Categories
Tag: CLUE
How to quantify the correlation of variants between cells?
How to quantify the correlation of variants between cells? 0 Hi! I’m going to compute the distance between cells by their variants, but I have no clue. For example, here’re variants of mitochondria from two cells: mttype_1 A73G,A210G,230delA mttype_2 A73G,220delT What’s the distance between these two mttype? correlation variant •…
Problem with DRAGEN RNAseq hashtable directory
Problem with DRAGEN RNAseq hashtable directory 1 Dear all, Recently I wrote a code to work with DRAGEN and RNAseq pipeline. I use this command: /opt/edico/bin/dragen -f -l \ -r refdir \ -1 ${forward} \ -2 ${reverse} \ -a ${gtf} \ –output-dir output/${sample} \ –output-file-prefix ${sample} \ –RGID ${sample}_group_id \…
Google Adds Gemini To Bard
Google has announced that Gemini Pro is available in Bard. This is described as the biggest upgrade to Bard since it launched. Google has also released a Gemini API and other AI tools for developers. Gemini is Google’s multimodal large language model developed by Google DeepMind. It has…
r – Problem with significance test using stat_signif() coupled with a ggplot2 boxplot
I am attempting to produce a boxplot with the results of a significance text, ideally with Student’s test and/or a Wilcoxon’s test comparing two groups of concentrations between two different auto-analysers. If I run the following code (Note the code does not include the input statements for the datafiles but…
ggplot2 – Should I update my ggplot code in R version 4.3.1?
I made code for a boxplot in R version 3.6.1: ggplot(Data_Addi, aes(x=as.factor(Sex), y=DEFS_SF, fill=as.factor(Diagnosis_Addison_Recoded))) + geom_boxplot(outlier.shape=NA, color=”black”) + geom_jitter(position=position_jitterdodge(),show.legend = FALSE) + theme_bw(base_size = 25) + scale_x_discrete(name=””, breaks=c(“1”, “2”),labels=c(“Females”, “Males”)) + scale_fill_manual(name=”Diagnostic Group”, breaks=c(“1”, “2”), labels=c(“Addison”,”Control”), values=c(“white”, “grey”)) + labs(title=”Executive function total”, x=”Sex”, y=”BDEFS-SF Total Score”) This gave the following…
FeatureCounts Invalid Parameter Error
FeatureCounts Invalid Parameter Error 0 Hello! I’m trying to use featureCounts, and it keeps on giving me this error: ERROR: invalid parameter: ‘SRR11860547.bam’ I’m pretty new at using featureCounts, so I have no clue what is wrong. I’ve tried changing the directory and location of the file, but it keeps…
STAT Health News: Medication abortion, mifepristone, pregnancy
Understand how science, health policy, and medicine shape the world everyday. Sign up for our Morning Rounds newsletter here. Good morning. Reproductive health is dominating the news and the newsletter this morning. We also have a look at the decade-long battle over a patent for CRISPR. It’s been a rollicking…
Understanding lupus: Chronic lifelong autoimmune disease
KUALA LUMPUR (Bernama) — When Dr Thipa Paneer Chelvam, 32, was diagnosed with lupus – a chronic disease that can cause inflammation and pain in any part of the body – she was in a state of denial. “I was in denial for many years. Accepting a chronic illness…
Re: Vertex AI Search Index stays forever with Crea…
From some weeks, we successfully created some Vertex AI Search Indexes in the console UI and with Terraform in several projects, some creations lasted around 30 mins, some even only 3 or 4 mins. From yesterday 27/11, all our Indexes creation are never ending, staying with the ‘Creating’ status for…
Automating API Documentation: A Journey from TypeScript to OpenAPI and Schema Governence with Optic
In the previous blog post Documenting and Testing Schemas of Serverless Stacks with Optic & Cypress, we focused on the benefits of schema testing and governance. Briefly, some of the core problems addressed were: Effortless API Documentation: Automating the API documentation creation and update, ensuring that our API documentation evolves…
Quast Genome assembly Quality (Galaxy Version 5.2.0+galaxy1) – usegalaxy.org support
Busrak November 29, 2023, 9:55am 1 Hi dear galaxy family, When I put my metagenome single read Megahit assembly data into Quast, I encounter the following error code. How can I solve this problem? Assembly_with_MEGAHIT_on_data_658 /usr/local/opt/quast-5.2.0/metaquast.py –single /jetstream2/scratch/main/jobs/53997042/inputs/dataset_f68c8b4a-bea0-4985-8324-4c64cdbe4d6d.dat –labels Assembly_with_MEGAHIT_on_data_658 -o outputdir –max-ref-num 50 –m 822: Quast on data 196…
