Tag: MD

Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment | BMC Infectious Diseases

Mokomane M, Kasvosve I, Melo Ed, Pernica JM, Goldfarb DM. The global problem of childhood diarrhoeal diseases: emerging strategies in prevention and management. Ther Adv Infect Dis. 2018;5(1):29–43. PubMed  Google Scholar  Organization WH. Rotavirus vaccines: WHO position paper–July 2021. Weekly Epidemiol Rec. 2021;96(28):301–219. Google Scholar  Bucardo F, Reyes Y, Svensson…

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Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

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Tramadol Therapy and CYP2D6 Genotype – Medical Genetics Summaries

Introduction Tramadol (brand names ConZip, Ultram, UltramER, Odolo) is an analgesic used to treat moderate to severe pain. It is used for a variety of pain conditions, including post-operative pain, cancer pain, and musculoskeletal pain. Tramadol is a centrally acting opioid analgesic with mu-opioid binding activity as well as weak…

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Differences in Germline Variant Spectrum Between Black and White Men With Prostate Cancer

By Matthew StengerPosted: 6/13/2022 10:50:00 AM Last Updated: 6/13/2022 10:00:21 AM In a study presented at the 2022 ASCO Annual Meeting (Abstract 10502) and simultaneously published in JCO Precision Oncology, Veda N. Giri, MD, and colleagues found that Black men with prostate cancer exhibited a lower frequency and narrower spectrum…

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73 Boys Enrolled for DMD Therapy Pamrevlumab’s Second Phase 3 Trial

FibroGen has completed patient enrollment for its Phase 3 trial evaluating pamrevlumab in combination with corticosteroids as a potential treatment for children with Duchenne muscular dystrophy (DMD). The LELANTOS-2 study (NCT04632940) has enrolled 73 boys with DMD, ages 6 to 12, who maintain their ability to walk. The trial, the second…

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Roles of circRNAs | CMAR

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

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First-of-its-kind platform generates antitumor immunity and improves responses to checkpoint inhibitors

Researchers at The University of Texas MD Anderson Cancer Center have developed an ultrasound-guided cancer immunotherapy platform that generates systemic antitumor immunity and improves the therapeutic efficacy of immune checkpoint blockade. The findings from the preclinical study were published today in Nature Nanotechnology. As the first-of-its-kind platform, the Microbubble-assisted UltraSound-guided…

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Learning how to write script for lammps in python – LAMMPS Beginners

Good day to all,I am trying to apply Monte Carlo method within the intervals of MD simulation.Specifically, I am trying to write python code that could be invoked from lammps(or vice versa) so that I could add a new calculation method. To begin with, I am currently running Lammps on…

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Porting GROMACS Across Heterogeneous Architectures

Porting GROMACS Across Heterogeneous Architectures In this second episode about GROMACS, one of the world’s most widely used open source molecular dynamics (MD) applications, we explore the quest to simplify portable, performant programming with Erik Lindahl, Biophysics Professor at Stockholm University & KTH Royal Institute of Technology, and Roland Schulz,…

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Researchers Develop Allogeneic CART for Relapsed or Refractory T-ALL Using Base Editing

A group of researchers at Children’s Hospital of Philadelphia (CHOP), in collaboration with Beam Therapeutics, have tested and developed an “off-the-shelf” chimeric antigen receptor T-cell (CART) using base editing, which is designed to allow for precise editing of the CART with less risk of unwanted and unforeseen outcomes that may…

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Regarding the use of -table and -tablep – User discussions

GROMACS version: 2018.3GROMACS modification: No Hi, I am trying to simulate a polymer-water system where the polymer beads interact by Weeks-Chandler-Andersen potential and all the other non-bonded interactions are LJ type. I have two tabulated potential files: (i) table.xvg (for LJ) and (ii) table_P_P.xvg (for WCA). In the .mdp file…

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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Twin pair analysis (MZ, DZ twin pairs)

Hi I have a question on how to deal with following experimental setup. I have data on microbiome and metabolomics for twins that are either MZ or DZ, and thus we have only pairs in the dataset. I would like to assume the twins are unrelated, to be generalizable to…

