Categories
Tag: nr
ZsGreen/Luciferase Safe-Harbor HEK293 Cell Line | BPS Bioscience
Product information “ZsGreen/Luciferase Safe-Harbor HEK293 Cell Line” Recombinant stable HEK293 cell line constitutively expressing ZsGreen (bright green fluorescent protein derived from Zoanthus sp. reef coral) and firefly luciferase, which have been stably integrated into the AAVS1 safe harbor locus on chromosome 19 using CRISPR/Cas9. Expression of ZsGreen and the luciferase…
Structure-guided discovery of anti-CRISPR and anti-phage defense proteins
Identification of putative anti-crispr proteins using structural features To identify Acrs in phage genomes, we began by retrieving ~66.5 million proteins from Integrated Microbial Genomes Virus database (IMG/VR)37. We excluded large proteins because over 90% of known Acrs contain less than 200 amino acids38 (Fig. 1A, Supplementary Data 1). To reduce computational…
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…
rstudio – Cannot deploy R-shiny app due to “fribidi was not found”
Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….
hypothetical protein LOTGIDRAFT_99224 partial, maker-scaffold1322_size48131-snap-gene-0.13 (gene) Tigriopus kingsejongensis
Associated RNAi Experiments Homology BLAST of hypothetical protein LOTGIDRAFT_99224 partial vs. L. salmonis genes Match: EMLSAG00000006769 (supercontig:LSalAtl2s:LSalAtl2s379:476161:478870:-1 gene:EMLSAG00000006769 transcript:EMLSAT00000006769 description:”maker-LSalAtl2s379-augustus-gene-4.10″) HSP 1 Score: 59.6918 bits (143), Expect = 4.225e-12Identity = 29/57 (50.88%), Postives = 39/57 (68.42%), Query Frame = 0 Query: 22 AANARERTRMRVLSKAFGRLKLTLPWVPPDTKLSKLDTLRLATSYISHLQRLLSDEE 78 +N +ER R + ++…
Gadolinium Oxide Nanoparticles reinforce immune response
Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…
Zanubrutinib Favored Over Bendamustine/Rituximab Combination Across Biomarker Subgroups in CLL/SLL Without del(17p)
Treatment with the BTK inhibitor zanubrutinib (Brukinsa) conferred a progression-free survival (PFS) benefit compared with bendamustine plus rituximab (Rituxan) across most biomarker subgroups of patients with treatment-naive chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL) without del(17p), according to findings from the phase 3 SEQUOIA trial (NCT03336333) presented as…
Human TIA1 activation kit by CRISPRa Clinisciences
Product Data Format 3 gRNAs (5ug each), 1 scramble ctrl (10ug) and 1 enhancer vector (10ug) Symbol TIA1 Locus ID 7072 Kit Components GA104875G1, TIA1 gRNA vector 1 in pCas-Guide-GFP-CRISPRa GA104875G2, TIA1 gRNA vector 2 in pCas-Guide-GFP-CRISPRa GA104875G3, TIA1 gRNA vector 3 in pCas-Guide-GFP-CRISPRa 1 CRISPRa-Enhancer vector, SKU GE100056 1…
A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception
Identification of novel TAS1R family members We identified homologues of TAS1R genes that are included in public genome/transcriptome databases for diverse taxa of jawed vertebrates (Supplementary Table 1). Except for jawed vertebrates, TAS1R genes were not identified in any Deuterostomia reference genomes (lampreys, hagfishes, tunicates, lancelets, sea urchins, starfish, hemichordate,…
Molecular Techniques | SpringerLink
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 CrossRef CAS PubMed PubMed Central Google Scholar Büyükköroğlu G, Dora DD, Özdemir F, Hızel C (2018)…
Heavy-chain antibody targeting of CD38 NAD+ hydrolase ectoenzyme to prevent fibrosis in multiple organs
Asano, Y. & Varga, J. Rationally-based therapeutic disease modification in systemic sclerosis: Novel strategies. Semin. Cell Dev. Biol. 101, 148–160. doi.org/10.1016/j.semcdb.2019.12.007 (2019). Article Google Scholar Allanore, Y. et al. Systemic sclerosis. Nat. Rev. Dis. Prim. 1, 15002. doi.org/10.1038/nrdp.2015.2 (2015). Article PubMed Google Scholar Varga, J. & Abraham, D. Systemic sclerosis:…
High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines
Almarez DN, Almarez FJS, Baulete EM. 2014. Bayug Island Aquasilvi Program: An Eco-Governance Strategy for Climate Change Adaptation and Mitigation. J Govern Dev 10(2): 35-54. DOI: 10.32890/jgd. Alongi DM. 2014. Carbon cycling and storage in mangrove forests. Ann Rev Mar Sci 6: 195-219. DOI: 10.1146/annurev-marine-010213-135020. Balint M, Pfenninger M, Grossart…
Snakemake rule error
Snakemake rule error 0 I have the following rule in snakemake: rule low_coverage_contig_reads: input: bam=”data/processed/bam_files/bam/{sample}_{fraction}.bam.bai”, output: r1=”data/processed/clean_reads/low_cov/low_cov_{sample}_{fraction}_R1.fq.gz”, r2=”data/processed/clean_reads/low_cov/low_cov_{sample}_{fraction}_R2.fq.gz” threads: 8 params: bam=”data/processed/bam_files/bam/{sample}_{fraction}.bam” log: log1=”logs/{sample}_{fraction}_low_coverage_reads.log”, shell: “”” (samtools coverage {params.bam} | awk ‘NR > 1 && $7 < 10 {{print $1}}’ | tr ‘\\n’ ‘ ‘ | samtools view -u {params.bam}…
How to restrain to some specified waters for OPC model – User discussions
Shin December 11, 2023, 1:24am 1 GROMACS version:2021.6GROMACS modification: NoHere post your questionDear Gromacs usersI have the same problem as inHow to treat specific water molecules as ligand?. I’m setting .top file for MD simulation with OPC model for water.I want to use positional constraints on the three waters(name: FIX)…
