PubMed Journals Articles About "Building Pipeline" RSS

17:57 EDT 25th June 2019 | BioPortfolio

Building Pipeline PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Building Pipeline articles that have been published worldwide.

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Showing "building pipeline" PubMed Articles 1–25 of 1,500+

ppsPCP: A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline.

Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe w...

Open-source pipeline for multi-class segmentation of the spinal cord with deep learning.

This paper presents an open-source pipeline to train neural networks to segment structures of interest from MRI data. The pipeline is tailored towards homogeneous datasets and requires relatively low amounts of manual segmentations (few dozen, or less depending on the homogeneity of the dataset). Two use-case scenarios for segmenting the spinal cord white and grey matter are presented: one in marmosets with variable numbers of lesions, and the other in the publicly available human grey matter segmentation c...

Nurturing a talent pipeline.

Vet nurse , who is a joint venture partner with Vets4Pets, has created a talent pipeline to develop her practices' staff and help with long-term recruitment.

Information and Statistical Analysis Pipeline for High-Throughput RNA Sequencing Data.

Applications of RNA sequencing have been wide-spreading in various subfields of life science. Construction of information and statistical analysis pipeline is indispensable to process raw RNA sequencing (RNA-seq) data generated by next-generation sequencers in order to extract biological implications. In this chapter, we introduce a common pipeline for RNA-seq data. A collection of notes on related advanced topics will be useful when conducting information and statistical analysis in practice.

Common Workflow Language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.

Here, we created an automated pipeline for the de novo-assembly of genomes from PacBio long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb) and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence data sets, and assessed the quality of the assemblies against curated reference genomes.

PhyloPi: An affordable, purpose built phylogenetic pipeline for the HIV drug resistance testing facility.

Phylogenetic analysis plays a crucial role in quality control in the HIV drug resistance testing laboratory. If previous patient sequence data is available sample swaps can be detected and investigated. As Antiretroviral treatment coverage is increasing in many developing countries, so is the need for HIV drug resistance testing. In countries with multiple languages, transcription errors are easily made with patient identifiers. Here a self-contained blastn integrated phylogenetic pipeline can be especially...

Optimising neonatal fMRI data analysis: Design and validation of an extended dHCP preprocessing pipeline to characterise noxious-evoked brain activity in infants.

The infant brain is unlike the adult brain, with considerable differences in morphological, neurodynamic, and haemodynamic features. As the majority of current MRI analysis tools were designed for use in adults, a primary objective of the Developing Human Connectome Project (dHCP) is to develop optimised methodological pipelines for the analysis of neonatal structural, resting state, and diffusion MRI data. Here, in an independent neonatal dataset we have extended and optimised the dHCP fMRI preprocessing p...

Pipeline Embolization of Vertebrobasilar Aneurysms - a Multicenter Case Series.

and purpose: The Pipeline Embolization Device (PED) is being increasingly utilized for treatment of posterior circulation aneurysms. The purpose of this study was to examine the clinical and angiographic outcomes of patients with vertebrobasilar aneurysms treated with the PED.

Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments.

We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data ou...

Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in non-model species.

Mitochondrial resources are of known utility to many fields of phylogenetic, population and molecular biology. Their combination of faster and slower-evolving regions and high copy number enables them to be used in many situations where other loci are unsuitable, with degraded samples and after recent speciation events. The advent of next-generation sequencing technologies (and notably the Illumina platform) has led to an explosion in the number of samples that can be studied at transcriptomic level, at rel...

Acceleration of spleen segmentation with end-to-end deep learning method and automated pipeline.

Delineation of Computed Tomography (CT) abdominal anatomical structure, specifically spleen segmentation, is useful for not only measuring tissue volume and biomarkers but also for monitoring interventions. Recently, segmentation algorithms using deep learning have been widely used to reduce time humans spend to label CT data. However, the computerized segmentation has two major difficulties: managing intermediate results (e.g., resampled scans, 2D sliced image for deep learning), and setting up the system ...

Evaluation of Radiological Features of the Posterior Communicating Artery and their Impact on Efficacy of Saccular Aneurysm Treatment with the Pipeline Embolization Device: A Case Series Study.

Posterior communicating artery segment aneurysms are one of the most frequent intracranial aneurysms. Currently, there is limited literature describing the use of the pipeline embolization device in these aneurysms.

Antibacterials in the pipeline and perspectives for the near future.

Antimicrobial resistance is a global threat to the management of infections in our patients. Sound stewardship of antibacterial agents at our disposal must be accompanied by a concerted effort to develop new agents to bolster our armamentarium. This review will cover the latest antibiotics that have come through the pipeline and the role they can play in the management of infections that are increasingly difficult to treat due to resistance mechanisms.

A Universal Analysis Pipeline of Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes (UMIs).

Hybrid capture-based targeted sequencing is increasingly used for genomic variants profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing PCR biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various studying groups for their own pu...

Efficiency and performance tests of the sorptive building materials that reduce indoor formaldehyde concentrations.