MIL-OSI USA: Whole Genome Sequencing: Cracking the Genetic Code for Foodborne Illness
Recommended Sponsor Painted-Moon.com – Buy Original Artwork Directly from the Artist Source: US Food and Drug Administration-1 A person commits a crime, and the detective uses DNA evidence collected from the crime scene to track the criminal down. An outbreak of foodborne illness makes people sick, and the U.S. Food…
Is not compatible with the current PyTorch installation
Eunhae_Lee (Eunhae Lee) November 28, 2023, 7:28am 1 Hello, I’m using Mobaxterm to access a server to work on training a model when I try to run the command to launch it, I have his error: NVIDIA GeForce RTX 3090 with CUDA capability sm_86 is not compatible with the current…
Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals
Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…
New molecule extends lifespan and boosts muscle function
Buck Institute researchers identify new pathway for mitophagy which highlights the gut/brain connection. Researchers at the Buck Institute for Research on Aging have identified a new drug-like molecule that keeps mitochondria healthy via mitophagy, a process that removes and recycles damaged mitochondria in multicellular organisms. The compound, dubbed MIC, is…
When Did Humans Arrive in the Americas? Lice Help Answer That Head-Scratcher | Science
Contact between Europeans and Native Americans is recorded in the DNA of head lice. Vincent Smith, Natural History Museum, London, CC-BY 4.0 The first humans to arrive in America left scattered evidence behind, from ancient stone tools to fossilized footprints. And among descendants on either side of the Bering Strait,…
Genes that shape facial features
After turning up hundreds of genes with hard-to-predict effects, some scientists are now probing the grander developmental processes that shape face geometry When Eric Mueller, who was adopted, first saw a photograph of his birth mother, he was overcome by how alike their faces were. It was, he wrote, “the…
Science news in review: Nov. 5
As we enter the November stretch of the semester, researchers around the world are also working hard to advance efforts that can be beneficial to human health. This week’s science news highlights endeavors to understand various health challenges and identify treatments to combat them. New drug for treating antimicrobial-resistant gonorrhea…
Magic of Genetic Diversity: How a Varsity Pool Could Change DNA Rules
The discovery of a microorganism that edits genes in a university pool not only changes our understanding of how DNA works but also throws into spotlight the importance of saving genetic diversity on the planet, writes Satyen K. Bordoloi. In many university campuses worldwide, the local pool has been the…
couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘
Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…
Novel Rett syndrome variant shines light on n
Rett syndrome is a rare devastating neurological disorder that primarily affects young girls and manifests as an impaired ability to walk and talk, along with characteristic ‘hand-wringing’ movements, seizures, and cognitive disability. This incurable condition results from mutations in the methyl-CpG binding protein 2 (MECP2) gene that impairs the role…
Error in Gviz (actually, rtracklayer)
Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…
New DNA technology has found the killer
Credit: Pixabay/CC0 Public Domain In the 1970s and 1980s, pine trees growing in various forestry plantations in South Africa’s Western Cape province began to die in patches. These trees succumbed to a mysterious root disease and the patches expanded gradually. Spontaneous regrowth of seedlings in the patches died dramatically. As…
java – Getting null for request for api calls in vertx when building from openapi specification in vertx
Im facing some strange issue where I update the vertx libraries in my project from 4.2.7 to 4.4.6 recently. After that the requests validations got failed saying that request body is null. These endpoints did worked well in previous version. Im building my endpoints using below open api specification. ‘/v1/marketSession/{marketId}’:…
Life with ‘an almost 100 per cent risk’ of getting cancer
Luana Locke has survived five different kinds of cancer. Her first diagnosis — breast cancer at age 25 while pregnant with her first child — triggered genetic testing that revealed she had a rare hereditary disorder that made it almost certain she would face the disease again in her lifetime….