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Identifying Mechanisms of Methylation in Stem Cells

Normal cells (red) survive much longer than Set1A-mutant cells (green) when ING5 is deleted. Northwestern Medicine scientists have identified critical regulatory processes that govern differentiation in embryonic stem cells, according to a study published in the Proceedings of the National Academy of the Sciences (PNAS). Bercin Cenik, MD, PhD, postdoctoral…

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Dosing of KIN-3248 Begins in Advanced Solid Tumors With FGFR2 and/or FGFR3 Alterations

The first patient has been dosed in the phase 1 KN-4802 trial (NCT05242822) examining the safety, tolerability, and preliminary efficacy of KIN-3248, a next-generation pan-FGFR inhibitor, in adult patients with advanced tumors harboring FGFR2 and/or FGFR3 gene alterations, according to a press release from Kinnate Biopharma Inc.1 KIN-3248 is an…

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Team develops method to increase gene editing efficiency while minimizing DNA deletion sizes

Targeting E. coli DNA pol I to DSBs increased the ratio of 1-bp deletions versus >1-bp deletions and TIS versus non-TIS. (A) Counteracting DNA resection (e.g. MRE11) by pol I fused to Cas9. The expected result is suppression of the MMEJ and SSA DNA repair pathways, which require DNA resection. (B)…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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The Fifth Annual YCC Trainee Colloquium

Yale Cancer Center (YCC) will hold its Fifth Annual Trainee Colloquium virtually on Friday, June 10, 2022 from 8:30am – 1:15pm. This will be a forum for Yale trainees to highlight their research, exchange ideas, and initiate collaborations. We invite predoctoral MD, PhD, MD-PhD students, postdoctoral associates, postdoctoral fellows, residents,…

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Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in , for Cedars-Sinai Medical Center

Details Posted: 26-Apr-22 Location: Nationwide Type: Full-time Salary: Open Internal Number: 20002022 At Cedars-Sinai, postdoctoral scientists and other junior researchers fulfill a critical role in expanding the horizons of medical knowledge through biomedical research. By hosting more than 100 postdocs, who conduct vital research and receive advanced training with expert…

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Biomedical/BioInformatics Intern in Rockville, MD

Description Job Description: The Government Health and Safety Solutions Group within the Health group has an opening for a  Biomedical/Bioinformatics Intern. The intern will work alongside data scientists and managers and use biomedical or genomics data to inform health-related research questions. Primary Responsibilities: Under the guidance of Leidos staff, the…

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Lenvatinib+Pembrolizumab Adverse Reactions in Advanced RCC Characterized

Investigators have characterized the adverse reactions (ARs) resulting from the use of lenvatinib plus pembrolizumab in patients with advanced renal cell carcinoma (aRCC) as well as how these ARs were managed. “Clinicians play a critical role in the prompt identification and management of ARs in patients with aRCC treated with…

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Endometriosis-related functional modules and hub genes

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

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CareDx Showcases Leadership with Over 25 Oral Presentations and Posters at the International Society for Heart and Lung Transplantation Meeting

CareDx, Inc. Data Highlights Clinical Utility of CareDx Solutions, Including Findings from Surveillance HeartCare Outcomes Registry (SHORE) Demonstrating Power of Multimodality Assessment for More Precise Interventions CareDx Symposia Feature Latest Advancements Including XenoSure and XenoMap SOUTH SAN FRANCISCO, Calif., April 20, 2022 (GLOBE NEWSWIRE) — CareDx, Inc. (Nasdaq: CDNA) –…

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TREEFROG THERAPEUTICS LAUNCHES A $100,000 RESEARCH GRANT IN REGENERATIVE MEDICINE

Bordeaux, France / April 19th, 2022 – TreeFrog Therapeutics, a biotechnology company aimed at making safer, more efficient and more affordable cell therapies based on induced pluripotent stem cells (iPSCs), today announced the launch of The Stem Cell SpaceShot Grant, a $100,000 research funding in the field of stem cell…

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Whole-genome analysis of coxsackievirus B3 reflects its genetic diversity in China and worldwide | Virology Journal

Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, et al. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol. 2020;6:2. doi.org/10.1093/ve/veaa048. Article  Google Scholar  Chen J, Han Z, Wu H, Xu W, Yu D, Zhang Y. A large-scale outbreak…

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SwissDock and Autodock Vina results comparison : comp_chem

Hi! I’m a chemistry undergrad. For my research, I performed docking using Autodock Vina. For further validation, I tried docking using SwissDock too. But now, the two programs give different results. They predict different ligands to give the most favorable binding. I read that Autodock is more reliable. So, should…

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Anaveon presents compelling data from the Phase I/II study of ANV419 during the AACR Annual Meeting 2022

Anaveon – ANV419 is very well-tolerated and demonstrates exceptional safety with strong pharmacodynamic effects and excellent IL-2Rβγ selectivity – – A Phase II program of ANV419 has been initiated in multiple tumor types, including melanoma, alongside multiple combination trials – BASEL, Switzerland, April 08, 2022 (GLOBE NEWSWIRE) — Anaveon, a…

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Biomea Fusion Reports Preclinical Data on BMF-219 and Trial

Covalent menin inhibitor BMF-219 showed strong cytotoxic activity as a single agent at similar concentrations across multiple preclinical patient derived (PDX) models ex vivo, including diffuse large B-cell lymphoma (DLBCL), multiple myeloma (MM), colorectal cancer (CRC), non-small cell lung cancer (NSCLC), and pancreatic cancer Single agent BMF-219 demonstrated pronounced anti-cancer activity…

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Postdoctoral Associate-Epidemiology and Bioinformatics – Medicine – Epidemiology & Population Science

Job Description Summary The Section of Epidemiology and Population Sciences at Baylor College of Medicine invites applications for postdoctoral research in systems epidemiology of cancer.  This is a 3-year flexible program with personalized educational curricula and individually tailored multidisciplinary teams of mentors with ongoing research in a variety of pediatric…

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Researchers identify sustainable source of im

image: Monkey iPSCs with edited CCR5 locus growing in culture. view more  Credit: Image Credit: Saritha D’Souza, Wisconsin National Primate Research Center, USA Genetic engineering can make immune cells resistant to infection with human or monkey (simian) immunodeficiency virus (HIV and SIV, respectively). Recently, treatment with HIV-resistant immune cells has given…

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How to edit a SAM file using pysam

How to edit a SAM file using pysam 0 Dear all – I have a template sam file and I want to change one of the columns (template_length) and replace it with a new value. The new value is a quick mathematical operation. template sam file: @HD VN:1.0 SO:unsorted @SQ…

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DESeq2 comparisons with multiple experimental variables?

Summary: I’m trying to get a series of pairwise comparisons of specific experimental variables while holding the other variables constant, and can’t figure out how to do it in DESeq2 I am running an circadian experiment with multiple disease states and experimental interventions, let’s say condition: high fat (HFC), normal…

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Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands Aysu Okbay, Hyeokmoon Kweon & Philipp D. Koellinger Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia Yeda Wu, Julia Sidorenko, Jian Yang, Loic Yengo & Peter M. Visscher National Bureau of Economic Research, Cambridge, MA, USA Nancy Wang, Hariharan Jayashankar, Michael Bennett, Grant Goldman, Tamara Gjorgjieva, Steven…

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Tacrolimus Measures Up in Lupus Nephritis Trial

In a phase III trial, oral tacrolimus (Prograf) proved non-inferior to intravenous cyclophosphamide for treating lupus nephritis, researchers said. Among 158 patients randomized to tacrolimus, 83.0% achieved complete or partial responses after 24 weeks versus 75.0% of 156 assigned to intravenous cyclophosphamide, according to Zhaohui Zheng, MD, of Zhengzhou University…

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Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

Continue Reading Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Extensively drug resistant E. coli LZ00114

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

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Polatuzumab Vedotin Plus R-CHP Recommended for EU Approval for Previously Untreated DLBCL

