Tag: IDR

What Is The Meaning Of The Score In Diffbind’S Occupancy/Overlap Analysis?

I have 3 chip-seq biological replicates, each with its own input control. I was interested in using diffBind to performs some IDR-style analysis – e.g. take only the peaks that come up in more than one sample. experiment <- dba(sampleSheet=”exp_samples.csv”) pdf(‘overlap_venn.pdf’) dba.plotVenn(experiment, experiment$masks$macs) dev.off() I got a nice Venn diagram:…

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Evolution of lysine-specific demethylase 1 and REST corepressor gene families and their molecular interaction

The RCOR gene repertoire expanded in the ancestor of jawed vertebrates To understand the duplicative history of the RCOR genes, we reconstructed gene phylogenies with different taxonomic samplings. The first analysis aimed to understand the evolution of RCOR genes in vertebrates (Fig. 2), whereas in the second, our sampling effort included…

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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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Phages could help to tackle antimicrobial resistance

Researchers have found what triggers bacteria to start the CBASS immune response to counter infections by phages. Predatory viruses called phages pose a great threat to bacteria, as they can infiltrate their cells to replicate and take over. Phage have been of interest to scientists as tools to understand fundamental…

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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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Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces

Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article  PubMed  PubMed Central  Google Scholar  Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article  Google Scholar  Kutter, E. & Sulakvelidze, A. Bacteriophages:…

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Direct Detection of Fluoroquinolone Resistance in Sputum Samples from Tuberculosis Patients by High Resolution Melt Curve Analysis

WHO (2022) Global Tuberculosis Report. WHO (2022) WHO consolidated guidelines on tuberculosis, Module 4: Treatment- Drug-resistant tuberculosis treatment: 2022 update. WHO (2020) Meeting report of the WHO expert consultation on the definition of extensively drug-resistant tuberculosis. Jabeen K, Shakoor S, Hasan R (2015) Fluoroquinolone-resistant tuberculosis: implications in settings with weak…

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Use of IDR after running MACS3 for ATAC-seq data

Use of IDR after running MACS3 for ATAC-seq data 0 Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice) I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:…

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EMDB < EMD-14025

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EMDB < EMD-16930

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EMDB < Search results

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EMDB < EMD-40454

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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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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Mycobacterium tuberculosis Sub Lineage 4.2.2/SIT149 as DR

Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…

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Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep

Global changes of the transcriptome during postnatal muscle growth The number of myofibers is thought to remain fixed following birth, muscle fiber hypertrophy growth is the primaryway of muscle growth. The average CSA is generally used to measure the hypertrophy of skeletal muscle fibers. To systematically identify the growth of postnatal…

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EMDB < EMD-25228

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae

Introduction Klebsiella pneumoniae (K. pneumoniae), which belongs to the family Enterobacteriaceae, is a common nosocomial pathogen that causes a variety of human infections, including bloodstream infection, respiratory tract infection, urinary tract infection, and abdominal infection.1,2 Carbapenems are generally considered to be a last choice for the treatment of multi-drug resistant…

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Integration of phenotypic, qPCR and genome sequencing methodologies for the detection of antimicrobial resistance and virulence in clinical isolates of a tertiary hospital, India

Azimi A, Peymani A, Pour PK (2018) Phenotypic and molecular detection of metallo-β-lactamase-producing Pseudomonas aeruginosa isolates from patients with burns in Tehran. Iran Rev Soc Bras Med Tro 51:610–615. doi.org/10.1590/0037-8682-0174-2017 Article  Google Scholar  Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology….

