Categories
Tag: DEL
Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics
Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82(11):801–11. Article CAS Google Scholar Jeon SA, Park JL, Park SJ, Kim JH, Goh SH, Han JY, Kim SY. Comparison between MGI and Illumina sequencing platforms for whole genome sequencing. Genes Genomics. 2021;43(7):713–24. Article CAS …
Horses drove societal transformation in South America – study
Horses on Argentina’s Valdes Peninsula. Photo by Cynthia del Río The introduction of horses to South America led to a rapid social and economic transformation, researchers report. “Perhaps nowhere in the ancient world was the impact of domestic horses on human societies more impactful than in the plains and foothills…
Extended Follow-up of ALPINE Randomized Phase 3 Study Confirms Sustained Superior Progression-free Survival of Zanubrutinib Versus Ibrutinib for Treatment of Relapsed/Refractory Chronic Lymphocytic Leukemia and Small Lymphocytic Lymphoma (R/R CLL/SLL)
Background ALPINE, a randomized, multinational phase 3 study (NCT03734016) in patients with R/R CLL/SLL, established the statistical and clinically meaningful superiority of zanubrutinib over ibrutinib on progression-free survival (PFS) and overall response rate (ORR) and confirmed the favorable safety/tolerability profile of zanubrutinib (Brown et al. NEJM; 2022). Now, with 3…
Sacramento bee obituaries for today
Sacramento,CA Obituaries. The Dignity Memorial® online obituary search tool gives you access to obituaries from thousands of locations across North America. You can search by first or last name, state and publication date. Once you find the obituary you are looking for, you can get important information about upcoming services,…
Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal
Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…
UChicago Medicine experts showcase blood cancer research at 65th ASH Annual Meeting
Faculty and trainees from the University of Chicago Medicine Comprehensive Cancer Center (UCCCC) joined the world’s largest hematology community to discuss the latest updates in blood cancers at the 65th American Society of Hematology (ASH) Annual Meeting and Exposition held December 9-12, 2023 in San Diego and online. At the meeting,…
machine learning – How to properly free GPU memory in Pytorch
I am using Pytorch with Pytorch-Lightning to train and validate a model. But during testing (test_step), I am faced with a CUDA memory error which I’m not sure how to resolve. The model trains and validates fine, and it is not an issue of batch size, data size or model…
Analysis of biomarkers in speculative CNS-enriched extracellular vesicles for parkinsonian disorders: a comprehensive systematic review and diagnostic meta-analysis
44. Zurück zum Zitat Thery C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, Antoniou A, Arab T, Archer F, Atkin-Smith GK, Ayre DC, Bach JM, Bachurski D, Baharvand H, Balaj L, Baldacchino S, Bauer NN, Baxter AA, Bebawy M, Beckham C, Bedina Zavec A, Benmoussa A, Berardi…
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 + ++…
Image:Gengis Khan empire-fr.svg – from the Schools Wikipedia
From Wikipedia, the free encyclopedia This is a file from the Wikimedia Commons. The description on its description page there is shown below.Commons is a freely licensed media file repository. You can help. Description Français : Carte de l’empire mongol au XIIIème siècle English: Genghis Khan empire, XIIIth century Source Own…
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…
Study uncovers vast genomic diversity in Aboriginal Australian communities
In a recent study published in the journal Nature, researchers investigated the previously underrepresented genomic diversity of four Aboriginal Australian communities. They used population-scale whole-genome (WGS) long-read sequencing. Study findings revealed unique alleles comprised of insertion-deletion variants, variable copy number regions, and structural variants, 62% of which are novel to…
Bioconductor – QTLExperiment (development version)