The European Medicines Agency’s Committee for Medicinal Products for Human Use has adopted a positive opinion in favor of the approval of polatuzumab vedotin for use in combination with rituximab plus cyclophosphamide, doxorubicin, and prednisone in patients with previously untreated diffuse large B-cell lymphoma. The European Medicines Agency’s Committee for…

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LAMMPS Patch Release 24 March 2022

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

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Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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Gopal Addresses Differences Between Real-World and Clinical Trial Data for DLBCL

During a Targeted Oncology case-based roundtable event, Ajay K. Gopal, MD, discussed the options for second-line and subsequent treatment of a patient with relapsed/refractory diffuse large B-cell lymphoma who refuses CAR T-cell therapy. Targeted OncologyTM: What are the recommended approaches for relapsed/refractory DLBCL in the second-line and subsequent therapies settings?…

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Trimmomatic/ linux system

Trimmomatic/ linux system 1 Hi all, I am trying to remove adapters and clean my RNA-seq.gz files using Trimmomatic, loaded on a Linux system (supercomputer server) Following the steps for Pair ends reads, explained in the manual (www.usadellab.org/cms/?page=trimmomatic) java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3…

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Parsing error(s): The input OpenAPI file is not valid for the OpenAPI specification #2770 | Support Center

ABP Framework version: v5.1 UI type: MVC DB provider: EF Core / MongoDB Tiered (MVC) or Identity Server Separated (Angular): yes / no Exception message and stack trace: Steps to reproduce the issue:” Add new solution add the Page with CURD operation using ABP Suite When we are validating the…

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Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

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Postdoctoral Associate job with Baylor College of Medicine

Summary The Cheng Lab at Baylor College of Medicine is searching for highly motivated and talented post-doc candidates to work on Bioinformatics and Computational Biology. The Lab is particularly interested in Cancer Systems Biology, Cancer Genomics and Cancer Immunology. Job Duties Assists in the development and application of computational approaches…

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Nvt.tpr -I couldn’t manage my nvt.tpr – User discussions

GROMACS version:2022-cp2k interface I couldn’t manage my nvt.tpr I tried to fix problem but I couldn’t. gmx_cp2k grompp -f nvt.mdp -c confout.gro -r confout.gro -p topol.top -n index.ndx -o nvt.tpr nvt.mdb file :; md-nvt.mdp – used as input into grompp to generate nma-nvt.tprintegrator = md ; MD using leap-frog integratordt…

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Human induced pluripotent stem cells improve visual acuity, vascular health — ScienceDaily

Researchers at Indiana University School of Medicine, in collaboration with the University of Alabama at Birmingham and five other institutions, are investigating novel regenerative medicine approaches to better manage vascular health complications from type 2 diabetes that could someday support blood vessel repair in the eye among diabetic patients with…

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Nurosene’s CSO And Director Of Bioinformatics Receives ‘Highly Cited Paper’ Award For AI-Based Alzheimer’s Research Findings

Nurosene’s Chief Scientific Officer, Dr. Joseph Geraci PhD, was recently recognized with an award for his work in Alzheimer’s disease utilizing Nurosene’s powerful AI platform. TORONTO, March 8, 2022 /CNW/ – Nurosene Health Inc. (“Nurosene” or the “Company”) (CSE: MEND) (Frankfurt: 8TV) (OTC: MNNDF), a healthtech company focused on delivering…

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Top 17 b cell lymphoma treatment in 2022

Below are the best information and knowledge on the subject b cell lymphoma treatment compiled and compiled by our own team tuhoangkaido: 1. Treating B-Cell Non-Hodgkin Lymphoma 2. Treatments for B-Cell Lymphoma 3. Diffuse Large B-Cell Lymphoma: Treatment Options 4. B-cell Lymphoma 5. B-cell Lymphoma: Types, Symptoms & Prognosis 6….

