Tag: EB

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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Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors

Akhoundi M, Downing T, Votypka J, Kuhls K, Lukes J, Cannet A, et al. Leishmania infections: molecular targets and diagnosis. Mol Aspects Med. 2017;57:1–29. Article  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. A historical overview of the classification, evolution, and…

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Comprehensive Review of Small Interfering RNAs (siRNAs)

Introduction Cancer, also called malignancy, is a group of diseases caused by the rapid multiplication and spread of malignant cells.1,2 According to statistics from the National Cancer Center, more than 100 types of cancer have been identified.3 The ability of malignant tumor cells to metastasize via the blood-lymphatic system and…

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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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Hybrid Friday Satellite Symposium on R/R DLBCL | Preceding the 65th ASH Annual Meeting & Exposition Tickets, Fri, Dec 8, 2023 at 3:00 PM

Hybrid Friday Satellite Symposium on R/R DLBCL | Preceding the 65th ASH Annual Meeting & Exposition Attend In-Person or Virtually for an exciting and informative event, Advances in Precision Medicine for Relapsed/Refractory Diffuse Large B-Cell Lymphoma Care, happening at the San Diego Convention Center on Friday, December 8, 2023, 3:00…

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Potential use of iPSCs for disease modeling, drug screening, and cell-based therapy for Alzheimer’s disease | Cellular & Molecular Biology Letters

Tarawneh R, Holtzman DM. The clinical problem of symptomatic Alzheimer disease and mild cognitive impairment. Cold Spring Harb Perspect Med. 2012;2(5): a006148. Article  PubMed  PubMed Central  Google Scholar  van der Flier WM, Scheltens P. Epidemiology and risk factors of dementia. J Neurol Neurosurg Psychiatry. 2005;76(suppl 5):v2-7. Article  PubMed  PubMed Central …

Continue Reading Potential use of iPSCs for disease modeling, drug screening, and cell-based therapy for Alzheimer’s disease | Cellular & Molecular Biology Letters

DNA methylation change in blood cells of FB and CFS patients

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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Unleashing the power of soft-decision decodin

image:  DNA digital storage (DDS) involves encoding information into nucleotide sequences, synthesizing DNA molecules, and storing them accordingly. Solid-phase synthesis using phosphoramidite-based chemical synthesis can be performed on a column or array solid support, enabling low-throughput or high-throughput synthesis. The synthesized DNA material can be stored in biological cells (in…

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Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis | Journal of Translational Medicine

Centore RC, Sandoval GJ, Soares LMM, Kadoch C, Chan HM. Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies. Trends Genet. 2020;36:936–50. Article  CAS  PubMed  Google Scholar  Pagliaroli L, Trizzino M. The Evolutionary conserved SWI/SNF subunits ARID1A and ARID1B Are Key modulators of pluripotency and cell-fate determination. Front Cell…

Continue Reading Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis | Journal of Translational Medicine

Unleashing the power of soft-decision decoding in DNA digital storage

DNA digital storage (DDS) involves encoding information into nucleotide sequences, synthesizing DNA molecules, and storing them accordingly. Solid-phase synthesis using phosphoramidite-based chemical synthesis can be performed on a column or array solid support, enabling low-throughput or high-throughput synthesis. The synthesized DNA material can be stored in biological cells (in vivo)…

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Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer

Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article  CAS  PubMed  PubMed Central  Google Scholar  Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article  CAS  PubMed  Google Scholar  Lawrence…

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[slurm-users] parastation (mpi)

On 11/24/23 06:16, Heckes, Frank wrote: > My colleagues are using this toolchains on Jülich cluster (especially > Juwels). My question is whether these eb files can be shared ? I would > be interested especially in the ones using NVHPC as core module. If Jülich developed that toolchain then…

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Immune-privileged tissues formed from immunologically cloaked mouse embryonic stem cells survive long term in allogeneic hosts

Mice C57BL/6N (strain 005304), C3H/HeJ (strain 000659), FVB/NJ (strain 001800), BALB/cJ (strain 000651) and NSG mice (stock 005557) were purchased from the Jackson Laboratory. CD-1 (stock 022) mice were purchased from Charles River. Mice (6–20-week-old) of each strain/background were used for teratoma assays. Mice were housed in a pathogen-free facility…

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Next-Generation Sequencing Data Analysis Market is Expected

Wilmington, Delaware, United States, Nov. 22, 2023 (GLOBE NEWSWIRE) — Transparency Market Research Inc. – The global next-generation sequencing data analysis market stood at US$ 1.17 billion in 2022 and the global market is projected to reach US$ 5.4 billion in 2032. The next-generation sequencing data analysis market is anticipated…

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ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry

Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article  Google Scholar  American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…

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Molecular detection and whole genome sequencing of Pectobacterium and Dickeya, the casual agents of soft rot disease in lettuce

Azadmanesh S, Marefat A (2013) and Kayhan Azadmanesh. Detection of Pectobacteria causal agents of potato soft rot in north-western provinces of Iran. J Plant Pathol Microbiol 4(1) Babadoost M (1990) Bacterial soft rot of vegetables, fruits and ornamentals. Rep Plant Dis 943:7 Google Scholar  Ben Fekih I, Zhang C, Li…

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Knockdown of GNL3L alleviates the progression of COPD

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic bronchitis disease characterized by persistent airflow limitation, which can be prevented and treated. COPD is the third leading cause of death in the world reported in 2020.1 With the progression of the disease, COPD will lead to respiratory failure, pulmonary…

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Gotta Get Rid of It All: Total Plaque Clearance Key for Clinical Benefit

18 Nov 2023 As researchers parse what makes amyloid immunotherapy work, one answer keeps bubbling up: Take out all plaque quickly, so that clinical benefits have time to show up. At last month’s Clinical Trials on Alzheimer’s Disease conference, held October 24 to 27 in Boston and online, several talks…

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The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment

Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…

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db2 – Connection to database using ibm_db on Python using Rstudio IDE

I am trying to connect to a database using ibm_db. I am working on Rstudio but with Pythomn not with R. I have the next code: import ibm_db import pandas as pd # Definir los parámetros de conexión dsn_driver = “{IBM DB2 ODBC DRIVER}” dsn_database = “BQ” dsn_hostname = “bq-stby.db2.***.**”…

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Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

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Partners turn to technology to develop gene editing therapy for EB

Healiva and C4U will collaborate to develop a next-generation gene editing therapy — focusing on new technology to correct gene mutations — for epidermolysis bullosa (EB) patients, who are sometimes known as butterfly children for their fragile skin. Combining C4U’s expertise in gene editing technology and Healiva’s experience with cell-based…

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BDQ resistance and molecular characterization of RR-TB

Enyu Tong,1,* Ying Zhou,1,* Zhengwei Liu,2 Yelei Zhu,2 Mingwu Zhang,2 Kunyang Wu,2 Junhang Pan,2 Jianmin Jiang1– 3 1School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China; 2Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China; 3Key Laboratory of…

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A New Hope for Epidermolysis Bullosa (“butterfly children”) Thanks to Novel CRISPR-Cas3 Platform

LUGANO, Switzerland & OSAKA, Japan–(BUSINESS WIRE)– Healiva SA (Healiva) and C4U Corporation (C4U) are pleased to announce that they have entered into a strategic alliance agreement regarding the development of CRISPR-Cas3 derived therapeutic solutions for Epidermolysis Bullosa (EB), also known as “butterfly children”. This press release features multimedia. View the…

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Significant Pathogenic Nontuberculous Mycobacteria | IDR

Introduction The Mycobacterium genus encompasses various species, including the Mycobacterium tuberculosis complex, which is responsible for tuberculosis (TB) infections, Mycobacterium leprae, which associated with leprosy, and a group of nontuberculous mycobacteria (NTM) species.1 The NTM species, also known as Mycobacteria other than tuberculosis (MOTT), can be widely found in the…

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Mass Spectrometer Market Anticipated to Reach a Robust USD 13.5 Billion by 2031, with a Steady 8.2% CAGR, States TMR

Surge in Adoption of Mass Spectrometers in Food & Beverage Industry to Drive Demand for Mass Spectrometers. WILMINGTON, DELAWARE , UNITED STATES, October 25, 2023 /EINPresswire.com/ — As per the latest market research report titled ‘ ,’ released by Transparency Market Research, the global mass spectrometry market is poised to…

Continue Reading Mass Spectrometer Market Anticipated to Reach a Robust USD 13.5 Billion by 2031, with a Steady 8.2% CAGR, States TMR

Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)

Aguilera F, McDougall C, Degnan BM (2017) Co-option and de novo gene evolution underlie molluscan shell diversity. Mol Biol Evol 34(4):779–792 CAS  PubMed  PubMed Central  Google Scholar  Alexa A, Rahnenfuhrer J (2020) topGO: Enrichment analysis for gene ontology. R package version 2.40.0 Google Scholar  Arivalagan J, Yarra T, Marie B,…

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Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

MacDonald SW, Li SC, Bäckman L. Neural underpinnings of within-person variability in cognitive functioning. Psychol Aging. 2009;24:792–808. Article  PubMed  Google Scholar  Haynes BI, Bunce D, Kochan NA, Wen W, Brodaty H, Sachdev PS. Associations between reaction time measures and white matter hyperintensities in very old age. Neuropsychologia. 2017;96:249–55. Article  PubMed …