DOI: 10.18129/B9.bioc.QTLExperiment This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…
Legend is not shown using ggplot2 – General
Hello, I’m new using RStudio. I’m trying to show the distribution of temperature values (min,max and mean) in a graphic, my database is called ‘datos_diarios’ and I already imported the library, but it doesn’t seem to work with this code…It also shows the values on the X axis way too…
Lee’s Famous Recipe Chicken to clone voices with AI for drive-thru
Lee’s Famous Recipe Chicken is using AI at the drive-thru. A quick-serve chicken chain will personalize the drive-thru experience with help from artificial intelligence (AI) – and the voice of a local football legend. Ohio-based Lee’s Famous Recipe Chicken, which operates more than 130 locations in 12 U.S. states and…
The landscape of genomic structural variation in Indigenous Australians
Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…
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…
Combine MAF, GISTIC, and clinical data using maftools
My goal is to produce an OncoPlot with somatic mutation, copy number, and clinical information. I’m able to produce a MAF file with clinical info: maf.plus.clin <- read.maf( maf = maf, clinicalData = clinical.all, ) and also a MAF file with GISTIC info: maf.plus.gistic <- read.maf( maf = maf, gisticAllLesionsFile…
[PyTorch] Delete Model And Free Memory (GPU / CPU)
Problem Last night I tried to improve some code about merge two models. Because my poor device, I cannot merge all layers totally, but need to merge them layer by layer for reducing my memory cost. I found how to free the memory of GPU is very easy, but CPU…
Comprehensive Review of Small Interfering RNAs (siRNAs)
Introduction Cancer, also called malignancy, is a group of diseases caused by the rapid multiplication and spread of malignant cells.1,2 According to statistics from the National Cancer Center, more than 100 types of cancer have been identified.3 The ability of malignant tumor cells to metastasize via the blood-lymphatic system and…
overlapping duplicate dispersed_repeat feature in stringtie
GFF Error: overlapping duplicate dispersed_repeat feature in stringtie 0 Hi. I got following error when I use stringtie. with repeatmasker annotation gff file and RNA-seq bam files which is already sorted with samtools. GFF Error: overlapping duplicate dispersed_repeat feature (ID=461) GFF Error: overlapping duplicate dispersed_repeat feature (ID=712) GFF Error: overlapping…
Screening for lipid nanoparticles that modulate the immune activity of helper T cells towards enhanced antitumour activity
Huang, Q., Zeng, J. & Yan, J. COVID-19 mRNA vaccines. J. Genet. Genomics 48, 107–114 (2021). Article CAS PubMed PubMed Central Google Scholar Huang, S., Zhu, Y., Zhang, L. & Zhang, Z. Recent advances in delivery systems for genetic and other novel vaccines. Adv. Mater. 34, e2107946 (2022). Article PubMed …
The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden Kaisa Thorell Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Chihuahua, México Zilia Y. Muñoz-Ramírez Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA Difei Wang, Yunhu Wan, Belynda Hicks, Bin Zhu, Meredith Yeager, Amy Hutchinson, Kedest Teshome, Kristie Jones & Wen Luo…
New Data Presented at ASH from the Phase 3 GLOW Study Show
Additional data from the Phase 2 CAPTIVATE study, show 82 percent of patients with previously untreated chronic lymphocytic leukaemia (CLL) treated with fixed-duration ibrutinib plus venetoclax did not need next-line treatment at 54 months1,2 BEERSE, BELGIUM, Dec. 11, 2023 (GLOBE NEWSWIRE) — The Janssen Pharmaceutical Companies of Johnson & Johnson…
Dural 10x scRNAseq
Mouse Brain Dural scRNAseq Database Other scRNAseq databases from Betsholtzlab Citation:We provide this database resource free to the scientific community. We encourage reproduction of data excerpts from the database in academic publications on the condition that it is cited with reference to the original publication (below) and the database website….
