Multi-omics analyses of the heterogenous immune microenvironment in triple-negative breast cancer implicate UQCRFS1 potentiates tumor progression by Yuhui Tang, Aiqi Xu, Zhongbiao Xu, Jindong Xie, Wei Huang, Liulu Zhang, Yitian Chen, Lu Yang, Shasha Du, Kun Wang

“…Methods The thorough analyses of different cell types within TME were conducted on the self-tested single-cell RNA sequencing dataset which contained nine TNBC treatment-naïve patients, including subclusters classification, CellChat algorithm, transcription factors (TFs) expression, pseudotime analysis and functional enrichment assay. …”
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Optimising Wastewater Sample Processing for Multiple Pathogen Detection by Miss Shannon Fitz, Debora Akortia, Richard Larbi, Richard Owusu, Gifty Nkrumah, Dr Joyce Akello, Catherine Troman, Dr Jaspreet Mahindroo, Dr Anton Spader, Dr Ben Bellekom, Piya Rajendra, Professor Yaw Adu-Sarkodie, Dr Ellis Owusu-Dabo, Dr Nicholas Grassly, Dr Dilip Abraham, Professor Venkata Raghava Mohan, Dr Michael Owusu, Dr Alex Shaw

“…The Wastewater Kit performed well in extracting RNA/DNA across the organisms, recovering 72.27% (cholera surrogate), 100% (typhi), and 88.2% (nOPV2) of the spike compared to the optimal extraction kit for each organism. …”
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Study the effect of Lactobacillus plantarum ATCC 14917 for caries prevention and anti-obesity by Wei Yang, Wei Yang, Mingxin Jiang, Bairu Chen, Bairu Chen, Kongzhao Jiang, Nan Ma, Nan Ma, Yimin Li, Yimin Li, Meng Wang, Meng Wang, Meihua Bao, Meihua Bao, Chengyue Wang, Chengyue Wang, Xiaopeng Yang, Xiaopeng Yang

“…These included the use of Mirco-CT to calculate the enamel volume, the staining of liver and fat cell sections, serological analysis, and 16S rRNA sequencing of feces.ResultsIt was proved that the L. plantarum could inhibit the proliferation of S. mutans and remove dental plaque biofilm in time, which showed the remarkable effects of anti-caries in vitro. …”
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Immune regulatory genes impact the hot/cold tumor microenvironment, affecting cancer treatment and patient outcomes by Mengmeng Sang, Jia Ge, Juan Ge, Juan Ge, Gu Tang, Qiwen Wang, Jiarun Wu, Liming Mao, Liming Mao, Xiaoling Ding, Xiaorong Zhou

“…Kyoto Encyclopedia of Genes and Genomes and Hallmark pathway enrichment were evaluated through gene set variation analysis. Additionally, hub genes that regulate the tumor microenvironment were identified, and their expression patterns were analyzed using single-cell RNA sequencing. …”
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High-expression of BCL10 inhibits cell-mediated immunity within the tumor immune microenvironment by Jinyi Gu, Jinyi Gu, Changshun Chen, Changshun Chen, Yuanjing Chen, Wei Lv, Fei Li, Puyuan Zhu, Pu He, Yunjie Du, Huiling Liu, Bingdong Zhu

“…The correlation between BCL10 expression and infiltrated immune cells was analyzed by immune algorithms such as xCELL, CIBERSORT, QUANTISEQ and MCPcounter using TCGA and GTEx databases. Furthermore, single-cell RNA sequencing data of the cervical squamous cell carcinoma(CESC)microenvironment were analyzed using the GEO database. …”
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Cell cycle checkpoint factor p15Ink4b is a novel regulator of osteoclast differentiation by Shunya Tsuji, Sora Mizukami, Akihiko Sakamoto, Kenji Takemoto, Tetsuya Seto, Kazuya Uehara, Kiminori Yukata, Takashi Sakai, Keiko Iwaisako, Norihiko Takeda, Ryoji Yanai, Masataka Asagiri

“…In this manuscript, we identified p15Ink4b, a member of the Ink4 family, as a novel regulator of osteoclastogenesis by comprehensive single-cell RNA sequence data reanalyzing. Furthermore, histological analysis and in vitro osteoclast differentiation assay revealed that p15Ink4b functionally regulates osteoclastogenesis. …”
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Epigenome-wide association study for dilated cardiomyopathy in left ventricular heart tissue identifies putative gene sets associated with cardiac pathology and early indicators of... by Konstanze Tan, Darwin Tay, Wilson Tan, Hong Kiat Ng, Eleanor Wong, Michael P. Morley, Gurpreet K. Singhera, Chang Jie Mick Lee, Pritesh R. Jain, Fei Li Tai, Paul J. Hanson, Thomas P. Cappola, Kenneth B. Margulies, Roger Foo, Marie Loh

