Tag: HYBRID

Data Scientist – Molecular Biology job with SRG

Data Scientist London (hybrid, some remote working is possible) Permanent Up to £40k per annum I’m partnering with an exciting and revolutionary MedTech organisation based in London who are hiring for a Data Scientist to join their assay development team. The organisation has developed unique wearable, personalised technology to inform…

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Transverse Sectioning of Mature Rice (Oryza sativa L.) Kernels for Scanning Electron Microscopy Imaging Using Pipette Tips as Immobilization Support

This protocol allows for the preparation of transverse sections of cereal seeds (e.g., rice) for the analysis of endosperm and starch granule morphology using scanning electron microscopy. This protocol allows seeds to be sliced intact so they don’t crumble, permitting visualization of starch granules in any seed that can fit…

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Pair_write with eam/alloy – error – LAMMPS General Discussion

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

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

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

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Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression

There is a need to determine which atherosclerotic lesions will progress in the coronary vasculature to guide intervention before myocardial infarction occurs. This article outlines the biomechanical modeling of arteries from Optical Coherence Tomography using fluid-structure interaction techniques in a commercial finite element solver to help predict this progression. Atherosclerosis…

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Applying manybody potential in Hybrid pair style – #4 by pranavkumar – LAMMPS General Discussion

pranavkumar: It will be great if you can quickly comment Bogus, too. You are ignoring core properties of the EAM model: every time you use multiple EAM pair styles in a hybrid setup, the embedding term will be incorrectly computed. Each instance will compute and apply only the contributions from…

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Using Minimap2 with FMLRC2

Using Minimap2 with FMLRC2 1 Hello all, I am using FMLRC2 (github.com/HudsonAlpha/rust-fmlrc) to correct PacBio reads with Illumina reads for hybrid genome assembly. Since FMLRC2 only corrects reads (does not do any assembly) another program is needed. In the paper published on FMLRC minimap (now succeeded by minimap2, github.com/lh3/minimap2) was…

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Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

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Addressing the Challenges of AAV Production

Adeno-associated virus (AAV) vectors are a versatile and appealing gene therapy delivery platform, capable of targeting a wide range of cell types. However, AAV must be produced in a living system, and issues with scalability and high production costs have so far limited the widespread adoption of the technology. Technology…

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Caribou Biosciences to Present at 40th Annual J.P. Morgan Healthcare Conference

BERKELEY, Calif., Jan. 04, 2022 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq:CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today that Rachel Haurwitz, Ph.D., Caribou’s president and chief executive officer, will present a corporate update at the 40th Annual J.P. Morgan Healthcare Conference on Thursday, January 13, 2022 at…

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RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

Abstract Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However,…

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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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Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

doi: 10.3389/fgene.2021.772557. eCollection 2021. Chun Huang  1 , Fei Ge  1 , Xiaoming Ma  1 , Rongfeng Dai  1 , Renqing Dingkao  2 , Zhuoma Zhaxi  3 , Getu Burenchao  3 , Pengjia Bao  1 , Xiaoyun Wu  1 , Xian Guo  1 , Min Chu  1 , Ping Yan  1 , Chunnian Liang  1 Affiliations Expand Affiliations 1 Key Laboratory of…

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48 Postdoctoral and Academic Positions at The European Molecular Biology Laboratory, Germany

Postdoctoral and Academic Positions at The European Molecular Biology Laboratory (EMBL), a molecular biology research institution, Germany Scientific Officer – Protein Expression and Purification Core Facility Staff Member at EMBL Heidelberg Closes 14 February 2022 |  Grading: Grading: 4, 5 or 6; depending on experience and qualifications (monthly salary starting from 3.1k – 3.8k EUR…

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Scientists Say They Could Bring Back Woolly Mammoths. But Maybe They Shouldn’t | THE DAILY TRIBUNE

Agencies | Washington The Daily Tribune – www.newsofbahrain.com Using recovered DNA to “genetically resurrect” an extinct species — the central idea behind the Jurassic Park films — may be moving closer to reality with the creation this week of a new company that aims to bring back woolly mammoths thousands of years…

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Where Do Species Come From?

The evolutionary biologist Jochen Wolf was working from home when we first spoke, in April, 2020. Germany was under lockdown, and his lab, at Ludwig Maximilian University, in Munich, had been closed for weeks. Still, a reminder of his research had followed him from the office. “I have a crow…

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Kaggle Jane Street competition

1 introduction Kaggle There are a lot of competitions sponsored by hedge funds , It may have become a new type of inner roll , Or maybe you really want to start from Kaggler Get some idea.This time we’re here to learn what has just ended Jane Street Sponsored competition…

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Micromotor-based localized electroporation and gene transfection of mammalian cells [Engineering],Proceedings of the National Academy of Sciences of the United States of America

Herein, we studied localized electroporation and gene transfection of mammalian cells using a metallodielectric hybrid micromotor that is magnetically and electrically powered. Much like nanochannel-based, local electroporation of single cells, the presented micromotor was expected to increase reversible electroporation yield, relative to standard electroporation, as only a small portion of…

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De-extinction Could Reverse Species Loss. But Should We Do It?