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Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes | BMC Microbiology

Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13:260–70. Article  CAS  PubMed  PubMed Central  Google Scholar  Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24:392 NIH Public Access. Article …

Continue Reading Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes | BMC Microbiology

Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers | Parasites & Vectors

Machado-Ferreira E, Vizzoni VF, Balsemao-Pires E, Moerbeck L, Gazeta GS, Piesman J, et al. Coxiella symbionts are widespread into hard ticks. Parasitol Res. 2016;115:4691–9. doi.org/10.1007/s00436-016-5230-z. Article  PubMed  Google Scholar  Jung M, Kho JW, Lee WG, Roh JY, Lee DH. Seasonal occurrence of Haemaphysalis longicornis (Acari: Ixodidae) and Haemaphysalis flava, vectors…

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Bioinformatics Market Sees USD 44.9 Billion Valuation by 2028 |

Bioinformatics Market The latest research study released by Transparency Market Research on “Bioinformatics Market Forecast to 2020 – 2028 ″ research provides accurate economic, global, and country-level predictions and analyses. It provides a comprehensive perspective of the competitive market as well as an in-depth supply chain analysis to assist businesses…

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Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology

Zhang L, Wang F, Wang L, Wang W, Liu B, Liu J, Chen M, He Q, Liao Y, Yu X, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012;379:815–22. Article  PubMed  Google Scholar  Collaboration GBDCKD. Global, regional, and national burden of chronic kidney disease, 1990–2017:…

Continue Reading Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology

The histone acetyl transferases CBP and p300 regulate stress response pathways in synovial fibroblasts at transcriptional and functional levels

Hypoxia, the formation of reactive oxygen species (ROS), and subsequent oxidative stress in synovial tissues are key events in the pathogenesis of RA1. We provide here evidence that CBP and p300 are pivotal regulators of the adaptive response of SF that integrate the cell`s transcriptional and functional regulation of stress…

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Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex

Adams RV, Burg TM (2015) Gene flow of a forest-dependent bird across a fragmented landscape. PLoS One 10:1–22 Article  Google Scholar  Aguillon S, Rohwer V (2022) Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times. Evolution 76:1082–1090 Article  PubMed  Google Scholar  Aktas C (2020)…

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The Therapeutic Effects of MUC1-C shRNA@Fe3O4 Magnetic Nanoparticles i

Introduction Breast cancer (BC) is a malignant tumor originating from the epithelial tissue of the breast and is the most common malignancy in women.1 It is estimated that by 2040, there will be 3,000,000 new cases of BC and 100,000 deaths worldwide. Triple-negative breast cancer (TNBC), which accounts for 15–20%…

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Gene Set – PPP6C

Symbol Name ACTR3 ARP3 actin-related protein 3 homolog (yeast) ADAR adenosine deaminase, RNA-specific ADNP activity-dependent neuroprotector homeobox ANAPC13 anaphase promoting complex subunit 13 ARF6 ADP-ribosylation factor 6 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 ATP5J2 ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2 ATP5L ATP…

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Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article  Google Scholar  Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…

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The Clinical Impact of mNGS for the Diagnosis of PJI

Introduction The total number of periprosthetic joint infection cases is increasing with the surging numbers of joint arthroplasties, internal fixation implantation and the use of immunosuppressive agents.1,2 Unfortunately, the identification of corresponding pathogens remains time-consuming and challenging because of inert bacteria, biofilm formation and prior antibiotic administration.3–8 Metagenomic next-generation sequencing…

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World Cup: Eb Eye First Win Against Hfc | Kolkata News

Kolkata: East Bengal FC seek momentum and first win against Hyderabad FC when Carles Cuadrat’s team welcomes the former champions here on Saturday.In their previous six meetings in the league, Hyderabad won four times while honours were shared on two occasions.Changing the script with a maiden win against Hyderabad now…

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Innovative strategies of reprograming immune system cells

Introduction Cancer is well characterized by genomic instability resulting in structural alterations that build up with tumor progression.1,2 A subpopulation of undifferentiated cancer cells, known as cancer stem cells (CSCs) are found within the tumor bulk. These cells are responsible for cancer initiation, recurrence and show therapeutic resistance and these…

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Borrelia persica infection in wild carnivores in Israel: molecular characterization and new potential reservoirs | Parasites & Vectors