Metagenomic species profiling using universal phylogenetic marker genes
Standard Metagenomic species profiling using universal phylogenetic marker genes. / Sunagawa, Shinichi; Mende, Daniel R.; Zeller, Georg; Izquierdo-Carrasco, Fernando; Berger, Simon A.; Kultima, Jens Roat; Coelho, Luis Pedro; Arumugam, Manimozhiyan; Tap, Julien; Nielsen, Henrik Bjørn; Rasmussen, Simon; Brunak, Søren; Pedersen, Oluf Borbye; Guarner, Francisco; de Vos, Willem M; Wang, Jun;…
Phase 3 KEYLYNK-008 Trial of Pembrolizumab Plus Olaparib in Metastatic Squamous NSCLC to Stop for Futility
The phase 3 KEYLYNK-008 trial (NCT03976362) evaluating pembrolizumab (Keytruda) plus olaparib (Lynparza) in patients with metastatic squamous non–small cell lung cancer (NSCLC) will be discontinued for futility, according to an announcement from Merck.1 The decision was based on a recommendation issued by an independent data monitoring committee (IDMC) after reviewing…
CircRNA and Stroke: New Insight of Potential Biomarkers and Therapeutic Targets
Diener HC, Hankey GJ (2020) Primary and secondary Prevention of ischemic Stroke and Cerebral Hemorrhage: JACC Focus Seminar. J Am Coll Cardiol 75(15):1804–1818 Article PubMed Google Scholar Dou Z, Yu Q, Wang G, Wu S, Reis C, Ruan W, Yan F, Chen G (2020) Circular RNA expression profiles alter significantly…
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…
Characterization of 16S rRNA of the gut microbiome in long-tailed macaque (Macaca fascicularis) with spontaneous type 2 diabetes mellitus
Ahmad A, Yang W, Chen G, Shafiq M, Javed S, Zaidi SSA, Shahid R, Liu C, Bokhari H. 2019. Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals. PLoS One. 14(12):1–15. doi:10.1371/ journal.pone.0226372. Arora A, Behl T, Sehgal A, Singh S, Sharma N, Bhatia S,…
Sen. Gary Peters Protects CCP-Linked Biotech Firm Accused of DNA Theft
Sen. Gary Peters (D-MI) is reportedly protecting a CCP-linked biotech firm that Republicans appear ready to ban from operating in the United States after it was accused of stealing Americans’ DNA. Peters’ decision to hold up the legislation might permanently prevent lawmakers from passing legislation to cause Beijing Genomics Institute (BGI)…
Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. | Virology Journal
Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…
Compute matrix skipping many regions stating not found in compute matrix output
Compute matrix skipping many regions stating not found in compute matrix output 0 Hello all I am working on Chip seq data and for generating the TSS Plots when I am computing the matrix it is giving a very long list stating “skipping NR_049895_r4, due to being absent in the…
Updated Data Show Efficacy of Tafasitamab/Lenalidomide in R/R DLBCL
CASE A 67-year-old man presented with fatigue, back pain, and lymphadenopathy. Medical history: Hypertension, well controlled with medication Physical exam: Left posterior cervical, 1.5-cm node; right anterior cervical node, 2.5-cm; left supraclavicular node, 2.0-cm. PET-CT scan: multiple enlarged mesenteric and retroperitoneal nodes, largest measuring 5.3 x 3.1 cm Bone marrow biopsy was…
WO2017055487A2 – A METHOD FOR DIAGNOSING A DISEASE BY DETECTION OF circRNA IN BODILY FLUIDS
“Current Protocols in Molecular Biology“, 1991, JOHN WILEY & SONS, pages: 6.3.1 – 6.3.6 “Quantitative monitoring of gene expression patterns with a complementary DNA microarray.“, SCIENCE, vol. 270, no. 5235, 1995, pages 467 – 70 ALTSCHUL ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403 – 410 ALTSCHUL ET…
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 …
mlogit function Error – RStudio IDE
Try cutting and pasting the below. library(mlogit) #> Loading required package: dfidx #> #> Attaching package: ‘dfidx’ #> The following object is masked from ‘package:stats’: #> #> filter data(“Game”, package = “mlogit”) g <- mlogit(ch ~ own | hours, Game, varying = 1:12, ranked = TRUE, reflevel = “PC”, idnames…
Germline PTEN genotype-dependent phenotypic divergence during the early neural developmental process of forebrain organoids
American Psychiatric Association Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5). Arlington, VA: American Psychiatric Publishing; 2013. Lewis MH, Bodfish JW. Repetitive behavior disorders in autism. Ment Retard Dev D R. 1998;4:80–9. Article Google Scholar Bodfish JW, Symons FJ, Parker DE, Lewis MH. Varieties of repetitive behavior in…
Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants
Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…
Sequence-Based Classification and Identification | SpringerLink
Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef PubMed Google Scholar Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef CAS PubMed Google Scholar Arahal DR,…
CIMP Gives The Green Light To Three New Orphan Drugs For Rare Diseases
The Interministerial Commission on Drug Prices (CIPM) proposed at its last meeting in November the total or partial financing of 8 new drugs (three of which are orphan drugs for rare diseases) and 3 new indications for 2 additional drugs, already authorized and previously funded. in other signs. The new…
Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70:5607–12. Article PubMed PubMed Central Google Scholar Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ. Bacillus species in soil…
Species coverage in the NCBI protein NR database ?
