Tag: PASS

A high-throughput multispectral imaging system for museum specimens

The two-dimensional nature of many pinned Lepidoptera specimens allows us to omit some technical considerations, such as the variable incident angles that need to be carefully considered when imaging 3D objects, and our multi-spectral imaging rig with its custom designed platform can image both the dorsal and ventral sides of…

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Backpropagation Network using Python

Backpropagation neural network is used to improve the accuracy of neural network and make them capable of self-learning. Backpropagation means “backward propagation of errors”. Here error is spread into the reverse direction in order to achieve better performance. Backpropagation is an algorithm for supervised learning of artificial neural networks that…

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Can you pass on COVID-19 if you’re testing negative?

Yes, it is possible to still spread COVID-19 if you test negative but have cold-like symptoms. This is true if you just started having symptoms, as well as if you’re testing negative after a COVID-19 infection. Rapid COVID-19 tests are quite good at telling if someone is infected and can…

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Scientific Manager – Immunology (Nanostring, Exome, RNA, CHIP) job with University of Texas MD Anderson Cancer Center

The Immunology department at MD Anderson Cancer Center seeks to determine the fundamental cellular and molecular mechanisms of a wide range of processes by which the body recognizes and eliminates pathogens and use these findings to unleash the patient’s own immune system against previously treatment-resistant cancers. Treating the immune system…

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No module named ‘upstream_ontologist.tests’ (and more)

Source: lintian-brush Version: 0.134 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of lintian-brush the autopkgtest of lintian-brush fails in testing when that autopkgtest is run with the binary packages of lintian-brush from unstable. It passes when run with only packages from testing. In tabular form:…

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logits to softmax pytorch

A tag already exists with the provided branch name. Join the PyTorch developer community to contribute, learn, and get your questions answered. Space – falling faster than light? We are converting the layers using ReLu and other neural networks. Learn more, including about available controls: Cookies Policy. In addition, the…

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Action is not authorized with current scopes; requires any of [read:servers] – JupyterHub

Hi all,I come from here.As it seems the error is coming from an strange behaviour with Traefik, I have decided to use nginx as proxy.However after configuring it, after log-in the server is stuck in “Your server is starting up” and the progress bar is not moving. If I reload,…

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Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

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17-Year-Old Indian American Student Becomes First To Sequence Angelfish DNA

Indeever Madireddy is an avid fish-keeper and biologist. Indeever Madireddy, an Indian American student studying at BASIS Independent Silicon Valley, a private school at the Silicon Valley has become the first person to sequence the genome of freshwater angelfish. He did the sequencing after his pet fish died in March…

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Samtools Convert Sam To Bam With Code Examples

Samtools Convert Sam To Bam With Code Examples In this session, we’ll try our hand at solving the Samtools Convert Sam To Bam puzzle by using the computer language. The code that follows serves to illustrate this point. # Basic syntax: samtools view -S -b sam_file.sam > bam_file.bam # Where:…

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pytorch transforms resize

Example 1 torchvision.transforms.functional.resize(img: Tensor, size: List[int], interpolation: InterpolationMode = InterpolationMode.BILINEAR, max_size: Optional[int] = None, antialias: Optional[bool] = None) Tensor [source] Resize the input image to the given size. If the image is torch Tensor, it is expected to have [, H, W] shape, where . In order to script the…

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advantages of electroporation

Therapeutic mRNAs can be stabilized by the incorporation of modified nucleosides, synthetic capping, and the addition of lengthy poly-A tails, and can be enhanced with codon optimization (1113). Maintains viability . Plant tissue culture is a collection of techniques used to maintain or grow plant cells, tissues or organs under…

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What sequencing/alignment artifact is this?