Third Generation Sequencing Market Growing a Remarkable CAGR
Third Generation Sequencing Market is anticipated to observe growth during the forecast period due to growing demand at the end user level. This market document gives a clue about the uncertainties that may come up due to changes in business activities or introduction of a fresh product in the market….
A Ballroom Dancer’s DLBCL Journey
October 19, 2023 Interviewed by: Alexis Moberger As an avid exerciser and ballroom dancer, Harriet knew something was wrong when she had difficulty after 2 minutes of walking. This led her to the ER, where she assumed she’d receive fluids because she was dehydrated. Doctors insisted she have a CAT…
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…
The chemistry behind Leonardo da Vinci’s paintings
A new analysis of microsamples from two of Leonardo da Vinci’s most famous artworks, theMona Lisa and theLast Supper, shows that Leonardo may have experimented with lead oxide as a drying agent in his primer formula (J. Am. Chem. Soc. 2023, DOI: 10.1021/jacs.3c07000). “You understand easily when you analyze his…
Cell banks in drug development – how frozen cells drive medical progress
(Photo : Single Use Support) Cell banks are generally known for various fields of application – while many are familiar with the concept of freezing cells for reproductive purposes, others may have come across cell banking in the context of stem cell preservation. What might be less known, though, is…
DESeq2 Error in Results Contrast and ResultsNames
Hi, I have a DESeq2 script that used to work until recently, I’m not sure if I updated a package which suddenly caused it to stop function properly, and I’m hoping to get some insight on what the issue might be stemming from. colData has 6 factors (A,B,C,D,E,F) dds <-…
How could we tell if those “alien bodies” in Mexico are legit?
Last week, I was contacted by a German documentary producer, asking if I was willing to be interviewed about two mummified bodies presented at a Mexican congressional hearing by TV personality Jaime Maussan, who claimed they were aliens. I declined, explaining that I didn’t have any inside knowledge about the…
strange behaviour of RStudio…have to restart RStudio in order to get right values
Hallo Community, i have a strange behavior in RStudio. In a script, I download crypto values from Coinmarketcap web server with the r package Coinmarketcapr.Later I want to do some matching with coloums of the dataframes aa and historiedf2. But the strange thing is, I get only correct values, when…
A New Clue Into the Cause, Spread of Parkinson’s Disease?
Damaged mitochondrial DNA (mtDNA) initiates and spreads Parkinson’s disease (PD) pathology, potentially opening new avenues for early diagnosis, disease monitoring, and drug development. While defects in mitochondrial functions and in mitochondrial DNA have been implicated in PD in the past, the current study demonstrates “for the first time how damaged…
Mitochondrial Inheritancega Mutation In Mtdna Creates New Restriction Site Destroys An Old One Crossword Clue
SPORCLE PUZZLE REFERENCE For the word puzzle clue of mitochondrial inheritancega mutation in mtdna creates new restriction site destroys an old one, the Sporcle Puzzle Library found the following results. Explore more crossword clues and answers by clicking on the results or quizzes. 25 results for “mitochondrial inheritancega mutation in…
OpenFold Drug Discovery AI Research Consortium Announces Funding of Large-Scale Protein Data Collection at Prof. Gabriel Rocklin’s Laboratory at Northwestern University
New first-in-class datasets will improve the capabilities of state of the art protein AI models to create new biologic drugs DAVIS, Calif., October 02, 2023–(BUSINESS WIRE)–The OpenFold group, a non-profit artificial intelligence (AI) research consortium of biotech and tech firms whose goal is to develop free and open-source software tools…
Metagenomics as new tool for diagnosis of scrub typhus
Introduction Scrub typhus, a kind of zoonotic bacterial infection, is becoming a threat to public health,1 which usually occurs to field operators, especially those living in remote and rural areas.2 Scrub typhus is caused by Orientia tsutsugamushi that is a kind of bacteria of gram-negative coccobacillus,3 the latent period is…
deep learning – Pytorch resource contention in cross validation loop
I am new to pytorch and am trying to train a model inside of a CV-Loop. For some reason I don’t understand it keeps on throwing the following error: RuntimeError: DataLoader worker (pid(s) 12796, 14968, 18532, 3432, 26096, 12980, 3712, 10588, 15712, 22028, 8976, 4852) exited unexpectedly It seems to…
Name Of Gengis Khan’s Grandson
Welcome to our dedicated page for CodyCross, a renowned crossword game that has topped the charts of the IOS App Store and Google Play Store from 2018 till 2023. Recognizing the intricate complexity of these puzzles, we’ve committed ourselves to assist you by providing answers for every possible Clue of…
Gene Therapy Among the New Possible Treatments for Wilson’s Disease, a Rare Liver Disease
Wilson’s disease is a rare disease that results in copper accumulating in hepatocytes, the cells that make up 80% of the liver. According to review paper recently published in the New England Journal of Medicine it occurs worldwide and has an estimated prevalence of about 30 cases per 1 million…
Split reads along the genome in my samples
Split reads along the genome in my samples 0 Hello, I am working with DNA sequencing libraries and I have found out that there are a lot of split reads randomly distributed (not clustered) along the genome in my samples. When I do a Blast of the sequence of these…
how do i convert my genomic data into proteome?
