Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes by Arthur Monjot, Jérémy Rousseau, Lucie Bittner, Cécile Lepère

“…Conclusions Although no universal marker for parasitism was identified, candidate genes can be proposed at a fine taxonomic scale. …”
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Proteomic Identification and Functional Analysis of Babesia microti Reveals Heparin-Binding Proteins by Yu Chun Cai, Bin Xu, Yan Hong Chu, Ying Fang Yu, Jia Hui Sun, Zi Ran Mo, Han Yin Yang, Shu Ning Yan, Mu Xin Chen, Jia Xu Chen

“…Bioinformatics was utilized to analyze the subcellular localization and biological functions of these proteins. Candidate genes encoding proteins with strong heparin affinity will be expressed in a prokaryotic system to produce recombinant proteins. …”
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The influence of the forest corridors to the north of the Andes on the diversification of the bright‐rumped Attila, Attila spadiceus (Passeriformes, Tyrannidae), during the climati... by Patrícia Mendonça, Lincoln Silva Carneiro, Victor Leandro‐Silva, Alexandre Aleixo, Juliana Araripe, Péricles S. Rêgo

“…Through a multilocus analysis of the mitochondrial (CytB and ND2) and nuclear genes (I7BF, I5BF, and G3PDH) of 41 samples representing six subspecies, we describe the existing molecular lineages of A. spadiceus, and estimate their demographic dynamics. …”
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2′-O-Methylperlatolic Acid Enhances Insulin-Regulated Blood Glucose-Lowering Effect through Insulin Receptor Signaling Pathway by Wang Yinghao, Guan Qiaoli, Liu Guanfu, Wu Xiaoyun, Wang Xuanjun, Sheng Jun

“…Next, qRT-PCR was performed to detect the mRNA expression of genes involved in lipid and glucose metabolism in the liver and muscle tissues. …”
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Alternaria leaf blight of clusterbean by Е. Е. Radchenko, R. A. Abdullaev, N. V. Alpatieva, O. V. Putina, E. L. Gasich

“…Therefore, to prevent epiphytotics, varieties protected by non-identical resistance genes  should  be grown.  At all VIR branches, accessions  k-52568 (Argentina) and k-52569 (Pakistan) were weakly damaged by Alternaria leaf blight, and some  accessions  were resistant only in the environmental conditions of one or two experimental stations. …”
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Negative Association of Gulf War Illness Symptomatology with Predicted Binding Affinity of Anthrax Vaccine Antigen to Human Leukocyte (HLA) Class II Molecules by Lisa M. James, Apostolos P. Georgopoulos

“…Method: Here, we tested this hypothesis by determining the association between severity of GWI symptoms in 458 GW veterans and the overall strength of the binding affinity of the PA epitopes to the specific six Human Leukocyte Antigen (HLA) Class II alleles carried by each individual (two of each of the HLA-II genes: DPB1, DQB1, DRB1), responsible for initiating the process of antibody production in otherwise immunocompetent individuals, estimated in silico. …”
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Study on hsa_circ_101209 in Plasma of Pregnant Women with Deep Venous Thrombosis by Zhang Y, Li J

“…Sixty women with DVT were selected as the DVT group, and 60 women without DVT as the non-DVT group. hsa_circ_14797 in plasma was detected, as well as D-dimer (D-D) concentration and P-selectin expression. Target genes that may be regulated by hsa_circ_14797 were predicted, and GO analysis and KEGG pathway enrichment analysis were performed.Results: hsa_circ_14797 was highly expressed in DVT. hsa_circ_14797 in plasma of DVT patients was positively correlated with D-D (r = 0.358, P = 0.001). …”
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Role and mechanism of dexmedetomidine in regulating bone metabolism in tail-suspended osteoporotic rats by GUO Yunliang, WANG Can, ZHANG Xinyu

“…The in vitro experiments showed that Dex treatment obviously improved ALP activity and the number of ALP-positive osteoblasts in primary osteoblasts isolated from tail-suspended rats (P<0.01), and up-regulated the expression levels of osteogenic differentiation-related genes, such as Ocn, Runx2, Osx and Col1 (P<0.01). …”
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p300/Sp1-Mediated High Expression of p16 Promotes Endothelial Progenitor Cell Senescence Leading to the Occurrence of Chronic Obstructive Pulmonary Disease by Zhihui He, Huaihuai Peng, Min Gao, Guibin Liang, Menghao Zeng, Xuefeng Zhang