What sequencing/alignment artifact is this? 0 I’m calling mitochondria variants with mutect2 and one variant looks like an artifact but I don’t understand what could be the cause. It looks like from IGV (picture below) that this variant is always at the same position on forward and backward reads. Also…

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MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network | BMC Bioinformatics

Problem description Limited by time and cost, exploring the correlations between circRNAs and human diseases based on biological experiments has encountered many difficulties and bottlenecks. Instead of traditional experiments, computational methods are proved to be an efficient and accurate way to discover the potential connections between circRNAs and diseases. Data…

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Report Exposes Rot In Middle East Studies Centers, Connection to CRT

Neetu Arnold, Senior Research Associate of the National Association of Scholars (NAS) has done what amounts to an expose of the politicization of campus Middle East studies centers. What began as – let’s say, a coincidence of timing between generous Arab donations to university study centers offering a pro-Arab, anti-Israel…

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NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) AND Cornelia de Lange syndrome 3 – ClinVar

NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) AND Cornelia de Lange syndrome 3 Based on: 1 submission [Details] Record status: current Accession: RCV000760292.1 Allele description [Variation Report for NM_005445.4(SMC3):c.181C>T (p.Arg61Trp)] NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) Gene: SMC3:structural maintenance of chromosomes 3 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 10q25.2 Genomic location: Preferred name:…

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Bioinformatics Analyst job in Lexington, Kentucky at University of Kentucky

Posting Details Posting Details Job Title Bioinformatics Analyst Requisition Number RE35885 Working Title Department Name 7H025:CANCER CENTER-CORE SUPPORT Work Location Lexington, KY Grade Level 46 Salary Range $50,981-84,115/year Type of Position Staff Position Time Status Full-Time Required Education MS Click here for more information about equivalencies: www.uky.edu/hr/employment/working-uk/equivalencies Required Related Experience…

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As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/man_0112a.html

NAME SYNOPSIS DESCRIPTION EXAMPLES BASIC OPTIONS SITE FILTERING OPTIONS INDIVIDUAL FILTERING OPTIONS GENOTYPE FILTERING OPTIONS OUTPUT OPTIONS COMPARISON OPTIONS AUTHOR NAME VCFtools v0.1.12a − Utilities for the variant call format (VCF) and binary variant call format (BCF) SYNOPSIS vcftools [ –vcf FILE | –gzvcf FILE | –bcf FILE]…

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Multiplex Chemical Imaging Based on Broadband Stimulated Raman Scattering Microscopy

We present a protocol to acquire chemical images with broadband stimulated Raman scattering (SRS) microscopy. Based on an SRS microscope that operates with differential multichannel-lock-in detection, the protocol describes the sample preparation, adjustment of the SRS apparatus, and chemometrics to disentangle different constituents of chemically heterogeneous samples. Our protocol describes…

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Language Modeling with LSTMs in PyTorch | by Essam Wisam | Sep, 2022

“Learning how to protect their affections at the genre, an assertive case of its own,” said the model. In the last three stories we discussed a lot about RNNs and LSTMs from a theoretical perspective. In this story, we will bridge the gap to practice by implementing an English language…

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Special Issue : Recent Advances in Chemical Biology to Study and Target ncRNAs

Dear Colleagues, In recent decades, ncRNAs have been shown to play a critical role in a myriad of cellular processes, impacting normal gene expression as well as disease progression, making them an attractive target for drug discovery. Moreover, their complex impacts on molecular biology still require revealing and studying. Recent…

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NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) AND Hereditary cancer-predisposing syndrome – ClinVar

NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) AND Hereditary cancer-predisposing syndrome Based on: 1 submission [Details] Record status: current Accession: RCV001012497.1 Allele description [Variation Report for NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr)] NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) Gene: SMAD4:SMAD family member 4 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 18q21.2 Genomic location: Preferred name: NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) HGVS:…

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Solved Fredrick Wilson and his colleagues studied members of

Transcribed image text: Fredrick Wilson and his colleagues studied members of a large family who had low levels of magnesium in their blood (see the pedigree). They argued that this disorder of magnesium (and associated high blood pressure and high cholesterol) is caused by a mutation in mtDNA (F. H….

