Increasingly efficient production of human pluripotent stem cells

Reliable production of high-quality iPS cells enables their increasingly efficient utilization in biomedical applications. Credit: Ras Trokovic, University of Helsinki Researchers at the University of Helsinki have developed a new, faster and more reliable technique for reverting human cells to the stem cell state. Pluripotent stem cells are a key…

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Multi-organoid system to simulate human liver-islet axis in normal and type 2 diabetes

Schematic of hiPSCs derived multi-organoid-on-chip system to model human liver-pancreatic islet axis in vitro. Credit: Tao Tingting Type 2 diabetes (T2DM) is a systematic multi-organ metabolic disease, which is characterized by dynamic interplay among different organs. Pancreatic islet-liver axis is closely associated with normal glucose regulation and homeostasis maintenance. The…

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The website is currently not available

The website you want to visit is currently not available. This may be due to that the website is being developed, that maintenance is underway or that the website is closed due to some other reason. Domain owner, please see your contact address (email) or contact support@loopia.com for more information….

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Bonnie Regalia found her niche selling bird seed, and much more

By Joanne Engelhardt More than 30 years ago, Birder’s Garden owner Bonnie Regalia found her true calling: as a small businesswoman. Not that she knew it then, of course. At that time Birder’s Garden was owned by Rich and Marsha Held who had the San Carlos franchise of a company…

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MultiProcessing on SeqIO biopython

MultiProcessing on SeqIO biopython 0 Hello, I would like to parse a wheat genome (13Gb) quickly, in order to cut each Sequence and count the fragment lengths and store it in a pandas dataframe. Is it recommendable to use multiprocessing on the SeqIO.parse command? Does it save time? Any experiences/recommendations…

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KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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Bug#995356: python-parameterized: autopkgtest regression: AssertionError in tearDownModule

Hi, On Thu, 30 Sep 2021 11:07:17 +0200 Paul Gevers <elb…@debian.org> wrote: With a recent upload of python-parameterized the autopkgtest of python-parameterized fails in testing when that autopkgtest is run with the binary packages of python-parameterized from unstable. It passes when run with only packages from testing. In tabular form:…

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A GPT-2 ChatBot implemented using Pytorch and Huggingface-transformers

A GPT-2 ChatBot implemented using Pytorch and Huggingface-transformers How to use install the required packages pip install -r requirements.txt Download and process the data train the model   you can train the model from a initial state python main.py –mode=”train”   also you can train a model from a specific…

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Image2_Construction and Comprehensive Analysis of a circRNA-miRNA-mRNA Regulatory Network to Reveal the Pathogenesis of Hepatocellular Carcinoma.TIF

Background: Circular RNAs (circRNAs) have been demonstrated to be closely related to the carcinogenesis of human cancer in recent years. However, the molecular mechanism of circRNAs in the pathogenesis of hepatocellular carcinoma (HCC) has not been fully elucidated. We aimed to identify critical circRNAs and explore their potential regulatory network…

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Python scikit-learn: Cannot clone object… as the constructor does not seem to set parameter

Without seeing your code, it’s hard to tell exactly what goes wrong, but you are violating a scikit-learn API convention here. The constructor in an estimator should only set attributes to the values the user passes as arguments. All computation should occur in fit, and if fit needs to store…

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Basilea reports updated interim results for iCCA patients with FGFR2 mutations and

Basel, Switzerland, January 24, 2022 Basilea Pharmaceutica Ltd. (SIX: BSLN), a commercial-stage biopharmaceutical company committed to meeting the needs of patients with cancer and infectious diseases, announced today that updated interim results from cohort 2 of the phase 2 study FIDES-01 (Fibroblast growth factor Inhibition with DErazantinib in Solid tumors)…

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To use rflp analysis to detect a snp. the snp must _______.

To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. cause disease occur in homozygous form occur within a restriction enzyme recognition sequence be present in…

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Install CUDA on NVIDIA Jetson Nano

Hardware Pre-requisite Jetson Nano A 5V 4Ampere Charger 64GB SD card Software Preparing Your Raspberry Pi Flashing Jetson SD Card Image Unzip the SD card image Insert SD card into your system. Bring up Etcher tool and select the target SD card to which you want to flash the image….