FibroGen Presents Data from Phase 3 MATTERHORN Trial of
A post hoc analysis of patients with higher transfusion burden at baseline showed a larger percentage of patients achieved transfusion independence ≥ 56 days with roxadustat vs. placebo (36.1% vs 11.5%; p=0.047ǂ). Dr. Moshe Mittelman’s presentation was selected for the “2024 Highlights of ASH” SAN FRANCISCO, Dec. 09, 2023 (GLOBE…
FIGURE S6. from Mitochondrial replication’s role in vertebrate mtDNA strand asymmetry
figure posted on 2023-12-08, 07:46 authored by André Gomes-dos-Santos, Nair Vilas-Arrondo, André M. Machado, Esther Román-Marcote, Jose Luís Del Río Iglesias, Francisco Baldó, Montse Pérez, Miguel M. Fonseca, L. Filipe C. Castro, Elsa Froufe GenomeScope2 k-mer (21) distributions displaying estimation of genome size (len), homozygosity (aa), heterozygosity (ab), mean k-mer…
Building tools for zebra mussel genetic biocontrol
December 7, 2023 Lindsey O’Brien and Victor Hernandez Elizarraga, UMGC Innovation Lab scientists Zebra mussels are a damaging invasive species that are spreading throughout the lakes and rivers of Minnesota and beyond. The UMGC Innovation Lab is building on previous work sequencing the zebra mussel genome and working to develop…
Geron Announces Fifty Percent Enrollment in the Phase 3 IMpactMF Clinical Trial Evaluating Imetelstat in Patients with Relapsed, Refractory Myelofibrosis -December 07, 2023 at 07:35 am EST
FOSTER CITY – Geron Corporation (Nasdaq: GERN), a late-stage clinical biopharmaceutical company, today announced achievement of fifty percent enrollment in the Phase 3 IMpactMF clinical trial investigating the Company’s first-in-class telomerase inhibitor, imetelstat, versus best available therapy (BAT) in patients with relapsed/refractory myelofibrosis (MF). ‘Reaching fifty percent enrollment in IMpactMF…
ClinVar and DGV
Hello, we are using UCSC in micro array reading support to help us evaluate CNVs but, this morning, the DGV and ClinVar databases have disappeared. The cause of this is an update and then everything will go back to the way it was before or will it stay that way…
A genomic mutational constraint map using variation in 76,156 human genomes
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Siwei Chen, Laurent C. Francioli, Julia K. Goodrich, Ryan L. Collins, Masahiro Kanai, Qingbo Wang, Jessica Alföldi, Nicholas A. Watts, Christopher Vittal, Timothy Poterba, Michael W. Wilson, Yekaterina Tarasova, William Phu, Riley Grant, Mary T. Yohannes, Namrata Gupta, Irina M. Armean, Samantha M. Baxter, Sarah E. Calvo, Katherine R. Chao, Sinéad Chapman, Beryl B. Cummings, Phil Darnowsky, Patrick…
Geron Announces Fifty Percent Enrollment in the Phase 3 IMpactMF Clinical Trial Evaluating Imetelstat in Patients with Relapsed/Refractory Myelofibrosis
IMpactMF is the first and only Phase 3 clinical trial to evaluate overall survival as the primary endpoint in R/R MF An interim analysis is expected in the first half of 2025, with a final analysis expected in the first half of 2026 FOSTER CITY, Calif., December 06, 2023–(BUSINESS WIRE)–Geron…
Inferring compound heterozygosity from large-scale exome sequencing data
Department of Neurology, Hospital of the University of the Pennsylvania, Philadelphia, PA, USA Michael H. Guo Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Michael H. Guo, Laurent C. Francioli, Sarah L. Stenton, Julia K. Goodrich, Nicholas A. Watts, Moriel Singer-Berk, Emily Groopman, Philip W. Darnowsky, Matthew Solomonson, Samantha Baxter, Jessica Alföldi, Irina M….
The Revolutionary DNA Sequencing Breakthrough
Space scientists at the University of Aberdeen have achieved a monumental breakthrough that is set to transform the field of DNA sequencing and its applications in the search for extraterrestrial life. Employing state-of-the-art technology, these researchers have developed an innovative technique capable of precisely detecting and characterizing soil DNA using…
Land transactions for Nov. 13-17 – Shelby County Reporter
Land transactions for Nov. 13-17 Published 3:34 pm Monday, December 4, 2023 The following deeds were transferred in Shelby County from Nov. 13-17: Nov. 13 -Freedom Driven Properties LLC to Kenneth Kirkes, for $188,500, for Lot 1 in Tucker Estate Survey Resubdivision of Lot 1A of a Resurvey of…
Geron Announces Publication in the Lancet of Results from the IMerge Phase 3 Clinical Trial Evaluating Imetelstat in Lower Risk MDS -December 04, 2023 at 05:00 am EST
Geron Corporation announced publication in The Lancet of results from the IMerge Phase 3 trial investigating imetelstat versus placebo in patients with lower risk myelodysplastic syndromes (MDS) relapsed/refractory or ineligible for erythropoiesis stimulating agents (ESAs). The publication is available online and will be available in print at a later date….