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GATK vs DeepVariant : bioinformatics

Hi everyone, I am currently working on a medium-sized WES cohort study and wanted to know what the bioinformatics community would regard a cutting-edge workflow. As the big labs usually utilize GATK I also started with that. The results for SNPs are ok, but manual inspection (IGV) still uncovers a…

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CRISPR – INSIGHTSIAS

GS Paper  3 Syllabus: Biotechnology   Source: Indian Express  Direction: Biotechnology is one of the favourites for UPSC mains as well as prelims. CRISPR has reached a decade of development this year. Those giving mains this time, plz don’t ignore this topic.  Context: Over the last 3 years, gene-editing technology…

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New Pre-Print Study Implies Airborne COVID-19 Antibodies Post-Vaccination

Since the rollout of mRNA COVID-19 vaccines, many researchers have speculated on the possibility of transmission of vaccine particles from the vaccinated to the unvaccinated, more commonly known as “vaccine shedding.” Though these speculations are routinely fact-checked, anecdotal stories of unvaccinated people who become infected with COVID-19 or have experienced…

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Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform

Reviewer #1 (Public Review): In this manuscript, Siepe et al. developed a high-throughput screen designed to identify novel protein-protein interactions in the extracellular human proteome. Their CRISPRa-based method induced the expression of transmembrane receptors such that they could be screened for binding to proteins of interest. Major strengths of this…

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Optrode Array for Simultaneous Optogenetic Modulation and Electrical Neural Recording

Here, we present the fabrication method of an optrode system with optical fibers for light delivery and an electrode array for neural recording. In vivo experiments with transgenic mice expressing channelrhodopsin-2 show the feasibility of the system for simultaneous optogenetic stimulation and electrophysiological recording. This protocol includes fabricating on optrode…

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Introduction to HybridNets using PyTorch

In deep learning and computer vision, models tackle a specific task. For example, we can find models for image classification, object detection, and image segmentation also. But there are very few models out there which perform end-to-end vision perception on both, object detection and semantic segmentation. But one of the…

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BBmap bbduk.sh for filtering reads

I’m looking to filter reads that contain a stretch of A’s, I found these posts looking for polyA tails, meaning this should work all the same (Identify RNA-seq reads containing polyA sequence, Identifying RNA-seq reads containing polyA stretch). However, I cannot get it to work. Given just these two reads,…

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mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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5 Smart Ways to Save Money on Your Pets & More Latest News Here

Money may not be able to buy you happiness, but it can buy treats, toys and training for your furry four-legged friend — and that’s basically the same thing. Though pet ownership has always been a financial commitment, it’s especially true today. Average annual costs now range between $1,270 and…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in WORLDWIDE

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. This opportunity is…

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Bug#1016498: rope: autopkgtest regression: No module named ‘pkg_resources’

Source: rope Version: 1.2.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of rope the autopkgtest of rope fails in testing when that autopkgtest is run with the binary packages of rope from unstable. It passes when run with only packages from testing. In tabular form:…

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Challenges facing AI in science and engineering

Join executives from July 26-28 for Transform’s AI & Edge Week. Hear from top leaders discuss topics surrounding AL/ML technology, conversational AI, IVA, NLP, Edge, and more. Reserve your free pass now! One exciting possibility offered by artificial intelligence (AI) is its potential to crack some of the most difficult…

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Researchers Suspect New Variants of Rapidly-Progressing Brain Degenerating Diseases from COVID-19 Vaccines

Things have not been the same since June 2021 for 53-year-old Douglas Howey from Colorado. Around a year after he received the second dose of the Moderna COVID-19 vaccine, the 6 foot 4 and a half inch paraplegic man who once weighed 262 pounds lost over 100 pounds after the…

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What You Need to Know to Become a Medical Scribe

Discover how and why to become a medical scribe.  There is a growing demand for medical scribes, and for good reason. They help with the efficiency and accuracy of data and records of patients.  Following the strict implementation of electronic health record (EHR) systems for recording patients’ medical data, clinics,…

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Competent Cells Market Top Companies and Industry Growth Insights

