Tag: LIU

A Simple Overview for Proteins Molecular Dynamics Simulations Using GROMACS

About Gromacs – Gromacs. s.d. Consulté le 5 mai 2023. www.gromacs.org/About_Gromacs Baker, D., Sali, A.: Protein structure prediction and structural genomics. Science 294(5540), 93–96 (2001). doi.org/10.1126/science.1065659 Beckstein, O., et al.: Ion channel gating: insights via molecular simulations. FEBS Lett. 555(1), 85–90 (2003). doi.org/10.1016/s0014-5793(03)01151-7 CrossRef  Google Scholar  Bowman, A.L., Ridder, L.,…

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Searching For Giant Exoplanets Around M-dwarf Stars (GEMS) I: Survey Motivation

Green triangles show an estimate of the heavyelement content (MZ ) of GEMS from planetary interior models (Thorngren et al. 2016) compared to the Class II disk dust mass (Md) estimates as orange squares (Manara et al. 2022) and the median (and 1-σ) trend seen in the Lupus sample (Ansdell…

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A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

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Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco

Zaman, S. B. et al. A review on antibiotic resistance: Alarm bells are ringing. Cureus doi.org/10.7759/cureus.1403 (2017). Article  PubMed  PubMed Central  Google Scholar  Peterson, E. & Kaur, P. Antibiotic resistance mechanisms in bacteria: Relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front. Microbiol. 9, 2928 (2018)….

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Author Correction: Prime editing using CRISPR-Cas12a and circular RNAs in human cells

New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China Ronghong Liang, Zixin He, Haocheng Zhu, Jiacheng Hu, Guanwen Liu, Meiyan Liu, Rui Zhang & Caixia Gao College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China Zixin He, Haocheng Zhu, Meiyan Liu & Caixia Gao Qi Biodesign, Beijing,…

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Investigation of the Flipping Dynamics of 1, N6-Ethenoadenine in Alkyladenine DNA Glycosylase

dataset posted on 2024-02-09, 02:43 authored by Bin Liu, Yanping Qi, Xiaowei Wang, Xin Gao, Yuan Yao, Lu Zhang Alkyladenine DNA glycosylase (AAG) is an essential enzyme responsible for maintaining genome integrity by repairing several DNA lesions damaged by alkylation or deamination. Understanding how it can recognize and excise the…

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Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

Continue Reading Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal

N6-methyladenosine modification positively regulate Japanese encephalitis virus replication | Virology Journal

Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev. 2021;35:1005–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Chambers…

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Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics

Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82(11):801–11. Article  CAS  Google Scholar  Jeon SA, Park JL, Park SJ, Kim JH, Goh SH, Han JY, Kim SY. Comparison between MGI and Illumina sequencing platforms for whole genome sequencing. Genes Genomics. 2021;43(7):713–24. Article  CAS …

Continue Reading Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics

Innovent, SanegeneBio to Co-Develop Hypertension Drug Candidate

Credit: Linda Bartlett/National Cancer Institute, via Wikimedia Innovent Biologics and SanegeneBio have entered into a collaboration and co-development agreement for SGB-3908, an siRNA drug candidate targeting angiotensinogen (AGT) for the treatment of hypertension. Under the terms of the deal, Innovent will gain an exclusive option to license future development, manufacturing,…

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High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange

High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange – Texas A&M University (TAMU) Scholar Search form   Overview   Research   Identity   Additional Document Info   Other   View All   Overview abstract Ethidium homodimer (EthD; lambda Fmax 620…

Continue Reading High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange

Neutrophil extracellular trap-induced intermediate monocytes trigger macrophage activation syndrome in adult-onset Still’s disease | BMC Medicine

Wang MY, Jia JC, Yang CD, Hu QY. Pathogenesis, disease course, and prognosis of adult-onset Still’s disease: an update and review. Chin Med J (Engl). 2019;132(23):2856–64. Article  CAS  PubMed  Google Scholar  Feist E, Mitrovic S, Fautrel B. Mechanisms, biomarkers and targets for adult-onset Still’s disease. Nat Rev Rheumatol. 2018;14(10):603–18. Article …