how do i convert my genomic data into proteome? 1 I need to convert my whole genome sequence data containing genome sequence into protein sequence. What tools I can use for this? proteome data • 29 views If this is homework, you should do it on your own. A general…
How Reproductive Genetics Is Helping To Shape Healthier Generations
Reproductive genetics, a rapidly evolving field at the intersection of medicine and genetics, has emerged as a pivotal tool in shaping the landscape of prenatal care. This comprehensive approach encompasses a range of diagnostic tests and screening procedures aimed at ensuring the health and well-being of both prospective parents and…
Researchers uncover novel physiological functions of CRISPR-Cas guard RNA
Graphical abstract. Credit: Cell Host & Microbe (2023). DOI: 10.1016/j.chom.2023.08.005 How the expression of Cas proteins in bacterial CRISPR-Cas immune system adapts to the constantly changing CRISPR structures and crRNA expression levels has been a long-standing unresolved question. Prof. Li Ming and Prof. Xiang Hua’s lab at Institute of Microbiology…
Top 10 In-Demand GenAI Skills
(Creativa-Images/Shutterstock) AI skills are in high demand, as companies seek to leverage emerging tech like generative AI for competitive advantage. But what specific skills are the most in-demand? The folks at Upwork provided a clue. A recent survey by Upwork found that generative AI job posts on the platform were…
Evaluation nested too deeply error for basic formula with many variables – RStudio IDE
I have the following error showing up in Rstudio when I run the code below:Error: evaluation nested too deeply: infinite recursion / options(expressions=)? redun.formula <- formula(paste(“~”, paste0(“X”, seq(1:2500), collapse = “+”))) I have tested it on 3 computers (2 OSX and 1 Windows) with recent (different but all 2023) versions…
R studio freezes when monocle3 is installed – RStudio IDE
Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…
Discussion: Human Genome Sequencing – 864 Words
Genome sequencing is the art of establishing DNA patterns or the order of DNA nucleotides, or bases, in a genome in an organism at a given time. This process narrows down to how a chromosomal and mitochondrion DNA is set up, which provides much information on important issues like the…
Dermatologist outlines how to spot early signs of melanoma
The British broadcaster and DJ, Chris Evans, has revealed that he has been diagnosed with a skin cancer called a “melanoma”. The 57-year-old says that he was tested for the disease after his masseuse noticed a mark on his shin. So, what exactly is melanoma? Julia Newton-Bishop is a professor…
Singleuser pod unable to register to hub on k8s – Zero to JupyterHub on Kubernetes
Hi,I am trying to deploy the zero to jupyterhub on k8s charts on my k8s cluster (microk8s with calico networking).I am stuck where I can access the hub UI (I am using domain name so I bind the hub to domain.com/jupyterhub) and I am able to login (with the dummy…
ggplot2 – How to merge multiple graphs of separate months, in R?