Geron Corp (GERN) Announces Publication in The Lancet of Results from the IMerge Phase 3 Clinical Trial Evaluating Imetelstat in Lower Risk MDS
Geron Corporation (Nasdaq: GERN), a late-stage clinical biopharmaceutical company, today announced publication in The Lancet of results from the IMerge Phase 3 trial investigating imetelstat versus placebo in patients with lower risk myelodysplastic syndromes (MDS) relapsed/refractory or ineligible for erythropoiesis stimulating agents (ESAs). The publication is available online and will…
Geron Announces Publication in The Lancet of Results from the IMerge Phase 3 Clinical Trial Evaluating Imetelstat in Lower Risk MDS
FOSTER CITY, Calif.–(BUSINESS WIRE)– Geron Corporation (Nasdaq: GERN), a late-stage clinical biopharmaceutical company, today announced publication in The Lancet of results from the IMerge Phase 3 trial investigating imetelstat versus placebo in patients with lower risk myelodysplastic syndromes (MDS) relapsed/refractory or ineligible for erythropoiesis stimulating agents (ESAs). The publication is…
The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism
Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article PubMed CAS Google Scholar Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…
Stream DjGengis | Listen to top hits and popular tracks online for free on SoundCloud
DJ Gengis Khan, nome d’arte di Loris Malaguti (Roma, 8 novembre 1982), è un disc jockey e beatmaker italiano, membro del duo romano Rubber Headz e DJ ufficiale del rapper italiano Noyz Narcos. Biografia Cresciuto alla periferia di Roma, Gengis si appassiona molto presto alla musica, avvicinandosi…
AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings
J Chem Inf Model. Author manuscript; available in PMC 2023 Nov 28. Published in final edited form as: PMCID: PMC10683950 NIHMSID: NIHMS1947068 Jerome Eberhardt aDepartment of Integrative Structural and Computational Biology, Scripps Research, La Jolla, 92037, California, USA Diogo Santos-Martins aDepartment of Integrative Structural and Computational Biology, Scripps Research, La…
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 …
Why rRNA is used for identification?
Why is strain identification for labeling accuracy of probiotic products important?5 answersStrain identification for labeling accuracy of probiotic products is important because probiotic health benefits are strain-specific. Different strains of probiotics have different effects on human health, and therefore it is crucial to include the correct strains in probiotic products…
DNA methylation change in blood cells of FB and CFS patients
Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…
Molecular consequences of PQBP1 deficiency, involved in the X-linked Renpenning syndrome
Kalscheuer VM, Freude K, Musante L, Jensen LR, Yntema HG, Gécz J, et al. Mutations in the polyglutamine binding protein 1 gene cause X-linked mental retardation. Nat Genet. 2003;35:313–5. Article CAS PubMed Google Scholar Lenski C, Abidi F, Meindl A, Gibson A, Platzer M, Kooy F, et al. Novel truncating…
Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer
Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article CAS PubMed PubMed Central Google Scholar Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article CAS PubMed Google Scholar Lawrence…
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,…
Implementing Early Convolutions for Improved Accuracy – vision
Thanks for helping me out. I am using a pre-trained ViT-b/16 model with pretrained CLIP. def load_clip_to_cpu(backbone_name): url = clip._MODELS[backbone_name] model_path = clip._download(url) try: model = torch.jit.load(model_path, map_location=”cpu”).eval() state_dict = None except RuntimeError: state_dict = torch.load(model_path, map_location=”cpu”) pretrained_dict = state_dict or model.state_dict() model = clip.build_model(pretrained_dict) return model The strucutre of…
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…
Development and evaluation of specific polymerase chain reaction assays for detecting Theileria equi genotypes | Parasites & Vectors
Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS PubMed PubMed Central Google Scholar Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…
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…
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
journal contribution posted on 2023-11-23, 11:51 authored by Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Rodrigo V Honorato, Charlotte van Noort, Joao MC Teixeira, Alexandre MJJ Bonvin, Ren Kong, Hang Shi, Xufeng Lu, Shan Chang, Jian Liu, Zhiye Guo, Xiao Chen, Alex Morehead, Raj S…
Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc Avise JC (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Philos Trans R Soc Lond B 312:325–342. doi.org/10.1098/rstb.1986.0011 Article CAS Google Scholar Baker CS, Steel D, Calambokidis J, Falcone E, González-Peral U, Barlow J,…