Hi Biostars, I am currently trying to build a Eukaryote version of the NCBI NR database and I am not really sure that I fully understand how the NR is implemented. Here is the code that I’m using to do so : #!/usr/bin/bash ############## # DOWNLOAD FULL NR ############## baseURL=”https://ftp.ncbi.nlm.nih.gov/blast/db/”…
NFIB Human shRNA Plasmid Kit (Locus ID 4781) Clinisciences
Product Data Locus ID 4781 Synonyms CTF; HMGIC/NFIB; MACID; NF-I/B; NF1-B; NFI-B; NFI-RED; NFIB2; NFIB3 Vector pGFP-V-RS E. coli Selection Kanamycin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components NFIB – Human, 4 unique 29mer shRNA constructs in retroviral GFP vector(Gene ID = 4781). 5µg purified plasmid DNA per…
Maintenance Selinexor Shows PFS in TP53 Wild-type Endometrial Cancer
Selinexor did not show a clinically meaningful improvement in the general study population. Maintenance selinexor (Xpovio) showed a significant progression-free survival (PFS) benefit compared with placebo in a subgroup of patients with TP53 wild-type advanced/recurrent endometrial cancer, according to findings from the phase 3 ENGOT-EN5/GOG-3055/SIENDO trial (NCT03555422).1,2 Data from the…
Pembrolizumab Plus Enzalutamide and ADT Falls Short in mHSPC
Pembrolizumab Plus Enzalutamide and ADT Falls Short in mHSPC Findings from the phase 3 KEYNOTE-991 trial demonstrated that adding pembrolizumab (Keytruda) to enzalutamide (Xtandi) and androgen deprivation therapy (ADT) did not improve radiographic progression-free survival (rPFS) compared with placebo in patients with metastatic hormone-sensitive prostate cancer (mHSPC). Findings were presented…
Integrating BLAST Searches into Data Science Projects with Biopython | by Bao Tram Duong | Nov, 2023
BLAST, or Basic Local Alignment Search Tool, is a powerful and widely used bioinformatics tool for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotide sequences of DNA. The main purpose of BLAST is to identify sequences in a database that are similar…
Falcon Plans To Return for Phase 3 Drilling at Central Canada, Renegotiates Pre-Production
Overview Ontario has always been a premier jurisdiction for mining in Canada. However, one of Ontario’s earliest gold camps in the province’s northwestern region is showing signs of high-grade revitalization. The town of Atikokan in Ontario is known for its two massive iron ore pits mined in the middle of…
Limma/DESeq2 for unbalanced nested design (paired samples)
I have an RNAseq dataset that I want to perform differential gene-expression analysis on. The dataset consists of 3 groups = macrophages deriving from adults (n=6), term-born infants (n=5), and preterm infants (n=3). Each sample has been treated with an immune-stimulus, or left untreated (paired samples). Group Treatment Sample_Nr Sample_within_group…
Small rigid molecules with constraints – User discussions
tnagai November 22, 2023, 1:47pm 1 GROMACS version: 2023.1GROMACS modification: No I modelled a small rigid-body nitrate ion (or NO3+) with 6 constraints.However, I observed weird and large oscillations during a simulation with LINCS (and many errors). It seems (at least visually) fine or OK with SHAKE.Could you please let…
Selinexor Maintenance Leads to PFS Benefit in TP53 Wild-Type Advanced/Recurrent Endometrial Cancer
Maintenance therapy with selinexor (Xpovio) improved progression-free survival (PFS) compared with placebo in patients with TP53 wild-type advanced or recurrent endometrial cancer, regardless of microsatellite instability (MSI) status, according to long-term follow-up data from the phase 3 ENGOT-EN5/GOG-3055/SIENDO trial (NCT03555422)presented at the 2023 IGCS Annual Global Meeting.1 At a median…
AK2 Human shRNA Plasmid Kit (Locus ID 204) Clinisciences
Product Data Locus ID 204 Synonyms ADK2 Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components AK2 – Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 204). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pGFP-C-shLenti…
Outcomes Associated With Nirmatrelvir or Monupiravir, FDA Authorizes Use of Novavax Vaccines, and More.