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Executive Search Firm – Recruitment Agenciespinpoint one

Our assignments are continuously exciting and relevant in this consistently challenging economy. our story A story that goes back to the 1st of May 1999 – “International Workers’ Day”as the world was nervous about the possible chaos of Y2K, we instead were confident about our business being an entrepreneurial business…

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Efficiently merge two BAM files while retaining reads from only one file in overlapping regions

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions 1 I have a WGS BAM file that is fairly large (>150GB) and a smaller BAM file (<5GB) with reads in a small 10Mbp region. I want to (efficiently) merge the two BAM files while…

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Writing Biopython output into csv

In your second block of code, your variable names talk about dictionaries, but your they are actually lists: journal_dict = [] datep_dict = [] place_dict = [] So, let’s fix that (this will also be useful later when writing to CSV): record_list = [] for record in records: record_dict =…

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CRAN Package Depends on Bioconductor Package Installing error

In R 3.0.2, the following works: At the time of this writing, the value ind can take a vector with values between 1 and 8, and the following meaning: 1: CRAN 2: BioC software 3: BioC annotation 4: BioC experiment 5: BioC extra 6: Omegahat 7: R-Forge 8: rforge.net This…

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Zachary Piper Solutions hiring 100% Remote Senior Bioinformatician in United States

Job DescriptionZachary Piper Solutions is looking for a Senior Bioinformatician supporting the Centers for Disease Control and Prevention (CDC). The ideal candidate would prepare for, prevent, and respond to infectious diseases, including outbreaks, bioterrorism, and other public health emergencies. Responsibilities: Experience with genomic epidemiology, genomic sequencing, identifying pathogen clusters and…

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Does anyone have experience making custom references for 10X Genomics’ cellranger VDJ pipeline?

I am working on getting expressed, paired IGH and IGL (immunoglobin) sequences from data we acquired by designing custom primers for IGH and IGL in horse and then preparing the samples using a 10X kit as we normally do with mouse, human, etc. Sadly, the horse genome has terrible annotations…

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ggplot2 – How to wrap graphs by categories while keeping the same width of bars with ggplot in R?

I am struggling with using facet_grid() and facet wrap() with ggplot(). I would like to be able to wrap the different stacked barcharts for every two categories (of the variable Department here) but at the same time have the same width of bars. The first action can be achieved with…

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r – ggplot two histograms in one plot

You can reference some of the other calculated values from stat functions using a notation that you may have seen before: ..value… I’m not sure the proper name for these or where you can find a list documented, but sometimes these are called “special variables” or “calculated aesthetics”. In this…

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Jupyterhub – nltk – unable to use stopwords – resource stopwords not found ( Python, Nltk )

Problem : ( Scroll to solution ) I am using below code to use stopwords through jupyter notebook. I have hosted jupyter on Linux server and using the notebook. python3 -m nltk.downloader stopwords python3 -m nltk.downloader words python3 -m nltk.downloader punkt python3 >>>from nltk.corpus import stopwords >>>stop_words = set(stopwords.words(“english”)) >>>print(stop_words)…

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An experimental OpenAPI -> Terraform Provider generator that does not yet function

An experimental OpenAPI -> Terraform Provider generator that does not yet function. The goal is to allow developers to incrementally generate and maintain their own simple Terraform Provider using an OpenAPI 3 specification. Other Solutions terraform-provider-openapi A single provider that configures itself at runtime given an OpenAPI specification. This is…

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Python – run indented code through keyboard shortcuts in spyder as in rstudio ( Python, R )

Problem : ( Scroll to solution ) I would like to be able to run an indented block of code in python in the same way I do in R. In particular, if in RStudio I have the following indented block of code: print(seq(from = 1, to = 10, by…

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Imaging Mitochondrial Ca2+ Uptake in Astrocytes and Neurons using Genetically Encoded Ca2+ Indicators (GECIs)

This proctocol aims to provide a method for in vitro and in vivo mitochondrial Ca2+ imaging in astrocytes and neurons. Demonstrating the procedure will be graduate student Zhe Zhang, research specialist Nannan Zhang, professors Illker Ozden and Shinghua Ding. The overall goal of this procedure is to develop cell type…

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Radiosensitizing and cytotoxic effects of nitroimidazoles in CHO cells expressing elevated levels of glutathione-S-transferase

doi.org/10.1016/0360-3016(89)90304-0Get rights and content Abstract A cell line, CHO-Chlr, which has elevated levels of glutathione-S-transferase (GST), is resistant to damage caused by bi-functional nitrogen mustards. This cell line has a similar radiation sensitivity to and value of oxygen enhancement ratio as the wild type cells, CHO-KI, from which the mutant…