Continue Reading Neutrophil extracellular trap-induced intermediate monocytes trigger macrophage activation syndrome in adult-onset Still’s disease | BMC Medicine

MAVS found to antagonize human stem cell senescence as a mitochondrial stabilizer

MAVS maintains mitochondrial homeostasis and regulates cellular senescence through stabilizing OPA1. A. Depletion of MAVS accelerates cellular senescence of human mesenchymal stem cells. B. MAVS deficiency compromises mitochondrial dynamics. C. A model illustrating the MAVS-OPA1 axis regulates mitochondrial homeostasis and human stem cell senescence. Credit: Research A recent study led…

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Exploring the Latest Advances in Transcriptomics

Since the idea of genetic regulation was first postulated back in the 1950s, our scientific understanding of the transcriptome has deepened greatly.1 Looking into the transcriptome of cells and tissues has helped scientists to understand the biological processes that drive both health and disease; however, the complex and occasionally mysterious…

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Enhancement and inactivation effect of CRISPR/Cas12a via extending hairpin activators for detection of transcription factors

Li Q, Song ZL, Zhang YX, Zhu LN, Yang Q, Liu XF, Sun XF, Chen XX, Kong RM, Fan GC, Luo XL (2023) Synergistic Incorporation of two ssDNA activators enhances the trans-cleavage of CRISPR/Cas12a. Anal Chem 95:8879–8888 Article  CAS  PubMed  Google Scholar  Ma JY, Wang SY, Du YC, Wang DX,…

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Apoptosis-resistant megakaryocytes produce large and hyperreactive platelets in response to radiation injury | Military Medical Research

Animals C57BL/6-Tg (Pf4-icre) Q3Rsko/J (Pf4-Cre) mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA). B6;129-Tmem173tm1(flox)Smoc (Stingfl) mice were purchased from Shanghai Model Organisms Center, Inc. (Shanghai, China). C57BL/6J-Ifnar1em1(flox)Cya (Ifnar1fl) mice were purchased from Cyagen Biosciences (Guangzhou, China). Stingcko and Ifnar1cko mice were generated by crossing Pf4-Cre mice with…

Continue Reading Apoptosis-resistant megakaryocytes produce large and hyperreactive platelets in response to radiation injury | Military Medical Research

Seroprevalence and Molecular Characterization of B. abortus

Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…

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Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillation [PeerJ]

Introduction The incidence and mortality rates of AF are continuously increasing, leading to serious complications such as heart failure and stroke (Fig. 1) (Sagris et al., 2021). The occurrence and development of AF involve different mechanisms and interactions (Kornej et al., 2020). AF often progresses from paroxysmal to persistent (Nattel…

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LncRNA/circRNA-mRNA networks in CARAS | JIR

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

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Characterization of the Spectrum of Mitochondrial DNA Nucleotide Substitutions in Human Populations in High Altitude Environments

Burtscher, J., Mallet, R.T., Pialoux, V., et al., Adaptive responses to hypoxia and/or hyperoxia in humans, Antioxid. Redox Signal., 2022, vol. 37, pp. 887—912. doi.org/10.1089/ars.2021.0280 Article  PubMed  Google Scholar  Chandel, N.S., McClintock, D.S., Feliciano, C.E., et al., Reactive oxygen species generated at mitochondrial complex III stabilize hypoxia-inducible factor-1alpha during hypoxia: a…

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The Next Chapter in Genome Editing? Tome Emerges from Stealth with $213M

Rahul Kakkar, MD, Tome Biosciences president and CEO While the CRISPR community celebrates the recent first FDA approval of a CRISPR-Cas9 therapy (Casgevy), new entities are making strides in their efforts to write perhaps the definitive new chapter in programmable genome editing. Last week, Tome Biosciences—a developer of genome editing…

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A super-pangenome of the North American wild grape species | Genome Biology

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

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Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Almeida OAC, Moreira GCM, Rezende FM et al (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 20:1–20. doi.org/10.1186/s12864-019-5811-1 Article  Google Scholar  Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and…