“…The expressions of p16, p300, and senescence-related genes were detected by RT-PCR and Western Blot. Then, we knocked down or overexpressed Sp1 and p300 and used the ChIP assay to detect the histone H4 acetylation level in the promoter region of p16, CCK8 to detect cell proliferation, flow cytometry to detect the cell cycle, and β-galactosidase staining to count the proportion of senescent cells. …”
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A 3D Clinical Face Phenotype Space of Genetic Syndromes Using a Triplet-Based Singular Geometric Autoencoder by Soha S. Mahdi, Eduarda Caldeira, Harold Matthews, Michiel Vanneste, Nele Nauwelaers, Meng Yuan, Giorgos Bouritsas, Gareth S. Baynam, Peter Hammond, Richard Spritz, Ophir D. Klein, Michael Bronstein, Benedikt Hallgrimsson, Hilde Peeters, Peter Claes

“…Experiments are designed to illustrate the following properties of CFPSs that can aid clinicians in narrowing down their search space: a CFPS can 1) classify syndromes accurately, 2) generalize to novel syndromes, and 3) preserve the relatedness of genetic diseases, meaning that clusters of phenotypically similar disorders reflect functional relationships between genes. The proposed model consists of three main components: an encoder based on GDL optimizing distances between groups of individuals in the CFPS, a decoder enhancing classification by reconstructing faces, and a singular value decomposition layer maintaining orthogonality and optimal variance distribution across dimensions. …”
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Two-Step Transfer Learning Improves Deep Learning–Based Drug Response Prediction in Small Datasets: A Case Study of Glioblastoma by Jie Ju, Ioannis Ntafoulis, Michelle Klein, Marcel JT Reinders, Martine Lamfers, Andrew P Stubbs, Yunlei Li

“…The oxaliplatin-based TL improved the performance probably by increasing the weights of cell cycle-related genes, which relates to the TMZ response processes. …”
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Associations of maternal night shift work during pregnancy with DNA methylation in offspring: a meta-analysis in the PACE consortium by Irene F. Marques, Carola Domènech-Panicello, Madelon L. Geurtsen, Thanh T. Hoang, Rebecca Richmond, Kristen Polinski, Lea Sirignano, Christian M. Page, Anne-Claire Binter, Todd Everson, Amber Burt, Michael Deuschle, Maria Gilles, Fabian Streit, Sunni L. Mumford, Per Magnus, Irwin K. M. Reiss, Marijn J. Vermeulen, Stephanie H. Witt, Inês Chaves, Edwina Yeung, Stephanie J. London, Mònica Guxens, Janine F. Felix

“…In a mouse model of prenatal jet lag exposure, information on offspring DNA methylation of ten homologous genes annotated to the 16 CpGs with P < 1 × 10−5 in our analysis was available, of which eight were associated (enrichment P: 1.62 × 10−11). …”
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IL-33 Mediates Lung Inflammation by the IL-6-Type Cytokine Oncostatin M by Fernando Botelho, Anisha Dubey, Ehab A. Ayaub, Rex Park, Ashley Yip, Allison Humbles, Roland Kolbeck, Carl D. Richards

“…Flow-sorted ILC2 responded in vitro to IL-33 (but not OSM or IL-6 stimulation). Matrix remodelling genes col3A1, MMP-13, and TIMP-1 were also decreased in IL-33-/- mice. …”
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The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity by Chiara Pesenti, Stefania Elena Navone, Laura Guarnaccia, Andrea Terrasi, Jole Costanza, Rosamaria Silipigni, Silvana Guarneri, Nicola Fusco, Laura Fontana, Marco Locatelli, Paolo Rampini, Rolando Campanella, Silvia Tabano, Monica Miozzo, Giovanni Marfia