According to a new report published by Allied Market Research, titled, “Competent Cells Market: Global Opportunity Analysis and Industry Forecast, 2021-2030” Bacterial cells that can take up the foreign DNA from the surroundings by a process called transformation are known as competent cells. These cells can be made competent by…

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

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autopkgtest needs update for new version of python-decorator)

Hi, I’d like to point out to this serious bug. Steffen, would you mind koordinating (not doing alone) an upgrade of the qiime infrastructure to make sure everything will go smoothly? Kind regards Andreas. Am Thu, Jun 30, 2022 at 11:30:21AM +0200 schrieb Paul Gevers: > Source: qiime > Version:…

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ARCH= -gencode arch=compute for NX: – Jetson Xavier NX

hi,i am working on jetson Xavier NX box,i updated to jetpack 5.0.1 and deepstream6.1 right now.before i setup ARCH= -gencode arch=compute 72 for NX to train some models.but i cmake another file yesterday it detected arch-gencode 75!so i am confuse right now, should i setup 72 or 75 for jetson…

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Robotic Left Hepatectomy using Indocyanine Green Fluorescence Imaging for an Intrahepatic Complex Biliary Cyst

Robotic liver surgery has gained more acceptance as a feasible, safe, and effective procedure for the treatment of both benign and malignant indications. However, robotic left hepatectomy is still technically demanding. We describe our surgical technique of a robotic left hepatectomy using indocyanine green fluorescence imaging for a large biliary…

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Left and right DataArray objects are not close

Source: python-xarray Version: 2022.06.0~rc1-1 Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of python-xarray the autopkgtest of python-xarray fails in testing when that autopkgtest is run with the binary packages of python-xarray from unstable. It passes when run with only packages from testing. In tabular form: …

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Ubuntu Manpage: Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. SYNOPSIS use Bio::Map::OrderedPosition; # the first marker in the sequence my $position = Bio::Map::OrderedPosition->new(-order => 1, -positions…

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Issue with streamlit as dependency when deploying my package to Bioconda repository – Using Streamlit

Hello,I am opening an issue here for a problem that I don’t think you guys can solve, but you never know. I recently developped a Python tool, and I need to get it onto the Bioconda repository . To do this, I have created a recipe that I must know…

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autopkgtest regression with openssl 3

I raised the issue to the upstream developer, and he is working on it: github.com/grke/burp/issues/904 He is very responsive and gentle. On Tue, 24 May 2022 20:53:39 +0200 Sebastian Ramacher <sramac…@debian.org> wrote: > Source: burp > Version: 2.4.0-3 > Severity: serious > Tags: sid bookworm > > burp’s autopkgtest fail…

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python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

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Five basic functions dealing with tensors in pytorch

Every beginner of deep learning should know these five basic functions of pytoch. It is one of the most sought after skills for recruiters to build neural networks in an accurate and effective way. Pytorch is a python library mainly used for deep learning. One of the most basic and…

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React Query Codegen from OpenAPI

Rapini is a new tool that can generate custom React Query hooks using OpenAPI (Swagger) files. The Command Line Interface (CLI) tool will take a path to an Open API file and generate a package that includes react hooks, typescript types and axios http requests – and this package is…

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PyMC3 Normal with variance per column

One can pass an argument for the shape parameter to achieve this. To demonstrate this, let’s make some fake data to pass as observed, where we use fixed values for epsilon that we can compare against the inferred ones. import numpy as np import pymc3 as pm import arviz as…

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clustalw and muscle in Biopython

First, try installing Biopython 1.63 from here, it may solve some of your problems. Second, make sure you’re using the latest Python from python.org – you might want to run the installer again just to ensure that none of your files are corrupted, if you’re still getting the same error…

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Mulugeta Metaferia – Academia.edu

Mulugeta Metaferia – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our…

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Special Issue : Methods and Tools in RNA Biology