Continue Reading Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer

Waters JK, Reznik SI. Update on management of squamous cell esophageal cancer. Curr Oncol Rep. 2022;24:375–85. Article  PubMed  Google Scholar  Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185…

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Perception of genomic newborn screening among peripartum mothers

Therrell BL, Padilla CD, Loeber JG, Kneisser I, Saadallah A, Borrajo GJC, et al. Current status of newborn screening worldwide: 2015. Semin Perinatol. 2015;39:171–87. Article  PubMed  Google Scholar  Battelino T, Kržišnik C, Pavlin K. Early detection and follow-up of children with phenylketonuria in Slovenia. Zdr Vestn. 1994;63:25–8. Google Scholar  Lampret…

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New updates on the use of Shapley value part3(Machine Learning Fall’23) | by Monodeep Mukherjee | Dec, 2023

Getting started with Shapely Values ONNXExplainer: an ONNX Based Generic Framework to Explain Neural Networks Using Shapley Values(arXiv) Author : Yong Zhao, Runxin He, Nicholas Kersting, Can Liu, Shubham Agrawal, Chiranjeet Chetia, Yu Gu Abstract : Understanding why a neural network model makes certain decisions can be as important as…

Continue Reading New updates on the use of Shapley value part3(Machine Learning Fall’23) | by Monodeep Mukherjee | Dec, 2023

TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

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Arsenic is a potent co-mutagen of ultraviolet light

Barnes, J. L., Zubair, M., John, K., Poirier, M. C. & Martin, F. L. Carcinogens and DNA damage. Biochem. Soc. Trans. 46, 1213–1224 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system…

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Gadolinium Oxide Nanoparticles reinforce immune response

Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…

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Diversity and dissemination of viruses in pathogenic protozoa

Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article  CAS  PubMed  Google Scholar  Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article  Google Scholar …

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PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660. Article  PubMed  Google Scholar  Hu G, Chong RA, Yang Q, Wei Y, Blanco…

Continue Reading PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International

Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

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Fatty Acid Metabolism-Related lncRNAs as Biomarkers for SKCM

Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…

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Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

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Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

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Genomic Predictors Associated With Exceptional Response to Systemic Therapy in Advanced Pancreatic Cancer

ABSTRACT Introduction: Exceptional response to therapy is rare in patients with advanced pancreatic cancer. This study explored potential genomic differences between typical and exceptional responses that could confer more favorable biology. Methods: We included exceptional responders and controls with advanced pancreatic cancer from Cleveland Clinic from April 2013 to August…

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Empowering Models with Performance: The Art of Generalized Model Transformation Approach

by Jackie (Jiaqi) Xu, Yanbo Liang, Jason Ansel, Chunzhi Yang, Jade Nie, Yuzhen Huang, CK Luk, Xiaodong Wang, Lu Fang, Menglu Yu, Jinwon Lee, Daohang Shi, Flavio Sales Truzzi Introduction PyTorch 2.0 (PT2) offers a compiled execution mode which rewrites Python bytecode to extract sequences of PyTorch operations, translating them…

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SOCS3 inhibiting JAK-STAT pathway enhances oncolytic adenovirus efficacy by potentiating viral replication and T-cell activation

Kaufman HL, Kohlhapp FJ, Zloza A. Oncolytic viruses: a new class of immunotherapy drugs. Nat Rev Drug Discov. 2015;14:642–62. Article  CAS  PubMed  PubMed Central  Google Scholar  Kessler T, Wick W. Oncolytic virotherapy: potentially a game-changing tumor treatment. Cancer Cell. 2021;39:753–5. Article  CAS  PubMed  Google Scholar  Koch J, Schober SJ, Hindupur…

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Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the Molecular Level with Real-Time PCR

Allam RM, Al-Abd AM, Khedr A, Sharaf OA, Nofal SM, Khalifa AE, Mosli HA, Abdel-Naim AB (2018) Fingolimod interrupts the cross talk between estrogen metabolism and sphingolipid metabolism within prostate cancer cells. Toxicol Lett 291:77–85 Article  CAS  PubMed  Google Scholar  Andrews S et al (2010) FastQC: a quality control tool…