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…
Detection of a novel Babesia sp. in Amblyomma javanense, an ectoparasite of Sunda pangolins | Parasites & Vectors
Yabsley MJ, Shock BC. Natural history of zoonotic Babesia: role of wildlife reservoirs. Int J Parasitol Parasit Wildl. 2013;2:18–31. Article Google Scholar Hersh MH, Tibbetts M, Strauss M, Ostfeld RS, Keesing F. Reservoir competence of wildlife host species for Babesia microti. Emerg Infect Dis. 2012;18:1951–7. Article PubMed PubMed Central Google…
Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies
Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…
Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics
Here, we report a proband with characteristic features of the clinical syndrome, including downward-slanting palpebral fissures; delayed development of bilateral optic nerve hypoplasia; facial deformity with a small mouth, thin lips, micrognathia, and blepharophimosis; short neck; abnormal deciduous teeth; and malformations of the thorax and short ribs. The proband showed…
A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics
Título: Autor: Haro-Moreno, José M.; Cabello-Yeves, Pedro J.; Garcillán-Barcia, M. Pilar; Zakharenko, Alexandra; Zemskaya, Tamara I.; Rodriguez-Valera, Francisco Palabras clave: Ca. PatescibacteriaLake BaikalLong-read metagenomics16S rRNA Fecha de publicación: 2023 Editor: Springer Nature Citación: Environmental Microbiome 18: 12 (2023) Resumen: [Background]: Lake Baikal, the world’s deepest freshwater lake, contains important numbers…
The total show at the Qube in Rome (Info and Tickets)
On 12 and 13 December, MArteLive – the total show – returns to Rome: in the rooms of the Qube (via di Portonaccio 212) the great event with a constantly updated line up. On stage more than 30 national and international guests, over 300 emerging artists (selected from the 5…
JupyterHubSingleUser – Failed to connect to my Hub at http://127.0.0.1:8081/hub/api – JupyterHub – Jupyter Community Forum
After updating the base notebook image to Quay (base-notebook:2023-10-31) getting these connection errors in single user server spawn. Earlier used version jupyter/base-notebook:2023-04-14 this working without any errors. (python3.10 version used in working docker image) Environment:Used helm chart version “3.0.3” to deploy the 4.0.2 version of application on AWS EKS Cluster….
Flumarina Mercado: impactos de covid-19 para 2023-2030
“Flumarina Escenario de mercado 2023-2030: El mercado Global Flumarina exhibe información completa que es una fuente valiosa de datos perspicaces para los estrategas comerciales durante la década 2030. Sobre la base de datos históricos, el informe de mercado Flumarina proporciona segmentos clave y sus subsegmentos, ingresos y datos de oferta…
Apple to Enhance Software Quality and Performance with Development Pause
In a surprising decision, Apple Inc. has chosen to temporarily halt the development of next year’s software updates for its range of devices, including the iPhone, iPad, and Mac. The company made this internal decision in order to address the numerous bugs found in earlier versions. Rather than introducing new…
Predoctoral Research Assistant for the Bioinformatics Unit ( AIPREBIOINF13) – National Center for Oncological Research – job portal
Referencia de la oferta: AIPREBIOINF13 Inicio de la oferta: 14/11/2023 Fin de la oferta: 13/12/2023 23:59:00 Descripción The Bioinformatics Unit (BU) within the Structural Biology Programme is seeking to recruit a highly motivated and talented student to conduct a PhD study as part of the GENCODE project to annotate the…
[Question] How to classify designs? – vision
Hello, I’m fairly new to this world of vision. But I want to train a network that tells me whether it’s product 1 or 2. The products are quite similar, and I’ve trained with many photos of these designs, but I always get disastrous results. Can someone help me or…
Detection of cellular traction forces via the force-triggered Cas12a-mediated catalytic cleavage of a fluorogenic reporter strand
Orr, A. W., Helmke, B. P., Blackman, B. R. & Schwartz, M. A. Mechanisms of mechanotransduction. Dev. Cell 10, 11–20 (2006). Article CAS PubMed Google Scholar Zhang, Y. et al. Platelet integrins exhibit anisotropic mechanosensing and harness piconewton forces to mediate platelet aggregation. Proc. Natl Acad. Sci. USA 115, 325–330…
How To Get Chromosome Position Given Rs Number?
How To Get Chromosome Position Given Rs Number? 3 I have a list of a few hundred SNPs given by rs number. I want to get the chromosome and position for each SNP. For example: input: rs4477212 output: chr1:82154 snp chromosome position • 29k views you can download this information…
The mystery of the ‘black box’ at the MacBook event. What is that object?