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Xenotransplantation: Argentina is about to produce genetically modified animals for human transplants

While the international medical community celebrates the first successful xenotransplantation, in Argentina two research teams from public universities are preparing to produce genetically modified animals so that their organs are suitable for human transplants and the first pigs of this type would be obtained at the end of this year…

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mirbase ftp error

mirbase ftp error 0 When I am running this link “wget mirbase.org/pub/mirbase/21/hairpin.fa.gz” in the terminal the below error is appearing for me. How can I fix it? -2022-01-21 16:35:30– mirbase.org/pub/mirbase/21/hairpin.fa.gz => ‘hairpin.fa.gz’ Resolving mirbase.org (mirbase.org)… 130.88.97.249 Connecting to mirbase.org (mirbase.org)|130.88.97.249|:21… failed: Connection refused. ftp mirbase • 225 views • link…

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log repeats until it times out)

Your message dated Sat, 22 Jan 2022 21:52:05 +0100 with message-id <f98ce279-5828-d2b5-8b7c-88287a3ab…@debian.org> and subject line Re: Bug#997845: bug 997845 has caused the Debian Bug report #997845, regarding growlight: autopkgtest regression: log repeats until it times out to be marked as done. This means that you claim that the problem has…

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Donor-derived cell-free DNA as a composite marker of acute lung allograft dysfunction in clinical care

This article was originally published here J Heart Lung Transplant. 2021 Dec 26:S1053-2498(21)02630-9. doi: 10.1016/j.healun.2021.12.009. Online ahead of print. ABSTRACT BACKGROUND: As a marker of underlying lung allograft injury, donor-derived cell-free DNA (dd-cfDNA) may be used to identify episodes of acute allograft injury in lung transplant recipients. We investigated the…

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Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs

doi: 10.1093/nar/gkac019. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA. 2 Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA. 3 Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA….

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WLQ #5.doc – BIOL/BNFO 541 Wet Lab Quizzes 5 Protocol 3 and 6 3 Agarose gel electrophoresis 6 Cloning 16S rRNA gene PCR fragments into pGEM u00ae-T Easy

BIOL/BNFO 541 Wet Lab Quizzes # 5, Protocol 3 and 6 – March 15, 2019 3. Agarose gel electrophoresis 6. Cloning 16S rRNA gene PCR fragments into pGEM ® -T Easy plasmid vector Deadline: March 14 , 2019, Thursday, midnight sharp! No copying and pasting! Use your own words. Mario…

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Scikit Learn Mean Squared Error

Module: metrics — skimage v0.19.0 docs – scikit-image Posted: (1 days ago) structural_similarity¶ skimage.metrics. structural_similarity (im1, im2, *, win_size = None, gradient = False, data_range = None, channel_axis = None, multichannel = False, gaussian_weights = False, full = False, ** kwargs) [source] ¶ Compute the mean structural similarity index between…

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PostDoc iPSCs for toxicology (m/w/d) – Biberach

OUR COMPANY At Boehringer Ingelheim we develop breakthrough therapies and innovative healthcare solutions in areas of unmet medical need for both humans and animals. As a family owned company, we focus on long-term performance. We believe that, if we have talented and ambitious people who are passionate about innovation, there…

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Loncastuximab tesirine: an effective therapy for relapsed or refractory diffuse large B-cell lymphoma

Background: Diffuse large B-cell lymphoma (DLBCL) is the most common type of Non-Hodgkin’s lymphoma in the United States, with approximately 40% of first-line DLBCL chemoimmunotherapy attempts failing. The FDA approved a new type of antibody-drug conjugate (ADC), Zynlonta (loncastuximab tesirine), once called ADCT-402, on April 23, 2021, for relapsed or…

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[pytorch/torchx] slurm: environment improvements

The current slurm scheduler specifies the working directory via the image field of the Role. This doesn’t match how any of the other schedulers work since local_cwd has been switched to use the current working directory. We should update the slurm scheduler to be more inline with the other schedulers….

