Tag: SOS

Stochastic biological system-of-systems modelling for iPSC culture

Cell proliferation and aggregation dynamics modeling The aggregation process is characterized by the dynamic evolution of a density profile of aggregates. Let \(\phi (x,t)\) denote the average number of aggregates or clusters of size \(x\) (i.e., mass and volume) at time \(t\), where mass is equal to a buoyant density…

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New Hope for Streamlining Induced Pluripotent Stem Cell Therapy Production

A novel framework developed by researchers at Northeastern University in Boston could revolutionize the production of therapies from induced pluripotent stem cells (iPSCs). The framework, called biological system-of-systems (Bio-SoS), incorporates a multi-scale bioprocess mechanistic model to simplify the scaling up of iPSC production. Traditionally, producing therapies from iPSCs involves numerous…

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Optimizing iPSC Manufacturing

By Mike May, PhD Making therapies from induced pluripotent stem cells (iPSCs) usually takes many experiments to scale up production. Wei Xie, PhD, assistant professor of mechanical and industrial engineering at Northeastern University in Boston, hopes to streamline that process with modeling. Recently, Xie and her colleagues described a biological…

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Multiple micronutrient deficiencies in early life cause multi-kingdom alterations in the gut microbiome and intrinsic antibiotic resistance genes in mice

Han, X., Ding, S., Lu, J. & Li, Y. Global, regional, and national burdens of common micronutrient deficiencies from 1990 to 2019: a secondary trend analysis based on the Global Burden of Disease 2019 study. eClinicalMedicine 44, 101299 (2022). Article  PubMed  PubMed Central  Google Scholar  Bailey, R. L., West, K….

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Multiple systems in a single simulation – LAMMPS Beginners

AMINA November 15, 2023, 10:20am 1 hello,I am simulating cacao butter which contain 3 triglyceride with different proportion (POS 48%, SOS 34%, POP 18%)Can you please tell me if there is any command which can do thisRegards,amina This is not a question that can be handled with a LAMMPS command….

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Practical 6 Final 320 GENE – GENE 320 Practical 6 Advanced BLAST Start with a brief introduction

GENE 320 Practical 6 Advanced BLAST Start with a brief introduction [150 words] and aim of the practical. [5] An Introduction should have relevant information relating to the practical, including at least 2 in-text citations from scientific literature (3 marks). The aim/s should be clearly stated. (2 mark) The aim…

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The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus

Clp proteases are not involved in the lytic phage cycle We initiated this study testing the possibility that the chromosomally encoded Clp ATPases or proteolytic subunits (Table S1) could control the life cycles of the prototypical S. aureus phages Φ11 and 80α, which have been extensively used as models for Gram-positive…

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Mitochondrial SOS: how mtDNA may act as a stress signal in Alzheimer’s disease

Review doi: 10.1186/s13195-023-01322-6. Affiliations Expand Affiliations 1 Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA. 2 Department of Family Medicine, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA. 3…

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Mitochondrial SOS: how mtDNA may act as a stress signal in Alzheimer’s disease | Alzheimer’s Research & Therapy

2021 Alzheimer’s disease facts and figures – 2021 – Alzheimer’s & Dementia – Wiley Online Library. Available from: alz-journals.onlinelibrary.wiley.com/doi/doi.org/10.1002/alz.12328. [Cited 2022 Nov 13]. Jack CR, Bennett DA, Blennow K, Carrillo MC, Dunn B, Haeberlein SB, et al. NIA-AA research framework: toward a biological definition of Alzheimer’s disease. Alzheimers Dement J…

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Protistan predation selects for antibiotic resistance in soil bacterial communities

Courtenay M, Castro-Sanchez E, Fitzpatrick M, Gallagher R, Lim R, Morris G. Tackling antimicrobial resistance 2019-2024–the UK’s five-year national action plan. J Hosp Infect. 2019;101:426–7. Article  CAS  PubMed  Google Scholar  D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, et al. Antibiotic resistance is ancient. Nature. 2011;477:457–61….

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Section 2: ggplot2 Functions (2 pts) In this section,

Transcribed image text: Section 2: ggplot2 Functions (2 pts) In this section, you will be asked to explain the purpose of various ggplot2 functions and their syntax. Each question has two parts, A and B. We’re looking to evaluate if you understand the use and syntax of the functions. Please…

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rstudio – How do I set a breakpoint and step through R code that is sourced from Github

I have an R library that I have installed from github using remotes::install_github. I have also downloaded the source code using git checkout When I call one of the library functions I’m getting an error (the parameters I’m using to connect to the database aren’t working) I am able to…

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How to deal with two dataset of RNA expression

How to deal with two dataset of RNA expression 1 Hi all. I am anaylzing two dataset from GEO database. One is data of RNAseq, and under CPM and RPKM processing. Another seems from microarray,which describes the data processing as “The data were analyzed with Microarray Suite GCOS using Affymetrix…

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Microorganisms | Free Full-Text | Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample

1. Introduction The pathogen Vibrio cholerae is widespread and has long coevolved with humans. It is the agent that causes cholera, a severe intestinal illness that can result in up to 140,000 fatalities and affects between 1 and 5 million people annually [1]. V. cholerae carries the cholera toxin and…

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Confusing about the dimension of Seq2Seq model – nlp