The mystery of the ‘black box’ at the MacBook event. What is that object? On October 30th, during the latter part of Apple’s new MacBook Pro unveiling event, a black machine box connected to the MacBook was briefly captured on camera. The presenter at the event was discussing the speed…
Myeloid/Lymphoid Neoplasms with ETV6::PDGFRB Fusion Gene
Introduction The ETV6::PDGFRB fusion gene is commonly associated with myeloid neoplasms with monocytosis (such as CMML), and with eosinophilia.1 The PDGFRB gene, located on 5q33, encodes PDGFRβ, a type III tyrosine kinase comprising an extracellular domain consisting of five immunoglobulin (Ig)-like domains, a single-transmembrane helix domain, a juxtamembrance domain, and…
Most large structural variants in cancer genomes can be detected without long reads
JaBbA v1 outperforms previous CN algorithms We enhanced our previous JaBbA (v0.1; ref. 4) model with several methodological innovations to increase robustness to read depth waviness, improve algorithm convergence and enforce junction balance for allele-specific as well as total CN (Extended Data Fig. 1a–d and Methods). We also rigorously defined…
Which type of ribosomal RNA Does E. coli have?
E. coli has ribosomal RNA (rRNA) in its ribosomes. The 16S and 23S rRNAs are specifically mentioned in the abstracts. The abstract by Nissley et al. states that MS2 tags were inserted in either the 16S or 23S rRNAs of E. coli 50S subunits. Pletnev et al. also mention rRNA…
Molecular diagnosis, phylogenetic analysis, and antifungal susceptibility profiles of Candida species isolated from neutropenic oncological patients | BMC Infectious Diseases
Eissa S, Khedr R, Romeih M, Halaby L, Elanany M, Madney Y. Clinical characteristics and outcome of invasive fungal sinusitis in children with hematological malignancies. Med Mycol. 2022;60(4):myac010. Article PubMed Google Scholar Lin G-L, Chang H-H, Lu C-Y, Chen C-M, Lu M-Y, Lee P-I, Jou S-T, Yang Y-L, Huang L-M,…
Targeted gene delivery to telencephalic inhibitory neurons by directional in utero electroporation
Título: Autor: Borrell, Víctor CSIC ORCID; Yoshimura, Yumiko; Callaway, Edward M. Fecha de publicación: 2005 Editor: Elsevier Citación: Journal of Neuroscience Methods 143(2): 151-158 (2005) Resumen: Telencephalic inhibitory neurons originate in the ganglionic eminences and migrate to the cerebral cortex following a tangential trajectory, before they differentiate and integrate within…
ncRNA | Free Full-Text | Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma
4. Dysregulation of lncRNAs in MM In recent years, numerous studies have focused on the role of lncRNAs in MM pathogenesis. Since then, the role of aberrantly expressed lncRNAs in MM has been reported, highlighting the potential in clinical applications. For instance, lncRNAs participate in the differentiation of erythroid, myeloid,…
Metagenomic analysis of the microbial community in kefir grains from different milk sources
Bengoa AA, Iraporda C, Garrote GL, Abraham AG. 2019. Kefir micro?organisms: their role in grain assembly and health properties of fermented milk. Journal of applied microbiology 126:686-700.doi.org/10.1111/jam.14107. Biçer Y, Telli AE, Sönmez G, Turkal G, Telli N, Uçar G. 2021. Comparison of commercial and traditional kefir microbiota using metagenomic analysis….