THE MOST BELOVED BIRD IN HISTORY may very well have been a 29-year-old pigeon by the name of Martha. It was the early 1900s, shortly before the United States entered the First World War, and Martha was at the height of her fame. Perched on her humble roost at the Cincinnati…

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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The Problem With the Idea To Bring Back Woolly Mammoths

An illustrated recreation of a woolly mammoth, on display at the Royal Victoria Museum, British Columbia. Credit: Thomas Quine/Flickr, CC BY 2.0 Like Sergey Zimov’s ‘Pleistocene Park’, George Church’s company Colossal plans to repopulate the Arctic tundra with woolly mammoths. Church, a genetic engineering expert, plans to splice mammoth genes…

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[lammps-users] Define different intramolecular and intermolecular forces – #2 by akohlmey – LAMMPS Mailing List Mirror

Groups are a dead end, since there is no way to restrict or differentiate pairwise interactions by groups. Thus I think the only way that you can currently realize such a model would be to have different atom types for each molecule and then use the hybrid pair style. So…

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Micromotor-based localized electroporation and gene transfection of mammalian cells

Significance A metallodielectric Janus particle–based micromotor system for local electroporation and gene transfection of a single mammalian cell is studied. This hybrid micromotor is magnetically and electrically propelled with magnetic steering to approach and contact a targeted cell. The targeted cell is then locally electroporated at its contact point with…

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Jennifer Doudna’s CRISPR startup Mammoth Biosciences goes unicorn

The gene-editing tool CRISPR is moving toward the market, promising better tests, disease cures — and maybe even a woolly mammoth. The big picture: CRISPR is already a historic scientific achievement, but we’re just now entering the moment when it will begin to impact patients and possibly the planet. Driving…

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My symmetry-equivalent sites don’t have the same energy

Hello! Help, my symmetry-equivalent sites don’t have the same energy! __The problem:__ My system is insulating and antiferromagnetic Cr2O3 with a positive interstitial H in a hexagonal supercell. There are 6 equivalent* sites in a ‘doughnut’ around a large interstitial region. When I compute the total energy of these sites…

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Scientists say they could bring back woolly mammoths, but maybe they shouldn’t

Artist’s impression of a woolly mammoth in a snow-covered environment. Leonello Calvetti/Stocktrek Imag / Getty Images/Stocktrek Images Using recovered DNA to “genetically resurrect” an extinct species — the central idea behind the Jurassic Park films — may be moving closer to reality with the creation this week of a new…

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scarlet star plant propagation

Humidity – high, Air Plants, Bromeliads, Flowering Plants, Foliage Plants, Garden Plants, Indoor Plants Keep geraniums in winter. For medium sized aquariums it is much better placed as a midground plant only use as a background plant in smaller aquariums. Another nice aspect of . In their natural habitat, most…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars…

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Mammoth-elephant hybrids could be created within the decade. Should they be?

The park’s vision of bringing back ancient grasslands is “an exciting hypothesis,” says University of Maine palaeoecologist Jacquelyn Gill, based on the effects that today’s elephants have on their habitats. However, she cautions that researchers still don’t know the full details of how woolly mammoths’ ecosystems functioned, which complicates efforts…

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A startup wants to bring mammoths back to the Arctic

It’s almost been a decade since Harvard geneticist George Church first talked about using synthetic biology to bring woolly mammoths back to life. Now, his idea to reverse history is pressing forward.  Today, Church and software entrepreneur Ben Lamm announced the launch of their biotech startup, Colossal, with seed funding…

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Strata Oncology Trial Data Support Robustness of NGS Assay for Challenging Samples

NEW YORK – Research from Strata Oncology on a large cohort of cancer patients has shown that the firm’s amplification-based sequencing assay can handle samples that don’t meet the usual requirements for comprehensive genomic profiling (CGP). The company also believes that assays like StrataNGS that only need little tumor tissue…

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Cisco targets net-zero by 2040, Illumina by 2050

Tech giant Cisco has pledged to reach net-zero emissions for operations by 2025 and the supply chain by 2040, while healthcare research and solutions firm Illumina has set a 2050 target. Cisco’s new targets involve reaching net-zero for Scope 1 (direct)…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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GALAXY Workflow for Bacterial Next-Generation Sequencing De Novo Assembly and Annotation

Whole-genome sequencing of prokaryotes is now readily available and affordable on next-generation sequencing platforms. However, the process of de novo assembly can be complicated and tedious for those without a background in computational biology, bioinformatics, or UNIX. Licenses for commercial bioinformatics software may be costly and limited in flexibility. GALAXY…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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chloramphenicol resistance

