Disentangling oncogenic amplicons in esophageal adenocarcinoma.

Esophageal adenocarcinoma is a prominent example of cancer characterized by frequent amplifications in oncogenes. However, the mechanisms leading to amplicons that involve breakage-fusion-bridge cycles and extrachromosomal DNA are poorly understood. Here, we use 710 esophageal adenocarcinoma cases with matched samples and patient-derived organoids to disentangle complex amplicons and their associated mechanisms.

Improving Student Attitudes Toward Autistic Individuals: A Systematic Review.

There is an increasing number of autistic students being educated alongside their neurotypical peers. However, placing a student in the general education setting is not sufficient for meaningful inclusion. Historically, autistic students have had fewer friendships, been less accepted, and experienced stigmatization.

Use of a non-endoscopic immunocytological device (Cytosponge™) for post chemoradiotherapy surveillance in patients with oesophageal cancer in the UK (CYTOFLOC): A multicentre feasibility study.

Background: Effective surveillance strategies are required for patients diagnosed with oesophageal squamous cell carcinoma (OSCC) or adenocarcinoma (OAC) for whom chemoradiotherapy (CRT) is used as a potentially-curative, organ-sparing, alternative to surgery. In this study, we evaluated the safety, acceptability and tolerability of a non-endoscopic immunocytological device (the Cytosponge™) to assess treatment response following CRT.

Methods: This multicentre, single-arm feasibility trial took place in 10 tertiary cancer centres in the UK.

Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity.

Barrett's esophagus is a pre-malignant lesion that can progress to esophageal adenocarcinoma. We perform a multi-omic analysis of pre-cancer samples from 146 patients with a range of outcomes, comprising 642 person years of follow-up. Whole genome sequencing reveals complex structural variants and LINE-1 retrotransposons, as well as known copy number changes, occurring even prior to dysplasia.

The utility of P53 immunohistochemistry in the diagnosis of Barrett's oesophagus with indefinite for dysplasia.

Aims: Barrett's oesophagus with indefinite for dysplasia (BE-IND) is a subjective diagnosis with a low interobserver agreement (IOA) among pathologists and uncertain clinical implications. This study aimed to assess the utility of p53 immunohistochemistry (p53-IHC) in assessing BE-IND specimens.

Methods And Results: Archive endoscopic biopsies with a BE-IND diagnosis from two academic centres were analysed.

Image-Enhanced Endoscopy and Molecular Biomarkers Vs Seattle Protocol to Diagnose Dysplasia in Barrett's Esophagus.

Background & Aims: Dysplasia in Barrett's esophagus often is invisible on high-resolution white-light endoscopy (HRWLE). We compared the diagnostic accuracy for inconspicuous dysplasia of the combination of autofluorescence imaging (AFI)-guided probe-based confocal laser endomicroscopy (pCLE) and molecular biomarkers vs HRWLE with Seattle protocol biopsies.

Methods: Barrett's esophagus patients with no dysplastic lesions were block-randomized to standard endoscopy (HRWLE with the Seattle protocol) or AFI-guided pCLE with targeted biopsies for molecular biomarkers (p53 and cyclin A by immunohistochemistry; aneuploidy by image cytometry), with crossover to the other arm after 6 to 12 weeks.

Charged aerosol detection in early and late-stage pharmaceutical development: selection of regressionmodels at optimum power function value.

In recent years, the use of quantitative liquid chromatography (LC) coupled charged aerosol detection (CAD) for poor UV absorbing analytes in multicomponent mixtures has grown exponentially across academic and industrial sectors. The ballpark of previous LC-CAD reports is focused on practical applications, as well as optimization of critical parameters such as: response dependencies on temperature, nebulization process, analyte volatility, and mobile-phase composition. However, straightforward approaches to deal with the characteristic nonlinear response of CAD still scarce.

Longitudinal tracking of 97 esophageal adenocarcinomas using liquid biopsy sampling.

Background: The incidence of esophageal adenocarcinoma (EAC) is rapidly rising and has a 5-year survival rate of <20%. Beyond TNM (tumor-node-metastasis) staging, no reliable risk stratification tools exist and no large-scale studies have profiled circulating tumor DNA (ctDNA) at relapse in EAC. Here we analyze the prognostic potential of ctDNA dynamics in EAC, taking into account clonal hematopoiesis with indeterminate potential (CHIP).