Dworkin MS, Schwan TG, Anderson DE, Borchardt SM. Tick-borne relapsing fever. Infect Dis Clin North Am. 2008;22:449–68. Article  PubMed  PubMed Central  Google Scholar  Barbour AG, Hayes SF. Biology of Borrelia species. Microbiol Rev. 1986;50:381–400. Article  CAS  PubMed  PubMed Central  Google Scholar  Parola P, Raoult D. Ticks and tickborne bacterial diseases…

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capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…

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First isolation of Rickettsia amblyommatis from Amblyomma mixtum in Colombia | Parasites & Vectors

Fang R, Blanton LS, Walker DH. Rickettsiae as emerging infectious agents. Clin Lab Med. 2017;37:383–400. doi.org/10.1016/j.cll.2017.01.009. Article  PubMed  Google Scholar  Verhoeve VI, Fauntleroy TD, Risteen RG, Driscoll TP, Gillespie JJ. Cryptic genes for interbacterial antagonism distinguish Rickettsia species infecting blacklegged ticks from other Rickettsia pathogens. Front Cell Infect Microbiol. 2022;12:880813….

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the dispersion estimation of edgeR and DESeq2

the dispersion estimation of edgeR and DESeq2 0 Hello, I am currently studying the dispersion estimation methods used in edgeR and DESeq2.And I wonder if someone can help me correct my understanding. The edgeR and DESeq2 both use the EB method to borrow information from genes in the dataset. In…

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Drug delivery systems for CRISPR-based genome editors

Li, Y., Glass, Z., Huang, M., Chen, Z. Y. & Xu, Q. Ex vivo cell-based CRISPR/Cas9 genome editing for therapeutic applications. Biomaterials 234, 119711 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Dong, W. & Kantor, B. Lentiviral vectors for delivery of gene-editing systems based on CRISPR/Cas: current state and…

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Electroporation Instruments Market Current Trends and Future

The latest research study released by Transparency Market Research on “Electroporation Instruments Market Forecast to 2020-2030 ″ research provides accurate economic, global, and country-level predictions and analyses. It provides a comprehensive perspective of the competitive market as well as an in-depth supply chain analysis to assist businesses in identifying major…

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r – Plotting multivariate time series along with mean and confidence interval in ggplot

I have a (very) multivariate time series, say 25 observations at different timepoints, for at least 15 different variables. I would like to plot all observations with respect to time and plot a mean-line and confidence interval for each timepoint (where mean and standard deviation is across the different variables…

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The genetic variability of grapevine Pinot gris virus (GPGV) in Australia | Virology Journal

Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, et al. A new grapevine virus discovered by deep sequencing of virus-and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 2012;163(1):262–8. doi.org/10.1016/j.virusres.2011.10.010. Article  CAS  PubMed  Google Scholar  Bertazzon N, Forte V, Filippin L, Causin R, Maixner…

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TCGAbiolinks not working anymore

TCGAbiolinks not working anymore 0 The script in this tutorial does not work anymore bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html I get to GDCprepare stage and get error: Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix paper_ brca…

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Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes

Strain identification The strain Phoma sp. CNCM I-4278 was previously isolated from the rhizosphere of Nicotiana tabacum (cv Xanthi, Solanaceae) grown under controlled conditions17. The fungus was identified according to the closest similarity of its 18 S rRNA sequence (HM16174323) with those present in GenBank by that time and it was…

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Java8 FIPS client connection to K8s server – General Discussions

We have RHEL8 FIPS enabled OS linux machines ( Red Hat Enterprise Linux release 8.8 (Ootpa), 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu May 18 10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux ) and have a very simple java client running on that machine to connect to K8s client to list the pods….

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Electroporation Instruments Market is Expected to Gain Popularity Across the Globe by 2030

PRESS RELEASE Published September 2, 2023 The Electroporation Instruments Market is anticipated to experience a growth rate of 6% during the projected timeframe from 2018 to 2028. The market analysis by Transparency Market Research offers insights into the market, highlighting key factors that are predicted to influence the market’s progress throughout…

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Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis | Parasites & Vectors

Miterpáková M, Trbolová A, Hurníková Z, Balicka A, Čabanová V, Valentová D, et al. Thelazia callipaeda in Slovakia—from sporadic cases to endemic areas. Parasitol Int. 2022;87:102495. doi.org/10.1016/j.parint.2021.102495. Article  PubMed  Google Scholar  Gama A, Pires I, Canado M, Coutinho T, Lopes AP, Latrofa MS, et al. First report of Thelazia callipaeda…

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IJMS | Free Full-Text | CRISPR/Cas9-Mediated HY5 Gene Editing Reduces Growth Inhibition in Chinese Cabbage (Brassica rapa) under ER Stress