Severe Outcomes Associated With Nirmatrelvir, Molnupiravir in Patients Treated for Omicron Subvarients1 A team of researchers investigated the outcomes associated with the use of nirmatrelvir or molnupiravir—ritonavir-boosted medications—in nonhospitalized patients with COVID-19 omicron subvariants, particularly BQ.1.1 and XBB.1.5. The cohort study consisted of 68,867 patients who received a diagnosis of…
GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21
Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…
CD96 Human shRNA Lentiviral Particle (Locus ID 10225)
Product Data Locus ID 10225 Synonyms TACTILE Vector pGFP-C-shLenti Format Lentiviral particles RefSeq NM_001318889, NM_005816, NM_198196, NR_134917, NM_198196.1, NM_198196.2, NM_005816.1, NM_005816.2, NM_005816.3, NM_005816.4, BC020749, BC027914, BM561433, NM_005816.5 UniProt ID P40200 Summary The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein. The…
standalone blastx of queries without NR annotations
standalone blastx of queries without NR annotations 0 I have to identify long non-coding RNA transcripts in Arabidopsis thaliana using expressed sequence tags. For that I have downloaded ESTs from dbEST NCBI. Next I need to blastx ESTs to nr database but can not be done through online database due…
Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli
Detecting antibiotic susceptibility based on deep learning of single-cell subcellular phenotypes We designed a method that takes as an input bacterial cultures grown in rich medium to a consistent optical density and then treated with an antibiotic of choice for a time sufficient to produce distinct, antibiotic-specific, cellular phenotypic changes…
trying to use the API for edirect tool (NCBI)
trying to use the API for edirect tool (NCBI) 1 Hi, I’m new to bioinformatics, so I apologize if my question seems a little bit basic. I wanted to use the tool Edirect to retrieve information about a list of samples that I have generated. I work on a cluster,…
Recent Clinical Trial Updates Shift DLBCL Treatment Paradigm
Although progress in the development of new treatment regimens for the management of patients with diffuse large B-cell lymphoma (DLBCL) has been relatively slow overall, recent developments in both the frontline and relapsed/refractory spaces have stirred optimism amongst clinicians in the field, according to a presentation given by Gilles A. Salles,…
Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron | Virology Journal
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021;593(7857):142–6. Article CAS PubMed PubMed Central Google Scholar Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2…
Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls
World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….
Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau
Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.). Front Plant Sci 6:813 Article PubMed PubMed Central Google Scholar Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 Article CAS PubMed …
An FcRn-targeted mucosal vaccine against SARS-CoV-2 infection and transmission
Mice and Golden Syrian hamsters All research experiments in this study comply with all relevant ethical regulations. The Institutional Animal Care and Use Committee approved the animal protocol at the University of Maryland (#R-APR-20-18 and #R-MAR-21-19). The animals were acclimatized at the animal facility for 4–6 days before initiating experiments….
The ongoing risk of Leishmania donovani transmission in eastern Nepal: an entomological investigation during the elimination era | Parasites & Vectors
World Health Organization. Leishmaniasis; 2023. www.who.int/news-room/fact-sheets/detail/leishmaniasis. Ruiz-Postigo JA, Jain S, Mikhailov A, Maia-Elkhoury AN, Valadas S, Warusavithana S, et al. Global leishmaniasis surveillance: 2019–2020, a baseline for the 2030 roadmap. Weekly epidemiological record. WHO; 2021. 3 September Report No.: 35. World Health Organization. Accelerating work to overcome the global impact…
Phase 3 KEYNOTE-564 Meets it Secondary Endpoint in RCC
Phase 3 KEYNOTE-564 Meets it Secondary Endpoint in RCC Merck has announced that adjuvant pembrolizumab (Keytruda) has met its key secondary end point of the phase 3 KEYNOTE-564 trial (NCT03142334), improving overall survival (OS) over placebo in patients with renal cell carcinoma (RCC) at intermediate-high or high risk of recurrence following…
Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]
Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…
sars cov 2 – contradiction in command line blast
I would like to perform blast+, using the command line, here is the code: -task blastn -db nr -outfmt 7 -query myQuery.fas -out result.txt -remote. I have to exclude SARS-CoV-2 hits from my results, so I must include -negative_taxids mentioning SARS-CoV-2 NCBI taxid number. However, the problem is, -negative_taxids is…
Optical detection using CRISPR-Cas12a of Helicobacter pylori for veterinary applications
. 2023 Nov 1;190(11):455. doi: 10.1007/s00604-023-06037-x. Affiliations Expand Affiliations 1 MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. 2 MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University,…
papain family cysteine protease containing protein, maker-scaffold1702_size30647-snap-gene-0.14 (gene) Tigriopus kingsejongensis
Associated RNAi Experiments Homology BLAST of papain family cysteine protease containing protein vs. L. salmonis genes Match: EMLSAG00000006045 (supercontig:LSalAtl2s:LSalAtl2s327:400616:404607:-1 gene:EMLSAG00000006045 transcript:EMLSAT00000006045 description:”augustus_masked-LSalAtl2s327-processed-gene-4.0″) HSP 1 Score: 590.497 bits (1521), Expect = 0.000e+0Identity = 283/525 (53.90%), Postives = 368/525 (70.10%), Query Frame = 0 Query: 49 GHVARPLGKSPPNFVRDPPPRTTPPAQWLWNNVNETNFLTVSRNQHLPTYCGSCWAHAATSSLSDRIKIARQGAWPDINLAPQVLISCGPGDGCHGGEAGDANAYMHAQGITDETCSIYRARGQDNGLPCSKLEICSTCE—SKCYQPQHFFTYRVDEFHDVEGESNGEQEANMMAEIHHRGPISCGIAVTQALV-NYTGGLFHDKTGAQEIDHDISVVGYGVDEGTQEKYWLIRNSWGTYWGEQGFFRLIRGVNNLGIESGTCSWATPADTWSDAARE—RAAILSNEITLQKP——LWKQLWTVVADFVDNTRDTDLFRRLKLMQKGCKKLSSPRVPVVNIRPRPQDYVSTADLPEALDWRSVNGTNFLSWSVNQHLPVYCGSCWAQAGLSSLADRFTIADRKRFANLALSVQYILNCQAGGSCHGGDAFPLYAFIQKQGVPDVTCQPYEALDEGPLTDCSKPSKLVCKDCTWPPPEPGQEGNCWAKEKFHRYYVDEYNGVEGADNMKKEILERGPVT 560 GH+ R G+…
Phase separation in cGAS-STING signaling
Sun L, Wu J, Du F, Chen X, Chen ZJ. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 2013; 339(6121): 786–791 Article CAS PubMed Google Scholar Wu J, Sun L, Chen X, Du F, Shi H, Chen C, Chen ZJ. Cyclic GMP-AMP…
coatomer subunit alpha, maker-scaffold52_size450388-snap-gene-3.16 (gene) Tigriopus kingsejongensis
Associated RNAi Experiments Homology BLAST of coatomer subunit alpha vs. L. salmonis genes Match: EMLSAG00000004199 (supercontig:LSalAtl2s:LSalAtl2s221:488387:561813:1 gene:EMLSAG00000004199 transcript:EMLSAT00000004199 description:”maker-LSalAtl2s221-augustus-gene-5.19″) HSP 1 Score: 208.379 bits (529), Expect = 8.743e-63Identity = 95/135 (70.37%), Postives = 99/135 (73.33%), Query Frame = 0 Query: 1 MLTKFETKSPRVKGLAFHPQRPWILASLHNGVIQLWDYRMCTLLEKFDEHEGPVRGIGFHAQQPLFVSGGDDYKIKVWNYKLKRCLFHLLGHLDYIRTTVFHAPVPHARRISPAGPAESSTYLAKIHGLWGWKAR 135 MLTKFETKSPRVKGLAFHP+RPWILASLHNGVIQLWDYRMC LLEKFDEHEGP GI H QPLFVSGGDDYKIKVWNYKLKRCLF LLGHLDYIR…
A novel tetra-primer ARMS-PCR approach for the molecular karyotyping of chromosomal inversion 2Ru in the main malaria vectors Anopheles gambiae and Anopheles coluzzii | Parasites & Vectors
Loughlin SO. The expanding Anopheles gambiae species complex. Pathog Glob Health. 2020;114:1. Article PubMed PubMed Central Google Scholar Coluzzi M, Sabatini A, Petrarca V, Di Deco MA. Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex. Trans R Soc Trop Med Hyg. 1979;73:483–97. Article CAS PubMed Google…
Answer: OMA in AWS cloud
Hi, you can use [AWS Batch][1] to execute OMA. You can use [AWS Batch Array Jobs][2] for parallelization and use [Amazon EFS as filesystem][3]. You can also use [Amazon FSx for Lustre][4] if you need higher filesystem performance. You can avoid [throttling of Docker Hub image][5] pulls by using [Amazon…
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee P-H, et al. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome. 2020;8:111. Article CAS PubMed PubMed Central Google Scholar Conrad R. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic…
Sobuzoxane Combo Extends Survival in Elderly DLBCL Group
“Our findings may suggest that R-PVP therapy is one of the safe and effective treatments for a subgroup of patients, i.e., those who may have high CCI [scores] or low tumor burden, among untreated DLBCL patients aged over 80 [years],” according to the authors of a retrospective analysis. Elderly patients…
GPP Web Portal – Gene Details
