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PubMed Journals Articles About "Quantitative Tracking Combinatorially Engineered Populations With Multiplexed Binary" RSS

09:35 EDT 19th September 2018 | BioPortfolio

Quantitative Tracking Combinatorially Engineered Populations With Multiplexed Binary PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Quantitative Tracking Combinatorially Engineered Populations With Multiplexed Binary articles that have been published worldwide.

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Showing "Quantitative tracking combinatorially engineered populations with multiplexed binary" PubMed Articles 1–25 of 11,000+

Tracking of Engineered Bacteria In Vivo Using Non-Standard Amino Acid Incorporation.

The rapidly growing field of microbiome research presents a need for better methods of monitoring gut microbes in vivo with high spatial and temporal resolution. We report a method of tracking microbes in vivo within the gastrointestinal tract by programming them to incorporate non-standard amino acids (NSAA) and labeling them via click chemistry. Using established machinery constituting an orthogonal translation system (OTS), we engineered Escherichia coli to incorporate p-azido-L-phenylalanine (pAzF) in p...


Elucidating the Burden of HIV in Tissues Using Multiplexed Immunofluorescence and In Situ Hybridization: Methods for the Single-Cell Phenotypic Characterization of Cells Harboring HIV In Situ.

Persistent tissue reservoirs of HIV present a major barrier to cure. Defining subsets of infected cells in tissues is a major focus of HIV cure research. Herein, we describe a novel multiplexed in situ hybridization (ISH) (RNAscope) protocol to detect HIV-DNA (vDNA) and HIV-RNA (vRNA) in formalin-fixed paraffin-embedded (FFPE) human tissues in combination with immunofluorescence (IF) phenotyping of the infected cells. We show that multiplexed IF and ISH (mIFISH) is suitable for quantitative assessment of HI...

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage.

A lack of analytically robust and multiplexed assays has hampered studies of the large, branched phosphosignaling network responsive to DNA damage. To address this need, we developed and fully analytically characterized a 62-plex assay quantifying protein expression and post-translational modification (phosphorylation and ubiquitination) after induction of DNA damage. The linear range was over 3 orders of magnitude, the median inter-assay variability was 10% CV and the vast majority (∼85%) of assays were ...


A multiplexed quantitative MALDI MS approach for assessing activity and inhibition of protein kinases based on post-enrichment dephosphorylation of phosphopeptides by MOF-templated porous CeO2.

Protein kinase is regarded as a potential target for anticancer therapeutics due to its relation to many diseases, in which more than one kinase participates in the cell signaling cascades. We herein demonstrate a multiplexed quantitative matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) approach to simultaneously assess the activity and inhibition of multiple protein kinases. In this design, substrate peptides phosphorylated by kinases of interest are specifically harvested by MOF-te...

Engineered reciprocal chromosome translocations drive high threshold, reversible population replacement in Drosophila.

Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions using gene drive provides a self-perpetuating method of disease prevention. Mechanisms that require the gene drive element and linked cargo to exceed a high threshold frequency in order for spread to occur are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminat...

Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster.

Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitation...

Visual Tracking via Dynamic Graph Learning.

Existing visual tracking methods usually localize a target object with a bounding box, in which the performance of the foreground object trackers or detectors is often affected by the inclusion of background clutter. To handle this problem, we learn a patch-based graph representation for visual tracking. The tracked object is modeled by with a graph by taking a set of non-overlapping image patches as nodes, in which the weight of each node indicates how likely it belongs to the foreground and edges are weig...

A digital approach to dynamic jaw tracking using a target tracking system and a structured-light three-dimensional scanner.

This technical procedure describes a method for tracking mandibular movement using a three-dimensional (3D) optical scanner and target tracking system to digitally portray the motion of the mandible and temporomandibular joints by merging cone beam computed tomography (CBCT) data.

Single-shot quantitative phase microscopy based on color-multiplexed Fourier ptychography.

We present a single-shot quantitative phase imaging (QPI) method based on color-multiplexed Fourier ptychographic microscopy (FPM). Three light-emitting diode (LED) elements with respective R/G/B channels in a programmable LED array illuminate the specimen simultaneously, providing triangle oblique illuminations matching the numerical aperture of the objective precisely. A color image sensor records the light transmitted through the specimen, and three monochromatic intensity images at each color channel ar...

High-Throughput Signaling Profiling in Blood Platelets by Multiplexed Phosphoflow Cytometry.

Multiplexed phosphoflow cytometry is a novel method that provides rapid and quantitative readouts on intracellular phosphoprotein signaling. In this approach, flow cytometry is combined with fluorescent cell barcoding (FCB) to facilitate high-throughput analyses of signaling events. After stimulation, fixed and permeabilized platelets are labeled with distinct dye intensities to create unique fluorescent signatures for individual samples. These uniquely labeled samples can be combined for simultaneous antib...

Detection of Sub-fM DNA with Target Recycling and Self-Assembly Amplification on Graphene Field Effect Biosensors.

All-electronic DNA biosensors based on graphene field effect transistors (GFETs) offer the prospect of simple and cost-effective diagnostics. For GFET sensors based on complementary probe DNA, the sensitivity is limited by the binding affinity of the target oligonucleotide, in the nM-range for 20-mer targets. We report a ~20,000× improvement in sensitivity through the use of engineered hairpin probe DNA that allows for target recycling and hybridization chain reaction. This enables detection of 21-mer targ...

Gender identity disparities in Pap test use in a sample of binary and non-binary transmasculine adults.

Modeling CNS Myelination Using Micropillar Arrays.