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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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Accelerating minimap2 for long-read sequencing applications on modern CPUs

Chaisson, M. J. et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun. 10, 1–16 (2019). Article  Google Scholar  Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 1–19 (2016). Article  Google Scholar  Beyter, D. et al. Long-read sequencing of…

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Change of protein-protein-interaction free energy upon ligand binding (procedure and controls) – User discussions

GROMACS version: 2021.1GROMACS modification: No Dear Gromacs and simulation community, in the course of my master’s thesis, I want to determine the protein-protein-binding free energy between two GTPases using PMF calculations via umbrella sampling. Especially I am interested in the contribution of the bound nucleotides (one per protein) which are…

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trollchu | coder – Coder Social

Qingzhao’s Projects AI-learns-to-play-the-dino-game AsFem A Simple Finite Element Method program (AsFem) aten Molecular / atomic coordinate editor atomman Atomistic Manipulation Toolkit awesome-python-chemistry A curated list of Python packages related to chemistry awesome-python-MD cantera Chemical kinetics, thermodynamics, and transport tool suite CFDPython A sequence of Jupyter notebooks featuring the “12 Steps…

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Polatuzumab Vedotin Plus R-CHOP May Improve Outcomes For DLBCL Patients

Thomas Habermann, MD, discusses R-CHOP and how it can be improved upon as a treatment method for diffuse large B-cell lymphoma. Thomas Habermann, MD, a hematologist with the Mayo Clinic, discusses the combination of rituximab (Rituxan), cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) as a treatment method for diffuse large B-cell…

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Highly Efficient Genome Editing in Plant Protoplasts by Ribonucleoprotein Delivery of CRISPR-Cas12a Nucleases

Review doi: 10.3389/fgeed.2022.780238. eCollection 2022. Affiliations Expand Affiliations 1 Department of Plant Science and Landscape Architecture, University of Maryland, College Park, College Park, MD, United States. 2 College of Agriculture, Nanjing Agricultural University, Nanjing, China. 3 Integrated DNA Technologies, Coralville, IA, United States. 4 U.S. Horticultural Research Laboratory, USDA-Agricultural Research…

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sam – Use Htslib to create auxilary tags in bam file C++

I am creating a threaded c++ file where i generate in silico bam files, using header, DNA sequence and read information. First i use bam_init1() to create the bam1_t structure just named “b”. Then i use bam_set1 to create the actual sequence entry in the bam file bam_set1(b,read_id_length,READ_ID,flag,chr_idx,min_beg,mapq,n_cigar,cigar,-1,-1,0,strlen(DNAsequence),DNAsequence,quality_string,l_aux) And finally…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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Selective targeting of multiple myeloma cells with a monoclonal antibody recognizing the ubiquitous protein CD98 heavy chain

Submission history Received: 29 April 2019 Accepted: 26 January 2022 Acknowledgments We thank T. Yamane (Osaka City General Hospital), K. Koh (Osaka General Hospital for West Japan Railway Company), and M. Ichii (Osaka University Graduate School of Medicine) for MM samples; T. Kitamura (The University of Tokyo) for the retroviral…

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Do I meet the basic requirements needed to study a PhD in computational chemistry? : comp_chem

I am an undergraduate who’ll graduate in 2 years. I think I want to get a PhD in computational chemistry (although not sure where, might want to study in the US), and I’ve had around 5 months of research experience in computational chemistry in an research internship. However, I’ve only…

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Axi-cel CAR-T significantly improves EFS among older patients with non-Hodgkin lymphoma

February 16, 2022 3 min read Source/Disclosures Published by: Source: van Meerten T, et al. Abstract PT02-1. Presented at: European Society for Blood and Marrow Transplantation-European Hematology Association 4th European CAR T-cell Meeting (virtual meeting); Feb. 10-12, 2022. Disclosures: van Meerten reports honoraria from Kite Pharma and…

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Issue with segmentation fault – User discussions

GROMACS version: 2021.2, 2019.6GROMACS modification: YesHere post your question I am facing a segmentation fault issue with GROMACS patched with plumed and I was wondering if you could help me. I am trying to run a replica averaged MD simulation by calculating the backbone chemical shifts for a protein (using…

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CRISPR-Cas9 Gene Therapy for Duchenne Muscular Dystrophy

Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169:5429–33. CAS  PubMed  PubMed Central  Google Scholar  Jansen R, van Embden JDA, Gaastra W, et al. Identification of genes…