library(“dplyr”) library(“rjson”) library(“ggplot2”) json_file = “./sliceA.json” # Main data. my.JSON = fromJSON(file=json_file, simplify = TRUE) df = lapply(my.JSON, function(d) { data.frame(matrix(unlist(d), ncol=3, byrow=TRUE)) }) df = do.call(rbind, df) names(df) = c(“Year”, “Month”, “Day”) m = table(df$Month) yr = table(df$Year) d = table(df$Day) yrChr = function(mon,year) { x = data.frame(ftable(df[df$Year ==…
Researchers uncover a critical role for an amyloid precursor protein in human neurogenesis
A recent research reveals how an amyloid precursor protein (APP) affects the growth of nerve cells in the cortex — the outer layer of the human brain — and plays a critical role in preserving the delicate equilibrium between neural stem cell proliferation and differentiation in the early stages of…
In ggplot2, why are bars not centered on ticks when position is dodged? – tidyverse
This is subtle, but theres a clue in the legend showing an NA, category. Gentoo and Adelie have NA sex entries, which is position dodged would be a column to the rightof the female and male columns. so the bars are centered but you dont see the rightmost bar because…
Researchers Capture Atomic View of Synthetic DNA
Researchers have utilized X-ray crystallography to view synthetic DNA, known as DNAzymes, at an atomic level, leading to a better understanding of its structure and potential for enhancing medical diagnosis and treatment technologies. Their findings, a crucial step in solving a 30-year-old question, could be used to develop effective treatments…
Intraspecific trait variability is relevant in assessing differences in functional composition between native and alien aquatic plant communities
Aschehoug, E. T. & R. M. Callaway, 2015. Diversity increases indirect interactions, attenuates the intensity of competition, and promotes coexistence. American Naturalist 186: 452–459. doi.org/10.1086/682901. Article PubMed Google Scholar Botta-Dukát, Z. & B. A. Lukács, 2021. Optimal pooling of data for the reliable estimation of trait probability distributions. Global Ecology…
Her Allergy Symptoms were actually Non-Hodgkin’s Lymphoma
July 27, 2023 Interviewed by: Alexis Moberger As a kindergarten teacher, Alesia assumed her fatigue, shortness of breath, and swelling around the face and throat were work-related symptoms or simply allergies. It wasn’t until her throat became swollen to the point of being unable to swallow that she visited the…
How to check if BAM file is result of ILLUMINA?
How to check if BAM file is result of ILLUMINA? 2 Given a BAM file that is only computer readable how can I check if it comes from a illumina machine? I tried doing grep -q “ILLUMINA” filename.sorted.bam To check if ILLUMINA word appeared but it did not appear, probably…
error reading from input file
Samtools mpileup : error reading from input file 0 I am writing a code to analyse yeast sequencing data using R. I was able to do the alignment using BWA and thus obtain a .bam file and its .bai index using samtools. My next step is to perform variant calling…
Germs, genes and soil: tales of pathogens past
The bacterium behind the plague has now been traced back centuries.Credit: Getty The first documented epidemic of syphilis broke out in the French army during its invasion of Naples in 1495. From there, the sexually transmitted disease spread quickly across Europe — but where did it come from? The timing…
New DNA repair test could revolutionize treatment for genetic disorders and cancers
A personalized test that tells how well chemotherapy, radiotherapy or gene therapy will work on individual patients is now approved for UK, US, EU and Japanese patents. Image Credit: Testavec It will give many people with serious diseases like cancer, heart disease, HIV and cystic fibrosis the choice to opt…
rstudio – Problems in R update
Hi I would like to update my R version but an errors occurs. Could I ask for help regarding to this, please? Thank you in advance! Here is the error. install.packages(“installr”) Installing package into ‘/home/ss2826/R/x86_64-pc-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) trying URL ‘cran.rstudio.com/src/contrib/installr_0.23.4.tar.gz’ Content type ‘application/x-gzip’ length 158533 bytes (154 KB)…
The quahog makes a tasty chowder, but it can also edit your genome
It’s been a really good week for bivalves. Why, just a week ago in the journal Science we found out that the shell hinge from the freshwater cockscomb mussel can be opened and closed 1,500,000 times in succession without suffering any fatigue damage (!), and we also learned the structural secret…
Very different QUAL scores on VCFs of same sample using different methods
Hello, I produced a few VCFs, using clara parabricks deepvariant and gatk haplotype caller (in the regular way and also using clara-parabricks haplotype caller, which yielded identical results) The problem is that the QUAL score of both different extremely; using haplotype caller a lot of variants were in the thousands,…
How to retrieve gene and CDS entries properly from GenBank files with Perl?