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Space Force Seeks Offers for 2 Lanes of National Security Space Launch Phase 3 Program

Seal of the United States Space Force by United States Space Force licensed under CC0 The U.S. Space Force has issued two solicitations for the third phase of the National Security Space Launch program. The service has adopted a dual-lane approach to acquisition under NSSL Phase 3 to ensure assured…

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Secondary infection surveillance | IDR

Introduction The coronavirus disease 2019 (COVID-19) caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continues to threaten human life worldwide. The disease severity of COVID-19 patients is very wide: from an asymptomatic carrier state to severe infection and critical illness with intensive care admission and/or mechanical…

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Genomic Analysis of CR-hvKP in a Chinese Tertiary Hospital

Introduction Klebsiella pneumoniae (KP) is a common opportunistic pathogen in clinical practice, capable of causing infectious diseases in the urinary tract, respiratory tract, blood, and soft tissues.1 Hypervirulent Klebsiella pneumoniae (hvKp) has a higher virulence than KP2 and can cause severe infectious diseases, including pyogenic liver abscess, endophthalmitis, and meningitis.3,4…

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Diagnostic value and clinical application of mNGS

Introduction Infection is one of the greatest challenges for critically ill patients and intensivists. Previous investigations reported that 30% to 60% of antimicrobials used in ICUs are unnecessary, inappropriate, or suboptimal,1,2 which might be partly attributed to the many defects of conventional microbiological tests (CMT). Culture is the most commonly…

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Genome-Based Prediction of Bacterial Antibiotic Resistance

Abdelbary M, Basset P, Blanc D et al (2017) In: Tibayrenc M (ed) Genetics and evolution of infectious diseases: the evolution and dynamics of methicillin-resistant Staphylococcus aureus, 2nd edn. Elsevier, pp 553–572. ISBN: 9780127999425 CrossRef  Google Scholar  Allard MW, Stevens EL, Brown EW (2019) All for one and one for…

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The Chromosomal Virulence D | IDR

Introduction The clinical symptoms and signs of pulmonary disease caused by nontuberculous mycobacteria (NTM) are very similar to tuberculosis, so differentiating the two becomes extremely challenging. Both diseases manifest cough, expectoration, hemoptysis, chest pain, and other respiratory symptoms, as well as systemic symptoms, such as fatigue and anorexia.1–3 Furthermore, NTM…

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Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador

Knight, G. M. et al. Antimicrobial resistance and COVID-19: Intersections and implications. Elife doi.org/10.7554/eLife.64139 (2021). Article  PubMed  PubMed Central  Google Scholar  Bong, C.-L. et al. The COVID-19 pandemic: Effects on low- and middle-income countries. Anesth. Analg. 131(1), 86–92. doi.org/10.1213/ANE.0000000000004846 (2020). Article  CAS  PubMed  Google Scholar  Alhalaseh, Y. N. et al….

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ST11 and ST15 carbapenem-resistant hypervirulent Klebsiella

Introduction Klebsiella pneumoniae is a gram-negative opportunistic pathogen that can cause both community and hospital-acquired pneumonia, urinary tract infections, and bacteremia primarily in immunocompromised patients.1 Most experts agree that carbapenems are an effective treatment for serious infections brought on by Enterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs).2–4 Because of the wide…

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Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing | BMC Infectious Diseases

Mboowa G, Sserwadda I, Bulafu D, Chaplain D, Wewedru I, Seni J, et al. Transmission Dynamics of Antimicrobial Resistance at a National Referral Hospital in Uganda. Am J Trop Med Hyg. 2021;105(2):498–506. Article  CAS  PubMed  PubMed Central  Google Scholar  Rossolini GM, Arena F, Pecile P. Pollini SJCoip. Update on the…

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Clinical efficiency of mNGS in sputum for pathogen detection

Introduction Lower respiratory infections (LRIs) are the world’s most deadly communicable disease and ranks fourth as the primary cause of death globally according to the World Health Organization (WHO) 2019 report.1,2 LRIs include hospital-acquired pneumonia (HAP), community-acquired pneumonia (CAP), bronchiolitis, bronchitis, and tracheitis.3,4 Immunocompromised patients have a higher risk of…

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Analysis of drug-resistance characteristics of MDR-TB

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), continues to pose a significant global public health challenge.1–3 In 2021, there were 10.6 million new TB cases worldwide, with China accounting for 780,000 cases, making it the third highest burden country for TB globally.4 The World Health Organization (WHO) estimates that…

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Emergence of ST248Pasteur-ST1068Oxford | IDR

Acinetobacter pittii is a crucial pathogen that mainly causes healthcare-associated infections, including pneumonia, bloodstream infections (BSIs) and urinary tract infections (UTIs).1 Carbapenem-resistant A. pittii (CRAP) poses a huge challenge in clinical settings. CRAP is increasingly recognized as a significant pathogen of hospital-acquired infections in the hospital.2 Carbapenem resistance in A….