A special issue of Non-Coding RNA (ISSN 2311-553X). Deadline for manuscript submissions: 30 November 2022 | Viewed by 9 Special Issue Editors Dr. Mirolyuba Ilieva E-Mail Website Guest Editor Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, DenmarkInterests: non-coding RNAs; stem cell biology; neuroscience Special…

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Blackrock Clinic launches new device to help combat AF

Electroporation systems being used to tackle a condition which one in four over-55s will develop THE Blackrock Clinic recently started its new program of electroporation for the treatment of patients with atrial fibrillation. Conventional catheter ablation for the treatment of cardiac arrhythmias uses tissue heating (radiofrequency current) to cauterize the…

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Error in BAFFromGVCFs – GenotypeGVCFs

Bug Report Affected module(s) or script(s) Module00c/BAFFromGVCFs/GenotypeGVCFs Affected version(s) Description I’m running GATKSVPipelineBatch and I got the following error in the GenotypeGVCFs task: A USER ERROR has occurred: Input /tmp/scratch/bean-resources/broad-references/v0/Homo_sapiens_assembly38.dbsnp138.vcf must support random access to enable queries by interval. If it’s a file, please index it using the bundled tool…

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Environmental Factor – May 2022: Scientific moonshot: Now is the time to sequence RNA, expert says

Rick Woychik, Ph.D., directs NIEHS and the National Toxicology Program. (Image courtesy of NIEHS) Almost two decades have passed since the first sequence of a complete set of DNA was released as part of the Human Genome Project. That initiative expanded understanding of certain cancers, boosted the effectiveness of some…

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Missing data per site

Hi, I want to calculate statistics of missing data per each site in my vcf file. Using vcftools –missing-site gives wrong stats for several sites. Is there is any other way to calculate it? Thank you! I have 36 samples and here is an example of the vcftools –missing-site output…

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AIM brings innovations from labs to hospitals and masses

Human body like the Space is an endless frontier made even more complex by the irreversibility of life by the arrow of time. Similar to the mystery of origin of the Universe some problems in the human body are so complex, for example, the problem of qualia or the Hard…

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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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Microsoft Store Web

Skip to main content Microsoft Windows Apps Software Microsoft 365 Office Windows Software for Mac Business Software Software support Games & Entertainment Xbox consoles Xbox games Xbox Game Pass Ultimate Xbox Live Gold PC games Movies & TV All Microsoft Software Software Windows Apps OneDrive Outlook Skype OneNote Teams…

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Reproduce incorrect goa generation of MapOf in OpenAPI body

goa version 3.7.2 Design The field name anyobject with Attribute MapOf(String, Any) should describe a map of string to any unknown value. For HTTP requests, the field anyobject can be sent like the following (i.e. any json object): { “anyobject”: { “testkey”: 10, “test1”: “testval”, “myarr”: [ { “nestedk”: {…

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Stacey Dash Bio, Age, Height, Career , Family, Salary, And Net Worth

Stacey Dash Biography Stacey Dash is a native American actress and former talk show host. In the 1995 feature picture clueless and its television series of the same name, she portrayed Dionne Marie Davenport. She appeared on television in the NBC 1982 drama pilot Farrell: For the people, that got…

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Limit Fragment Duration Polymorphisms (RFLP) Style of DNA Profiling

Limit Fragment Duration Polymorphisms (RFLP) Style of DNA Profiling Conceptual The amazing strength regarding DNA technical as the a recognition product got lead a tremendous change in crimnal fairness . DNA studies legs is an information capital into forensic DNA typing neighborhood having informative data on popular quick tandem repeat…

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Bioinformatics Specialist (Pathology and Laboratory Medicine) at University of Pennsylvania in Philadelphia, Pennsylvania

Job Description: Bioinformatics Specialist (Pathology and Laboratory Medicine) University Overview The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey….