Gene: Human LOC642131 (642131) immunoglobulin IGHV1OR15-3-like pseudogene Source: NCBI, updated 2019-09-11 Taxon: Homo sapiens (human) Chromosome: 15 Wildtype Transcripts: NR_135667.1 Additional Resources: NBCI Gene record: LOC642131 (642131) NCBI Gene records for discontinued versions of this gene: LOC102724835 (102724835) sgRNA constructs originally intended to target this gene (CRISPRko, NGG PAM) NOTE:…
Genome-wide association study of traumatic brain injury in U.S. military veterans enrolled in the VA million veteran program
Helmick KM, Spells CA, Malik SZ, Davies CA, Marion DW, Hinds SR. Traumatic brain injury in the US military: Epidemiology and key clinical and research programs. Brain Imaging Behav. 2015;9:358–66. Article PubMed Google Scholar DoD Numbers for Traumatic Brain Injury Worldwide – Totals (Defense Health Agency) (2021). Karr JE, Areshenkoff…
Frontline Sobuzoxane Plus Etoposide and Rituximab is Safe and Effective in Older DLBCL Population
The combination of sobuzoxane (MST-16) and etoposide plus rituximab (Rituxan; R-PVP) prolonged survival and showcased a tolerable safety profile in patients with previously untreated diffuse large B-cell lymphoma (DLBCL) aged 80 years and older, according to findings from a retrospective analysis, which were presented at the 2023 ESMO Congress.1 At…
Frontline Sobuzoxane/Etoposide/Rituximab is Safe and Effective in DLBCL Subgroup
Lymphomas: © David A Litman – stock.adobe.com Sobuzoxane (MST-16), etoposide, and rituximab (Rituxan; R-PVP) used in combination were found to prolong survival and showcase a tolerable safety profile in patients with previously untreated diffuse large B-cell lymphoma (DLBCL) who were aged 80 years and older, according to findings from a…
Phase 3 innovaTV 301 Trial Shows Potential of Tisotumab Vedotin in Cervical Cancer
Ignace B. Vergote, MD, PhD In the phase 3 innovaTV 301/ENGOT-cx12/GOG-3057 trial (NCT04697628), tisotumab vedotin-tftv (Tivdak) demonstrated a 30% reduction in the risk of death compared with investigator’s choice of chemotherapy when utilized in the second- or third-line for patients with recurrent or metastatic cervical cancer with disease progression on…
KEYNOTE-991 Pembrolizumab plus Enzalutamide and Androgen Deprivation Therapy or Patients with Metastatic Hormone-Sensitive Prostate Cancer
(UroToday.com) The 2023 ESMO annual meeting included a session on prostate cancer, featuring a presentation by Dr. Christian Gratzke discussing results of the phase 3 KEYNOTE-991 trial assessing pembrolizumab + enzalutamide and ADT for patients with metastatic hormone-sensitive prostate cancer (mHSPC). Indeed, new therapeutic options are needed to delay disease…
Maintenance Durvalumab Plus Olaparib Improves PFS in Advanced or Recurrent Endometrial Cancer
Shannon N. Westin, MD, MPH, FACOG The addition of durvalumab (Imfinzi) to first-line chemotherapy, followed by maintenance treatment with durvalumab plus olaparib (Lynparza) significantly improved progression-free survival (PFS) in patients with newly diagnosed advanced or recurrent endometrial cancer, according to data from the phase 3 DUO-E/GOG-3041/ENGOT-EN10 trial (NCT04269200) presented at…
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,…
Durvalumab/Olaparib Maintenance Induces PFS Benefit in Advanced, Recurrent Endometrial Cancer
The addition of durvalumab (Imfinzi) to first-line chemotherapy, followed by maintenance therapy with the anti-PD-L1 antibody plus olaparib (Lynparza) improved progression-free survival (PFS) in patients with newly diagnosed advanced or recurrent endometrial cancer, according to data from the phase 3 DUO-E/GOG-3041/ENGOT-EN10 trial (NCT04269200) presented at ESMO Congress 2023.1-3 In particular,…
Perioperative Nivolumab Significantly Improves EFS in Previously Untreated Resectable NSCLC
Neoadjuvant treatment with nivolumab (Opdivo) plus chemotherapy followed by surgery and adjuvant nivolumab resulted in a statistically significant improvement in event-free survival (EFS) vs placebo plus chemotherapy, in patients with previously untreated resectable stage II to IIIB non-small cell lung cancer (NSCLC), according to data from the phase 3 CheckMate…
problem with bcftools syntax
problem with bcftools syntax 1 Hi all! I am having difficulty with creating a bcftools command. I have a .vcf.gz file downloaded from the 1000G site and a csv file with columns chrom/pos/id/ref/alt. I would like to manipulate the downloaded vcf file so that it uses only the snps I…