Using these strains, it is possible to integrate plasmids that carry the complementary ΦC31 att site onto the chromosome (attP, in this figure). Because the mtDNA codes for key OXPHOS polypeptides, genetic alterations in the mtDNA will affect energy metabolism. Proc Natl Acad Sci U S A. 1969 Jun;98(3):1248-57 eCollection…

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Satellite DNA-mediated diversification of a sex-ratio meiotic drive gene family in Drosophila

1. Sandler, L. & Novitski, E. Meiotic drive as an evolutionary force. Am. Nat. 91, 105–110 (1957). Article  Google Scholar  2. Lindholm, A. K. et al. The ecology and evolutionary dynamics of meiotic drive. Trends Ecol. Evol. 31, 315–326 (2016). Article  PubMed  Google Scholar  3. Lyttle, T. W. Segregation distorters….

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Caribou Biosciences Announces Publication of Data Demonstrating High Specificity Genome Editing with its Proprietary chRDNA Technology

Data published in Molecular Cell provide a mechanistic framework to explain the enhanced specificity and key differentiation of Caribou’s proprietary chRDNA technology for therapeutic applications BERKELEY, Calif., Sept. 02, 2021 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq:CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today the publication of data…

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PROPER-Seq Uses NGS to ID Undiscovered Protein-Protein Interactions

NEW YORK – A new method for profiling protein-protein interactions (PPIs) using next-generation sequencing as a readout has the potential to reveal thousands of previously undiscovered combinations in human cells. The method, called PROPER-seq (protein-protein interaction sequencing), tags proteins with RNA barcodes that form chimeric sequences when brought into proximity with…

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Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Caribou Biosciences Announces Publication of Data

Data published in Molecular Cell provide a mechanistic framework to explain the enhanced specificity and key differentiation of Caribou’s proprietary chRDNA technology for therapeutic applications BERKELEY, Calif., Sept. 02, 2021 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq:CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today the publication of data…

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Indian Wolf Among World’s Most Endangered and Distinct Wolves

The Indian wolf could be far more endangered than previously recognized, according to a study from the University of California, Davis, and the scientists who sequenced the Indian wolf’s genome for the first time.  The findings, published in the journal Molecular Ecology, reveal the Indian wolf to be one of…

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Modification of endoglin-targeting nanoliposomes | IJN

Introduction Today, malignant tumors (cancer) still severely imperil human health and cause millions of global mortality rates.1,2 Deep-seated solid tumors are challenging to cure by most therapeutic tools, mainly blamed on the complex tumor microenvironment (TME).3,4 Adoptive cell therapy (ACT), as one of the effective immunotherapeutic means for cancer treatment,…

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Hybrid assembly SPAdes (Ox. Nanopore + Illumina)

Hybrid assembly SPAdes (Ox. Nanopore + Illumina) 0 Hi all, I have both Oxford Nanopore and Illumina sequencing data of a bacterial genome. I would like to perform an hybrid assembly combining the two sequencing techniques. Is SPAdes the most appropriate software to do it? And, I typed the following…

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Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Feasibility of genomic skimming on the ONT minION sequencer The term ’genomic skimming’ was first coined by in 2012 by Straub et al. (2012)20 as a way to utilize shallow sequencing of gDNA to obtain relatively deeper coverage of high-copy portions of the genome, including mitogenomes. In combining genomic skimming…

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Blocking Melanin to Boost Commercial Demand for Tilapia

Source: The CRISPR Journal Scientists at Israel’s Agricultural Research Organization (ARO), Volcani Center in Rishon Lezion, have used CRISPR-Cas9 genome editing tools to create a new strain of tilapia that does not develop suspicious blotches on their skin and instead acquires appealing, uniform, red skins that drive up their commercial…

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lammps – KSpace style for hybrid/overlay table and dipole?

I’m trying to run lammps for a system subject to a custom short-range potential, that I have in a table, as well as the lammps lj/cut/dipole/long interaction (with LJ epsilon set to 0 because I do not want its contribution) with ewald summation. I need to provide a kspace_style for…

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UMAP of TRA/B

Hello, I have output from a single cell sequencing run that has both the VDJ and gene expression data. For the same cells, we also used a hybrid capture approach to sequence the TCR sequences. I have compared the TCR sequences across the two approaches and I have found a…

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[lammps-users] pair_style hybrid/overlay command – #2 by akohlmey – LAMMPS Mailing List Mirror

Dear all, I want to model three different types of atoms in my copper/titanium nitride (Cu/TiN) material model where Cu is deposited on a TiN substrate: Cu is type 1, N is type 2, and Ti is type 3. I want to use an EAM potential to model the interaction…

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