In my goal to write a Perl script without modules that retrieves all simple gene and CDS entries (without the GenBank operators, since I have no clue how to handle them) in a specified range, I’ve come up with the following: use strict; use warnings; my $gene=””; my $CDS =…
While Starting Up, Keep Your Passion Aside And See If The Idea Has Potential To Make Money: Sam Santhosh
Sam Santhosh, Founder of MedGenome Sam Santhosh is a self-made entrepreneur who has spent 20 years in the software industry followed by 15 years in biotech. He started his entrepreneurial career with US California Software Company Limited and took it public in India. He then wanted to go deep…
Scientists create cell zoo to study developmental time
In humans, pregnancy lasts around nine months. In mice, only 20 days, and in rhinoceroses, as long as 17 months. Although many mammalian species go through the same stages during embryo development, the speed of development differs substantially across animals. Another example of an event that differs in time across…
GenomicsDBImport from Mutect2 output
I am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with: gatk Mutect2 \ -R ${REF} \ -L ${EXOME_INPUT_INTERVALS} \ -I ${BAM} \ –sequence-dictionary ${DICT} \ –max-mnp-distance 0 \ -O ${SAMPLE_NAME}.mutect2.vcf but I see that the tool is unable…
Postdoctoral Researcher for In-Silico Drug Repurposing for FIMM job with UNIVERSITY OF HELSINKI
Description: The Computational Systems Medicine group led by Tero Aittokallio focuses on developing and applying integrated computational-experimental approaches to tackle biomedical questions, such as how genes function as interaction networks to carry out and regulate cellular processes, how perturbations in these networks contribute to complex traits, such as human diseases,…
Homer not finding hg38 genome – Support scientifique et technique
Hi everyone,I am trying to annotate a .bed file using homer annotatePeaks.pl module load homer/ annotatePeaks.pl ConsensusPeaks.bed hg38 -gtf gencode.v43.annotation.gtf.gz > ConsensusPeaks.annotatedPeaks I obtain the following error message !!!!Genome /shared/ifbstor1/software/miniconda/envs/homer-4.11/share/homer/hg38 not found in /shared/ifbstor1/software/miniconda/envs/homer-4.11/share/homer/.//config.txt To check if is available, run “perl /shared/ifbstor1/software/miniconda/envs/homer-4.11/share/homer/.//configureHomer.pl -list” If so, add it by typing “perl…
New Visualization Method for Force-Sensing Neurons
A recent study by researchers at Texas Children’s Hospital, Baylor College of Medicine, and Scripps Research Institute has discovered fluorescent dye FM 1-43 as an effective and versatile tool to visualize PIEZO2 ion channel activity in mechanosensory neurons. The study, published in Neuron, was led by Dr. Kara Marshall, assistant…
Need help editing text in the shell
Need help editing text in the shell 1 Hello. I’m learning how to edit text with shell scripting, and I need to change the format of this: > chr1 204073115 204127743 > chr6 31164337 31170682 > chr17 42313412 42388540 I want to change it to this: chr-204073115:204127743 chr6-31164337:31170682 chr17:42313412-42388540 I…
r – Overlapping Boxplot and Cloudplot with two Y-Axes in ggplot
I have a dataframe like df: df <- structure(list(VarBinariaY = c(“1”, “1”, “0”, “1”, “0”, “1”, “1”, “1”, “1”, “1”), VarContinuaX = c(0.42125112307258, 0.403089860687032, 0.501541076926515, 0.285735354525968, 0.838761311257258, 0.728340754751116, 0.547309613088146, 0.758638551225886, 0.664854867151007, 0.730170585680753 ), VarContinuaY = c(0.62294910964556, 0.153794215992093, 0.173481315141544, 0.441902326885611, 0.556428883690387, 0.300496574025601, 0.778148024342954, 0.358530796831474, 0.163795455591753, 0.658571016974747)), row.names = c(NA, 10L), class…
Import torch gives Segmentation fault on Jetson Orin Nano – Jetson Nano
Hi.I’m having troubles with torch on my Jetson Orin NanoWhen I try to import it in python the interpreter crashes.I tried to run it with the fault handler here is the output: python3 -q -X faulthandler >>> import torch Fatal Python error: Segmentation fault Current thread 0x0000ffff8411c010 (most recent call…
Handling NA’s in Deseq2
Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…
Analysis of tRNA-derived small RNAs
Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…
Genetic variation discovery offers Alzheimer’s disease clue