“…Indeed, the heatmap reporting Gain/Loss State for 21022 coding/noncoding genes demonstrated high interpatient divergence. …”
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Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges by Margaret E. Knight, Kata Farkas, Matthew Wade, Gordon Webster, Daniel A. Pass, William Perry, Peter Kille, Andrew Singer, Davey L. Jones

“…This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). …”
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Integrated serum metabolomics and network pharmacology reveal molecular mechanism of Qixue Huazheng formula on peritoneal fibrosis by Xiaohui Meng, Xiaohui Meng, Li Sheng, Yongqing You, Yongqing You, Huibo Dai, Manshu Yu, Funing Wang, Funing Wang, Ziren Zhou, Ziren Zhou, Yun Shan, Meixiao Sheng

“…Qixue Huazheng formula (QXHZF), comprising Astragalus membranaceus, Centella asiatica, and Ligusticum sinense, is applied to treat PD-related peritoneum injury related; however, the active components, core genes, and underlying mechanism involved remain unclear.MethodsThe anti-PF effects of QXHZF were verified in vivo and in vitro. …”
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Engineering aortic valves via transdifferentiating fibroblasts into valvular endothelial cells without using viruses or iPS cells by Peng Tang, Fuxiang Wei, Weihua Qiao, Xing Chen, Chenyang Ji, Wanzhi Yang, Xinyu Zhang, Sihan Chen, Yanyan Wu, Mingxing Jiang, Chenyu Ma, Weiqiang Shen, Qi Dong, Hong Cao, Minghui Xie, Ziwen Cai, Li Xu, Jiawei Shi, Nianguo Dong, Junwei Chen, Ning Wang

“…These iAECs and hiVECs express VEC-associated genes and proteins and VEC-specific marker NFATC1 and are functional in culture and on decellularized porcine aortic valves, like mouse aortic endothelial cells or human primary aortic valvular endothelial cells. …”
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SMRT sequencing and ddPCR reveal the complexity of developmental trajectories and temporal dynamics of gut bifidobacterial communities in infants by Xu Gao, Tao Zhang, Xiaoye Bai, Qiannan Wen, Dongyu Li, Lai-Yu Kwok, Heping Zhang, Zhihong Sun

“…A total of 28 fecal samples from 4 infants (GF, ZZ, QM, TN, respectively) were collected and analyzed after 5, 15, 30, 60, 90, 120, 150, and 180 days of birth by a bifidobacteria-target method (based on single-molecule real-time sequencing of partial bifidobacterial rpsK genes) in conjunction with droplet digital polymerase chain reaction (ddPCR). …”
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Pre-operative DNA methylation marks as predictors of weight loss outcomes after sleeve gastrectomy by Guillermo Paz-López, Teresa M. Linares-Pineda, Andrés González-Jiménez, Raquel Sancho-Marín, Luis Ocaña-Wilhelmi, Francisco J. Tinahones, Sonsoles Morcillo, Carolina Gutiérrez-Repiso

“…Of them, 59,308 DMPs were annotated to genes. KEGG enrichment analysis showed that pathways involved in the signalling of MAPK, Wnt, mTor, FoxO and AMPK, among others, were involved in weight loss trajectory.A stepwise logistic regression using the DMPs with an absolute Δβ >0.2 showed that higher methylation levels in the CpG sites cg02405213 (mapping to JAK2) (OR: 1.20098, [0.9586, 1.5044]) and cg01702330 (OR: 2.4426, [0.5761, 10.3567]), were shown to be associated with a higher probability of achieving >60 %EWL after sleeve gastrectomy, whereas higher methylation levels in the CpG site cg04863892 (mapping to HOXA5) were associated with lower probability of achieving >60 %EWL after sleeve gastrectomy (OR: 0.7966, [0.5637, 1.1259]). …”
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Exploring the Underlying Mechanism of Weiling Decoction Alleviates Cold-Dampness Diarrhea Based on Network Pharmacology, Transcriptomics, Molecular Docking and Experimental Validat... by Yannan Zhang, Shuai Zhang, Yimeng Fan, Sijuan Huang, Shimin Wang, Zhihui Hao, Jianzhong Shen

“…Additionally, WLD influenced key genes in immune-related pathways. Molecular docking revealed strong binding affinities between the main components of WLD and key targets within these pathways. …”
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