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PubMed Journals Articles About "Open Source Solution Robust Reproducible Analysis High Content" RSS

15:45 EDT 16th June 2019 | BioPortfolio

Open Source Solution Robust Reproducible Analysis High Content PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Open Source Solution Robust Reproducible Analysis High Content articles that have been published worldwide.

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We have published hundreds of Open Source Solution Robust Reproducible Analysis High Content news stories on BioPortfolio along with dozens of Open Source Solution Robust Reproducible Analysis High Content Clinical Trials and PubMed Articles about Open Source Solution Robust Reproducible Analysis High Content for you to read. In addition to the medical data, news and clinical trials, BioPortfolio also has a large collection of Open Source Solution Robust Reproducible Analysis High Content Companies in our database. You can also find out about relevant Open Source Solution Robust Reproducible Analysis High Content Drugs and Medications on this site too.

Showing "open source solution robust reproducible analysis High Content" PubMed Articles 1–25 of 65,000+

The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.

Affinity proteomics (AP-MS) is growing in importance for characterizing protein-protein interactions (PPIs) in the form of protein complexes and signaling networks. The AP-MS approach necessitates several different software tools, integrated into reproducible and accessible workflows. However, if the scientist (e.g., a bench biologist) lacks a computational background, then managing large AP-MS datasets can be challenging, manually formatting AP-MS data for input into analysis software can be error-prone, a...


Automated Fluorescence Lifetime Imaging High-Content Analysis of Förster Resonance Energy Transfer between Endogenously Labeled Kinetochore Proteins in Live Budding Yeast Cells.

We describe an open-source automated multiwell plate fluorescence lifetime imaging (FLIM) methodology to read out Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) labeling endogenous kinetochore proteins (KPs) in live budding yeast cells. The low copy number of many KPs and their small spatial extent present significant challenges for the quantification of donor fluorescence lifetime in the presence of significant cellular autofluorescence and photobleaching. Automated FLIM data ...

Society of Biomolecular Imaging and Informatics High-Content Screening/High-Content Analysis Preclinical Translational Imaging Colloquium: How Emerging Technologies in Disease Models, High-Content Imaging, and Data Analytics Are Changing Our Approach to Drug Discovery.


High content analysis enables high-throughput nematicide discovery screening for measurement of viability and movement behavior in response to natural product samples.

Historically, monitoring nematode movement and mortality in response to various potential nematicide treatments usually involved tedious manual microscopic analysis. High-content analysis instrumentation enables rapid and high-throughput collection of experimental data points on large numbers of individual worms simultaneously. The high-throughput platform outlined here should accelerate discovery of unique classes and types of promising lead molecules and sample types to control these plant pests. Also, th...

3D Organ Modeling with Open-Source Software.

To date, 3D organ modeling has not reached widespread clinical use, despite showing promise in medical literature. The majority of anatomic modeling that is presented in the literature is performed with proprietary software, presenting certain barriers to use such as price for usage rights. Open-source software not only circumvents this barrier, but also often provides greater customization offered by global communities. In this proof-of-concept experiment, a HeartMate II LVAD was "virtually fit" in a patie...

PyHab: Open-source real time infant gaze coding and stimulus presentation software.

Infant looking-time paradigms often use specialized software for real time manual coding of infant gaze. Here, I introduce PyHab, the first open-source looking-time coding and stimulus presentation solution designed specifically with open science in mind. PyHab is built on the libraries of PsychoPy (Peirce, 2007). PyHab has its own graphical interface for building studies and requires no programming experience to use. When creating a study, PyHab saves a folder that contains all of the code required to run ...

Quantification of Parasite Loads by Automated Microscopic Image Analysis.

High content analysis enables automated, robust, and unbiased evaluation of in vitro Leishmania infection. Here, we describe a protocol based on the infection of THP-1 macrophages with Leishmania promastigotes and the quantification of parasite load by high content analysis. The technique is capable of detecting and quantifying intracellular amastigotes, providing a multiparametric readout of the total number of cells, ratio of infected cells, total number of parasites, and number of parasites per infected ...