1. Introduction Crops such as rapeseed, along with vegetables like cabbage and Chinese cabbage, all of which belong to the Brassica genus, are widely cultivated across the world. Chinese cabbage, in particular, holds significant commercial importance as a vegetable extensively consumed in Asian countries [1,2,3]. Chinese cabbage thrives well in…

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Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Pan-cancer WGS data sources GrCh37/hg19 BAM alignments for 2,489 primary tumour and matched normal whole-genome sequencing data were obtained as previously described18. In brief, 989 tumour–normal (T/N) pairs were obtained from The Cancer Genome Atlas (TCGA) Research Network (Genomic Data Commons at portal.gdc.cancer.gov/, accession: phs000178.v11.p8). Additional WGS data were obtained for 874 T/N pairs…

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Processing frozen cells for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP

B. Adapter Ligation and Clean-Up 1. Spin down the AMX-F, Quick T4 ligase, and LNB, then return to ice. Note: Do not allow AMX-F to remain at room temperature for too long. 2. Thaw LNB at RT and mix by pipetting up and down (vortexing is ineffective due to viscosity)….

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Jazz Is: Now – Tomoki Sanders Visage – A Gengis Don Curation, The National Jazz Museum in Harlem, New York, August 18 2023

Tomiki Sanders presented by Gengis Don About this Event Child of the late saxophone legend, Pharoah Sanders, multi-instrumentalist, producer & artist Tomoki Sanders will be performing with his band Visage. They bring a mix of vapor wave, fusion, jazz, & hip hop, combined with elements of digitally produced music. Tomoki (they/them) was born in…

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Low-dose radiation induces unstable gene expression in developing human iPSC-derived retinal ganglion organoids

RGCs from human iPSCs for genomic analysis We developed neuronal organoids, including RGCs from human iPSCs, to assess the effects of low-dose irradiation. Phase-contrast microscopy (Supple Fig. S1a) indicated time-dependent morphological changes in the embryonal body formed from human iPSCs, which corresponded to previous reports14, 15. Retinal development was evaluated…

Continue Reading Low-dose radiation induces unstable gene expression in developing human iPSC-derived retinal ganglion organoids

Large-scale analysis of flavivirus sequences, with no unknowns, in Aedes aegypti whole-genome DNA sequence data | Parasites and vectors

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, et al. Flavivirus integration Aedes aegypti Limited and highly conserved across samples from different geographic regions, unlike integration Aedes albopictus. vectors of parasites. 2021; 14 (1): 332. Palatini U, Contreras CA, Gasmi L, Bonizzoni M. Endogenous viral elements…

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Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole-genome DNA sequencing data

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, et al. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions in contrast to integrations in Aedes albopictus. Parasite vectors. 2021;14(1):332. Palatini U, Contreras CA, Gasmi L, Bonizzoni M. Endogenous viral…

Continue Reading Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole-genome DNA sequencing data

Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data | Parasites & Vectors

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, et al. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasit Vectors. 2021;14(1):332. Palatini U, Contreras CA, Gasmi L, Bonizzoni M. Endogenous viral elements in…

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cp2k 2023.2 – Download, Browsing & More

cp2k 2023.2 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of cp2k-2023.2.tar.bz2 (27 Jul 10:02, 68243435 Bytes) About: CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material,…

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Illumina short-read genome sequencing of knockout mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system

Description: This dataset contains sequencing reads of the wild type strain S. suis P1/7 and two knockout mutants constructed using a novel CRISPR-Cas9 genome editing system for S. suis. Our data shows that our laboratory stock of strain P1/7 has 2 SNPs and one 5bp deletion relative to the reference…

Continue Reading Illumina short-read genome sequencing of knockout mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system

Age-related self-DNA accumulation may accelerate arthritis in rats and in human rheumatoid arthritis

Statement of ethics and regulations Our clinical data collection was approved by the Research Ethics Committee of the Affiliated Hospital of Southwest Medical University (KY 2021010). The animal study was conducted according to the guidelines of the Institutional Animal Care and Use Committee of Macau University of Science and Technology…

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Grifols completes enrollment in phase 3 study of long-term Albutein (albumin-human injection) therapy for patients with decompensated cirrhosis

Barcelona, Spain – Grifols (MCE: GRF, MCE: GRF.P NASDAQ: GRFS), one of the world’s leading producers of plasma-derived medicines, today announced it has completed enrollment in PRECIOSA (NCT03451292), its phase 3 clinical trial designed to determine the potential of long-term albumin treatment with Grifols Albutein® to increase survival time in…

Continue Reading Grifols completes enrollment in phase 3 study of long-term Albutein (albumin-human injection) therapy for patients with decompensated cirrhosis

Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…

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Grifols Completes Enrollment in Phase 3 Study of Long-term