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Kaggle Machine Learning

In this article, we’ll learn step by step an entire process of machine learning to solve a challenge in Kaggle Competition and make a submission. We’ll explore through Kaggle Competition joining, Data Exploration, Feature Engineering, Model Training, Testing, Scoring, and Evaluation. Then, we’ll go ahead and submit our result to…

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No rule to make target ‘/usr/lib/x86_64-linux-gnu/libpython3.10.so’

Source: opm-grid Version: 2021.10-3 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of opm-grid the autopkgtest of opm-grid fails in testing when that autopkgtest is run with the binary packages of opm-grid from unstable. It passes when run with only packages from testing. In tabular form:…

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python – Creating a phylogenetic tree with domain annotations using BioPython

You could use ETE3 to implement this as well – it can load the tree as a newick, and then you can set it up with the motifs – from how I understand the documentation you’ll have to have a list of lists for each organism, like so: motifs =…

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Issues with searching Swissprot #25

Eddykay310 Hi @cruizperez Please help me understand the problem here and how I can fix it. I have successfully generated my DBs but I get this error during analysis. The .dmnd files do not exist in the folders as the error says but I don’t know how I can generate…

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filtering host and gut material #340

Pdawyndt Pierre Rouzé yesterday hinted on a possible application of the Unipept Shotgun Metagenomics/Metaproteomics Analysis Pipeline. They are sequencing a marine organism (forgot about the name), but after DNA extraction and sequencing, they end up both with DNA reads and transcript data from the marine organism they want to sequence…

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Cardior Appoints Dr. Russell Greig as Independent Chairman of the Board

HANOVER, Germany–(BUSINESS WIRE)–Cardior Pharmaceuticals, a clinical-stage biotech company developing non-coding RNA (ncRNA)-based therapeutics for patients with cardiac diseases, today announced the appointment of Dr. Russell Greig, as independent Chairman of its Board of Directors. Dr. Greig brings more than 35 years of experience in the pharmaceutical industry from GlaxoSmithKline, with…

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Python scikit learn pipelines (no transformation on features)

Yes, you can simply do pipe = Pipeline(steps=[(‘clf’, RandomForestClassifier())]) Also, if you had some custom base transformation you almost always wanted, and it also had certain hyperparameters or added functionality you could also do something like (somewhat lame example, but just for ideas..) from sklearn.base import TransformerMixin class Transform(TransformerMixin): def…

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Establishment of a Mouse Severe Acute Pancreatitis Model using Retrograde Injection of Sodium Taurocholate into the Biliopancreatic Duct

A mouse model of severe acute pancreatitis is described herein. The procedure presented here is very rapid, simple, and accessible, thereby potentially allowing the study of the molecular mechanisms and different therapeutic interventions in acute pancreatitis in a convenient way. The overall goal of this video is to establish a…

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Solved Question 14 1 pts Hirschsprung disease (aka

Transcribed image text: Question 14 1 pts Hirschsprung disease (aka congenital aganglionic megacolon) stems from a failure of enteric nervous system (ENS) innervation of the distal colon resulting in the inability to pass stool. Scientists studying this disease are interested in modeling the ENS in culture beginning with human iPSCs….

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dx: error: unrecognized arguments: running swiss army knife plink2

Hi, I was trying to run regenie workflow in ukb rap (part E). github.com/dnanexus/UKB_RAP/blob/main/GWAS/regenie_workflow/partE-step2-qc-filter.sh All the previous steps ran perfectly without any error. But in this step partE-step2-qc-filter.sh I am getting dx: error: unrecognized arguments: –bfile ukb23155_c22_b0_v1 –no-pheno –keep natd_wes_200k.phe –autosome –maf 0.01 –mac 20 –geno 0.1 –hwe 1e-15 –mind…

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What is genetic engineering and how can it benefit healthcare?