I am new to Seq2Seq and hope to find a proper guildances, advices. I am doing a Project from an online course so I can not give the material but I got my Project notebook on Github I want to ask about my understanding about the architecture as well as…

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pytorch – NLP Transformers Machine Translation

Training transformer in pytorch train loss reduces but fails in validation. I have taken only one example just to test whether model architecture is fine or not. I have tested it on a larger dataset and still have the same results. I guess there is some problem with decoder greedy…

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TLJH always serves /hub/ regardless of base_url parameter in config.yaml

Update by Erik – 2021-10-26 This was also reported in #655 with relevant logs. Bug description I am running a TLJH server on Ubuntu 20.04.3 LTS (Focal Fossa). I would like the login to be available at a path on a subdomain I own, some.domain.org/jupyter/hub (and eventually be able to…

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Sparse tensor based nuclear gradients for periodic Hartree-Fock and low-scaling correlated wave function methods in the CP2K software package: A massively parallel and GPU accelerated implementation

. 2023 Apr 28;158(16):164109. doi: 10.1063/5.0144493. Affiliations Expand Affiliations 1 Department of Chemistry, University of Zurich, CH-8057 Zürich, Switzerland. 2 CP2K Foundation, CH-8006 Zurich, Switzerland. Item in Clipboard Augustin Bussy et al. J Chem Phys. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Apr 28;158(16):164109. doi: 10.1063/5.0144493. Affiliations…

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A two-part resurrection tale (2|2)

by Christoph  In continuation of the first part of the tale: what is the “resurrection” in the title about? A bit of nostalgia, as I will “resurrect” a story that is based on research from ~30 years ago (and today mainly known by dedicated plasmid specialists, if at all). A…

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Materials Cloud Archive

Augustin Bussy1*, Ole Schütt2, Jürg Hutter1* 1 Department of Chemistry, University of Zurich, CH-8057 Zürich, Switzerland 2 CP2K Foundation, CH-8006 Zurich Switzerland * Corresponding authors emails: augustin.bussy@chem.uzh.ch, hutter@chem.uzh.ch How to cite this record Augustin Bussy, Ole Schütt, Jürg Hutter, Sparse tensor based nuclear gradients for periodic Hartree–Fock and low-scaling correlated…

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KEGG ENZYME: 1.1.1.88

Entry EC 1.1.1.88                 Enzyme                                  Name hydroxymethylglutaryl-CoA reductase;beta-hydroxy-beta-methylglutaryl coenzyme A reductase (ambiguous);beta-hydroxy-beta-methylglutaryl CoA-reductase (ambiguous);3-hydroxy-3-methylglutaryl coenzyme A reductase (ambiguous);hydroxymethylglutaryl coenzyme A reductase (ambiguous) Class Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname (R)-mevalonate:NAD+ oxidoreductase (CoA-acylating) Reaction(IUBMB) (R)-mevalonate + CoA + 2 NAD+ = 3-hydroxy-3-methylglutaryl-CoA + 2 NADH +…

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‘Listeria Is Everywhere’ | MedPage Today

Here’s a medical story that recently caught my eye: “Five sick in French Listeria outbreak linked to cheese alternative.” Published on January 21 in Food Safety News, the report referenced four pregnant women in France who ate the same Listeria-tainted, plant-based food, then suffered serious infections and delivered prematurely. The…

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6 notorious tiger poachers arrested in Tamil Nadu

The non-governmental organisation Wildlife SOS in collaboration with the Tamil Nadu Wildlife Crime Control Bureau brought to end a major tiger poaching operation which spanned across the country. Six members of a notorious big cat poaching gang who had travelled from Delhi to Ooty to kill tigers in the rich…

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Identification of brain cell types underlying genetic association with word reading and correlated traits

Lyon GR. Part I defining dyslexia, comorbidity, teachers’ knowledge of language and reading. Ann Dyslexia. 2003;53:1–14. Google Scholar  Hendren RL, Haft SL, Black JM, White NC, Hoeft F. Recognizing psychiatric comorbidity with reading disorders. Front Psychiatry 2018;9:101. Google Scholar  Doust C, Fontanillas P, Eising E, Gordon SD, Wang Z, Alagoz…

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Is there a way to run docker on an R Markdown from Linux command line?

Is there a way to run docker on an R Markdown from Linux command line? 0 I have created a docker with certain genetics files I want to keep private. Is there a command I can use for R markdown to run it from command line such as people use…

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python – having problem with multi-gpu in pytorch transformer

I am currently trying to make a translation model with Trnasformer model through PyTorch. Since I have 2 GPUs (2080ti x 2) available for training, I want to train the model through multi-gpu. Currently, the gpu is assigned to 0 and 1 respectively. The way I use multi-gpu is to…

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[Bug 1960996] Autopkgtest regression report (sosreport/4.3-1ubuntu0.20.04.1)

All autopkgtests for the newly accepted sosreport (4.3-1ubuntu0.20.04.1) for focal have finished running. The following regressions have been reported in tests triggered by the package: sosreport/4.3-1ubuntu0.20.04.1 (amd64) 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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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Unable to download fastq files in parallel / SOS

Unable to download fastq files in parallel / SOS 0 Hi! Very new to all this so bear with me if I’m using incorrect terminology. Also english is my second language. I’m trying to download my fastq files in parallel but it doesn’t work and I keep receiving this error:…

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