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Tree size diversity is the major driver of aboveground carbon storage in dryland agroforestry parklands

Albrecht, A. & Kandji, S. T. Carbon sequestration in tropical agroforestry systems. Agric. Ecosyst. Environ. 1–3, 15–27 (2003). Article  Google Scholar  Nair, P. K. R. Agroforestry systems and environmental quality: Introduction. J. Environ. Qual. 40, 784–790 (2011). Article  CAS  PubMed  Google Scholar  Schroth, G. & McNeely, J. A. Biodiversity conservation,…

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CRISPR opens doors for novel probiotic functions and applications

Humans can benefit significantly from symbiotic relationships with probiotics-;live bacteria and microorganisms that influence the gut microbiota. When consumed in appropriate amounts, probiotics can promote gut health, support the immune system, and enhance metabolism. Probiotics, widely regarded as a treasure in the field of microbiology, are currently finding new applications…

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Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships | BMC Genomics

Johnson DV, Al-Khayri JM, Jain SM. Introduction: Date Production Status and Prospects in Africa and the Americas. In: Al-Khayri J, Jain S, Johnson D, editors. Date Palm Genetic Resources and Utilization: Volume 1: Africa and the Americas. Springer Netherlands, Dordrecht; 2015. p. 1–18. doi.org/10.1007/978-94-017-9694-1_1 Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic…

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Molecular Techniques | SpringerLink

Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Büyükköroğlu G, Dora DD, Özdemir F, Hızel C (2018)…

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Heavy-chain antibody targeting of CD38 NAD+ hydrolase ectoenzyme to prevent fibrosis in multiple organs

Asano, Y. & Varga, J. Rationally-based therapeutic disease modification in systemic sclerosis: Novel strategies. Semin. Cell Dev. Biol. 101, 148–160. doi.org/10.1016/j.semcdb.2019.12.007 (2019). Article  Google Scholar  Allanore, Y. et al. Systemic sclerosis. Nat. Rev. Dis. Prim. 1, 15002. doi.org/10.1038/nrdp.2015.2 (2015). Article  PubMed  Google Scholar  Varga, J. & Abraham, D. Systemic sclerosis:…

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Cas9-induced targeted integration of large DNA payloads in primary human T cells via homology-mediated end-joining DNA repair

Khan, S. et al. Role of recombinant DNA technology to improve life. Int. J. Genomics Proteomics 2016, 2405954 (2016). Google Scholar  Spolski, R., Li, P. & Leonard, W. J. Biology and regulation of IL-2: from molecular mechanisms to human therapy. Nat. Rev. Immunol. 18, 648–659 (2018). Article  CAS  PubMed  Google…

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High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines

Almarez DN, Almarez FJS, Baulete EM. 2014. Bayug Island Aquasilvi Program: An Eco-Governance Strategy for Climate Change Adaptation and Mitigation. J Govern Dev 10(2): 35-54. DOI: 10.32890/jgd. Alongi DM. 2014. Carbon cycling and storage in mangrove forests. Ann Rev Mar Sci 6: 195-219. DOI: 10.1146/annurev-marine-010213-135020. Balint M, Pfenninger M, Grossart…

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Galaxy Macau officially launches the newest phase of its resort

Galaxy Entertainment Group (GEG) held a formal ceremony today to mark the completion of its Phase 3 expansion project, almost two years after it announced the end of construction in February 2022.  Phase 3 consists of three buildings – the 700-room Andaz hotel, the 450-suite Raffles hotel and the 40,000-square-metre…

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The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

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Characterizing viral species in mosquitoes (Culicidae) in the Colombian Orinoco: insights from a preliminary metagenomic study

Kraemer, M. U. et al. The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus. Elife 4, e08347. doi.org/10.7554/eLife.08347 (2015). Article  PubMed  PubMed Central  Google Scholar  Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507. doi.org/10.1038/nature12060 (2013). Article  ADS  CAS  PubMed  PubMed Central …

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Diagnostic efficacy of mNGS in spinal infection patients

Introduction Spinal infection, an uncommon condition, was first recorded in 1779.1 When the intervertebral disk is infected, it is commonly referred to as spondylodiscitis,2 whereas infection of the vertebral body or endplates is more precisely termed vertebral osteomyelitis or spondylitis.3 The definitive diagnosis of spinal infection is often delayed by…

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A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article  CAS  PubMed  Google Scholar  Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article  CAS …

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How does mtdna tells about depression?