Genomic copy number predicts esophageal cancer years before transformation.

Recent studies show that aneuploidy and driver gene mutations precede cancer diagnosis by many years. We assess whether these genomic signals can be used for early detection and pre-emptive cancer treatment using the neoplastic precursor lesion Barrett's esophagus as an exemplar. Shallow whole-genome sequencing of 777 biopsies, sampled from 88 patients in Barrett's esophagus surveillance over a period of up to 15 years, shows that genomic signals can distinguish progressive from stable disease even 10 years before histopathological transformation.

Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data.

Background & Aims: Esophageal adenocarcinomas (EACs) are heterogeneous and often preceded by Barrett's esophagus (BE). Many genomic changes have been associated with development of BE and EAC, but little is known about epigenetic alterations. We performed epigenetic analyses of BE and EAC tissues and combined these data with transcriptome and genomic data to identify mechanisms that control gene expression and genome integrity.

Revealing the inner workings of the power function algorithm in Charged Aerosol Detection: A simple and effective approach to optimizing power function value for quantitative analysis.

In recent years, charged aerosol detection (CAD) has become a valuable tool for fast and efficient quantitative chromatographic analysis of drug substances with weak UV absorption. In analytical method development using CAD, the power function settings available in the instrument software are key for linearization of the signal response with respect to analyte concentration. However, the relatively poor understanding of the power function algorithm has limited a more widespread use of CAD for quantitative assays, especially in the late stage of method validation and GMP laboratories.

Kinetics and Degradation Mechanism of Adrenaline Derivative CpQ in Diluted Aqueous Solutions.

The degradation kinetics of an adrenaline (epinephrine) derivative, CpQ, was studied in solution in the pH range of 1-12 at 40-80 °C by high-performance liquid chromatography and ultraviolet-visible spectroscopy. The pH-rate profile exhibits a bell-shaped curve with two sigmoidal regions in the specific acid-catalyzed and specific base-catalyzed regions. The pH range of maximum stability was 2.

A four parameter optimization and troubleshooting of a RPLC - charged aerosol detection stability indicating method for determination of S-lysophosphatidylcholines in a phospholipid formulation.

A four parameter optimization of a stability indicating method for non-chromophoric degradation products of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1-stearoyl-sn-glycero-3-phosphocholine and 2-stearoyl-sn-glycero-3-phosphocholine was achieved using a reverse phase liquid chromatography-charged aerosol detection (RPLC-CAD) technique. Using the hydrophobic subtraction model of selectivity, a core-shell, polar embedded RPLC column was selected followed by gradient-temperature optimization, resulting in ideal relative peak placements for a robust, stability indicating separation. The CAD instrument parameters, power function value (PFV) and evaporator temperature were optimized for lysophosphatidylcholines to give UV absorbance detector-like linearity performance within a defined concentration range.

Cleaning verification: A five parameter study of a Total Organic Carbon method development and validation for the cleaning assessment of residual detergents in manufacturing equipment.

A Total Organic Carbon (TOC) based analytical method to quantitate trace residues of clean-in-place (CIP) detergents CIP100 and CIP200 on the surfaces of pharmaceutical manufacturing equipment was developed and validated. Five factors affecting the development and validation of the method were identified: diluent composition, diluent volume, extraction method, location for TOC sample preparation, and oxidant flow rate. Key experimental parameters were optimized to minimize contamination and to improve the sensitivity, recovery, and reliability of the method.

Failure of Cleaning Verification in Pharmaceutical Industry Due to Uncleanliness of Stainless Steel Surface.

The aim of this work is to identify the parameters that affect the recovery of pharmaceutical residues from the surface of stainless steel coupons. A series of factors were assessed, including drug product spike levels, spiking procedure, drug-excipient ratios, analyst-to-analyst variability, intraday variability, and cleaning procedure of the coupons. The lack of a well-defined procedure that consistently cleaned the coupon surface was identified as the major contributor to low and variable recoveries.

A simplified guide for charged aerosol detection of non-chromophoric compounds-Analytical method development and validation for the HPLC assay of aerosol particle size distribution for amikacin.