Have you heard of purple tomatoes? Or golden rice? If you haven’t, you might be surprised to know that these have actually been created by scientists via genetic engineering. These are genetically modified foods, with purple tomatoes containing 10 times more antioxidants than a normal red tomato. On the other…

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golang-github-albenik-go-serial: autopkgtest regression on ppc64el: undefined: unix.TCGETS2

Source: golang-github-albenik-go-serial Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of golang-github-albenik-go-serial the autopkgtest of golang-github-albenik-go-serial fails in testing when that autopkgtest is run with the binary packages of golang-github-albenik-go-serial from unstable. It passes when run with only packages from testing. In tabular form:…

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[Kernel-packages] [Bug 1966093] Autopkgtest regression report (nvidia-graphics-drivers-390/390.147-0ubuntu0.18.04.1)

All autopkgtests for the newly accepted nvidia-graphics-drivers-390 (390.147-0ubuntu0.18.04.1) for bionic have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-390/390.147-0ubuntu0.18.04.1 (i386) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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#1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’

#1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’ – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Joel Rosdahl <joel@debian.org>:Bug#1007732; Package src:ccache. (Tue, 15 Mar 2022 20:27:05 GMT) (full text, mbox, link). Acknowledgement sent to Paul Gevers <elbrus@debian.org>:New Bug report received…

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python – using scikit-learn preprocesser to select subset of rows in pandas dataframe

You can use a FunctionTransformer to do that. To a FunctionTransformer, you can pass any Callable that exposes the same interface as standard scikitlearn transform calls have. In code import pandas as pd from sklearn.preprocessing import FunctionTransformer class RowSelector: def __init__(self, rows:list[int]): self._rows = rows def __call__(self, X:pd.DataFrame, y=None) ->…

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python – Pytorch: Which class weights I need to pass to BCELoss

I’m trying to build a Resnet model with Sigmoid with BCELoss lose. Since my data is imbalance, I guess I need to use “class weights” as an argument for the “BCELoss“. But which weight I should pass, is it for the positive (with 1) or negative (with 0). Of course,…

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bedtools -u not giving unique files

bedtools -u not giving unique files 1 The following are the steps Im following: First step to extract sample using bed file is this (here the bedfile is input bedfile converted to Hg38): tabix -h -R Hg19_to_Hg38_sorted.bed.gz gnomad.genomes.v{g_version}.hgdp_tgp.chr{chr}.vcf.bgz | perl {vcftools} -c {sample_name} > {sample_name}_out.vcf’ output({sample_name}_out.vcf’) chr2 113982416 rs56177103 TATAAAATAAAATAAA…

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#1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error

#1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>:Bug#1007013; Package src:freecad. (Thu, 10 Mar 2022 14:21:07 GMT) (full text, mbox, link). Acknowledgement sent to Paul Gevers…

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Function plot in ggplot incorrectly displayed as constant line-Tech Notes

Technical otaku 2022-03-08 I want to plot a high degree polynomial function with given coefficients.I created this functionf_erzeuger() is for writing a polynomial functionf to be able to use ggplot2 and stat_function(fun=f).coef is the coefficient vector of the polynomial function. f_erzeuger <- function(coef) { f <- function(x) { x_vec <-…

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AlphaFold, GPT-3 and How to Augment Intelligence with AI

This is the first post in a two-part series. Read Part 2 here. Around the same time that Alan Turing was shaping his theories of machine intelligence in Manchester, another future giant of the computing world, Douglas Engelbart, was developing an alternative computing paradigm over 5,000 miles away in…

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A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

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CORS issues behind nginx ingress after updating to JupyterHub 2.1.1 – JupyterHub

Hi there, I noticed multiple issues after upgrading to JupyterHub 2.1.1 from 2.0.0. I stopped seeing spawn progress when starting the singleuser server. Logs: [I 2022-03-04 20:57:47.436 JupyterHub log:189] 302 GET /hub/spawn -> /hub/spawn-pending/konstantin.taletskiy@labshare.org (konstantin.taletskiy@labshare.org@192.168.15.108) 1006.02ms [I 2022-03-04 20:57:47.524 JupyterHub pages:405] konstantin.taletskiy@labshare.org is pending spawn [I 2022-03-04 20:57:47.528 JupyterHub log:189]…

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Demystifying RNAi and creating experimental myths