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An eQTL variant of ALDH1A2 is associated with Kashin-Beck disease in Chinese population

Introduction: The aims of the study were to investigate the relationship between aldehyde dehydrogenase 1 family member A2 (ALDH1A2) and Kashin-Beck disease (KBD), explore the effects of the rs3204689 polymorphism and methylation status on the expression levels of ALDH1A2, and further clarify the pathogenesis of KBD. Materials and methods: The…

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man subfuse (1): merge Genbank submissions

subfuse(1) merge Genbank submissions SYNOPSIS subfuse [–] [-o filename] [-p path] [-x ext] DESCRIPTION subfuse is a utility to consolidate multiple Genbank submissions into a single batch submission. OPTIONS A summary of options is included below. – Print usage message -o filename Output file (stdout by default) -p path Path to files -x ext Input filename…

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Their DNA Hides a Warning, but They Don’t Want to Know What It Says

“I was like, wait a minute. Where is this information going? How will it be utilized?” she later asked. “I don’t know if there are any implications for life and health insurance for me or my family, but why risk it?” What should happen when researchers, while sequencing a participant’s…

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Senior Biocurator (LIPID MAPS) at Cardiff University

Division of Infection and ImmunitySchool of MedicineCollege of Biomedical and Life Sciences We have an exciting opportunity to join the LIPID MAPS team, as a Biocurator.  You will be based at Cardiff University, and will provide core support for a new curation project, building lipid biochemical pathways in LIPID MAPS (www.lipidmaps.org) and…

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Pair_write with eam/alloy – error – LAMMPS General Discussion

Dear LAMMPS Users, I encountered a problem while trying to use pair_write command with an eam/alloy potential. pair_style hybrid eam/alloy table spline 100000 zbl 1.0 4.0pair_coeff * * eam/alloy Be_Agrawal.eam.alloy Be NULLpair_coeff 1 2 table DBe.potential-table DFT_DBEpair_coeff 2 2 zbl 1.0 1.0pair_write 1 1 100 r 1.0 6.0 table.txt metal…

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[gmx-users] Why gyration radius keep dropping?

Post by ZHANG ChengDear Gromacs,I am running MD at 500 K for my protein.I used this to analyse the gyration radiusecho 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvgI thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a…

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[BioC] problem with GEOquery

Hi to everybody, i have a little problem with GEOquery .i when I’m trying to download the GSE2841 dataset I encounter the gse <- getGEO(“GSE2841”) try with URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz’Error in downloading the.file(myurl, destfile, mode = mode) :impossible to open URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz'&#8221; why???????????? Please help me Best regards Dr Alberto GoldoniMedical Genetics UnitS….

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High school student learning ML with a short-term goal of placing top on Kaggle? : learnmachinelearning

I’m an 11th grade student who’s fairly interested in machine learning and the AI industry. I have coding experience but haven’t learned ML yet. My short term goal is to place high on a Kaggle competition because there aren’t that many tangible goals I can place as a high school…

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Bioinformatician job with EMBL | 1401746299

Are you creative, curious, and ambitious and like to tackle challenging biological data analysis problems? We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). In this…

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Deciphering Protein Structure-Dynamics-Function Relationships in the Post AlphaFold Era

AI techniques have come of age – Google DeepMind’s AlphaFold, and other competitive approaches such as RosettaFold, and the more recent efforts at folding RNA structures using Atomic Rotationally Equivariant Scorer (ARES), have enabled accurate predictions of protein and RNA three-dimensional (3D) structures starting with just their primary sequences….

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Post-doctoral Fellow – Analyst Bioinformatics in Oklahoma City, OK for Oklahoma Medical Research Foundation

Details Posted: 20-Jan-22 Location: Oklahoma City, Oklahoma Type: Full Time Required Education: Doctorate Categories: Biomedical Engineering Years of Experience: Less than 2 Post-doctoral Fellow – Analyst Bioinformatics OverviewOMRF is an independent, not-for-profit biomedical research institute adjacent to the University of Oklahoma Health Sciences Center (OUHSC) campus in Oklahoma City. Oklahoma…

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Guardant Health Staff Site Reliability Engineering / DevOps: Bioinformatics

Covid Vaccination Policy:  Starting January 7, 2022, Guardant Health will require all employees to be fully vaccinated to either (a) establish that they have been fully vaccinated against COVID-19; or (b) request and obtain an approved exemption from Guardant’s COVID-19 U.S. Vaccination Policy as a reasonable accommodation, as consistent with applicable…

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BD unveils high-throughput cell sorter that merges fluorescence with visual imaging

For researchers trying to find a single type of cell among tens of thousands, BD has outlined a new high-speed sorting technology that could help do more than just find the proverbial needle in the haystack, but also categorize each individual strand of hay itself. By combining flow cytometry methods…

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Which method works best for analysing ONE sample of scRNA-seq data?