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EMDB < EMD-40539

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Soligenix Announces Recent Accomplishments And Second Quarter 2023 Financial Results

(MENAFN– PR Newswire) PRINCETON, N.J., August 21, 2023 /PRNewswire/ —Soligenix, Inc. (NASDAQ: sngx ) (Soligenix or the Company), a late-stage biopharmaceutical company focused on developing and commercializing products to treat rare diseases where there is an unmet medical need,announced today its recent accomplishments and financial results for the quarter ended…

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Potential pathogenicity of Non-O1, Non-O139 V. cholerae

Introduction Vibrio cholerae is a Gram-negative bacterium that can be classified into different serotypes based on the O surface antigen, with O1 and O139 being responsible for causing cholera in humans. Cholera is a highly infectious and severe diarrheal disease that is prevalent worldwide, particularly in Africa, South Asia, and…

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how to merge peaks when finished IDR consistency test in ATAC-seq data?

how to merge peaks when finished IDR consistency test in ATAC-seq data? 1 hi, I have 3 biological replicates of ATAC-seq data, named a,b,c. I want to find some consistent peaks among these replicates. And I apply idr —compare ab,ac,bc respectively. Thus, I get three bed files, but I don’t…

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Clinical Value of Sampling Time of mNGS

Introduction Severe pneumonia is associated with high morbidity and mortality, especially in the ICU, and is one of the global burdens of infectious diseases.1,2 For patients with severe pneumonia, rapid identification of pathogens and timely initiation of appropriate anti-infective therapy are the most critical determinants of prognosis. Furthermore, pathogen diagnosis…

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Human genome sequencing revolutionizes medical treatment – Sat, August 12 2023

Tjandra Yoga Aditama (The Jakarta Post) PREMIUM Jakarta   ●   Sat, August 12 2023 When the COVID-19 pandemic reared its ugly head, discussions about whole genome sequencing (WGC) stole the limelight. WGC gave us a better understanding of the virus, its variants and subvariants and measures to control them….

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Clinical Evaluation of Metagenomic Next-Generation Sequencing and Iden

Introduction Infection is one of the major causes of death in patients with acute and critical illnesses. Especially, lower respiratory tract infections (LRTIs) are the most common infectious diseases worldwide, with a high mortality rate.1,2 As estimated, there are about 10 million new cases of LRTIs in China each year.3,4…

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EMDB < EMD-12919

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Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Cell culture HCC2429 cells were a kind gift from the Hamon Center for Therapeutic Oncology Research at UT Southwestern Medical Center. The cells were grown in RPMI 1640 medium (Thermo Fisher Scientific, #11875119) with addition of 10% heat-inactivated Fetal Bovine Serum (Thermo Fisher Scientific, #10-438-026) and 1% penicillin—streptomycin (Thermo Fisher…

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Mycobacterium tuberculosis Rv0494 protein | IDR

Introduction Persisters are assumed to be defined as non-replicating or slow-growing bacteria that are not killed by antibiotics, which can return to a growth state upon removal of antibiotics, and are sensitive to the same antibiotics.1 Persisters play an important role in medicine pose a major challenge to the treatment…

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Proviral HIV-1 DNA Genotyping for People Living with HIV

Introduction Antiretroviral therapy (ART) can effectively suppress HIV-1 replication and maintain plasma viral load (VL) below the detection limit for most of the people living with HIV (PLWH) who adhere to the regimens prescribed,1 which helps reduce morbidity, mortality, and HIV-1 transmission, and consequently result in improving life expectancy of PLWH. However,…