Addition of Adjuvant Nivolumab Improves EFS in NSCLC
Surgery and adjuvant nivolumab (Opdivo) given after a treatment regimen of neoadjuvant nivolumab plus chemotherapy, showed a significant event-free survival (EFS) benefit for patients with previously untreated resectable stage II to IIIB non-small cell lung cancer (NSCLC), according to data presented at the 2023 ESMO Congress.1 These data came from…
Neoadjuvant, Adjuvant Nivolumab Improves EFS in Resectable NSCLC
Neoadjuvant treatment with nivolumab (Opdivo) plus chemotherapy followed by surgery and adjuvant nivolumab significantly improved event-free survival (EFS), compared with placebo plus chemotherapy, in patients with previously untreated resectable stage II to IIIB non-small cell lung cancer (NSCLC), according to data from the phase 3 CheckMate 77T trial (NCT04025879) presented…
Macrophage polarization and metabolism in atherosclerosis
Organization WH the top 10 causes of death. www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death, 2019. Rana JS, Khan SS, Lloyd-Jones DM, Sidney S. Changes in mortality in Top 10 causes of death from 2011 to 2018. J Gen Intern Med. 2021;36:2517–8. Article PubMed Google Scholar Libby P. The changing landscape of atherosclerosis. Nature. 2021;592:524–33. Article …
Enzalutamide data published in NEJM as FDA weighs nonmetastatic HSPC approval
Data from the phase 3 EMBARK trial supporting a potential FDA approval of enzalutamide (Xtandi) for nonmetastatic hormone-sensitive prostate cancer (nmHSPC) have been published in the New England Journal of Medicine.1,2 The 5-year MFS rate 87.3% for those treated with enzalutamide plus leuprolide compared with 71.4% for those given leuprolide…
Generating a wrong xx.gro file during Simulation of a Water Box – User discussions
GROMACS version:GROMACS modification: NoHello everyone,I am a new user of GROMACS who wishes to study specific radial distribution functions (RDF). So I am learning a code from starting and facing a problem during water molecule optimization.I am generating xx.gro file using “edit_gro” script where H and O should be converted…
IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation
1. Introduction Human population genetics benefitted from the completion of the human genome sequence [1], which was further advanced by creating the reference of global genome variation [2] and, finally, the establishment of regional references assessing fine details of local variation in whole-genome sequences. Although European populations are relatively well…
Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?
Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb? 1 I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason…
Functional annotation with nr database followed by GO enrichment analysis
Functional annotation with nr database followed by GO enrichment analysis 0 Dear Stars, I am working in the field of plant biology. I usually performed functional annotation using Araport database (i.e. Arabidopsis database) After functional annotation, I could perform GO enrichment analysis using R wherein there is library called “Org.At.tair.db”…
ONT methylation data normalization
ONT methylation data normalization 0 I have methylation data from ONT sequencing expressed as percentage of methylation and/or number of reads. I don’t know if I’m supposed to normalize the data and how to handle replicates. Some ideas: I have data in triplicate. I want to normalize the data (quantile…
pysam – Is it possible to, all in memory without writing a file, given a list of AlignedSegments and a bam header, build a bam, index and get coverage?
Assuming you are on an operating system that supports them, like Linux, you can try using named pipes in a ramdisk or tmpfs. Not the most elegant approach, but I don’t know if what you are asking for is possible (it may very well be, I just don’t know) and…
DNA damage induced by CDK4 and CDK6 blockade triggers anti-tumor immune responses through cGAS-STING pathway
Patients’ tumor tissues and clinical data This study recruited 125 breast cancer patients for immunohistochemical (IHC) analysis and 10 breast cancer patients for RNA-seq analysis from the Affiliated Tumor Hospital of Nantong University. Tumor tissues collected from surgical patients were fixed with formalin and embedded with paraffin and then examined….