“…Methods We mapped DNA methylation at ~ 850,000 CpG sites, performed array-based genotyping and conducted RNA sequencing on left ventricular tissue samples from failing and non-failing hearts across two independent DCM cohorts (discovery n = 329, replication n = 85). …”
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Integrating Gut Microbiome and Metabolomics with Magnetic Resonance Enterography to Advance Bowel Damage Prediction in Crohn’s Disease by Huang L, Meng J, Lin S, Peng Z, Zhang R, Shen X, Zheng W, Zheng Q, Wu L, Wang X, Wang Y, Mao R, Sun C, Li X, Feng ST

“…Patients underwent MRE, fecal 16S rRNA gene sequencing, and fecal/serum metabolomic analysis. …”
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Primary and metastatic cellular landscapes in human pancreatic cancer by Nina G. Steele, Veerin R. Sirihorachai, Ahmed M. Elhossiny, Ian M. Loveless, Padma Kadiyala, Monica Bonilla, Emily L. Lasse-Opsahl, Carinna Solano Vargas, Katelyn L. Donahue, Samantha B. Kemp, Valerie Gunchick, Yatrik M. Shah, Timothy L. Frankel, Filip Bednar, Arvind Rao, Benjamin L. Allen, Jiaqi Shi, Vaibhav Sahai, Howard C. Crawford, Eileen S. Carpenter, Marina Pasca di Magliano

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Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study. by Vijay R Varma, Youjin Wang, Yang An, Sudhir Varma, Murat Bilgel, Jimit Doshi, Cristina Legido-Quigley, João C Delgado, Anup M Oommen, Jackson A Roberts, Dean F Wong, Christos Davatzikos, Susan M Resnick, Juan C Troncoso, Olga Pletnikova, Richard O'Brien, Eelko Hak, Brenda N Baak, Ruth Pfeiffer, Priyanka Baloni, Siamak Mohmoudiandehkordi, Kwangsik Nho, Rima Kaddurah-Daouk, David A Bennett, Shahinaz M Gadalla, Madhav Thambisetty

“…Participants in the BLSA autopsy cohort (AD/CON) were approximately 50%/77% male with a mean age of 87/82 years. We analyzed single-cell RNA sequencing (scRNA-Seq) data to compare brain BA receptor gene expression between AD and CON samples from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort (N = 46). …”
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Intrinsic immunosuppressive features of monocytes suppress CAR-T19 through IL-1 pathway modulation in mantle cell lymphoma by Kun Yun, R. Leo Sakemura, Ismail Can, Omar Gutierrez Ruiz, Ekene J. Ogbodo, Shuwen Zhang, Ateka Saleh, Truc N. Huynh, Claudia Manriquez Roman, Olivia L. Sirpilla, Carli M. Stewart, James H. Girsch, Jennifer M. Feigin, Long Mai, Hong Xia, Brooke Kimball, Lionel A. Kankeu Fonkoua, Mehrdad Hefazi, Michael W. Ruff, Fariborz Rakhshan Rohakhtar, Vernadette Simon, Elizabeth L. Siegler, Mike Mattie, Sao-Mai Nguyen-Mau, Simone Filosto, Saad S. Kenderian

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Multiomics Assessment of the Gut Microbiome in Rare Hyperoxaluric Conditions by Nadim Zaidan, Chan Wang, Ze Chen, John C. Lieske, Dawn Milliner, Barbara Seide, Melody Ho, Huilin Li, Kelly V. Ruggles, Frank Modersitzki, David S. Goldfarb, Martin Blaser, Lama Nazzal

“…Participants completed a food frequency questionnaire recording their dietary oxalate content while fecal oxalate levels were ascertained. DNA and RNA were extracted from stool samples and sequenced. …”
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First Molecular Identification of Zoonotic <i>Babesia odocoilei</i> in Ticks from Romania by Ioan Cristian Dreghiciu, Diana Hoffman, Simona Dumitru, Ion Oprescu, Mirela Imre, Tiana Florea, Anamaria Plesko, Vlad Iorgoni, Sorin Morariu, Gheorghe Dărăbuș, Marius Stelian Ilie

“…The presence of <i>Babesia</i> spp. was assessed using real-time PCR with primers and a Taq Man probe targeting 116 bp fragments of 18S rRNA genes. Molecular analysis was used to detect <i>Babesia</i> spp. …”
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