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Space Systems Command releases National Security Space Launch Phase 3 Draft RFP

ADVERTISEMENT Space Systems Command releases National Security Space Launch Phase 3 Draft RFP by Brad Bartz Los Angeles CA (SPX) Jul 14, 2023 In a recent announcement, the Space Systems Command (SSC) reported that it has issued a second round of draft Requests for Proposals (RFPs) as part…

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Clinical Value of Metagenomics | IDR

Introduction Mycoplasma pneumoniae is an important infectious pathogen of lower respiratory tract infection in children and adolescents. M. pneumoniae pneumonia (MPP) accounts for 30% to 40% of community-acquired pneumonia in children.1 The first-line antibiotic for treating MPP is macrolides. Due to the widespread use of macrolides, instances of M. pneumoniae…

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EMDB < EMD-33674

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Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR

Wanyang Dong,1,&ast; Qi Peng,1,&ast; Xiaohua Tang,1,2,&ast; Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…

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EMDB < EMD-17118

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Differential Binding of NLRP3 to non-oxidized and Ox-mtDNA mediates NLRP3 Inflammasome Activation

NLRP3 expression and purification Both wild-type NLRP3 and CAPS mutants were cloned in the mammalian expression vector pcDNA3.1HisB. Plasmid was purified using Qiagen Giga Prep up to 2000 ng/μl and subsequently transfected into Expi293 with Expifectamine per manufacturer instructions. Expression was allowed to proceed for 3 days before harvesting. Cells were…

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EMDB < EMD-10691

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Pathogen Diagnosis Value of Nanopore Sequencing

Introduction Severe hospital-acquired pneumonia (SHAP) is the most common acquired infection in the intensive care unit (ICU) and one of the main causes of increased mortality in ICU patients.1,2 Potential multidrug-resistant pathogens are very common in ICU-acquired pneumonia, including Pseudomonas aeruginosa, Acinetobacter spp., methicillin-resistant Staphylococcus aureus (MRSA), and ultrabroad spectrum…

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E. coli & K. pneumoniae strains produce NDM-5 & OXA-181

1Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China; 2Department of Clinical Laboratory, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China Correspondence: Qian Chen, Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China, Tel +8618951768213, Email [email protected]…

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Genomic and phylogenetic analysis of Klebsiella michiganens

Introduction Multidrug-resistant Enterobacteriaceae infection is a severe threat to public health that is worsening globally and is associated with increasing mortality rates.1 Klebsiella pneumoniae is a significant pathogen that contributes to the dissemination of multidrug-resistant strains in healthcare environments.2 K. michiganensis is a novel specie of pathogenic Klebsiella genus. Since…

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Antimicrobial activity of Limosilactobacillus fermentum strains isolated from the human oral cavity against Streptococcus mutans

Welch, J. L. M., Dewhirst, F. E. & Borisy, G. G. Biogeography of the oral microbiome: The site-specialist hypothesis. Annu. Rev. Microbiol. 73, 335–358. doi.org/10.1146/annurev-micro-090817-062503 (2019). Article  CAS  Google Scholar  Cornejo Ulloa, P., van der Veen, M. H. & Krom, B. P. Review: Modulation of the oral microbiome by the…

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Resistance of Nosocomial Acinetobacter baumannii

Chenxing Wei,1,&ast; Jian Chen,1,&ast; Tanveer Muhammad Anwar,2,&ast; Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…

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peak caller choice and typical peak size profile

CUT&Tag data processing: peak caller choice and typical peak size profile 1 Greetings everyone, I am currently analysing CUT&Tag data (a recent technique, variant of the ChIP-seq), capturing different histone variants. To do so, I tried all the different suggested tools for peaks calling: the more general MACS2 (broad peaks,…

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Nontuberculous mycobacteria and MAB_0540 mutations