Open access•Journal Article•DOI Na Cai, Yihan Li, Simon Chang, Jieqin Liang, Chongyun Lin, Xiufei Zhang, Lu Liang, Jingchu Hu, Wharton Chan, Kenneth S. Kendler, Tomas Malinauskas, Guo-Jen Huang, Qibin Li, Richard Mott, Jonathan Flint  – Show less +14 more The paper discusses the relationship between mitochondrial DNA (mtDNA) and major…

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Construction of a risk stratification model integrating ctDNA to predict response and survival in neoadjuvant-treated breast cancer | BMC Medicine

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Giaquinto AN, Sung H, Miller KD, Kramer JL, Newman LA,…

Continue Reading Construction of a risk stratification model integrating ctDNA to predict response and survival in neoadjuvant-treated breast cancer | BMC Medicine

Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Wang, W. T. Revision of Adonis (Ranunculaceae). Bull. Bot. Res. 14, 1–31 (1994). Google Scholar  Gao, T. et al. Evaluating the feasibility of using candidate DNA Barcodes in discriminating species of the large Asteraceae family. BMC Evol. Biol. 10, 324 (2016). Article  Google Scholar  Conti, F. et al. Adonis fucensis…

Continue Reading Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine

Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article  PubMed  Google Scholar  Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…

Continue Reading Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

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RPTOR mutation: a novel predictor of efficacious immunotherapy in melanoma

Li Z, Gao Y, Cao Y et al (2023) Extracellular RNA in Melanoma: advances, challenges, and opportunities. Front Cell Dev Biol 11:1141543. doi.org/10.3389/fcell.2023.1141543 Article  PubMed  PubMed Central  Google Scholar  Hamid O, Cowey CL, Offner M, Faries M, Carvajal RD (2019) Efficacy, Safety, and tolerability of approved combination BRAF and MEK…

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Wide bovine tick-borne pathogen spectrum: Predominancy of Theileria annulata and the first molecular detection of Ehrlichia minasensis in Turkey

Agina OA, Shaari MS, Isa NMM, Ajat M, Zamri-Saad M, Hamzah H (2020) Clinical pathology, immunopathology and advanced vaccine technology in bovine theileriosis: A review. Pathogens 9:697. doi.org/10.3390/pathogens9090697 Article  PubMed  PubMed Central  CAS  Google Scholar  Aktas M (2014) A survey of ixodid tick species and molecular identification of tick-borne pathogens….

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The emergence of CRISPR-Cas engineered strains

CRISPR-based genome editing in probiotics. Credit: BioDesign Research Probiotics, defined as live microorganisms beneficial to health, have shown promise in areas like anti-inflammatory activity and brain function, etc. However, challenges remain due to variability in tolerance and colonization among species and strains. Recent advances in genome engineering, including CRISPR-Cas, have…

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Genetic architecture of cardiac dynamic flow volumes

Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article  PubMed  Google Scholar  Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article  CAS …

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Study Links Gene Network To Diabetes 2

In a collaborative effort co-led by teams from Vanderbilt University Medical Center (VUMC) and the University of Michigan, a comprehensive study that integrates multiple analytic approaches has linked a regulatory gene network and functional defects in insulin-producing pancreatic beta cells to Type 2 diabetes. The study, published in the journal…

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Origin and evolution of the triploid cultivated banana genome

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

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A CNN based m5c RNA methylation predictor

Hammad, M. et al. A novel end-to-end deep learning approach for cancer detection based on microscopic medical images. Biocybern. Biomed. Eng. 42(3), 737–748 (2022). Article  Google Scholar  Hammad, M. et al. Efficient multimodal deep-learning-based covid-19 diagnostic system for noisy and corrupted images. J. King Saud Univ.-Sci. 34(3), 101898 (2022). Article …