A new study conducted by researchers at the University of Eastern Finland discovered that the APP A673T genetic variant, which protects against Alzheimer’s disease (AD), alters levels of several proteins and peptides linked to amyloid-beta metabolism in human biofluids and cell culture models, including amyloid beta itself. These new data…
Periodic Boundary Conditions Error, Molecule Trajectory Collapses to 2D – User discussions
GROMACS version: 2020.4GROMACS modification: No I have been running simulations of small proteins in water. Nothing fancy. Have been doing them without a hitch for awhile now. This last one I tried to do, however, behaved very strangely. The simulation seems to run for 125ns without any problems, but when…
Bartholin’s gland cyst caused by Sneathia amnii: a case report | BMC Infectious Diseases
S amnii is an important but underappreciated pathogen affecting women’s health because of its complex nutritional requirements, slow growth patterns, and requirement of anaerobic conditions. S amnii causes bacterial vaginosis and poor reproductive and perinatal outcomes. Sneathia species (spp.) have been identified as members of Community State Type IV (CST-IV)…
How Breast Cancer Arises | Harvard Medical School
Many human cancers arise in this manner during cell division, when chromosomes get rearranged and awaken dormant cancer genes that can trigger tumor growth. One such chromosomal scramble can occur when a chromosome breaks, and a second copy of the broken chromosome is made before the break gets fixed. Then,…
Bacterial metatransciptome antimicrobial resistance genes workflow?
Bacterial metatransciptome antimicrobial resistance genes workflow? 0 Hi everyone! I’m trying to analyse some metatranscriptomics data from different samples, the final goal is to determine wether one group of samples has a higher expression of antimicrobial resistance genes. I’m completely new to RNAseq and I have no clue where to…
High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq
Overview of the droplet-based snRandom-seq method for FFPE tissues The main workflow of snRandom-seq is shown in Fig. 1. For single nucleus isolation of FFPE tissues, the areas of interest of banked FFPE tissue block were first selected and placed into tubes. Deparaffinization and rehydration were carried out with standard xylene…
google cloud vertex ai – Sudden ImportError: cannot import name ‘appengine’ from ‘requests.packages.urllib3.contrib error on pipeline
My pipelines and schedulers were running smoothly without any problems. After I went out to lunch, I changed the number of epochs a Neural Network would run, save the .yaml file again and leave it in the bucket named “budgetff”. Afterwards, everything stopped working. There are the errors and I…
My first small project – Titanic
Hello everyone! My name is Jacob and this is my first ML project that I’m doing on my own. It’s also my first blog post, hope you will like it. This project comes from Kaggle’s competition “Titanic – Machine Learning from Disaster”. Here is the link to the competition: www.kaggle.com/competitions/titanic/data…
Genomic and transcriptomic profiling reveal molecular characteristics of parathyroid carcinoma
Clinical and biochemical characteristics of parathyroid carcinoma In total, 50 thyroid tissues were collected from three groups, 12 parathyroid carcinomas, 28 parathyroid adenomas, and 10 normal parathyroid tissues, for genomic and transcriptomic profiling (Fig. 1). The detailed protocols and quality control procedures are described in the Materials and Methods section….
Scientists sequenced the genome of Balto, famous sled dog of 1925 “Serum Run”
Enlarge / After Balto died in 1933, his taxidermy mount was put on display at the Cleveland Museum of Natural History. Cleveland Museum of Natural History In 1925, a sled dog named Balto led his plucky canine team on the last leg of a grueling 127-hour dogsled relay across Alaska…
Study identifies an unknown SARS-CoV-2 lineage on three mink farms in Poland
In a recent study published in the Eurosurveillance Journal, researchers detected a cryptic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage on mink farms in Poland. Study: Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022…
Is third-generation sequencing/long-read-sequencing the only way to identify the full length sequence of a novel transcript?