Which method works best for analysing ONE sample of scRNA-seq data? 1 Hello, I currently have a single-cell RNA-seq (scRNA-seq) data of a single person (sample) and i want to perform DE analysis. However, when I run the DESeq() in the DESeq2 package, it shows an error about only one…

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ggplot2 – Create graphs by group using ggplot in R

I’m relatively new to using ggplot2 in R and have been struggling with this for awhile. I have figured out how to get everything from one data frame on a graph (that is pretty easy…), and how to write a loop function to get each observation (id in the example…

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Fixing abrupt changes/transitions in animated ggplot

I was wanting to make an animated ggplot of daily values for countries over the course of a year. I was able to do that thanks to some helpful questions/answers here. While the code below successfully makes a gif, the changes/transitions when countries move up or down/overtake one another is…

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provider-opentelekomcloud – KMSv1 unexpected state

Terraform v1.1.4 on linux_amd64 provider registry.terraform.io/hashicorp/external v2.2.0 provider registry.terraform.io/hashicorp/local v2.1.0 provider registry.terraform.io/opentelekomcloud/opentelekomcloud v1.27.3 opentelekomcloud_kms_key_v1 main.tf resource “opentelekomcloud_identity_project_v3” “projects” { for_each = local.projects name = “${local.otc_region}_${each.value}” description = “Dedicated project space for ${each.value}” } resource “opentelekomcloud_s3_bucket” “tf_remote_states” { for_each = local.projects bucket = “${each.value}-tfstate-bucket” acl = “private” region = local.otc_region versioning…

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Python – canvas selection – Developer Questions

Hi from krita import * def selectRGB(node, red, green, blue, selectionLevel=255): # get pixels data from node projection # for RGBA/8bit, pixel data format: Blue, Green, Red, Alpha pdata=node.projectionPixelData(node.bounds().left(), node.bounds().top(), node.bounds().width(), node.bounds().height()) bred=red.to_bytes(1, ‘big’) bgreen=green.to_bytes(1, ‘big’) bblue=blue.to_bytes(1, ‘big’) # prepare selection (0=no selection, 255=full selection) selectionPixels=[0]*(node.bounds().width()*node.bounds().height()) offset=0 for index in…

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[Solved] Sanger products using ddGTP Mononucleotide Decanucleotide Trinucleotide 12-nucleotide Tetranucleotide 13-nucleotide Pentanucleotide 14-nucle…

A Sanger product of the sequencing of a template DNA is presented… A Sanger product of the sequencing of a template DNA is presented below. Determine the sequence of template DNA and the mRNA sequence from this template DNA. Briefly explain.  Image transcription text Sanger products using ddGTP Mononucleotide Decanucleotide…

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spring boot – Centralized Swagger/OpenAPI UI for all the different microservices on a single swagger URL i.e accessing all the URLs through one

If all you µservices use the same host, you can create a Spring Boot µservice which acts as a openAPI gateway using spring-doc. (If they are not using the same host, you will have to deal with CORS issues) First, add the following dependencies to your new gateway µservice <dependency>…

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Muv-Luv Alt Shiranui Second Phase3 Yuya Bridges Ki – Muv-Luv Alt Shiranui Second Phase3 Yuya Bridges Ki

More Info: Product Description The result of the XFJ Program, a Japan-America Joint Tactical Surface Fighter Development Program. From Muv-Luv Alternative Total Eclipse, SHIRANUI SECOND PHASE3, piloted by the protagonist Yuya Bridges, finally joins Kotobukiya’s plastic model kit lineup! The Phase 3 version is the final evolution of Shiranui Second,…

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Trimal – Names and nicknames style for Trimal

We have almost all kind of nicknames like Free Fire nicknames, Arena of Valor nicknames (Liên Quân Mobile), Mobile Legends nicknames, PlayerUnknown’s Battlegrounds nicknames, PUBG nicknames, League of Legends: Wild Rift nicknames (Liên Minh Huyền Thoại: Tốc Chiến), League of Legends nicknames (Liên Minh Huyền Thoại), Dota 2 nicknames, Love…

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Localization of small nuclear RNA by EM autoradiography in Chinese Hamster Ovary (CHO) cells

doi.org/10.1016/0014-4827(83)90345-2Get rights and content Abstract The ultrastructural localization of small nuclear RNA (snRNA) was studied by EM autoradiography in Chinese Hamster Ovary (CHO) cells. Conditions were set where most (>85 %) of the nuclear [3H]uridine label consisted of snRNA, the most abundant species being U1, U2 and the nucleolar species…