Diamond blast running in a loop
Diamond blast running in a loop 0 Hi ! I am using diamond blast (blastx) to align nanopore reads against NR database. The process runs fine until the last bin but suddenly gets in a loop and restarts the complete process again. It works fine on 1000 reads but dowmsampling…
OMA in AWS cloud
OMA in AWS cloud 2 Dear colleagues, I am new in cloud environment and I would like to run OMA standalone in AWS environment. Firstly I would like to know if it is possible. Secondly, if it is, what are the parameters to use (AWS configuration specialy for all versus…
Ligand not planar after energy minimisation – User discussions
GROMACS version: 2021.4GROMACS modification: NoI am using Amber99 parmbsc0 forcefield for DNA and I prepared the ligand topology using GAFF from acpype webserver. After energy minimisation the ligand which is aromatic is losing its planarity. This is the ligand topology [ moleculetype ]; Name nrexclUNL 3 [ atoms ]; nr…
The effect of vitrification on blastocyst mitochondrial DNA dynamics and gene expression profiles
Bosch E, De Vos M, Humaidan P. The future of cryopreservation in assisted reproductive technologies. Front Endocrinol (Lausanne). 2020;11:1–15. Article Google Scholar De Geyter C, Calhaz-Jorge C, Kupka MS, Wyns C, Mocanu E, Motrenko T, et al. ART in Europe, 2015: results generated from European registries by ESHRE†. Hum Reprod…
Solved 1) Carry out a BLASTX search of the sequence below
1) Carry out a BLASTX search of the sequence below NCBI BLASTXsearching the non-redundant protein (nr) sequences database and using the invertebrate mitochondrial genetic code. Answer these 3 questions. 1) What protein does this sequence code for? 2) Which is the correct reading frame? 3) Which organism is the closest…
[Solved] NCBI blast database – Biochemistry (Bsc221)
The NCBI Blast Database is a collection of sequence databases that can be used with the BLAST (Basic Local Alignment Search Tool) program. BLAST is a widely used bioinformatics tool for comparing nucleotide or protein sequences against a database to identify similarities and infer functional or evolutionary relationships. The NCBI…
18S taxonomy assignment SILVA database formatting
Hi Bioinformatic community, I would like to classify 18S data (V7) of Fungi with assignTaxonomy from dada2. For that I downloaded SILVA_132_SSURef_tax_silva.fasta.gz from the SILVA website and need to format it, what I do with some Linux command line oneliner. But some species in the database have a different number…
University of Washington hiring BIOINFORMATICS ENGINEER in Seattle, Washington, United States
Req #: 226825 Department: LABORATORY MEDICINE AND PATHOLOGY Posting Date: 10/02/2023 Closing Info: Open Until Filled Salary: $6843 – $11120 per month Shift: First Shift Notes: As an employee you will enjoy generous benefits and work/life programs. For detailed information on Benefits for this position, click here. ( hr.uw.edu/benefits/wp-content/uploads/sites/3/2018/02/benefits-professional-staff-librarians-academic-staff-20230119_a11y.pdf) The…
RNA sequencing and gene expression analysis in a Mouse model
Introduction Chronic obstructive pulmonary disease (COPD) is a condition that is characterized by persistent respiratory symptoms and airflow limitations that are not fully reversible. The severe complications of the disease may adversely affect its morbidity and mortality.1 According to World Health Organization (WHO) statistics, over 3 million people per year…
Epstein-Barr virus infection: the micro and macro worlds | Virology Journal
Epstein MA, Achong BG, Barr YM. VIRUS PARTICLES IN CULTURED LYMPHOBLASTS FROM BURKITT’S LYMPHOMA. Lancet. 1964;1(7335):702–3. Article CAS PubMed Google Scholar Cohen JI, Jaffe ES, Dale JK, Pittaluga S, Heslop HE, Rooney CM, et al. Characterization and treatment of chronic active Epstein-Barr virus disease: a 28-year experience in the United…
Repeated low doses of psilocybin increase resilience to stress, lower compulsive actions, and strengthen cortical connections to the paraventricular thalamic nucleus in rats
Agin-Liebes GI, Malone T, Yalch MM, Mennenga SE, Ponté KL, Guss J, et al. Long-term follow-up of psilocybin-assisted psychotherapy for psychiatric and existential distress in patients with life-threatening cancer. J Psychopharmacol. 2020;34:155–66. PubMed Google Scholar Johnson MW, Garcia-Romeu A, Griffiths RR. Long-term follow-up of psilocybin-facilitated smoking cessation. Am J Drug…
Invalid order for directive atom type – User discussions
Saeed September 29, 2023, 12:00pm 1 GROMACS version:2023.1GROMACS modification: Yes/No Hi.I am almost new to using the Gromacs and sorry If this question is a boring one for you!I have two separate itp files for two different molecules from the LigPargen server!I used the insert-molecules command and mixed these two…
Comparing multiple columns from two files using AWK
Dear all, I need your help to solve the following problem. I have the following two files (indicated as A and B): FILE A: head 129N.final-test_taxid-120686.txt A00270:507:H3KTJDSX5:4:1105:31747:1736 1187 chr1 205559197 60 144M6S = 205559203 152 GAGCATTTAGGCAAGAGAAAGGAACAAAGGGTATCCAAATTGAAAAACAGGAGTCAAATTGTCCCTTTGCAGACAACAGGATTTTACATATAGAAAAATCTAAAAGATCACACACACACACACACACACACACACACACACACACACAAA FFFFFFFFFFFFFFF:FFFFFFFFFFF:FF:FFFF,FFFFF:FFFF:F:FFFFFF:F:FFFFFF:FFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFF::,FFFF::,FFF,F:FFFFFFFFFFFFFFFF,FFFFFFFFFF:,F,FF,FF: NM:i:0 AS:i:288 nn:i:0 tp:A:P cm:i:18 s1:i:120 s2:i:0 de:f:0 rl:i:86 MQ:i:50 MC:Z:102M4I44M ms:i:4398 A00270:507:H3KTJDSX5:4:1105:31747:1736…
Epcoritamab Wins European and Japanese Approval for Select Types of R/R LBCL
The European Commission (EC) has granted conditional marketing authorization to epcoritamab-bysp (Tepkinly) for use as a single agent in adult patients with relapsed or refractory diffuse large B-cell lymphoma (DLBCL) following 2 or more lines of systemic treatment.1 Additionally, Japan’s Ministry of Health, Labour, and Welfare has approved the agent…