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ST23 Klebsiella pneumoniae in China

Introduction Klebsiella pneumoniae (KP), a member of the Enterobacteriaceae family, inhabits aquatic environments and can colonise respiratory and gastrointestinal tracts in humans, making it a significant opportunistic pathogen. It may result in pneumonia, meningitis, urinary tract infections, and bloodstream infections. Hypervirulent Kp (HvKp) is believed to cause severe community-acquired invasive…

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Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts

Benjamin, E. J. et al. Heart disease and stroke statistics-2019 update: A report from the American Heart Association. Circulation 139, e56–e528 (2019). Article  PubMed  Google Scholar  Yusuf, S. et al. Effect of potentially modifiable risk factors associated with myocardial infarction in 52 countries (the INTERHEART study): Case-control study. Lancet 364,…

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FGFR2 point mutation in 2 cases of pleomorphic adenoma progressing to myoepithelial carcinoma

1. Carlson ER, Schlieve T. Salivary gland malignancies. Oral Maxillofac Surg Clin North Am 2019; 31: 125-144. 2. Seethala RR. Salivary gland tumors: current concepts and controversies. Surg Pathol Clin 2017; 10: 155-176. 3. Bradley PJ, McGurk M. Incidence of salivary gland neoplasms in a defined UK population….

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Glabridin improves autoimmune disease in Trex1-deficient mice by reducing type I interferon production | Molecular Medicine

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55:611–22. Article  CAS  PubMed  Google Scholar  Chen Q, Sun L, Chen ZJ….

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The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

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HER2 low expression breast cancer subtyping and their correlation with prognosis and immune landscape based on the histone modification related genes

Barzaman, K. et al. Breast cancer: Biology, biomarkers, and treatments. Int. Immunopharmacol. 84, 106535 (2020). Article  CAS  PubMed  Google Scholar  Siegel, R. L., Miller, K. D., Wagle, N. S. & Jemal, A. Cancer statistics, 2023. CA Cancer J. Clin. 73(1), 17–48 (2023). Article  PubMed  Google Scholar  Mueller, C., Haymond, A.,…

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CircRNA and Stroke: New Insight of Potential Biomarkers and Therapeutic Targets

Diener HC, Hankey GJ (2020) Primary and secondary Prevention of ischemic Stroke and Cerebral Hemorrhage: JACC Focus Seminar. J Am Coll Cardiol 75(15):1804–1818 Article  PubMed  Google Scholar  Dou Z, Yu Q, Wang G, Wu S, Reis C, Ruan W, Yan F, Chen G (2020) Circular RNA expression profiles alter significantly…

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Google’s Gemini launch tells Chinese AI developers: latecomers can bridge gap with determination

Photo: VCG  While OpenAI has been continuously iterating and gaining widespread attention in the past few months, Google finally dropped a bombshell by unveiling its long-awaited multimodal model, Gemini, which Google itself touted as “the most capable model” they’ve ever built.  Chinese analysts say it can help Google catch up…

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Metagenomic next-gene sequencing for respiratory infections

Introduction Respiratory tract infections are common and occur frequently. Rapid and accurate microbial detection is essential for timely and appropriate treatment. Traditional microbial detection methods have some limitations such as dependence on morphology, long duration, low sensitivity, and high variability.1,2 Metagenomic next-generation sequencing (mNGS) is a new detection technology characterized…

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Illumina RNA Sequencing – SeqCenter, LLC

RNA, the intermediate stage in the flow of genetic information from DNA to protein, contains many systems of expression and regulation that can be studied through RNA sequencing. While whole genome sequencing reveals information at the DNA level, next generation RNA sequencing (RNA-seq) characterizes the transcriptome and provides additional context…

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CRISPR Continuous to Innovate! Exploring the Future of Cell & Gene Therapy, Industry Leaders Converge at the 2024 GenScript Biotech Global Forum

NANJING, China, Dec. 7, 2023 /PRNewswire/ — The rapid advancement of technology has propelled the field of life sciences into unprecedented growth, constantly expanding our understanding and imagination. Particularly in the field of cellular gene therapy, a series of recent positive developments have been overwhelming. Recently, the world’s first CRISPR/Cas9…

