Sangre Por Salud (SPS) Biobank: cohort profile by Richard R Sharp, Euijung Ryu, Janet E Olson, Karen Meagher, James R Cerhan, Davinder Singh, Suzette Bielinski, Emmil Zarrugh, Marlene E Girardo, Giovanna Moreno Garzon, Valentina Hernandez, Sharon Levey, Crystal Gonzalez, Daniela B Pompa, Gabriel Q Shaibi, Lawrence Mandarino, Steven Thibodeau, Elena De Filippis

“…In addition, participants had serum, plasma and DNA samples isolated and stored at the Mayo Clinic Arizona Biorepository Laboratory for long-term storage and future access. …”
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Suppressing recurrence in Sonic Hedgehog subgroup medulloblastoma using the OLIG2 inhibitor CT-179 by Yuchen Li, Chaemin Lim, Taylor Dismuke, Daniel S. Malawsky, Sho Oasa, Zara C. Bruce, Carolin Offenhäuser, Ulrich Baumgartner, Rochelle C. J. D’Souza, Stacey L. Edwards, Juliet D. French, Lucy S. H. Ock, Sneha Nair, Haran Sivakumaran, Lachlan Harris, Andrey P. Tikunov, Duhyeong Hwang, Coral Del Mar Alicea Pauneto, Mellissa Maybury, Timothy Hassall, Brandon Wainwright, Santosh Kesari, Gregory Stein, Michael Piper, Terrance G. Johns, Marina Sokolsky-Papkov, Lars Terenius, Vladana Vukojević, Leon F. McSwain, Timothy R. Gershon, Bryan W. Day

“…We find that CT-179 disrupts OLIG2 dimerization, phosphorylation and DNA binding and alters tumor cell-cycle kinetics, increasing differentiation and apoptosis. …”
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First detection and molecular characterization of Jingmen tick virus with a high occurrence in Rhipicephalus (Boophilus) microplus collected from livestock in Cameroon (2024) by Paloma Kiwan, Eva Lopez, Morena Gasparine, Geraldine Piorkowski, Agathe Colmant, Achille Paguem, Stephanie Mvodo, Laurence Thirion, Xavier de Lamballerie, Remi Charrel, Alessandra Falchi

“…Ticks were identified morphologically and molecularly. Total RNA/DNA was extracted from tick pools and screened for JMTV RNA using a segment 2 RT-qPCR system. …”
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Comprehensive genomic and transcriptomic profiling of pulmonary nodules in synchronous multiple primary lung cancer by Xingsheng Liu, Kun Qian, Lei Su, Xiaoru Tian, Xin Zhao, Tengteng Wang, Li Han, Zhenzhen Li, Peilong Zhang, Ruotian Wang, Baodong Liu, Yuanbo Li, Xiaogang Tan, Yi Zhang

“…Methods We performed targeted DNA sequencing on tumor specimens and conducted bulk RNA transcriptome analysis on 53 multiple nodules originating from 26 lung cancer patients. …”
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Phase II trial of nab-paclitaxel plus ramucirumab in combination with nivolumab for unresectable advanced or recurrent gastric cancer after progression on first-line treatment incl... by Hidekazu Hirano, Naoki Takahashi, Yusuke Amanuma, Nobumi Suzuki, Daisuke Takahari, Takeshi Kawakami, Chie Kudo-Saito, Kengo Nagashima, Narikazu Boku, Ken Kato, Hirokazu Shoji

“…Biomarker analyses of serial blood and tumor samples are planned to clarify predictive markers and molecular mechanisms underlying treatment resistance by multifaceted analytical methods (e.g., flow cytometry, DNA sequencing [DNAseq]/RNA sequencing [RNAseq]). …”
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Permafrost pore structure and its influence on microbial diversity: Insights from X-ray computed tomography by Nathan D. Blais, Joy M. O’Brien, Hannah Holland-Moritz, Lauren Farnsworth, Robyn A. Barbato, Thomas A. Douglas, Alexandra Contosta, Julie Bobyock, Erin C. Rooney, Taylor Sullivan, Jessica Gilman Ernakovich

“…The Euler characteristic number was used to measure pore connectivity and serve as a proxy for potential hydrological connectivity, as direct measurement of hydrological connectivity was not possible. DNA and RNA were extracted from the scanned permafrost and analyzed via amplicon sequencing of the 16S region to quantify the total and active microbial community diversity. …”
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Single-cell profiling reveals a reduced epithelial defense system, decreased immune responses and the immune regulatory roles of different fibroblast subpopulations in chronic atro... by Lin Lin, Tingxuan Huang, Lizhi Li, Yang Lin, Feng Chen, Ziyi Zheng, Jie Zhou, Yizhe Wang, Weihao You, Yujie Duan, Yawen An, Shiwei He, Weimin Ye