Structural Variants in gnomAD v4
Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…
Geron IMerge Phase 3 Presentations at Upcoming ASH Annual Meeting Reinforce Significant Durability and Breadth of Effect of Imetelstat in Lower Risk MDS
FOSTER CITY, Calif.–(BUSINESS WIRE)–Geron Corporation (Nasdaq: GERN), a late-stage clinical biopharmaceutical company, today announced the publication of abstracts from the IMerge Phase 3 clinical trial evaluating its first-in-class investigational telomerase inhibitor imetelstat in patients with lower risk myelodysplastic syndromes (MDS). Four abstracts have been accepted for presentation at the 65th…
Epigenetic regulation during cancer transitions across 11 tumour types
Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…
DNA damage response(DDR): a link between cellular senescence and human cytomegalovirus | Virology Journal
Hayflick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res. 1961;25:585–621. Article CAS PubMed Google Scholar Hayflick L. THE LIMITED IN VITRO LIFETIME OF HUMAN DIPLOID CELL STRAINS. Exp Cell Res. 1965;37:614–36. Article CAS PubMed Google Scholar Schmitt CA, Tchkonia T, Niedernhofer LJ, Robbins PD,…
ESMO 2023: Gynecologic Cancer Studies May Change Practice
Phase 3 studies presented at the ESMO Congress 2023 may change the way gynecologic cancers are treated, immediately or in the near future, according to researchers. An immediate change may be prompted by results from the INTERLACE trial, which suggest that induction chemotherapy before chemoradiotherapy (CRT) should be the new…
Apple unveils new MacBook Pro featuring M3 chips
October 30, 2023 PRESS RELEASE Apple unveils the new MacBook Pro featuring the M3 family of chips, making the world’s best pro laptop even better 14-inch MacBook Pro with M3 now starts at $1,599 14- and 16-inch models with M3 Pro and M3 Max are available in a gorgeous new space black…
MtDNA variation, oxygen and nutrient sensing pathways in the penetrance of mitochondrial disease
[eng] Mitochondrial diseases (MDs) are metabolic rare disorders impairing the OXPHOS system. mtDNA is polyplasmic, therefore mutant and wild-type alleles can coexist in the same mitochondria or cell in a state known as heteroplasmy. The regulation of heteroplasmy is poorly understood and some nutrient sensing pathways seem to have…
need interpretations for the vg call output
need interpretations for the vg call output 0 I successfully obtained the output VCF using the following command: vg call ${gbz_file} \ -k ${pack_file} \ -r ${snarls_file} \ -s ${sample_name} \ -t $SLURM_CPUS_PER_TASK \ -z -a > ${output_vcf_file} I need some interpretations for the VCF data. It appears that the…
Seasonal dynamics of Amblyomma cajennense (Fabricius, 1787) sensu stricto in a degraded area of the Amazon biome, with notes on Rickettsia amblyommatis infection | Parasites & Vectors
Szabó MPJ, Pinter A, Labruna MB. Ecology, biology and distribution of spotted-fever tick vectors in Brazil. Front Cell Infect Microbiol. 2013;3:27. Article PubMed PubMed Central Google Scholar Luz HR, Costa FB, Benatti HR, Ramos VN, Serpa A, Martins MC, et al. Epidemiology of capybara-associated Brazilian spotted fever. PLoS Neg Trop…
eClinical Solutions and Software Market Poised to Achieve
NEWARK, Del, Oct. 25, 2023 (GLOBE NEWSWIRE) — By the end of 2023, the global eClinical solutions and software market is projected to be valued at US$ 9.3 billion, and by 2033, it is projected to grow at a compound annual growth rate (CAGR) of 12.1% to reach a valuation…
vg call problem request
vg call problem request 0 Hello, recently I’m genotyping some SVs using illumila data, however, I have met some problems that I can not figure it out. The questions are as follows: For some large DEL SVs, for example, SV length > 1kb, the variants will be filtered in the…
Genome-wide analyses identify NEAT1 as genetic modifier of age at onset of amyotrophic lateral sclerosis | Molecular Neurodegeneration
van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, van den Berg LH. Amyotrophic Lateral Sclerosis. Lancet (London England). 2017;390:2084–98. Article PubMed Google Scholar Liu MS, Cui LY, Fan DS. Age at onset of Amyotrophic Lateral Sclerosis in China. Acta Neurol Scand. 2014;129:163–7. Article CAS PubMed …
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes | BMC Microbiology
Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13:260–70. Article CAS PubMed PubMed Central Google Scholar Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24:392 NIH Public Access. Article …
geom_abline and ggplot2 in R