Introduction Nontuberculous mycobacteria (NTM), a mycobacterium other than the Mycobacterium tuberculosis complex (MTC) and M. leprae, are conditional pathogens widely found in the environment.1 Studies have shown that the probability of NTM transmission is extremely low, and exposure comes primarily from the environment, soil, water, etc.1 In recent years, lung…

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EMDB < EMD-16884

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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EMDB < EMD-29544

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Phenotypic and Genetic Analysis of KPC-49

Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…

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Phase-separated nucleocapsid protein of SARS-CoV-2 suppresses cGAS-DNA recognition by disrupting cGAS-G3BP1 complex

SARS-CoV-2 infection induces mtDNA release and recognition by cGAS Recent studies revealed that SARS-CoV-2 stimulation could cause the accumulation of intracellular and intercellular DNA due to cell fusion, cell death and even tissue damage.17,19,27 To detect SARS-CoV-2-triggered release of DNA during infection, we first detected the cytosolic dsDNA pattern by…

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EMDB < EMD-14480

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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EMDB < EMD-15267

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Molecular Epidemiology and Characterization of Multidrug-Resistant MRS

Introduction Increasing antibiotic resistance is a worrisome trend being observed worldwide. Methicillin-resistant Staphylococcus aureus (MRSA) was first reported in the United Kingdom (UK) in 1961 and has since been reported throughout the world as a nosocomial pathogen.1 A steady increase in the occurrence of MRSA strains has been reported in…

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Coverage From ACCC 2023 Spring Business Summit

Stops and Starts Abound in the Oncology Payment Landscape The landscape of policies and processes surrounding cancer treatment and financial aspects of care is evolving, with each new rule affecting oncologists and patients. In a presentation March 10 at the Association of Community Cancer Centers (ACCC) 2023 Annual Meeting and Cancer Center Business…

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Diagnostic Significance of Targeted Next-Generation Sequencing in Cent

Introduction Neurosurgical infections affecting the central nervous system (CNS) encompass post-operative epidural abscesses, subdural pus, meningitis, brain abscesses, intracranial infections resulting from craniocerebral trauma, extraventricular and lumbar pool drainage, shunts, and meningitis associated with implants.1,2 In children, CNS infections can have a profound impact on neurological development. Acute symptoms may…

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RPA/CRISPR-cas12a as a specific, sensitive and rapid method for diagnosing Ehrlichia canis and Anaplasma platys in dogs in Thailand

Almazán C, González-Álvarez VH, Fernández de Mera IG, Cabezas-Cruz A, Rodríguez-Martínez R, De la Fuente J (2016) Molecular identification and characterization of Anaplasma platys and Ehrlichia canis in dogs in Mexico. Ticks Tick Borne Dis 7:276–283. doi.org/10.1016/j.ttbdis.2015.11.002 Article  PubMed  Google Scholar  Aman R, Mahas A, Marsic T, Hassan N, Mahfouz…

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Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation

Introduction Infections are the major cause of human deaths worldwide and present a rising threat to public security.1 Antimicrobial resistance is a major concern that is threatening our ability to treat bacterial infections.2 Delayed administration of antibiotics significantly increases the in-hospital mortality rate.3 The tragic outcome of infection highlights the…

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The status and future direction of advanced urine testing: multiplex PCR

Stephanie Gleicher, MD, MPH More than half of adult women in the United States will have at least 1 urinary tract infection (UTI) with an estimated annual cost burden of $1.6 billion.1 Among these women, 25% to 50% will develop recurrent UTI (rUTI), which is defined as at least 2…

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Merge replicates for CHIP-seq analysis

Merge replicates for CHIP-seq analysis 0 I am performing for the first time CHIP-seq analysis with two replicas, I used MACS2 to find the peaks of the two respective replicas, I used IDR to find the percentage of peaks in common and bedtools intersect to get a bed file that…

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A Nanobar-Supported Lipid Bilayer System for the Study of Membrane Curvature Sensing Proteins in vitro

Here, a nanobar-supported lipid bilayer system is developed to provide a synthetic membrane with a defined curvature that enables the characterization of proteins with curvature sensing ability in vitro. This nanobar-supported lipid bilayer system can be used to study the role of membrane curvature in regulating the dynamics and distribution…