PRECIOSA clinical trial is designed to evaluate efficacy and safety of Grifols Albutein® plus standard medical treatment to increase survival time in patients with decompensated cirrhosis awaiting transplant Albumin’s antioxidant and anti-inflammatory properties have the potential to mitigate the complications associated with decompensated cirrhosis Grifols continues innovating across its plasma-protein…

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The predictive power of phylogeny on growth rates in soil bacterial communities

Schimel J, Schaeffer S. Microbial control over carbon cycling in soil. Front Microbiol. 2012;3:348. Article  CAS  PubMed  PubMed Central  Google Scholar  Wallenstein MD, Hall EK. A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning. Biogeochemistry. 2012;109:35–47. Article  Google Scholar  Green JL, Bohannan…

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GROMACS – LUMI Software Library

[package list] License information GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL), version 2.1. You can redistribute it and/or modify it under the terms of the LGPL as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any…

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r – ggplot2 – geom_point with pattern fill of shapes does not change even though I change the colors

I have been struggling since yesterday with this issue. I am trying to make the following geom_point figure with a black border for the points and two different colors, one per condition grey for the LF-EB and white for the HF-EB. However, even though I used other suggestions from different…

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5’/3′ RACE method for sequencing the 5′ and 3′ untranslated regions of Zika virus

Akiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS (2016) Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science 354:1148–1152 Article  CAS  PubMed  PubMed Central  Google Scholar  Alvarez DE, Lodeiro MF, Ludueña SJ,…

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Differential contribution of nitrifying prokaryotes to groundwater nitrification

Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. Article  CAS  PubMed  Google Scholar  Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol. 2018;103:177–89. Article  PubMed  PubMed Central  Google Scholar  Lehtovirta-Morley LE Ammonia oxidation: ecology,…

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LifeArc program aims to help people living with rare diseases

LifeArc, a self-funded, non-profit medical research organization and charity, is launching a new program to invest more than £100 million ($127.2 million) by 2030 to deliver new breakthroughs to improve the lives of people living with a rare disease. The Rare Disease Translational Challenge will bring together researchers in rare…

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Role of invasive carnivores (Procyon lotor and Nyctereutes procyonoides) in epidemiology of vector-borne pathogens: molecular survey from the Czech Republic | Parasites & Vectors

Braks M, Medlock JM, Hubalek Z, Hjertqvist M, Perrin Y, Lancelot R, et al. Vector-borne disease intelligence: strategies to deal with disease burden and threats. Front Public Heal. 2014. doi.org/10.3389/fpubh.2014.00280. Article  Google Scholar  Faburay B. The case for a “one health” approach to combating vector-borne diseases. African J Disabil. 2015;5:1–4….

Continue Reading Role of invasive carnivores (Procyon lotor and Nyctereutes procyonoides) in epidemiology of vector-borne pathogens: molecular survey from the Czech Republic | Parasites & Vectors

Genetic diversity of vector-borne pathogens in ixodid ticks infesting dogs from Pakistan with notes on Ehrlichia canis, Rickettsia raoultii and Dirofilaria immitis detection | Parasites & Vectors

Chomel B. Tick-borne infections in dogs—an emerging infectious threat. Vet Parasitol. 2011;179:294–301. Article  PubMed  Google Scholar  Dantas-Torres F, Otranto D. Best practices for preventing vector-borne diseases in dogs and humans. Trends Parasitol. 2016;32:43–55. Article  PubMed  Google Scholar  Zhang J, Liu Q, Wang D, Li W, Beugnet F, Zhou J. Epidemiological…

Continue Reading Genetic diversity of vector-borne pathogens in ixodid ticks infesting dogs from Pakistan with notes on Ehrlichia canis, Rickettsia raoultii and Dirofilaria immitis detection | Parasites & Vectors

Molecular characterisation of human adenoviruses associated with respiratory infections in Uganda | BMC Infectious Diseases

Weigt SS, Gregson AL, Deng JC, Lynch JP 3rd, Belperio JA. Respiratory viral infections in hematopoietic stem cell and solid organ transplant recipients. Semin Respir Crit Care Med. 2011;32(4):471–93. Article  PubMed  PubMed Central  Google Scholar  Lynch JP, Kajon AE. Adenovirus: Epidemiology, Global Spread of Novel Serotypes, and Advances in Treatment…

Continue Reading Molecular characterisation of human adenoviruses associated with respiratory infections in Uganda | BMC Infectious Diseases

Exosomal circRNA: emerging insights into cancer progression and clinical application potential | Journal of Hematology & Oncology

