis Chang.
Conclusions

These findings greatly expand the gene resources of S. cathayensis Chang and provide basic data for the study of the biosynthetic pathways and molecular mechanisms of terpenoids.
Growing Season Harvests of Shrub Willow Have Higher Nutrient Removals and Lower Yields Compared to Dormant Season Harvests
Authors: de Souza Daniel PL , Eisenbies Mark , Volk Timothy 
Published: January 2022

Abstract
The commercial establishment of shrub willow biomass crops with three- or four-year harvest cycles raises concerns about nutrient removals. Furthermore, commercial harvesters in the northeast United States have begun to open the harvest season in late summer to early fall in order to ensure access on poorly drained, marginal sites because the ground no longer reliably freezes in winter. The potential impact that increased leaf-on harvesting has on nutrient export and its implications for crop management are not well known. This study examined the effects of six harvest dates over 10 months on the nutrient removal and second rotation biomass production of four shrub willow cultivars on a site in central New York State. First rotation harvests yielded between 77 and 85 Mg ha-1 during the growing season, and was between 93 and 104 Mg ha-1 after dormancy. There was a significant effect of harvest timing on the removal of N, K, Ca, Mg, and S. Willow harvested in October removed comparatively higher amounts of N (77.1 kg ha-1 y-1), P (11.2 kg ha-1 y-1), Ca (163.7 kg ha-1 y-1), Mg (9.9 kg ha-1 y-1), and S (8.9 kg ha-1 y-1) than in other harvests. Potassium removal was greater for plants harvested in June and August (51.2 and 52.5 kg ha-1 y-1 respectively). Significant interactions between harvest timing and cultivars suggest that targeted cultivar selection and deployment could maintain yields and limit excess nutrient losses.
Cytotoxic Effect of Samarium(III)-Based Complexes: Synthesis, Characterization and Photoluminescence Properties
Authors: SARIOGLU AHMET ORAL , kahraman demet taşdemir , köse Aysegül , sönmez mehmet 
Published: January 2022

Abstract
Three new homoleptic six-coordinate Sm(III) complexes have been synthesized from diketone ligand with different substituent groups. The structural properties of these compounds have been investigated using elemental analysis, UV-Vis, and FT-IR approaches. Then, their photoluminescence properties of the synthesized Sm complexes have been examined.Also, the cytotoxic activities of the complexes have been studied against to human epidermoid carcinoma cell (HTB-54) and normal bronchus epithelial cell (BEAS-2B). According to result, the [Sm(MPBP-1,3PPon)3]·H2O) (IC50: 11.05 μM) complex was more active than [Sm(BMP-1,3PPon)3]·2H2O (IC50:58.64 μM) and [Sm(BCP-1,3PPon)3]·H2O (IC50: >500 μM) complexes. Otherwise it was no effect on normal cell (BEAS-2B). This result shows that complex [Sm(MPBP-1,3PPon)3]·H2O) has the potential to be the ideal chemotherapeutic drug.
Economic Burden of Rheumatoid Arthritis in Iran: A Societal Perspective Economic Burden of R.A.
Authors: Rezaee Mehdi , Lotfi Farhad , Gholami Ahmad , Azizpoor Jassem , Aflaki Elham , Vazin Afsaneh , Keshavarz Khosro 
Published: January 2022

Abstract
Background: Rheumatoid arthritis (RA) is a progressive, chronic systemic inflammatory disease and impose a significant economic burden on patients and societies if not controlled. This study aimed to determine the economic burden of RA in southern Iran in 2019. Methods: This economic burden study was carried out as cross-sectional research in 2019 in southern Iran, in which 765 patients were included. The prevalence-based and bottom-up approaches were also used to prepare the cost information and calculate the costs, respectively. The human capital approach was used to calculate the indirect costs as well. Results: The results showed that the economic burden of RA in Iran was $ 3,744,967,993 PPP in 2019. In addition, the mean annual costs of RA per patient in remission, low, and moderate-to severe states and the total cost were $ 11,925.98, $ 11,887.49, $ 12,803.45, and $ 12,155.08 PPP, respectively in 2019.Conclusions: RA imposed a significant economic burden on the community and patients, and DMC, especially the cost of drugs, were the most important component. It is suggested to provide necessary facilities to produce RA drugs in the country and expand home care services in order to reduce the economic burden.