Tag: IDR

Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* 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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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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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…

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]…

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…

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…

Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* 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…

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,…

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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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…

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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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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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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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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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….

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,…

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…

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….

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;…

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…

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,…

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…

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…