He G, Peng X, Wei S, Yang S, Li X, Huang M, et al. Exosomes in the hypoxic TME: from release, uptake and biofunctions to clinical applications. Mol Cancer. 2022;21:19. Article  PubMed  PubMed Central  Google Scholar  Downs-Canner SM, Meier J, Vincent BG, Serody JS. B cell function in the tumor…

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Cross-phenotype relationship between opioid use disorder and suicide attempts: new evidence from polygenic association and Mendelian randomization analyses

Degenhardt L, Grebely J, Stone J, Hickman M, Vickerman P, Marshall BDL, et al. Global patterns of opioid use and dependence: harms to populations, interventions, and future action. Lancet. 2019;394:1560–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Patten DK, Schultz BG, Berlau DJ. The Safety and Efficacy of Low-Dose Naltrexone…

Continue Reading Cross-phenotype relationship between opioid use disorder and suicide attempts: new evidence from polygenic association and Mendelian randomization analyses

Ubuntu Manpage: cacheebeyesearch – Generates server cache file for EB-eye search domains

Provided by: emboss_6.6.0+dfsg-7ubuntu2_amd64 NAME cacheebeyesearch – Generates server cache file for EB-eye search domains SYNOPSIS cacheebeyesearch [-outfile outfile] -cachefile outfile cacheebeyesearch -help DESCRIPTION cacheebeyesearch is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the “Data resources” command group(s). OPTIONS Input section…

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Scoping review of Culex mosquito life history trait heterogeneity in response to temperature | Parasites & Vectors

Zell R. Global climate change and the emergence/re-emergence of infectious diseases. Int J Med Microbiol IJMM. 2004;293:16–26. PubMed  Google Scholar  Gage KL, Burkot TR, Eisen RJ, Hayes EB. Climate and vectorborne diseases. Am J Prev Med. 2008;35:436–50. Article  PubMed  Google Scholar  Elbers ARW, Koenraadt CJM, Meiswinkel R. Mosquitoes and Culicoides…

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Assessment of genetic polymorphisms associated with malaria antifolate resistance among the population of Libreville, Gabon | Malaria Journal

WHO. World malaria report 2022. Geneva: World Health Organization; 2022. Google Scholar  WHO. Regional data and trends briefing kit. Geneva: World malaria report; 2022. Google Scholar  Lalremruata A, Jeyaraj S, Engleitner T, Joanny F, Lang A, Belard S, et al. Species and genotype diversity of Plasmodium in malaria patients from…

Continue Reading Assessment of genetic polymorphisms associated with malaria antifolate resistance among the population of Libreville, Gabon | Malaria Journal

Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness

Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…

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Genomic characteristics of ESBL-producing E. coli in China

Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…

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A familial SAMD9 variant present in pediatric myelodysplastic syndrome

Cold Spring Harb Mol Case Stud. 2023 Apr; 9(2): a006256. ,1,2 ,1,2 ,1,2 ,2,3 ,4 and 1,2 Mahvish Q. Rahim 1Pediatric Hematology Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA; 2Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA; April Rahrig 1Pediatric Hematology Oncology,…

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Fine-scale genomic tracking of Ross River virus using nanopore sequencing | Parasites & Vectors

Flaxman JP, Smith DW, Mackenzie JS, Fraser JRE, Bass SP, Hueston L, et al. A comparison of the diseases caused by Ross River virus and Barmah Forest virus. Med J Aust. 1998;169:159–63. Article  Google Scholar  El-Hage CM, Bamford NJ, Gilkerson JR, Lynch SE. Ross River virus infection of horses: appraisal…

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Adipocyte-Specific ATAC-Seq with Adipose Tissues Using Fluorescence-Activated Nucleus Sorting

We present a protocol for assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) specifically on adipocytes using nucleus sorting with adipose tissues isolated from transgenic reporter mice with nuclear fluorescence labeling. ATAC-seq is a powerful technique to understand gene expression regulatory mechanisms. However, adipose tissue is difficult using this technique…

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Characterization of metagenome-assembled genomes from the International Space Station | Microbiome

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

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the monitor in mcallen, texas obituaries

If you are interested in reading The Monitor McAllen Texas obituaries, you can find them online or in the print edition of the newspaper. Learn About Online Memorials 269 talking about this. I was honored to have known Jeannie while living and growing up in McAllen. Mrs. Stroud, may you…

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Epigenetic regulation of human-specific gene expression in the prefrontal cortex | BMC Biology

Preuss TM. The human brain: rewired and running hot. Ann N Y Acad Sci. 2011;1225 Suppl 1(Suppl 1):E182-191. Article  PubMed  Google Scholar  Roth G, Dicke U. Evolution of the brain and intelligence in primates. Prog Brain Res. 2012;195:413–30. Article  PubMed  Google Scholar  Laland K, Seed A. Understanding human cognitive uniqueness….