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Investigating binding dynamics of trans resveratrol to HSA for an efficient displacement of aflatoxin B1 using spectroscopy and molecular simulation

Spectroscopic studies The binding and interactive mode of flavonoid trans-resveratrol with HSA was investigated before its use as a dislodging agent for HSA bound AFB1. The binding behavior was studied using spectroscopic tools like fluorescence spectroscopy and UV–visible spectroscopy. UV-absorption spectroscopy was used to ascertain the structural changes induced by…

Continue Reading Investigating binding dynamics of trans resveratrol to HSA for an efficient displacement of aflatoxin B1 using spectroscopy and molecular simulation

How to generate a free energy Ramachandran plot from a GROMACS MD trajectory if protein has more than 2 residues? : comp_chem

I ran some REMD calculations with GROMACS and wish to create a plot which depicts the free energies of the different regions on the Ramachandran plot of my protein at a specific temperature, similar to figure 2 in the following paper below. Article Antifreeze Glycoproteins Bind Reversibly to Ice via…

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Associate Operations Manager Job Opening in Houston, TX at NuProbe USA Inc.

Associate Operations Manager NuProbe USA is hiring one Associate Operations Manager for its Houston (TX) location. The successful candidate will have the opportunity to join the NuProbe family in the G&A Department reporting directly to the Director of Operations. Essential Job Duties and Responsibilities: Essential responsibilities and duties include, but…

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Bioconductor – AHLRBaseDbs

DOI: 10.18129/B9.bioc.AHLRBaseDbs     LRBaseDbs for AnnotationHub Bioconductor version: Release (3.14) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido…

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NCS v1.8.0: OpenThread: nrf-config.h: No such file or directory – Nordic Q&A – Nordic DevZone

I have a project using NCS v1.8.0 where I enabled openthread. For some reason, when trying to build `mbedtls/library/ecjpake.c`, the make command uses `-DMBEDTLS_CONFIG_FILE=”nrf-config.h”` and fails on: > nrf-config.h: No such file or directory I’m not sure why it tries to use this file because `MBEDTLS_CFG_FILE` is set to `config-tls-generic.h`….

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Novel CRISPR Tool Activates Instead of Editing Human Immune Cell Genes

Scientists at Gladstone Institutes and UC San Francisco (UCSF) say they have co-opted the CRISPR-Cas9 system to forcibly activate genes—rather than edit them—in human immune cells. The method, known as CRISPRa, lets them discover genes that play a role in immune cell biology more thoroughly and rapidly than previously possible,…

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AWS IoT Core Integration with NVIDIA DeepStream error in make command – #3 by AnamikaPaul – DeepStream SDK

Please provide complete information as applicable to your setup. • Hardware Platform (Jetson / GPU) Jetson nano• DeepStream Version 6.00• JetPack Version (valid for Jetson only)• TensorRT Version• NVIDIA GPU Driver Version (valid for GPU only)• Issue Type( questions, new requirements, bugs)• How to reproduce the issue ? (This is…

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DLBCL : Lymphoma_MD_Answers

Hello Doctor (u/Erel_Joffe_MD) , DLBCL, non-germinal, Stage 1A lymphoma diagnosis. However, MRI indicates contiguous infiltration. Please help to advise on the current reported observation of MRI . “MRI indicates soft tissue lesion infiltrating into the right perivertebral region ( infiltrates the perivertebral muscles and abuts the lateral aspects) . vertebrae…

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[gmx-users] why not coordinates from cpt file

Post by gromacs queryHi allI have very simple query. While continuing simulations why we need to use*.gro (-c) with grompp as *.cpt (-t) has all the information (as checkedwith gmxcheck)?cpt file should suffice all the purposes. I tried using grompp providing -t*.cpt file but without -c *.gro file, it does…

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Quip potential – LAMMPS Development

Hi,I am trying to run quip pair_style in lammps ( 9 Nov 21) to perform MD using my trained gap potential. I trained GAP potential for sodium data using distance_2b and soap as descriptors. But when I run the input file, I get the following warnings and no data are…

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[gmx-users] Adaptive Biasing Force method

Post by k***@mech.sharif.irDear GROMACS usersIs there any way� to employ the adaptive biasing force (ABF) methodwith GROMACS ?! If so,� could you please introduce me a tutorial orarticle about it ? I really appreciate it. Available features are described in the manual. Tutorials are found via Google. -Justin—================================================== Justin A….