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Advancements in Non-human Forensic DNA Analysis

Alahi MEE, Mukhopadhyay SC (2017) Detection methodologies for pathogen and toxins: a review. Sensors 1885:17 Google Scholar  Aly SM, Sabri DM (2015) Next generation sequencing (NGS): a golden tool in forensic toolkit. Archiwum Medycyny Sądowej i Kryminologii/Archives of Forensic Medicine and Criminology 65(4):260–271 Google Scholar  Amendt J, Richards CS, Campobasso…

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Advanced Emerging Techniques for Forensic DNA Analysis: STRs, SNPs, and mtDNA Analysis

Alshehhi A, Almarzooqi A, Alhammadi K, Werghi N, Tay GK, Alsafar H (2023) Advancement in human face prediction using DNA. Genes (Basel) 14:136. doi.org/10.3390/genes14010136 CrossRef  CAS  PubMed  Google Scholar  Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314. doi.org/10.7717/peerj.7314 CrossRef  PubMed Central  PubMed …

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Applications of NGS Technology in Forensic DNA Analysis

Caratti S, Turrina S, Ferrian M et al (August 2015) MiSeq FGx sequencing system: a new platform for forensic genetics. Forensic Sci Int Genet Suppl Ser 5:e98–e100. doi.org/10.1016/j.fsigss.2015.09.040 Elkins KM, Garloff AT, Zeller CB (2023) Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen…

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Zea mays genotype influences microbial and viral rhizobiome community structure

Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article  CAS  PubMed  Google Scholar  Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article  PubMed  Google Scholar  Pratama AA, Terpstra J, de Oliveria ALM,…

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A natural product YSK-A blocks SARS-CoV-2 propagation by targeting multiple host genes

Hoareau, L. & DaSilva, E. J. Medicinal plants: A re-emerging health aid. Electron. J. Biotechnol. 2, 3–4 (1999). Google Scholar  Jahan, I. & Ahmet, O. Potentials of plant-based substance to inhabit and probable cure for the COVID-19. Turk. J. Biol. 44, 228 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar …

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Characterization of 16S rRNA of the gut microbiome in long-tailed macaque (Macaca fascicularis) with spontaneous type 2 diabetes mellitus

Ahmad A, Yang W, Chen G, Shafiq M, Javed S, Zaidi SSA, Shahid R, Liu C, Bokhari H. 2019. Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals. PLoS One. 14(12):1–15. doi:10.1371/ journal.pone.0226372. Arora A, Behl T, Sehgal A, Singh S, Sharma N, Bhatia S,…

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A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article  CAS  PubMed  Google Scholar  International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….

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In-depth analyses of lncRNA and circRNA expression in the hi… : NeuroReport

Zhang, Yongcanga,*; Tang, Liangb,c,*; Wang, Yanb; Zhu, Xiaoyana; Liu, Lana Author Information aMedical College, Tibet University, Lhasa, Tibet bDepartment of Basic Medicine, Changsha Medical University cHunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative Diseases, Changsha Medical University, Changsha, People’s Republic of China Received 19…

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Bioinformatics analysis of immune characteristics in tumors with alternative carcinogenesis pathways induced by human papillomaviruses | Virology Journal

de Martel C, Georges D, Bray F, Ferlay J, Clifford GM. Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob Health. 2020;8:e180–90. Article  PubMed  Google Scholar  McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head…

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Correlation Between the Levels of ANGPTL3, ANGPTL4, ANGPTL8 and Postpr

Introduction As the prevalence of hyperlipidemia has increased, the assessment of blood lipids is increasingly important.1 At present, fasting lipid indices, including total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) levels are most commonly assessed in clinical practice.2 Among them, the TG level is one of the most…

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Bioconductor – octad (development version)

DOI: 10.18129/B9.bioc.octad   This is the development version of octad; for the stable release version, see octad. Open Cancer TherApeutic Discovery (OCTAD) Bioconductor version: Development (3.19) OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene…

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Identification and validation of key miRNAs for colon cancer

Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…

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Key Genes for Pyroptosis-induced Salivary Gland Inflammation

Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

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Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

Yang J, Liu X, Cao S, Dong X, Rao S, Cai K. Understanding esophageal cancer: the challenges and opportunities for the next decade. Front Oncol. 2020;10:1727. Article  PubMed  PubMed Central  Google Scholar  Li J, Xu J, Zheng Y, Gao Y, He S, Li H, et al. Esophageal cancer: epidemiology, risk…

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NOTCH1 mutations predict superior outcomes, NSCLC

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

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tRNA therapeutics for genetic diseases

Huang, X. et al. The landscape of mRNA nanomedicine. Nat. Med. 28, 2273–2287 (2022). Article  CAS  Google Scholar  Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022). Article  CAS  Google Scholar  Brown, A., Shao, S.,…

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Borrelia puertoricensis in opossums (Didelphis marsupialis) from Colombia | Parasites & Vectors

Oppler Z, Keeffe K, McCoy K, Brisson D. Evolutionary genetics of Borrelia. Curr Issues Mol Biol. 2021;42:97–112. doi.org/10.21775/cimb.042.097.2. Article  PubMed  Google Scholar  Margos G, Fingerle V, Cutler S, Gofton A, Stevenson B, Estrada-Peña A. Controversies in bacterial taxonomy: the example of the genus Borrelia. Ticks Tick Borne Dis. 2020;11:101335. doi.org/10.1016/j.ttbdis.2019.101335….

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The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes

Kornberg, R. D. & Lorch, Y. Primary role of the nucleosome. Mol. Cell 79, 371–375 (2020). Article  CAS  PubMed  Google Scholar  Zhu, F. et al. The interaction landscape between transcription factors and the nucleosome. Nature 562, 76–81 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Lee, C. K., Shibata, Y.,…

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Advances in Gene Editing Technology: Revolutionizing Healthcare and Beyond | by Amirali Banani | Dec, 2023

Amirali Banani December 3, 2023 Credit: vchal/Shutterstock “The power to control our species’ genetic future is awesome and terrifying. Deciding how to handle it may be the biggest challenge we have ever faced.” ― Jennifer A. Doudna In recent years, gene editing technology has witnessed remarkable advancements, transforming the landscape…

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Addgene: pDM002-sgRNA-lenti-ZeoR

These plasmids were created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the plasmids were described, and include Addgene in the Materials and Methods of your future publications. For your Materials & Methods section: pDM002-sgRNA-lenti-ZeoR was a gift from Britt Glaunsinger (Addgene plasmid # 200060…

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2023 Year in Review: Business Developments

By Alex Philippidis At the start of 2023, the website for Pfizer CenterOne posted an article titled, “What Trends Will Shape the Pharma and Biotech Industries in 2023?” It quoted Rick L. Knight, the company’s global head of strategic account management, as follows: “We can continue to expect to see…

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Lower-limb ulcers in participants with leprosy sequelae

Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…

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Targeting the epigenome to reinvigorate T cells for cancer immunotherapy | Military Medical Research

Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, et al. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature. 2022;609(7926):354–60. Article  CAS  PubMed  PubMed Central  Google Scholar  Zhu L, Zhou X, Gu M, Kim J, Li Y, Ko CJ, et al. Dapl1 controls NFATc2…

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The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article  PubMed  CAS  Google Scholar  Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…

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Survey of the infant male urobiome and genomic analysis of Actinotignum spp.

Wolfe, A. J. et al. Evidence of uncultivated bacteria in the adult female bladder. J. Clin. Microbiol. 50, 1376–1383 (2012). Article  PubMed  PubMed Central  Google Scholar  Hilt, E. E. et al. Urine is not sterile: Use of enhanced urine culture techniques to detect resident bacterial flora in the adult female…

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Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection

Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Żaczek A, Dziadek J (2016) Methodological and clinical aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clin Microbiol Rev 29:239–290. doi.org/10.1128/cmr.00055-15 Article  PubMed  PubMed Central  CAS  Google Scholar  Niemann S, Merker M, Kohl T, Supply P…

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