A Flexible Open-Source Decision Model for Value Assessment of Biologic Treatment for Rheumatoid Arthritis.

The nature of model-based cost-effectiveness analysis can lead to disputes in the scientific community. We propose an iterative and collaborative approach to model development by presenting a flexible open-source simulation model for rheumatoid arthritis (RA), accessible to both technical and non-technical end-users.

IsoProt: A complete and reproducible workflow to analyse iTRAQ/TMT experiments.

Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence a manuscript's methods section is often insufficient to completely describe and reproduce a data analysis workflow. Here we present IsoProt: A complete and reproducible bioinformatic workf...

Analysis of major carotenoids and fatty acid composition of freshwater microalgae.

Considering the nutraceutical properties, the high commercial value from pigments and essential lipids and the environmental sustainability, the purposes of this study were to assess the major carotenoids and fatty acids composition of nine microalgae species as a source of nutraceutical compounds and as fatty raw material for biodiesel production. The carotenoid and fatty acid content were analyzed by high performance liquid chromatography tandem mass spectrometry detection method with atmospheric pressure...

Attitude confidence and source credibility in information foraging with social tags.

There is growing concern that online information searchers are overconfident and therefore largely search for information which reinforces their prior attitudes, blinded by confirmation bias. This study tests if this effect can be reduced in content aggregation platforms, when social tag clouds show popular topics among experts. We manipulated (1) confidence in prior attitudes, and (2) the credibility of the expert community that tagged the content. We found that both factors influence navigation in differe...

Exactly Robust Kernel Principal Component Analysis.

Robust principal component analysis (RPCA) can recover low-rank matrices when they are corrupted by sparse noises. In practice, many matrices are, however, of high rank and, hence, cannot be recovered by RPCA. We propose a novel method called robust kernel principal component analysis (RKPCA) to decompose a partially corrupted matrix as a sparse matrix plus a high- or full-rank matrix with low latent dimensionality. RKPCA can be applied to many problems such as noise removal and subspace clustering and is s...

Can People Accurately Estimate the Calories in Food Images? An Optimised Set of Low- and High- Calorie Images from the food-pics database.

Calorie intake plays an important role in maintaining a healthy weight. As such, researchers often use the calorie content of food as a distinction when investigating appetite related brain processes and eating behaviour. This distinction assumes that observers accurately perceive caloric content. However, there is evidence suggesting this is not always the case. The current study examined how accurately observers could estimate the caloric content of food images from the widely used "Food-pics" database. E...

OpenCASA: A new open-source and scalable tool for sperm quality analysis.

In the field of assisted reproductive techniques (ART), computer-assisted sperm analysis (CASA) systems have proved their utility and potential for assessing sperm quality, improving the prediction of the fertility potential of a seminal dose. Although most laboratories and scientific centers use commercial systems, in the recent years certain free and open-source alternatives have emerged that can reduce the costs that research groups have to face. However, these open-source alternatives cannot analyze spe...

Diurnal biomarkers reveal key photosynthetic genes associated with increased oil palm yield.

To investigate limiters of photosynthate assimilation in the carbon-source limited crop, oil palm (Elaeis guineensis Jacq.), we measured differential metabolite, gene expression and the gas exchange in leaves in an open field for palms with distinct mesocarp oil content. We observed higher concentrations of glucose 1-phosphate, glucose 6-phosphate, sucrose 6-phosphate, and sucrose in high-oil content palms with the greatest difference being at 11:00 (p-value ≤0.05) immediately after the period of low morn...

3D Cell-Based Assays for Drug Screens: Challenges in Imaging, Image Analysis, and High-Content Analysis.

The introduction of more relevant cell models in early preclinical drug discovery, combined with high-content imaging and automated analysis, is expected to increase the quality of compounds progressing to preclinical stages in the drug development pipeline. In this review we discuss the current switch to more relevant 3D cell culture models and associated challenges for high-throughput screening and high-content analysis. We propose that overcoming these challenges will enable front-loading the drug discov...