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River BioMedics Raises Seed Investment to Progress its Cardiovascular Disease Programs

River BioMedics Raises Seed Investment to Progress its Cardiovascular Disease Programs • Eur 1.8 million seed funding to progress its pipeline of cardiovascular disease targets • Company appoints Nicky Cooper as its Chief Executive Officer • Financing round co-led by FIRST Fund, KIKK Capital and Oost NL Enschede, The Netherlands,…

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A cell-based phenotypic library selection and screening approach for the de novo discovery of novel functional chimeric antigen receptors

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

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c-Fos protein shRNA blockade in the central amygdala nucleus interfere with rats emotional reactivity on behavioral and autonomic level

Abstract This report is focusing on a function of the c-Fos protein in an associative, stress-induced memory. The shRNA vector injections were utilised to functionally silence the central amygdala nucleus in adult Wistar rats. Subsequently the operated animals and their control counterparts were screened in a selection of an emotionally-dependent…

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hash – SHA256 digest disagrees in Python vs. mbedTLS (STM32)

Problem: I am trying to compute the SHA256 digests of single blocks (512 bit) on an STM32L552ZE-Q using mbedTLS. Unfortunately, the digest doesn’t agree with that of Python’s SHA256 implementation, even for a single block of all-zeros. Sample output: Python: f5a5fd42d16a20302798ef6ed309979b43003d2320d9f0e8ea9831a92759fb4b mbedTLS, data-type= 1 bit: B20941D6177356919BCDF1F716029D5F53C81932439D59B98F04A5EE0E192A25 mbedTLS, data-type != 1…

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variant – Where should you put you cache for ensembl-vep using conda

I’ve installed vep in conda like so: conda install ensembl-vep=105.0-0 And then I installed the human cache like so: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep –CONVERT But when I try and run vep I get an error: vep –dir_cache /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep -i /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf -o /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated_vep.vcf Am I doing…

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[Bug 1786013] Autopkgtest regression report (linux-meta-oem-5.14/5.14.0.1021.18)

All autopkgtests for the newly accepted linux-meta-oem-5.14 (5.14.0.1021.18) for focal have finished running. The following regressions have been reported in tests triggered by the package: virtualbox-hwe/6.1.26-dfsg-3~ubuntu1.20.04.2 (amd64) virtualbox/6.1.26-dfsg-3~ubuntu1.20.04.2 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

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variant – Error running gatk HaplotypeCaller with allele specific annotations

I’ve got HaplotypeCaller working nicely in standard mode, like so: # Run haplotypcaller gatk –java-options “-Xmx4g” HaplotypeCaller –intervals “$INTERVALS” -R “$REF” -I “$OUT”/results/alignment/${SN}_sorted_marked_recalibrated.bam -O “$OUT”/results/variants/${SN}_g.vcf.gz -ERC GVCF But when I try in allele-specific mode, I get the following error. All I’ve done is add the -G annotations at the end,…

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organizing a Bed file for bedtools getfasta

organizing a Bed file for bedtools getfasta 0 I am trying to use bedtools getfasta on some bed files, but the issue is that the peaks bed file columns are mixed up such that the first column with the chromosome names contains the peak location as well for some of…

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Strange behavior in detection reference code

Solved it by adding a copy of the inital dataset object in the convert_to_coco_api function, which gives the following: def convert_to_coco_api(ds): ds_copy = copy.deepcopy(ds) # Create copy here coco_ds = COCO() # annotation IDs need to start at 1, not 0, see torchvision issue #1530 ann_id = 1 dataset =…

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DE analysis model matrix for paired samples

DE analysis model matrix for paired samples 1 @tkapell-14647 Last seen 2 hours ago Helmholtz Center Munich, Germany Hi, I am analyzing a NanoString dataset where the metadata look as below: The factor of interest is the “group” and both groups are found in each mouse (“mouseID”) (paired samples). I…

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Combining multiple 10x scRNAseq datasets

Hi everyone, Wondering if someone can provide me with some guidance. I have previously sequenced 4 skin cancers using 10X chemistries and I would like to combine them into one dataset. My research question is to look at cancer stem cell populations, so I will need sensitivity. I have done…

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How to get Agglomerative Clustering “Centroid” in python Scikit-learn