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how to decide the if the IDR result is good or not

how to decide the if the IDR result is good or not 1 Use IDR to do the Irreproducible Discovery Rate for two replicates of ATAC seq, the results are in the picture, is it shows good quality, as the log10 score at the right top, the percentage of the…

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Vancomycin-resistant E. faecium SJ2 strain carrying vanA

Introduction Enterococcus is a genus of Gram-positive, facultative anaerobe and oxidase-negative cocci classified as lactic acid bacteria and belonging to the Enterococcaceae family.1 Enterococci is a type of bacteria that is often found in the gastrointestinal tract of humans and other mammals.2,3 It comprises a ubiquitous group of bacteria that…

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Chip-seq Analysis

Chip-seq Analysis 0 Hi everyone, I am analyzing chipseq data and I am trying to figure out the handling of biological replicates and the best tools to use. I tried to dig into the former questions, but it is hard to navigate thorough so many information. I have 2 different…

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Chlamydia psittaci, Metagenomic Next-Generation Sequencing

Introduction Human psittacosis infection, also known as ornithosis or Parrot Disease, is a relatively rare zoonosis caused by Chlamydia psittaci. Zoonotic transmission of C. psittaci has been documented through contact with infected excreta and secretions, as well as through inhalation.1 A recent study showed that C. psittaci has the potential…

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P. aeruginosa retrieved from broiler chickens

Introduction Pseudomonas species are ubiquitous microorganisms that are retrieved from various origins, such as poultry, drinking water, domestic and wild animals, human cases, and different food products.1,2 Pseudomonas infections in poultry are of the highest significance as the infection might spread speedily among the poultry flocks resulting in elevated mortalities…

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EMDB < EMD-20232

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Aspera: Command ‘ascp’ not found

Aspera: Command ‘ascp’ not found 1 I am trying to download files from the idr website using aspera. I am running the following command however I get the error Command ‘ascp’ not found. The ssh key exists and the file path is correct. ascp -TQ -l40m -P 33001 -i “path/to/key/asperaweb_id_dsa.openssh”…

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EMDB < EMD-28585

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Molecular epidemiology of CRKP | IDR

Introduction Klebsiella pneumoniae (Kp; K. pneumoniae) is an important hospital and community-acquired pathogen that primarily causes pneumonia, urinary tract infections, bloodstream-associated infections, meningitis, and pyogenic liver abscess.1–3 Carbapenem antibiotics represent the most important treatment for Enterobacteriaceae; however, with the widespread use of such antibiotics, carbapenem-resistant K. pneumoniae (CRKP) is increasingly…

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The 2nd Booster Vaccine Discourse is Paid, How Much Does it Cost?

Vaccines, vaccinations. (Pixabay) Himedik.com – The discourse on paid vaccines has emerged since the beginning of the production of the Covid-19 vaccine, however, the Indonesian government itself has finally provided free subsidies to people who will be vaccinated because it is mandatory. Then, how much is the actual official price…

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EMDB < EMD-13594

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Epidemiology of Clostridioides difficile infection

Introduction Clostridioides difficile (C. difficile) is an anaerobic, gram-positive, spore-forming bacillus and important pathogen of antimicrobial-associated diarrhea and nosocomial diarrhea in humans.1 Clostridioides difficile infection (CDI) can progress from self-resolving diarrhea to colitis, life-threatening pseudomembranous colitis and toxic megacolon, and death.2,3 CDI is a toxin-mediated disease, and the major virulence…

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Establishment and Methodological Evaluation of a Method for Rapid Dete

Introduction Helicobacter pylori (H. pylori) is a Gram-negative, spiral microaerophilic bacterium that infects more than half of the world’s population.1,2 Studies have shown that this bacterium is the main pathogenic factor in chronic gastritis and peptic ulcers, and is related to the occurrence and development of gastric cancer.3,4 For several…

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EMDB < EMD-20433

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Multidrug resistance microbial therapy | VMRR