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BRAFV600E, BRAFK601E, NRAS, HRAS, and KRAS mutational status

Agnes Stephanie Harahap,1– 3 Imam Subekti,4 Sonar Soni Panigoro,5 Asmarinah,6 Lisnawati,1 Retno Asti Werdhani,7 Hasrayati Agustina,8 Dina Khoirunnisa,1 Mutiah Mutmainnah,1 Salinah,1 Alvita Dewi Siswoyo,9 Maria Francisca Ham1,2 1Department of Anatomical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia; 2Human Cancer Research Center-Indonesian Medical Education and Research Institute,…

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Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7. Article  CAS  PubMed  Google Scholar  Waldrop MP, Holloway JM, Smith DB, Goldhaber MB, Drenovsky RE, Scow KM, et al. The interacting roles of climate, soils, and…

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Screening and verification of key ubiquitination genes

Introduction Liver cancer is the third most common cause of cancer death globally with hepatocellular carcinoma (HCC) accounting for the majority of liver cancer.1,2 Early HCC (stage I/II) treatment mainly includes radical surgical resection, radiofrequency ablation and liver transplantation.3,4 However, there is a lack of typical clinical symptoms with early-stage…

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FDA okays Vyjuvek for dystrophic epidermolysis bullosa

The U.S. Food and Drug Administration has approved Vyjuvek, a herpes-simplex virus type 1 (HSV-1) vector-based gene therapy, for the treatment of wounds in patients 6 months of age and older with dystrophic epidermolysis bullosa (DEB) with mutation(s) in the collagen type VII alpha 1 chain (COL7A1) gene.   The approval…

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FDA okays gene therapy for dystrophic epidermolysis bullosa

The U.S. Food and Drug Administration has approved Vyjuvek, a herpes-simplex virus type 1 (HSV-1) vector-based gene therapy, for the treatment of wounds in patients 6 months of age and older with dystrophic epidermolysis bullosa (DEB) with mutation(s) in the collagen type VII alpha 1 chain (COL7A1) gene.   The approval…

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From 24 Hours to 7 Minutes, Huawei OceanStor Pacific Accelerates Genome Sequencing – High-Performance Computing News Analysis

Challenges & Requirements [SPONSORED GUEST ARTICLE]   International Supercomputing Conference (ISC) is an annual conference that showcases the key technologies in the supercomputing field. It brings together experts from multiple specialist fields, including research into life sciences and genetics to shed light on the origins and mysteries in our lives. HPC,…

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Immune-related transcripts, microbiota and vector competence differ in dengue-2 virus-infected geographically distinct Aedes aegypti populations | Parasites & Vectors

Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. Article  CAS  PubMed  PubMed Central  Google Scholar  Stanaway JD, Shepard DS, Undurraga EA, Halasa YA, Coffeng LE, Brady OJ, et al. The global burden of dengue: an…

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Genetically corrected, iPSC-derived epithelial sheets to treat RDEB

Researchers at Stanford have developed a targeted gene therapy approach to treat patients with recessive dystrophic epidermolysis bullosa (RDEB). Epidermolysis bullosa (EB) represents a group of debilitating inherited skin disorders in which blisters develop after minor trauma to the skin. Symptoms and severity depend on type of EB. RDEB is…

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Multi-ancestry meta-analysis and fine-mapping in Alzheimer’s disease

Tanzi RE, Bertram L. New frontiers in Alzheimer’s disease genetics. Neuron. 2001;32:181–4. Article  CAS  PubMed  Google Scholar  Holland D, Frei O, Desikan R, Fan C-C, Shadrin AA, Smeland OB, et al. The genetic architecture of human complex phenotypes is modulated by linkage disequilibrium and heterozygosity. Genetics. 2021;217:iyaa046. Article  PubMed  PubMed…

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Hallmarks of cardiovascular ageing | Nature Reviews Cardiology

Bergmann, O. et al. Evidence for cardiomyocyte renewal in humans. Science 324, 98–102 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  Senyo, S. E. et al. Mammalian heart renewal by pre-existing cardiomyocytes. Nature 493, 433–436 (2013). Article  CAS  PubMed  Google Scholar  Bergmann, O. et al. Dynamics of cell generation and…

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Abeona Therapeutics Announces – GuruFocus.com

CLEVELAND, May 16, 2023 (GLOBE NEWSWIRE) — Abeona Therapeutics Inc. ( ABEO) today announced new data regarding three internally developed preclinical gene therapy product candidates from its adeno-associated virus (AAV) ophthalmology program that will be presented at the 26th Annual Meeting of the American Society of Gene & Cell Therapy…

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