Is third-generation sequencing/long-read-sequencing the only way to identify the full length sequence of a novel transcript? 0 Thanks for your attention, TLDR: How to get the full length sequence of a novel transcript? Details: There is a novel transcript A I identified using short-read sequencing, through assembly. It contains an…
Error in R: incorrect number of subscripts on matrix
I have a dataset, and I am trying to make another dataset that is based on the previous dataset. Obviously, I will use a for loop to do that! Below is the data set used, and represented by the variable data. So I want to use rows 1 to 501…
Why do some people get UTIs over and over? A new report holds clues
Willa Rubin is a 26-year-old high school teacher in San Antonio, Texas, and like millions of other women, she suffers from recurrent urinary tract infections. “It’s really painful. It’s one of these situations that you just can’t really ignore. It’s sort of on the front of your mind until it…
The Search for Alien Life Moves to Icy Moons
The search for life beyond Earth “follows the water,” reports the Economist (since water is vital for earth’s lifeforms, and the laws of chemistry are universal). “For most of the space age that insight led scientists to Mars.” But… More and more, though, planetary scientists are following the water to…
Q. BioPython: CodeML FileNotFoundError: [WinError 2]
Q. BioPython: CodeML FileNotFoundError: [WinError 2] 0 I’m trying to run codeml in Biopython, following by Biopython cookbook. But it doesn’t work with an FileNotFoundError: [WinError 2]. I found ctl file does not contain file’s full path, like seqfile = seq2.phy outfile = result.out treefile = template.tree Files are on…
Can Scientists Learn to Prevent Brain Tumors?
David Ashley, MD, PhD, the Rory David Deutsch Distinguished Professor of Neuro-Oncology and director of the Preston Robert Tisch Brain Tumor Center at Duke, calls his choice to focus his career on brain cancers “a compulsion to defeat this terrible problem.” “When I was 23 years old, my father…
Perform the following Expasy analyses. Provide
Transcribed image text: Perform the following Expasy analyses. Provide screenshots of analyses for both translate and protparam calculations. a) Translate the recA gene sequence to protein using “EXPASY: translate” tool. Copy and paste the RecA protein sequence into your answer sheet. (1 point) b) Use “EXPASY Protparam” tool to calculate…
Transmictomic analysis with draft reference genome
Transmictomic analysis with draft reference genome 1 Hello, ultra noob here but is it possible to perform a transcriptome analysis but using a draft genome as a reference? I’m working with an assembled draft genome (a fasta file with a bunch of contigs) and I have no clue if bowtie…
Where are all the jobs? A sector guide for students
At the start your career, entering the world of work may seem daunting. The requirements of the jobs market always appear to be changing, thanks to technological shifts, while application processes can feel inscrutable and building up your skills from a limited foundation looks like an uphill battle. If you…
Why does a leukemic mutation not always lead to leukemia? A new clue from a mouse study
Credit: Pixabay/CC0 Public Domain Why do some people with a genetic mutation associated with leukemia remain healthy, while others with the same mutation develop the blood cancer? In a new study published in Blood, scientists from the USC Stem Cell laboratory of Rong Lu discovered a mechanism that linked a…
How to extract proteins from PCs in plot_pca in DEP package?
How to extract proteins from PCs in plot_pca in DEP package? 1 I am using DEP package to analyze proteomics data. I did PCA for my samples (see the following plot) and wish to extract proteins in PC1 for further analysis. However, the objects x and y generated by the…
How an Electrical Engineer Solved Australia’s Most Famous Cold Case
Dead, and in a jacket and tie. That’s how he was on 1 December 1948, when two men found him slumped against a retaining wall on the beach at Somerton, a suburb of Adelaide, Australia. The Somerton Man’s body was found on a beach in 1948. Nobody came forward to…
Scientists parse another clue to possible origins of Covid-19 as WHO says all possibilities ‘remain on the table’ – CENTRAL
But because viruses don’t survive in the environment outside of their hosts for long, finding so much of the genetic material from the virus intermingled with genetic material from raccoon dogs is highly suggestive that they could have been carriers, according to scientists who worked on the analysis. The analysis…
Debugging story: The case of the flaky Dynamo export tests
Keep asking why. For months, Dynamo export tests have been intermittently failing with “AssertionError: whole graph export entails exactly one call”. Flaky tests that you can’t reproduce are pretty difficult to debug, since you can’t easily make a change and see if it fixes the problem or not. So when…