Introduction Antimicrobials are the most important and useful therapeutic discovery in the history of medicine. It allows living beings to survive the microbial disease, enhances invasive surgical procedures, ensures animal health, and protects the food chain since 1928 after the discovery of penicillin. However, the indiscriminate use of antibiotics and…

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Understanding Chip-seq data (ENCODE and other resources)

Understanding Chip-seq data (ENCODE and other resources) 0 Hello, I am a beginner in understanding Chip-seq data analysis and just got introduced to Chip-seq data by studying the ENCODE portal documentation (www.encodeproject.org/data-standards/terms/#concordance). I am focusing on Chip-seq for transcription factors. Although, I still have some question such as: Why each…

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Euro-BioImaging Bio-Hub – FAIR Image Data Steward at European Molecular Biology Laboratory (EMBL)

About the team/job Euro-BioImaging ERIC (www.eurobioimaging.eu) is a leading pan-European research infrastructure that provides the research community open access to cutting-edge imaging services. The Euro-BioImaging Bio-Hub hosted by European Molecular Biology Laboratory (EMBL) is looking for a highly motivated FAIR Image Data Steward to develop general guidelines and technically support…

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Extensively drug resistant E. coli LZ00114

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

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LAMP-CRISPR-Cas12a-lateral flow immunochromatographic strip | IDR

Introduction About 700,000 people die from “superbugs” globally every year. Antibiotic abuse is the culprit of extensive spread of superbugs. Currently, carbapenemase-producing organisms are among the most important pathogens of hospital infections. Especially the plasmid-mediated highly transmissible carbapenem-resistant Enterobacterales (CRE) has become an important public health issue of global concern….

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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P. aeruginosa isolated from patients with aural infections

Introduction Aural infections are one of the most common diseases of the head and neck and are predominantly caused by bacterial infections of the ear canal. Several studies from different countries have reported that Pseudomonas aeruginosa is the most common pathogen isolated from ear canal secretions, followed by Staphylococcus aureus.1…

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Image Data Specialist – Euro-BioImaging at European Molecular Biology Laboratory (EMBL)

About the team/job The Euro-BioImaging Bio-Hub hosted by the European Molecular Biology Laboratory (EMBL) is looking for a highly motivated image data specialist to technically support the Image Data Services of the European research infrastructure Euro-BioImaging ERIC (www.eurobioimaging.eu). Euro-BioImaging is building and offering image data services to the research community….

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Antibiotic Resistance Genes | IDR

Witawat Tunyong,1 Weewan Arsheewa,2 Sirijan Santajit,3,4 Thida Kong-ngoen,1 Pornpan Pumirat,1 Nitat Sookrung,5,6 Wanpen Chaicumpa,6 Nitaya Indrawattana1 1Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; 2Department of Microbiology, Phrapokklao Hospital, Chanthaburi, 22000, Thailand; 3School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, 80161, Thailand;…

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Emergence of the Coexistence of mcr-1, blaNDM-5, and blaCTX-M-55 in Kl

Introduction Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen and the leading cause of healthcare-associated infections.1 Multidrug-resistant (MDR) K. pneumoniae isolates are rapidly spreading, thus limiting the choice of antimicrobial agents for empiric treatment of infections caused by these microorganisms; hence, this is a public health challenge.2 Polymyxins are last-resort…

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Prevalence and Molecular Characteristics Based on Whole Genome Sequenc

Introduction Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent (ranking above HIV/AIDS).1 In 2020, World Health Organization (WHO) reported that 7.1 million people with tuberculosis were newly diagnosed and notified in 2019,…

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Helicobacter pylori in Pakistan | IDR

Introduction Helicobacter pylori, an infectious agent of human chronic active gastritis and also associated with other gastric ailments such as peptic ulcer, gastric cancer, and mucosa-associated lymphoid tissue lymphoma.1 Clarithromycin is considered the best option among other antibiotics for the management of this bacterial infection.2 However, increasing resistance against this…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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