“…The mucous neck cells in CAG lesions showed upregulation of genes related to cell cycle transition, which may lead to aberrant DNA replication. Additionally, cells with the T exhaustion phenotype infiltrated under CAG condition. …”
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The anti-PD-L1/CTLA-4 bispecific antibody KN046 plus lenvatinib in advanced unresectable or metastatic hepatocellular carcinoma: a phase II trial by Da Xu, Hongwei Wang, Quan Bao, Kemin Jin, Ming Liu, Wei Liu, Xiaoluan Yan, Lijun Wang, Yanqiao Zhang, Guangyu Wang, Yue Ma, Zhigang Ma, Chunhui Zhang, Jiebing Tang, Sha Wang, Jiaohui Pang, Ting Xu, Kun Wang, Baocai Xing

“…The median overall survival (OS) was 16.4 (95% CI, 11.20-not estimable) months, and 12-month OS rate was 60.0% (95% CI, 45.87-71.55). Circulating tumor DNA status before the third cycle of treatment was associated with prognosis. …”
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Molecular characterization of ST15 carbapenem-resistant Klebsiella pneumoniae isolated in a single patient by Yongjin Hu, Rong Tang, Shanshan Jin, Jiahao Guan, Xiaoxiao Meng, Zengpeijie Dan, Ruilan Wang, Hong-Yu Ou, Jian Lu

“…Results: Our results revealed that 9 KP strains, isolated from the same patient, exhibited ‘resistance-sensitivity-resistance-sensitivity’ alternately to carbapenems. The differences in DNA fingerprint bands among the nine KP isolates were ≤3, which can be classified as the same PFGE type. …”
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Impact of donor CYP3A5 genotype on pharmacokinetics of tacrolimus in South African paediatric liver transplant patients by C Wheeler, C Masimirembwa, B Mthembu, J Botha, J Scholefield, J Fabian

“…Blood samples from 46 living liver donors were collected, their genomic DNA was extracted, and their CYP3A5 genotype was established (polymerase chain reaction and restriction fragment length polymorphism analysis, validated by Sanger sequencing). …”
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Shaoyao Gancao decoction alleviates paclitaxel-induced cognitive impairment by activating PTEN/PI3K/AKT pathway to inhibit NETs formation by Xu Ying, Su Yue, Hu Yuwen, Li Xiang, Zhou Ziyan, Yuan Ningning, Ji Xiaowei, Jiang Ruoyu, Wang Wenzhu, Zhang Yafeng, Zhai Guojie, Cheng Xiaolan

“…In addition, SGD could inhibit NETs formation, evidenced by decreasing the level of plasma MPO-DNA complex, as well as MPO and PAD4 expression. …”
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NPRL2 gene therapy induces effective antitumor immunity in KRAS/STK11 mutant anti-PD1 resistant metastatic non-small cell lung cancer (NSCLC) in a humanized mouse model by Ismail M Meraz, Mourad Majidi, Renduo Song, Feng Meng, Lihui Gao, Qi Wang, Jing Wang, Elizabeth J Shpall, Jack A Roth

“…Restoration of NPRL2 induces DNA damage, apoptosis, and cell-cycle arrest. We investigated NPRL2 antitumor immune responses in aPD1R/KRAS/STK11mt NSCLC in humanized-mice. …”
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Coupling of an Au@AgPt nanozyme array with an micrococcal nuclease-specific responsiveness strategy for colorimetric/SERS sensing of Staphylococcus aureus in patients with sepsis by Xueqin Huang, Yingqi Yang, Hanlin Zhou, Liping Hu, Annan Yang, Hua Jin, Biying Zheng, Jiang Pi, Jun Xu, Pinghua Sun, Huai-Hong Cai, Xujing Liang, Bin Pan, Junxia Zheng, Haibo Zhou

“…In the presence of S. aureus, the secreted MNase preferentially cut the nucleobase AT-rich regions of DNA sequences on magnetic beads (MBs) to release alkaline phosphatase (ALP), which subsequently mediated the oxTMB reduction for inducing the colorimetric/SERS signal fade away. …”
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Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors by Kristopher Amirault, Michael Collins, Luca Beker, Brandon Mills, Martina Werner, Jonathan Andreas, Daniel Hartman, Jordan Dargert, Vanessa Process, Sean Cederlund, Thuy Dao, Linnea Menin, Molly Ferrara, Andrew Briggs, Joshua Shreve, Daniel Metzger, Angela Stout, Erin Deblasi, Jie An, Taylor Jensen, Shengle Zhang, Vinesh Rana, Bryn Burlingame, Ulrich Thomann, Durga Prasad Dash, Sha Liao, Jeffrey M. Conroy, Eugenio Daviso