I believe you can use Agglomerative Clustering and you can get centroids using NearestCentroid, you just need to make some adjustment in your code, here is what worked for me: from sklearn.neighbors import NearestCentroid y_predict = clusterer.fit_predict(X) #… clf = NearestCentroid() clf.fit(X, y_predict) print(clf.centroids_) The only thing I think was…

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NCBI looking for testers for a new web-only (for now) clustered `nr` database

News:NCBI looking for testers for a new web-only (for now) clustered `nr` database 0 Find details about how to participate by going to this link. Clustered nr is the standard NCBI nr database clustered with each sequence within 90% identity and 90% length to other members of the cluster. Your…

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Pluristyx, panCELLa, and Implant Therapeutics Announce a Strategic Alliance to Manufacture and Distribute Genetically Modified, Clinical-grade Human-induced Pluripotent Stem Cells

SEATTLE–(BUSINESS WIRE)–Pluristyx, Inc., an advanced therapy tools and services biotechnology company, panCELLa, a privately held biotechnology company, and Implant Therapeutics, a developer of genetically engineered stem cells, today announced they have entered into a manufacturing and distribution strategic alliance that offers cell therapy companies streamlined access to the next generation…

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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

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Read bam/cram file with IGV from aws s3

Hi all, We store our alignment files on aws s3. I would like to be able to open them with IGV without needing to download them completely, but I can’t find an optimal solution. If I get a pre-signed url it works but it’s not convenient. I try to follow…

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r – How to parallelize future_pmap() across multiple slurm nodes

I have access to a large computing cluster with many nodes each of which has >16 cores, running Slurm 20.11.3. I want to run a job in parallel using furrr::future_pmap(). I can parallelize across multiple cores on a single node but I have not been able to figure out the…

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Tabix file download error eQTL analysis

I am trying to download a tabix file to perform an analysis on an eQTL dataset, however I have the following error each each file I try to try from the eQTL – catalogue library(ggplot2) library(readr) library(coloc) library(GenomicRanges) library(seqminer) tabix_paths = read.delim(“https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv”, sep = “t”, header = TRUE, stringsAsFactors =…

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Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project

Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project We’re sorry, but GBIF doesn’t work properly without JavaScript enabled. Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. Citation McVeigh R (2013)….

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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Avian mtDNA primers

Avian mtDNA Primers The PDF file below provides details on a complete set of primers for amplifying and sequencing avian mitochondrial DNA. All of the primers have been designed to work with most or all birds and most perform very well in this regard. The document is intended as a…

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Introduction to RNA-seq data analysis – Extended Materials

Introduction to RNA-seq data analysis – Extended Materials | cruk-summer-school-2021 Github repo for 2021 CRUK-CC Bioinformatics Summer School (tinyurl.com/crukss2021) Taught remotely Bioinformatics Training, Craik-Marshall Building, Downing Site, University of Cambridge Supplementary materials These files contain some additional information and exercises not included during the taught course. Obtaining public data Raw…

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(PDF) AntiHunter: searching BLAST output for EST antisense transcripts | Alessandro Guffanti

(PDF) AntiHunter: searching BLAST output for EST antisense transcripts | Alessandro Guffanti – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn more, view our Privacy Policy. ×…

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Samtools flagstat confusing result of a merged bam file

Hi, I am a bioinformatics student and I am struggling with an issue, I had paired-end fastq files for one sample with some low-quality bases at the end and adapter contamination, so I went and I trimmed my reads with trimmomatic, it gave me 4 files that I used for…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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genepattern/Salmon.Indexer: Salmon indexer wrapper module for GenePattern.

GitHub – genepattern/Salmon.Indexer: Salmon indexer wrapper module for GenePattern. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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Correlation Distance Metric and Sum of Squared Errors

The sum of squared error is more easily implemented than the correlation distance metric, so I would advise you to use biopython together with the following helper function. It should compute the sum of squared errors for you from the data (assumed to be a numpy array) and biopython’s clusterid…

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LargeBuffer (BioJava-1.4 API)

LargeBuffer (BioJava-1.4 API) org.biojava.utils.io Class LargeBuffer java.lang.Object org.biojava.utils.io.LargeBuffer public class LargeBuffer extends Object Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs. Author: Matthews Pocock   Method Summary  void force()              byte get()              byte get(long pos)              char getChar()              char getChar(long pos)              double getDouble()            …

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[BioC] removal of affymetrix control probes from ExpressionSet