Transfection with siRNA is unstable, and symptoms disappear after a few passages of cells, so protein should be extracted and analyzed immediately after a few days (1-3) of transfection. The shRNA in the plasmid is used for transfection. If the plasmid contains antibiotic sites, it can be screened to obtain…

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Bug#1006850: python-munch: autopkgtest regression: No module named ‘pkg_resources’

Source: python-munch Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of python-munch the autopkgtest of python-munch fails in testing when that autopkgtest is run with the binary packages of python-munch from unstable. It passes when run with only packages from testing. In tabular form:…

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Mechanisms involved in the transmission of genetic diseases from mother to child

Mitochondria are the organelles that produce most of the chemical energy needed by the cell. Mitochondrial DNA (mtDNA) contains 16,569 nucleotides that can be mutated. Some of these mutations can lead to the development of mitochondrial diseases. While nuclear DNA (the well-known double helix, which encodes most of the genome)…

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LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Published: 4 March 2022| Version 1 | DOI: 10.17632/2289cnrdtz.1 Contributors: Description The first version of this code (Mackay et al., 2013) [10] implemented long-range hydrodynamic interactions into the open-source molecular dynamics package LAMMPS. This was done through the creation of a fix, lb/fluid which was subsequently included as a user-package…

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Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Download Galaxy Genome [Space Sim] Mod Varies with device for android apk & iphone ios 4.4 and up Galaxy Genome is an open world sci-fi space simulator. You can upgrade your ship and customize each component as you hunt, explore, fight, mine, smuggle, trade and survive in a brutal galaxy….

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in PEORIA, IL

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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The Information Age needs a new data storage powerhouse. With an expanded molecular alphabet and a 21st century twist, DNA may just fit the bill. — ScienceDaily

Imagine Bach’s “Cello Suite No. 1” played on a strand of DNA. This scenario is not as impossible as it seems. Too small to withstand a rhythmic strum or sliding bowstring, DNA is a powerhouse for storing audio files and all kinds of other media. “DNA is nature’s original data…

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Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

This protocol presents a complete experimental workflow for studying RNA-protein interactions using optical tweezers. Several possible experimental setups are outlined including the combination of optical tweezers with confocal microscopy. The overall goal of the following method article is to demonstrate a protocol useful to study RNA interactions with proteins or…

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Linear Transformation to incoming data in Pytorch

We could apply linear transformation to the incoming data using the torch.nn.Linear() module in PyTorch. This module is designed to create a Linear Layer in the neural networks. A linear layer computes the linear transformation as below-   Where Please note that weights  and biases  are initialized randomly. Stepwise Implementation Below are…

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Passing a parameter into a slurm script (matlab)

I am using slurm to submit jobs to the university supercomputer. My matlab function has one parameter: function test(variable_1) and my slurm file is (I am not sure if it is correct. I know how to define the value of the parameter in the slurm file, but I would like…

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File “sage/symbolic/pynac_impl.pxi”, Exception. Unhandled SIGSEGV: A segmentation fault occurred

I am not sure if this is a bug in Python or sagemath. Using sagemath 9.5 on Linux Arch. I’ll describe the problem in words, then given MWE to reproduce it. I have an integrand integrand = “F(x)*(-x^2+x)^(1/2)” as string. I pass it to a subprocess using multiprocessing. When I…

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Validea Motley Fool Strategy Daily Upgrade Report – 2/26/2022

The following are today’s upgrades for Validea’s Small-Cap Growth Investor model based on the published strategy of Motley Fool. This strategy looks for small cap growth stocks with solid fundamentals and strong price performance. EXLSERVICE HOLDINGS, INC. (EXLS) is a mid-cap growth stock in the Business Services industry. The rating…

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u-net deployment based on tensorrt

The code used in this project is pytorch-Unet, Link to :GitHub – milesial/Pytorch-UNet: PyTorch implementation of the U-Net for image semantic segmentation with high quality images. The project is based on the scale of the original image as the final input , This for data If the size of the…

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