Myelination necessitates axons to initiate concentric membrane wrapping by oligodendroglia in the CNS. Here, we describe an in vitro system that models CNS myelination with a minimally permissive environment, termed Binary Indicant for myelination using Micropillar Arrays (BIMA). Engineered with conical micropillar arrays, BIMA allows for rapid translation of oligodendroglial wrapping and differentiation into binary readout under confocal microscopy. Fabricated into 96- or 384-well plates, BIMA serves as a ...

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging.

The immune system is critical in modulating cancer progression, but knowledge of immune composition, phenotype, and interactions with tumor is limited. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to simultaneously quantify in situ expression of 36 proteins covering identity, function, and immune regulation at sub-cellular resolution in 41 triple-negative breast cancer patients. Multi-step processing, including deep-learning-based segmentation, revealed variability in the composition of...

Evaluation of the accuracy of the CyberKnife Synchrony Respiratory Tracking System using a plastic scintillator.

The Synchrony Respiratory Tracking System of the CyberKnife Robotic Radiosurgery System (Accuray, Inc., Sunnyvale CA) enables real-time tracking of moving targets such as lung and liver tumors during radiotherapy. Although film measurements have been used for quality assurance of the tracking system, they cannot evaluate the temporal tracking accuracy. We have developed a verification system using a plastic scintillator that can evaluate the temporal accuracy of the CyberKnife Synchrony.

Investigating MLC tracking in stereotactic arrhythmic radioablation (STAR) treatments for atrial fibrillation.

Stereotactic arrhythmia radioablation (STAR) is an emerging treatment option for atrial fibrillation (AF). However, it faces possibly the most challenging motion compensation scenario: both respiratory and cardiac motion. MLC tracking is clinically used for lung cancer treatments but its capabilities with intracardiac targets is unknown. We report the first experimental results of MLC tracking for intracardiac targets. Methods: Five AF STAR plans of varying complexity were created. All delivered...

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile.

Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) in 189 C. difficile samples. The binary typing, ribotyping and MLST typed the samples into 53 binary types (BTs),...

An extended Kalman filter for mouse tracking.

Animal tracking is an important tool for observing behavior, which is useful in various research areas. Animal specimens can be tracked using dynamic models and observation models that require several types of data. Tracking mouse has several barriers due to the physical characteristics of the mouse, their unpredictable movement, and cluttered environments. Therefore, we propose a reliable method that uses a detection stage and a tracking stage to successfully track mouse. The detection stage detects the su...

What is "Non-Binary" and What Do I Need to Know? A Primer for Surgeons Providing Chest Surgery for Transgender Patients.

The majority of transgender research focuses on patients who fall within the gender binary of either trans-male or trans-female. This largely omits understanding of the "non-binary" gender identity, as it pertains to surgical care.

The Usability and Acceptability of a Patient-Centered Mobile Health Tracking App Among a Sample of Adult Radiation Oncology Patients.

The usability and acceptability of patient-centered mobile health tracking apps among most clinical populations are unknown. This mixed-methods feasibility study evaluated the usability and acceptability of the Health Storylines app among 32 adult radiation oncology patients in a 2-week trial. Data were collected via pre- and post-app use surveys and digital analytics. Participants accessed the app platform a total of 711 times. The overall usability of the Heath Storylines app was rated favorably, and 81% ...

Hilbert-Huang single-shot spatially multiplexed interferometric microscopy.

Hilbert-Huang single-shot spatially multiplexed interferometric microscopy (H2S2MIM) is presented as the implementation of a robust, fast, and accurate single-shot phase estimation algorithm with an extremely simple, low-cost, and highly stable way to convert a bright field microscope into a holographic one using partially coherent illumination. Altogether, H2S2MIM adds high-speed (video frame rate) quantitative phase imaging capability to a commercially available nonholographic microscope with improved pha...

DNA-Mediated Size-Selective Nanoparticle Assembly for Multiplexed Surface Encoding.

Multiplexed surface encoding is achieved by positioning two different sizes of gold nanocubes on gold surfaces with precisely defined locations for each particle via template-confined, DNA-mediated nanoparticle assembly. As a proof-of-concept demonstration, cubes with 86 and 63 nm edge lengths are assembled into arrangements that physically and spectrally encrypt two sets of patterns in the same location. These patterns can be decrypted by mapping the absorption intensity of the substrate at λ = 773 and 68...

Methylcellulose and polyacrylate binary hydrogels used as rectal suppository to prevent type I diabetes.

The purpose of this study was to fabricate a novel binary hydrogel, and the insulin-loaded hydrogel was used as rectal suppository to prevent type I diabetes. The binary hydrogel was synthesized via solution polymerization. Its structure was studied by Fourier transform infrared spectroscopy (FTIR) and Raman spectra. The swelling behaviors of binary hydrogels were revealed in pH 1.2, 6.8 and 7.4 buffers, respectively. Their inner morphologies were observed with a scanning electron microscope (SEM). Insulin ...

Multiplexed Quantitation of Intraphagocyte Mycobacterium tuberculosis Secreted Protein Effectors.

The pathogenic potential of Mycobacterium tuberculosis largely depends on ESX secretion systems exporting members of the multigenic Esx, Esp, and PE/PPE protein families. To study the secretion and regulation patterns of these proteins while circumventing immune cross-reactions due to their extensive sequence homologies, we developed an approach that relies on the recognition of their MHC class II epitopes by highly discriminative T cell receptors (TCRs) of a panel of T cell hybridomas. The latter were e...

The effect of concurrent hand movement on estimated time to contact in a prediction motion task.

In many activities, we need to predict the arrival of an occluded object. This action is called prediction motion or motion extrapolation. Previous researchers have found that both eye tracking and the internal clocking model are involved in the prediction motion task. Additionally, it is reported that concurrent hand movement facilitates the eye tracking of an externally generated target in a tracking task, even if the target is occluded. The present study examined the effect of concurrent hand movement on...


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