Construction of Mini-Chemostats for High-throughput Strain Characterization.

To achieve large-scale, high-throughput experiments for systems biology research of microorganisms, reliable data from robust cultivation systems are needed. Chemostats are such systems, ensuring reproducibility and quality by providing a stable, well controlled environment for the cells. However, many of the available chemostat systems require large amounts of media and are complex to set up and expensive to purchase and maintain. To address these concerns, we developed a mini-chemostat system with 16 reac...

Development and validation of an open source Monte Carlo dosimetry model for wide-beam CT scanners using Fluka.

Development and validation of an open source Fluka-based Monte Carlo source model for diagnostic patient dose calculations.

Correction to: Collaborative and Reproducible Research: Goals, Challenges, and Strategies.

The paper below had been published originally without open access, but has been republished with open access.

Genotypic Variation and Biofortification with Selenium in Brazilian Wheat Cultivars.

Selenium is essential to human and animal health, as it regulates glutathione peroxidase activity. Although not considered essential to plants, it may be beneficial to plant growth and development at low concentrations. This study evaluated the effect of selenate application on Se biofortification, macro- and micronutrient content, and the expression of genes involved in Se uptake and assimilation in 12 Brazilian wheat ( L.) cultivars. This nutrient-solution experiment was performed in a greenhouse and cons...

The conventional gait model, an open-source implementation that reproduces the past but prepares for the future.

The Conventional Gait Model (CGM), known by a variety of different names, is widely used in clinical gait analysis. We present pyCGM2, an open-source implementation of the CGM with two versions. The first, CGM1.0, is a clone of Vicon Plug In Gait (PiG) with all its variants. CGM1.0 provides a platform to test the effect of modifications to the CGM on data collected and processed retrospectively or to provide backward compatibility. The second version, CGM1.1, offers some practical modifications and includes...

Quantification of T-Cell Migratory Phenotypes Using High-Content Analysis.

The exploration screening of phenotypic changes in motile T-cells within a signaling environment has always been an arduous task due to the sheer population of these microscopic cells. In recent years, High-Content Analysis (HCA) has gained epochal momentum and has allowed for a wider range of quantitative multiplexed cell-based assays in the field of lymphocyte signaling. In this chapter, we consolidate our understanding and describe the technical approach and methodology to quantify T-cell migratory pheno...

Applicability assessment of empty fruit bunches from palm oil mills for use as bio-solid refuse fuels.

Palm kernel shells (PKS), empty fruit bunches (EFB), and trunks are by-products of the palm oil industry and form approximately 50 wt % of fresh fruit bunch (FFB). In particular, EFB accounts for approximately 20 wt % of FFB. Although large amounts of EFB are generated from palm oil mills every year in Indonesia and Malaysia, EFB is treated as waste because commercial technologies for thermo-chemical conversion of EFB into renewable energy are still under development. A robust conversion method can tran...

Technical Note: Design and Implementation of a High Throughput Pipeline for Reconstruction and Quantitative Analysis of CT Image Data.

With recent substantial improvements in modern computing, interest in quantitative imaging with CT has seen a dramatic increase. As a result, the need to both create and analyze large, high-quality datasets of clinical studies has increased as well. At present, no efficient, widely-available method exists to accomplish this. The purpose of this technical note is to describe an open-source high-throughput computational pipeline framework for the reconstruction and analysis of diagnostic CT imaging data to co...

Polymer Microarrays for the Discovery and Optimization of Robust Optical Fibre-based pH Sensors.

Polymer microarrays were utilized for the high-throughput screening and discovery of optimal polymeric substrates capable of trapping functional ratiometric fluorescence-based pH sensors. This lead to the identification of poly (methyl methacrylate-co-2-(dimethylamino) ethyl acrylate) (PA101) that allowed, via dip coating, the attachment of fluorescent pH sensors onto the tip of optical fibres that exhibited robust, rapid and reproducible sensing of physiological pH's.


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