The adsorption of volatile organic compounds by building materials reduces the pollutant concentrations in indoor air. We collected three interior building materials with adsorption potentials-latex paint, micro-carbonized plywood, and moisture-buffering siding-used the sorptive building materials test (SBMT) to determine how much they reduced indoor formaldehyde (HCHO) concentrations, and then assessed the consequent reduction in human cancer risk from HCHO inhalation. Adsorption of HCHO by building materi...

Building a Global Culture of Science - The Vietnam Experience.

We detail the lessons learned, challenges, achievements, and outlook in building a chemistry research center in Vietnam. Through the principles of 'global science', we provide specific insight into the process behind establishing an internationally-competitive research program - a model that is scalable and adaptable to countries beyond Vietnam. Furthermore, we highlight the prospects for success in advancing global science education, research capacity building, and mentorship.

Pipeline embolization device treatment of internal carotid artery terminus aneurysms.

The pipeline embolization device (PED) is approved for the treatment of large aneurysms of the proximal internal carotid artery (ICA). Its off-label application in treating aneurysms located specifically at the ICA terminus (ICA-T) has not been studied.

Reinventing the antimicrobial pipeline in response to the global crisis of antimicrobial-resistant infections.

The pipeline for new antibiotics is dry. Despite the creation of public/private initiatives like Combating Antibiotic Resistant Bacteria Biopharmaceutical Accelerator (Carb-X) and the Antimicrobial Resistance (AMR) Centre, the current focus on 'push-pull' incentives for the pharmaceutical industry still relies on economic return. We propose a joint, internationally-funded antimicrobial development institute that would fund permanent staff to take on roles previously assigned to pharmaceutical companies. Thi...

Outcomes and complications after the use of the pipeline embolization device in the treatment of intracranial aneurysms of the posterior circulation: A systematic review and meta-analysis.

and purpose: The use of the pipeline embolization device (PED) for posterior circulation aneurysms remains controversial. In this meta-analysis, we aimed to explore the safety and efficacy of PED for these aneurysms. Meta regression was used to identify predictors for incomplete aneurysm occlusion and procedure-related complications.

Hemodynamic Fate of the Precommunicating Anterior Cerebral Artery is Predicted by Vessel Dominance after Pipeline Embolization Device Deployment Across the Internal Carotid Artery Terminus.

The Pipeline Embolization Device (PED) is commonly used for treatment of distal internal carotid artery (ICA) aneurysms which often requires placing the stent across the origin of the precommunicating segment of the anterior cerebral artery (ACA-A1). We sought to characterize the clinical and angiographic consequences of this maneuver.

Dementia Matters: User-Building Interactions Shaping Institutional Life in the Netherlands.

In this article, I examine building-user interactions on three dementia wards in the Netherlands. I coin the concept of "sociomaterial awareness" to articulate a collective situational sensitivity to the ways in which the built environment invites its users (professionals, but also people with dementia themselves) to act in specific ways, as well as to possibilities to adjust (elements of) the building. I argue that along with different enactments of dementia, different positions become available for reside...

MRI safety of retained tip and protective coils after faulty deployment of an intracranial Pipeline embolization device: a case report.

The development of flow-diverters such as the Pipeline embolization device (PED) have allowed for safe/effective treatment of challenging and/or previously untreatable intracranial aneurysms. A rare but serious complication during PED deployment involves fracture of single or multiple components, which can lead to retained hardware. To date, there is little data regarding the safety of performing magnetic resonance imaging (MRI) when tip or capture coils remain intracranially.

Prediction and mitigation of train-induced vibrations of large-scale building constructed on subway tunnel.

Among all the recent improvements in the railway industry, ground vibration remains an important showstopper in metropolitan cities. In some particular cases, significant levels of vibration are felt by residents. The role of engineers is to propose mitigation solutions and to ensure that they are efficient in the long-term. This paper presents a numerical study of a large-scale building close to underground networks. A two-step time-frequency prediction method for train-induced vibrations of a superstructu...

Curse: Building expression atlases and co-expression networks from public RNA-Seq data.

Public RNA-Sequencing (RNA-Seq) datasets are a valuable resource for transcriptome analyses, but their accessibility is hindered by the imperfect quality and presentation of their metadata and by the complexity of processing raw sequencing data. The Curse suite was created to alleviate these problems. It consists of an online curation tool named Curse to efficiently build compendia of experiments hosted on the Sequence Read Archive, and a lightweight pipeline named Prose to download and process the RNA-Seq ...

Full-scale practice of domestic wastewater source separation and collection in a semicentralized treatment system: a case study.

Semicentralized supply and treatment systems (SCSTSs), which can realize water, nutrition, and energy recycling via separate water supply and discharge systems, have been developed for fast-growing urban areas. The world's first full-scale SCSTS was implemented in Qingdao in China. Greywater (GW) and blackwater (BW) are collected and treated separately, but the parallel setting of the BW and GW pipelines means that connection mistakes can easily occur. Taking Qingdao as an example, this article analyzes the...

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