Hi Brian, library(genefilter)filtered<-featureFilter(eset, require.entrez=F, remove.dupEntrez=F) Cheers,Yuan Hi,What’s the easiest way, given an ExpressionSet object, to remove just thecontrol probes (i.e. those that start with AFFX-….)?Thanks!Brian.[[alternative HTML version deleted]]_______________________________________________Bioconductor mailing listBioconductor at r-project.orgstat.ethz.ch/mailman/listinfo/bioconductornews.gmane.org/gmane.science.biology.informatics.conductor Read more here: Source link

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normalization for unsupervised analysis by DESeq2

normalization for unsupervised analysis by DESeq2 1 Hi friends I want to use DESeq2 to normalize the raw count data to do PCA. I dont have colData. What code should I use? because in the DESeq2 workflow we need colData and design. thanks RNA-Seq • 216 views • link updated…

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Senior Bioinformatics Scientist, Assay Development Analytics Job in California

About KariusKarius is a venture-backed life science startup focused on transforming the way infectious diseases are diagnosed. Combining Next-Generation Sequencing and proprietary data analysis, we can identify over 1,000 pathogens from a single blood sample with typical turnaround time in one business day. By unlocking the information present in…

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Postdoc bad for industry? : bioinformatics

I have a postdoc offer from a national lab but my goal is to eventually go to industry (software and AI research in the molecular bio/drug discovery area). The reason I like this postdoc is because my role is developing open-source AI software, with a big focus on accelerators like…

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Are you looking for a job? These are the six most requested items in 2022

1.Fintech With sustained growth, driven by a digital finance and payment market in the midst of a revolution, fintech companies are showing their full potential for development, driving more and more employment in the professional segment. In this context, fintech companies continue to open more and more searches since many…

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Editas (EDIT) Focuses on Developing Gene-Editing Eye Drug

This story originally appeared on Zacks Editas Medicine, Inc. EDIT has made rapid progress in the development of its lead pipeline candidate, EDIT-101, which employs CRISPR gene editing, to treat Leber congenital amaurosis type 10 (LCA10) — a rare genetic illness that causes blindness. – Zacks The company is evaluating…

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Distinguish the grafts in bulk RNA-seq

Distinguish the grafts in bulk RNA-seq 0 I have bulk RNA-seq data for a tissue and tissue-graft mixture. Is there a way to eliminate the tissue data from the tissue-graft mixture and only get the graft sequencing data? RNA-seq • 24 views • link updated 1 hour ago by seidel…

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KEGG REACTION: R00226

Entry R00226                      Reaction                                Name pyruvate:pyruvate acetaldehydetransferase (decarboxylating);(S)-2-acetolactate pyruvate-lyase (carboxylating) Definition (S)-2-Acetolactate + CO2 <=> 2 Pyruvate Equation Comment Reaction class Enzyme Pathway rn00290   Valine, leucine and isoleucine biosynthesis rn00660   C5-Branched dibasic acid metabolism rn00770   Pantothenate and CoA biosynthesis rn01110   Biosynthesis of secondary metabolites rn01210   2-Oxocarboxylic acid metabolism rn01230   Biosynthesis of amino…

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Plotting date intervals in ggplot2

I have a dataset which has a bunch of date intervals (i.e. POSIXct format start dates and end dates). In the example provided, let’s say it’s each period is associated to when someone was in school or out of school. I’m interested in plotting the data in ggplot2, each row…

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Writing ggplot custom geometry function

stat_accum <- function(mapping = NULL, data = NULL, geom = “point”, position = “stack”, …, show.legend = NA, inherit.aes = TRUE) { layer( data = data, mapping = mapping, stat = StatAccum, geom = geom, position = position, show.legend = show.legend, inherit.aes = inherit.aes, params = list( na.rm = na.rm,…

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NuProbe Technology Showcases Quantitative PCR for

Houston, January 18, 2022 (GLOBE NEWSWIRE) – NuProbe, a genomics and molecular diagnostics company that develops ultra-sensitive tests for precision cancer research, today released research demonstrating new technology to qualitatively and quantitatively detect multiple low-grade variants frequency in a quantitative PCR (qPCR reaction). The new allele-specific BDA technology (As-BDA) uses…

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MySQL always no result – Discussion

So I’ve been trying to create a custom system (kinda lika a garage system, but different) for my server.As I got to the part where I display the player all vehicles he ownes I need to create a server callback where the script gets all vehicles from the database using…

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