RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding.

Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology optimized for samples of fresh cells. Complexes of one cell paired with one barcoded bead are stabilized by a chemical linker and dispersed in a hydrogel in the liquid state. Upon gelation on ice the complexes are immobilized and physically separated without requiring nanowells or droplets.

High-sensitivity SARS-CoV-2 group testing by digital PCR among symptomatic patients in hospital settings.

Background: Worldwide demand for SARS-CoV-2 RT-PCR testing is still high as testing remains central to follow the disease spread and vaccine efficacy. Group testing has been proposed as a solution to expand testing capabilities but sensitivity concerns may limit its impact on the management of the pandemic. Digital PCR (RT-dPCR) has been shown to be highly sensitive and could help by providing larger testing capabilities without compromising sensitivity.

Correction: C797S, T790M and sensitizing mutations in non-small cell lung cancer revealed by six-color crystal digital PCR.

[This corrects the article DOI: 10.18632/oncotarget.26446.

C797S, T790M and sensitizing mutations in non-small cell lung cancer revealed by six-color crystal digital PCR.

Background: Detection of sensitizing and p.T790M and p.C797S resistance mutations is particularly important for non-small cell lung cancer (NSCLC) patient therapy management.

Detection of lipoarabinomannan in urine and serum of HIV-positive and HIV-negative TB suspects using an improved capture-enzyme linked immuno absorbent assay and gas chromatography/mass spectrometry.

TB diagnosis and treatment monitoring in resource limited regions rely heavily on serial sputum smear microscopy and bacterial culture. These microbiological methods are time-consuming, expensive and lack adequate sensitivity. The WHO states that improved TB diagnosis and treatment is imperative to achieve an end to the TB epidemic by 2030.

The effects of iatrogenic blood contamination on total nucleated cell counts and protein concentrations in canine cerebrospinal fluid.

Background: Cerebrospinal fluid (CSF) might be altered by iatrogenic blood contamination, precluding accurate diagnostic interpretation.

Objectives: Available formulas to correct for iatrogenic blood contamination are likely unreliable. Study objectives were to determine the effects of blood contamination on total nucleated cell counts (NCCs) and protein concentrations in canine CSF.

Nod2 is required for antigen-specific humoral responses against antigens orally delivered using a recombinant Lactobacillus vaccine platform.

Safe and efficacious orally-delivered mucosal vaccine platforms are desperately needed to combat the plethora of mucosally transmitted pathogens. Lactobacillus spp. have emerged as attractive candidates to meet this need and are known to activate the host innate immune response in a species- and strain-specific manner.

Crystal digital droplet PCR for detection and quantification of circulating EGFR sensitizing and resistance mutations in advanced non-small cell lung cancer.

Over the past years, targeted therapies using tyrosine kinase inhibitors (TKI) have led to an increase in progression-free survival and response rate for a subgroup of non-small cell lung cancer (NSCLC) patients harbouring specific gene abnormalities compared with chemotherapy. However long-lasting tumor regression is rarely achieved, due to the development of resistant tumoral subclones, which requires alternative therapeutic approaches. Molecular profile at progressive disease is a challenge for making adaptive treatment decisions.

Metabolic differentiation of early Lyme disease from southern tick-associated rash illness (STARI).

Lyme disease, the most commonly reported vector-borne disease in the United States, results from infection with Early clinical diagnosis of this disease is largely based on the presence of an erythematous skin lesion for individuals in high-risk regions. This, however, can be confused with other illnesses including southern tick-associated rash illness (STARI), an illness that lacks a defined etiological agent or laboratory diagnostic test, and is coprevalent with Lyme disease in portions of the eastern United States. By applying an unbiased metabolomics approach with sera retrospectively obtained from well-characterized patients, we defined biochemical and diagnostic differences between early Lyme disease and STARI.

Type 1 Reaction in Patients With Leprosy Corresponds to a Decrease in Proresolving Lipid Mediators and an Increase in Proinflammatory Lipid Mediators.

Background: Type 1 reaction (T1R) is an acute T-helper type 1 (Th1) inflammatory episode in patients with leprosy. While immunological responses associated with T1R have been investigated, the corresponding metabolic responses that could contribute to T1R pathology have received little attention.

Methods: Metabolomics-based analyses of sera from 7 patients with and 9 without T1R were conducted via liquid chromatography-mass spectrometry.

Temporal and Spatial Variability of Entomological Risk Indices for West Nile Virus Infection in Northern Colorado: 2006-2013.

West Nile virus (WNV) is enzootic in northern Colorado. Annual surveillance activities in Fort Collins, CO, include collecting female Culex mosquitoes and testing them for the presence of WNV RNA in order to calculate 1) Culex female abundance, 2) WNV infection rate, and 3) the vector index (VI). These entomological risk indices inform public policy regarding the need for emergency adulticiding.

Semi-automated query construction for content-based endomicroscopy video retrieval.

Content-based video retrieval has shown promising results to help physicians in their interpretation of medical videos in general and endomicroscopic ones in particular. Defining a relevant query for CBVR can however be a complex and time-consuming task for non-expert and even expert users. Indeed, uncut endomicroscopy videos may very well contain images corresponding to a variety of different tissue types.

Online blind calibration of non-uniform photodetectors: application to endomicroscopy.

We present an original method for the online blind calibration of non-uniform photodetectors. The disparity of the detectors may arise from both irregular spatial arrangement and distinct slowly time-varying photometric transfer functions. As natural images are mostly continuous, the signal collected by neighboring detectors is strongly correlated over time.

Software for automated classification of probe-based confocal laser endomicroscopy videos of colorectal polyps.

Aim: To support probe-based confocal laser endomicroscopy (pCLE) diagnosis by designing software for the automated classification of colonic polyps.

Methods: Intravenous fluorescein pCLE imaging of colorectal lesions was performed on patients undergoing screening and surveillance colonoscopies, followed by polypectomies. All resected specimens were reviewed by a reference gastrointestinal pathologist blinded to pCLE information.

Learning semantic and visual similarity for endomicroscopy video retrieval.

Content-based image retrieval (CBIR) is a valuable computer vision technique which is increasingly being applied in the medical community for diagnosis support. However, traditional CBIR systems only deliver visual outputs, i.e.

Retrieval evaluation and distance learning from perceived similarity between endomicroscopy videos.

Evaluating content-based retrieval (CBR) is challenging because it requires an adequate ground-truth. When the available groundtruth is limited to textual metadata such as pathological classes, retrieval results can only be evaluated indirectly, for example in terms of classification performance. In this study we first present a tool to generate perceived similarity ground-truth that enables direct evaluation of endomicroscopic video retrieval.

A smart atlas for endomicroscopy using automated video retrieval.

To support the challenging task of early epithelial cancer diagnosis from in vivo endomicroscopy, we propose a content-based video retrieval method that uses an expert-annotated database. Motivated by the recent successes of non-medical content-based image retrieval, we first adjust the standard Bag-of-Visual-Words method to handle single endomicroscopic images. A local dense multi-scale description is proposed to keep the proper level of invariance, in our case to translations, in-plane rotations and affine transformations of the intensities.

An image retrieval approach to setup difficulty levels in training systems for endomicroscopy diagnosis.

Learning medical image interpretation is an evolutive process that requires modular training systems, from non-expert to expert users. Our study aims at developing such a system for endomicroscopy diagnosis. It uses a difficulty predictor to try and shorten the physician learning curve.