“…The Sonication STAR automated DNA and RNA methods from FFPE Tissues was created as a collaboration between Hamilton Company, Covaris, and Labcorp and it offers the potential reduction in quantity not sufficient (QNS) samples and sequencing performance improvements resulting in a 16 % increase in fully reported tumor profiles for patients. …”
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Implementation of a genotyped African population cohort, with virtual follow-up: A feasibility study in the Western Cape Province, South Africa [version 2; peer review: 2 approved,... by Robert J Wilkinson, Francisco Lakay, Nicki Tiffin, Joel A Dave, Catherine Riou, Peter Raubenheimer, Anna K Coussens, Tsaone Tamuhla, Melissa J Blumenthal, Maleeka Abrahams

“…Methods We piloted a scalable virtual genotyped cohort in South Africa that was affordable in this resource-limited context, cost-effective, scalable virtual genotyped cohort in South Africa, with participant recruitment using a tiered informed consent model and DNA collection by buccal swab. Genotype data was generated using the H3Africa Illumina micro-array, and phenotype data was derived from routine health data of participants. …”
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Loss of MEF2C function by enhancer mutation leads to neuronal mitochondria dysfunction and motor deficits in mice by Ali Yousefian-Jazi, Suhyun Kim, Jiyeon Chu, Seung-Hye Choi, Phuong Thi Thanh Nguyen, Uiyeol Park, Min-gyeong Kim, Hongik Hwang, Kyungeun Lee, Yeyun Kim, Seung Jae Hyeon, Hyewhon Rhim, Hannah L. Ryu, Grewo Lim, Thor D. Stein, Kayeong Lim, Hoon Ryu, Junghee Lee

“…MEF2C localizes and binds to the mitochondria DNA, and directly modulates mitochondria-encoded gene expression. …”
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Diethyldithiocarbamate-copper complex ignites the tumor microenvironment through NKG2D-NKG2DL axis by Daciana C. Dumut, Daciana C. Dumut, Marian Hajduch, Marian Hajduch, Amanda M. Zacharias, Qingling Duan, Qingling Duan, Ivo Frydrych, Zuzana Rozankova, Zuzana Rozankova, Miroslav Popper, Miroslav Popper, Dusan Garic, Radu Alexandru Paun, Radu Alexandru Paun, Amanda Centorame, Amanda Centorame, Juhi Shah, Martin Mistrik, Martin Mistrik, Petr Dzubak, Petr Dzubak, Juan B. De Sanctis, Juan B. De Sanctis, Danuta Radzioch, Danuta Radzioch, Danuta Radzioch, Danuta Radzioch

“…Advanced metastatic colorectal cancer (CRC) with deficient DNA mismatch repair (MMR-d), or immune-hot CRCs, show significantly improved clinical outcomes compared to MMR-proficient (MMR-p), or immune-cold CRCs. …”
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Diel changes in the expression of a marker gene and candidate genes for intracellular amorphous CaCO3 biomineralization in Microcystis by Bruley, Apolline, Gaëtan, Juliette, Gugger, Muriel, Pancrace, Claire, Millet, Maxime, Gaschignard, Geoffroy, Dezi, Manuela, Humbert, Jean-François, Leloup, Julie, Skouri-Panet, Fériel, Callebaut, Isabelle, Benzerara, Karim, Duprat, Elodie

“…Moreover, several genes directly co-localized upstream and downstream of ccyA, on the same DNA strand show a similar expression pattern, including a cax gene encoding a calcium/proton exchanger and a gene encoding a protein with a domain also present in the N-terminal region of calcyanins in many iACC-forming cyanobacteria. …”
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STR profiling in a cohort of Saudi patients with acute leukemia by Husein A. Alhatim, PhD Student, Muhammad NH Abdullah, PhD, Suhaili A. Jamaludin, PhD, Armania B. Nurdin, PhD, Sayed A. Amer, PhD

“…Methods: Blood and saliva samples were collected from 27 patients diagnosed with acute leukemia in Riyadh City, KSA. DNA was extracted, and 15 STR loci were amplified. …”
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Effective gene therapy for metachromatic leukodystrophy achieved with minimal lentiviral genomic integrations by Lucas Tricoli, Sunetra Sase, Julia L. Hacker, Vi Pham, Maxwell Chappell, Laura Breda, Stephanie N. Hurwitz, Naoto Tanaka, Carlo Castruccio Castracani, Amaliris Guerra, Zhongqi Hou, Lars Schlotawa, Karthikeyan Radhakrishnan, Matthew Hogenauer, Aoife Roche, John Everett, Frederic Bushman, Peter Kurre, Rebecca Ahrens-Nicklas, Laura A. Adang, Adeline L. Vanderver, Stefano Rivella

“…To address this need, we increased the expression of ARSA cDNA at single integration by generating novel LVs, optimizing ARSA expression and enhancing safety. …”
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