I have the following code and I need help on geom_line and being able to add the 45° line chile_1980 <- data %>% filter(Country == “Chile” & Year == 1980) chile_1980 = chile_1980[,26:35] chile_1980 = t(chile_1980) PorcPobl = seq(10, 100, by = 10) chile_1980 = data.frame(Por_Acum_Pob = PorcPobl, DecilAcum =…
Central Venous Catheter Market Analysis: Anticipating a
NEWARK, Del, Oct. 19, 2023 (GLOBE NEWSWIRE) — The central venous catheter market size is anticipated to surpass US$ 3,238.1 million in 2023 and is likely to attain a valuation of US$ 5,314.5 million by 2033. The central venous catheter market share is projected to thrive at a CAGR of…
Pytorch-Dataloader throws multiprocessing exception when deployed inside gunicorn/flask server
I am deploying my pytorch model in aws-sagemaker container and using gunicorn server for inference imports i have Dependency versions matplotlib = 3.0; pandas = 2.0; PyTorch = 2.0.1; tqdm = 4.0; cuda = 11.7 import logging import os import shutil import pandas as pd import torch from time import…
Pysam pileup and Rsamtools pileup output discrepancy
I have mRNA sequencing data that I’ve aligned to a genome. Specifically, I am interested in determining the total number of reads at each base and the percentage of occurrences of A, T, G, C, deletions, and insertions at these bases. I have utilized both pysam pileup and Rsamtools pileup…
Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
Ceballos, G., Ehrlich, P. R. & Raven, P. H. Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction. Proc. Natl Acad. Sci. USA 117, 13596–13602 (2020). Article CAS PubMed PubMed Central Google Scholar Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the…
Generating Positional List from VCF
I think one of the ways to achieve your goal is by converting your VCF file to a MAF (Mutation Annotation Format) file. To this end, you may want to check out the fuc package I wrote: >>> from fuc import pyvcf, pymaf >>> data = { … ‘CHROM’: [‘chr1’,…
Aligner with statistics included?
Aligner with statistics included? 1 Hello, Is there a long range aligner that could make a statistics outlook listing how many SNP, indels etc are observed in the alignment itself? Thank you aligner alignment • 203 views BBTools’ callvariants.sh calls variants only from the alignments. So: callvariants.sh in=nxyxx.bam ref=ref.fa yields:…
XRCC1 R194W and R399Q Polymorphisms and Colorectal Cancer Risk in a Northeastern Mexican Population
. 2023 Oct 4:2023:5565646. doi: 10.1155/2023/5565646. eCollection 2023. Affiliations Expand Affiliations 1 Facultad de Medicina e Ingeniería en Sistemas Computacionales de Matamoros, Universidad Autónoma de Tamaulipas, Sendero Nacional km 3, CP 87349, Col. San José, Matamoros, Tamaulipas, Mexico. 2 Centro Universitario del Sur, Universidad de Guadalajara, Av. Enrique Arreola Silva…
Behold, the Human Brain Like Never Seen Before
12 Oct 2023 Understanding the human brain has entered a new era with the birth of a comprehensive cell atlas. Scientists used single-cell RNA sequencing, epigenetic analyses, and spatial mapping to study millions of brain cells from 100 brain regions, distinguishing 3,300 cell types. Researchers compared cell types to one…
How To Find Computer Password Without Changing It Windows 10
In today’s digital age, passwords play a crucial role in keeping our personal and sensitive information secure. However, there may be times when you find yourself needing to access a computer without knowing its password. This could be due to various reasons such as forgotten passwords, inheriting a computer with…
Novel GPR156 variants confirm its role in moderate sensorineural hearing loss
G protein coupled receptors (GPCR) are known to have an important role in several physiological processes crucial for normal functioning of a human body8,9,10. In recent decades researchers have shown that more than 30 GPCR are expressed in cochlea in different mouse models10. The accurate function of this huge number…
Genetic analysis challenges the presence of Ixodes inopinatus in Central Europe: development of a multiplex PCR to distinguish I. inopinatus from I. ricinus | Parasites & Vectors
Estrada-Peña A, de la Fuente J. Host distribution does not limit the range of the tick Ixodes ricinus but impacts the circulation of transmitted pathogens. Front Cell Infect Microbiol. 2017;7:1–10. doi.org/10.3389/fcimb.2017.00405. Article Google Scholar Al-Khafaji AM, Clegg SR, Pinder AC, Luu L, Hansford KM, Seelig F, et al. Multi-locus sequence…
Cuban genome, a particular witness to history
Our time is a specialist in creating absences. Ailton Krenak, Brazilian indigenous leader Most of us have heard or treasure in our personal lineage the story of a great-grandmother or great-great-grandfather who came to Cuba to found, whether voluntarily or involuntarily, a new family history and, also, that of…