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Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

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Manufacturing Associate Job Opening in Houston, TX at Nuprobe USA Inc.

MANUFACTURING ASSOCIATE (T1 or T2) NuProbe USA is hiring one Manufacturing Associate (T1 or T2) for its Houston (TX) location. The successful candidate will have the opportunity to join the NuProbe family in the Manufacturing Department reporting directly to the Manufacturing Manager. PRIMARY PURPOSE OF POSITION The new hire will…

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Researchers use CRISPR activation method to reveal “Rosetta Stone” of immune cell function

SAN FRANCISCO, CA—February 4, 2022—CRISPR genome editing has served as a powerful tool for deleting or altering DNA sequences and studying the resulting effect. Now, researchers at Gladstone Institutes and UC San Francisco (UCSF) have co-opted the CRISPR-Cas9 system to forcibly activate genes—rather than edit them—in human immune cells. The…

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[gmx-users] sudden jumps in RMSD etc.

Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, Istill find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then…

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bwa , 2 files fastq to 1 sam

bwa , 2 files fastq to 1 sam 1 i have this problem, please, help me, I’m trying it too from Mac OS Catalina I am creating a sam file, with 2 fastq files, using bwa I apply the following command bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz > V350019555_L03_B5GHUMqcnrRAABA-556.sam…

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Postdoctoral Fellow (Bioinformatics) – Jos Melenhorst Lab

Highly motivated individuals with a PhD or MD/PhD in relevant area are encouraged to apply. This training position, under the direct supervision of a Cleveland Clinic Principal Investigator will provide practical training and experience in a research setting. This position is appointed through the Lerner Research Institute. The successful applicant…

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Front-Line Treatment of DLBCL – NewsBreak

Dr. Lenz on the Rationale for the CheckMate 9X8 in Metastatic CRC Heinz-Josef Lenz, MD, FACP, discusses the rationale for the phase 2/3 CheckMate 9X8 trial in metastatic colorectal cancer. Heinz-Josef Lenz, MD, FACP, associate director, Clinical Research, J. Terrence Lanni Chair in Gastrointestinal Cancer Research, co-director, University of Southern…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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log repeats until it times out)

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

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[gmx-users] Why gyration radius keep dropping?

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

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

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

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Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS  Article  PubMed  Google Scholar  Altamirano C, Illanes A, Casablancas A, Gámez X,…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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ggplot2 – R knitr Markdown: Output Plots within For Loop

I am using child Rmd files in markdown, also works in sweave. in Rmd use following snippet: “`{r run-numeric-md, include=FALSE} out = NULL for (i in c(1:num_vars)) { out = c(out, knit_child(‘da-numeric.Rmd’)) } “` da-numeric.Rmd looks like: Variabele `r num_var_names[i]` ———————————— Missing : `r sum(is.na(data[[num_var_names[i]]]))` Minimum value : `r min(na.omit(data[[num_var_names[i]]]))`…

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Stream episode Is CAR-T Therapy Superior to ASCT for Relapsed/Refractory DLBCL? by Healthcare Unfiltered podcast

published on 2022-01-11T11:58:44Z Continuing his ASH Annual Meeting coverage, Chadi invites Matt Maurer (@MaurerStats), MS, principal biostatistician, Mayo Clinic, and Alan Skarbnik (@ASkarbnik), MD, director of the lymphoma and CLL program, Novant Health (Charlotte, NC), to review the three prominent CAR-T studies in relapsed/refractory DLBCL presented at the meeting. Why…

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Question about MD lammps : comp_chem

Hello everyone, I am trying to model the deposition of a polyelectrolyte on a glass surface to find the time it takes to fully coat the surface. This deposition is based on the difference of charge between the polyelectrolyte and the glass surface. I have created the water model and…

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Solved: rsa_varification using mbedtls libs