Amikacin, an aminoglycoside antibiotic lacking a UV chromophore, was developed into a drug product for delivery by inhalation. A robust method for amikacin assay analysis and aerosol particle size distribution (aPSD) determination, with comparable performance to the conventional UV detector was developed using a charged aerosol detector (CAD). The CAD approach involved more parameters for optimization than UV detection due to its sensitivity to trace impurities, non-linear response and narrow dynamic range of signal versus concentration.

Cleaning verification: Exploring the effect of the cleanliness of stainless steel surface on sample recovery.

The parameters affecting the recovery of pharmaceutical residues from the surface of stainless steel coupons for quantitative cleaning verification method development have been studied, including active pharmaceutical ingredient (API) level, spiking procedure, API/excipient ratio, analyst-to-analyst variability, inter-day variability, and cleaning procedure of the coupons. The lack of a well-defined procedure that consistently cleaned coupon surface was identified as the major contributor to low and variable recoveries. Assessment of acid, base, and oxidant washes, as well as the order of treatment, showed that a base-water-acid-water-oxidizer-water wash procedure resulted in consistent, accurate spiked recovery (>90%) and reproducible results (S≤4%).

Effects of clary sage oil and its main components, linalool and linalyl acetate, on the plasma membrane of Candida albicans: an in vivo EPR study.

The effects of clary sage (Salvia sclarea L.) oil (CS-oil), and its two main components, linalool (Lol) and linalyl acetate (LA), on cells of the eukaryotic human pathogen yeast Candida albicans were studied. Dynamic and thermodynamic properties of the plasma membrane were investigated by electron paramagnetic resonance (EPR) spectroscopy, with 5-doxylstearic acid (5-SASL) and 16-SASL as spin labels.

Analysis of Research Activity in Gastroenterology: Pancreatitis Is in Real Danger.

Objective: Biomedical investment trends in 2015 show a huge decrease of investment in gastroenterology. Since academic research usually provides the basis for industrial research and development (R&D), our aim was to understand research trends in the field of gastroenterology over the last 50 years and identify the most endangered areas.

Methods: We searched for PubMed hits for gastrointestinal (GI) diseases for the 1965-2015 period.

Galectin-1 is a local but not systemic immunomodulatory factor in mesenchymal stromal cells.

Background Aims: Mesenchymal stromal cells (MSCs) have powerful immunosuppressive activity. This function of MSCs is attributed to plethora of the expressed immunosuppressive factors, such as galectin-1 (Gal-1), a pleiotropic lectin with robust anti-inflammatory effect. Nevertheless, whether Gal-1 renders or contributes to the immunosuppressive effect of MSCs has not been clearly established.

Structural background for serological cross-reactivity between bacteria of different enterobacterial serotypes.

The structure of the oligosaccharide repeating units of endotoxins from Gram-negative bacteria is characteristic for the different serogroups and serotypes of bacteria. Detailed examination of the cross-reactions of three enterobacterial serotypes, Proteus morganii O34, Escherichia coli O111, and Salmonella enterica sv. Adelaide O35, was performed using sensitive tests (ELISA, immunoblotting).

Regulation of the unbalanced redox state in a Schizosaccharomyces pombe tert-butyl hydroperoxide-resistant mutant.

The one-gene mutation in the tert-butyl hydroperoxide-resistant mutant hyd1-190 of the fission yeast Schizosaccharomyces pombe led to a 4-fold increase in resistance to t-BuOOH and decreased specific concentrations of superoxide and total thiols in comparison with the parental strain hyd+. It suggested an unbalanced redox state of the cells, which induced continuously increased specific activities of glutathione peroxidase, glutathione reductase and glutathione S-transferase and decreased activities of the antioxidant enzymes superoxide dismutases and glucose-6-phosphate dehydrogenase to regulate the redox balance of the mutation-induced permanent, low-level but tolerable internal stress. These results may contribute to the understanding of internal, oxidative stress-related human diseases.

Citrinin-induced fluidization of the plasma membrane of the fission yeast Schizosaccharomyces pombe.

Citrinin (CTN) is a toxic fungal metabolite that is a hazardous contaminant of foods and feeds. In the present study, its acute toxicity and effects on the plasma membrane of Schizosaccharomyces pombe were investigated. The minimum inhibitory concentration of CTN against the yeast cells proved to be 500 μM.