I was trying to verify a signature of a binary file using mbedtls library (v2.26.0) I took the reference code from github.com/ARMmbed/mbedtls/blob/v2.26.0/programs/pkey/rsa_verify.c  In the reference code, they are using the mbedtls_md_file() function to calculate the hash of the file.But I’m using the FATFS library to access the files. so I had to modify…

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How to build mbedtls for arm gcc

I want to use mbedtls for my stm32 projects, but I have some problems with building. I have to build mbedtls with arm-none-gcc compiler, right? My command is :(in build directory). CC=/home/jareeeeczek/Arczbit/Firmware/ProgramingRelated/ARM_GCC/gcc-arm-none-eabi-10-2020-q4-major/bin/arm-none-eabi-gcc CFLAGS=’-fstack-protector-strong’ cmake -DUSE_SHARED_MBEDTLS_LIBRARY=On ../ and I have error while compiling test program: none-eabi-10-2020-q4-major/bin/arm-none-eabi-gcc CFLAGS=’-fstack-protector-strong’ cmake – DUSE_SHARED_MBEDTLS_LIBRARY=On ../…

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NIH Study Shows Using CareDx’s AlloSure Lung for Transplant Surveillance is More Effective than Diagnostic Bronchoscopy at Identifying Rejection

SOUTH SAN FRANCISCO, Calif., Jan. 07, 2022 (GLOBE NEWSWIRE) — CareDx, Inc.,  (Nasdaq: CDNA) – The Transplant Company™ focused on the discovery, development, and commercialization of clinically differentiated, high-value healthcare solutions for transplant patients and caregivers – today announced the results of a study led by the National Institutes of…

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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List of software for nanostructures modeling

Three dimensional molecular model of an all-carbon tubular fullerene. This is a list of computer programs that are used to model nanostructures at the levels of classical mechanics[1] and quantum mechanics. Ascalaph Designer Atomistix ToolKit and Virtual NanoLab[2] CST Studio Suite[3] CoNTub Deneb[4] – graphical user interface (GUI) for SIESTA,…

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Sr. Manager of Manufacturing – Resumetojobs.com

NuProbe USA is seeking an experienced Sr. Manager, In-Vitro Diagnostics Operations who will be responsible for all aspects of manufacturing, including design transfer of newly developed products from research & development. The successful candidate will control production planning, scheduling and forecasting. The candidate will lead continuous improvements in manufacturing as…

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[Buildroot] [PATCH 1/2] package/mbedtls3: new package

[Buildroot] [PATCH 1/2] package/mbedtls3: new package * [Buildroot] [PATCH 1/2] package/mbedtls3: new package @ 2021-12-28 15:33 Fabrice Fontaine 2021-12-28 15:33 ` [Buildroot] [PATCH 2/2] package/hiawatha: needs mbedtls3 Fabrice Fontaine 2021-12-28 15:49 ` [Buildroot] [PATCH 1/2] package/mbedtls3: new package Thomas Petazzoni 0 siblings, 2 replies; 5+ messages in thread From: Fabrice…

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Structure relaxation using SIESTA : comp_chem

I want to relax an interface using SIESTA with a method similar to ISIF = 2 in VASP. However, SIESTA has the following options for relaxation, MD.VariableCell = which is analogous to ISIF = 3 in VASP, Constant.Volume = which is analogous to ISIF = 4 in VASP and MD.RelaxCellOnly…

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La Jolla Institute for Immunology hiring Bioinformatics Postdoc – Systems Immunology of Infectious Diseases in San Diego, California, United States

The Peters Lab at the La Jolla Institute for Immunology (LJI) is looking for a bioinformatics postdoc to join our efforts in profiling immune system responses to a variety of infectious agents, such as M. tuberculosis and B. Pertussis, as well as various cancers. Qualified applicants will have the opportunity…

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Visualisation for MD simulations data : comp_chem

I’m a second year phd student running mostly orca calculations on a range of MOFs and quantifying their properties (mostly reaction free energies of adsorption for small molecules). However, from next year I’ll be running some MD simulations to track diffusion of ions through MOF pores. I’m already familiar with…

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