Variations in pre-analytical FFPE sample processing and bioinformatics: challenges for next generation molecular diagnostic testing in clinical pathology

Advances in cellular pathology techniques will improve diagnostic medicine. However, such improvements have to overcome many challenges including variations in pre-analytical sample processing, bioinformatics data analysis and clinical interpretation of data. In order to resolve such challenges, bioinformatics needs to become more tightly coupled to the experimental methodology development

Complete Sequence of pSAM7, an IncX4 Plasmid Carrying a Novel bla[sub]CTX-M-14b Transposition Unit Isolated from ' Escherichia coli ' and ' Enterobacter cloacae ' from cattle

The same plasmid carrying blaCTX-M-14b was identified from an Escherichia coli isolate and an Enterobacter cloacae isolate collected from cattle in the United Kingdom by complete plasmid sequencing. This 35,341-bp plasmid, pSAM7, had an IncX4 backbone that is 99% identical to that of pJIE143 from a human isolate in Australia. PCR screening identified pSAM7-like plasmids in three other E. coli isolates of different multilocus sequence types isolated from cattle on different farms in the United Kingdom

SARS-CoV-2 Infection in the COPD Population is Associated with Increased Healthcare Utilization: An Analysis of Cleveland Clinic\u27s COVID-19 Registry

Background: We sought to determine whether COPD conferred a higher risk for healthcare utilization in terms of hospitalization and clinical outcomes due to COVID-19. Methods: A cohort study with covariate adjustment using multivariate logistic regression was conducted at the Cleveland Clinic Health System in Ohio and Florida. Symptomatic patients aged 35 years and older who were tested for SARS-CoV-2 between March 8 and May 13, 2020 were included. Findings: 15,586 individuals tested for COVID-19 at the Cleveland Clinic between March 8, 2020 and May 13, 2020 met our inclusion criteria. 12.4% of COPD patients (164/1319) tested positive for COVID-19 compared to 16.6% (2363/14,267) of the non-COPD population. 48.2% (79/164) of COVID-19 positive COPD patients required hospitalization and 45.6% (36/79) required ICU admission. After adjustment for covariates, rates of COVID-19 infection were not significantly different than the non-COPD population (adj OR 0.97; CI: 0.89-1.05), but COPD patients had increased healthcare utilization as demonstrated by risk for hospitalization (adj OR 1.36; CI: 1.15-1.60), ICU admission (OR 1.20; CI: 1.02-1.40), and need for invasive mechanical ventilation (adj OR 1.49; CI: 1.28-1.73). Unadjusted risk for in-hospital mortality was higher in the COPD population (OR 1.51; CI: 1.14-1.96). After adjusting for covariates however, the risk for in-hospital mortality was not significantly different than the non-COPD population (adj OR 1.08: CI: 0.81-1.42). Interpretation: Our analysis demonstrated that COPD patients with COVID-19 had a higher risk for healthcare utilization, although adjusted in-hospital mortality risk was not different than the non-COPD patients with COVID-19

(Liquid plus liquid) equilibria of (water plus propionic acid plus dibasic esters) ternary systems

(Liquid + liquid) equilibrium (LLE) data for the solubility curves and tie-line compositions were examined for mixtures of {water (1) + propionic acid (2) + dimethyl succinate or dimethyl glutarate or dimethyl adipate (3)} at T = 298.15 K and atmospheric pressure, (101.3 +/- 0.7) kPa. The relative mutual solubility of the propionic acid is higher in the dibasic esters phases than in the aqueous phase. The reliability of the experimental tie-line data were confirmed by using the Othmer-Tobias correlation. The LLE data of the ternary systems were predicted by UNIFAC and modified UNIFAC methods. Distribution coefficients and separation factors were evaluated for the immiscibility region. (c) 2007 Elsevier Ltd. All rights reserved

Distribution of butyric acid between water and several solvents

Distribution of butyric acid between water and trioctylamine dissolved in 17 solvents (isoamyl alcohol, 1-nonanol, 1-decanol, 1-dodecanol, oleyl alcohol, methyl ethyl ketone, isopropyl methyl ketone, isobutyl methyl ketone, 4-heptanone, ethyl acetate, cyclohexyl acetate, dimethyl phthalate, dibutyl phthalate, tert-butyl methyl ether, kerosene, n-hexane, toluene) and 4 vegetable oils (haselnut, corn, soybean, olive) have been studied at T) 298.15 K. The highest distribution coefficient for butyric acid is shown by trioctylamine dissolved in isoamyl alcohol. As the molar mass of the alcohol increases, the value of the distribution coefficient decreases. In the amine extraction, it was observed that the use of trioctylamine dissolved in alcohol increased the distribution coefficient between 6 and 7 times; dissolving in ketones increased the distribution between 3 and 5 times; dissolving in esters increased it 4 to 9 times; dissolving in tert-butyl methyl ether increased it 2.3 times; dissolving in hydrocarbons increased it 10 to 18 times; and dissolving in vegetable oils increased it 12.5 times, all as compared to use of the pure solvents as extractant

Effects of Variations in Dwyer Osteotomy Determined by 3D-Printed Patient-Specific Modeling

Category: Hindfoot Introduction/Purpose: Dwyer osteotomy is commonly used in surgical correction of heel varus deformity but few studies have reported on the size of wedge removed, and none have reported on location of the osteotomy or angle at which the osteotomy should be made. The purpose of this study is to determine these optimal parameters for surgical correction in patients undergoing Dwyer osteotomy using pre-operative imaging analysis with 3D-printed modeling. Methods: Patients with hindfoot varus deformity who had undergone Dwyer calcaneal osteotomy in a single institution were evaluated. Pre-operative CT scans were used to create a 3D-printed model of the ankle and foot sparing the calcaneus. Multiple identical calcaneus models were 3-D printed to perform different variations of the osteotomy. Osteotomies were done at 10, 15 and 20 mm distal to the posterior calcaneal tuberosity at 3 different angles of 30, 45, and 60 degrees of obliquity and taking out 5 or 10 mm of bony wedge giving us 18 osteotomies for each patient. After fixation, each model was mounted to a fixed platform and posterior and Harris heel views was obtained. The angle between the tibial-talus axis and calcaneal-tuber axis was measured digitally and compared to pre-osteotomy state. We used paired t-test to compare corrections (Figure 1). Results: 54 osteotomies were done on 3 patient specific models. We focused on angles 30 and 45 degrees cuts. 60 degree cuts were excluded from the study, because most of them were impossible to do due to anatomical landmarks. The average degree correction of deformity per mm of bone resected was found to be 2.99 degrees in the posterior view and 1.84 degrees in the Harris Heel view. This correction was not statistically different between 30 and 45 degree cuts or between the location of the osteotomy from the posterior calcaneal tuberosity. Conclusion: This is the first study that a 3D-printed model was used in the analysis of pre-operative imaging prior to Dwyer osteotomy to help determine optimal realignment of the hindfoot. The average degree of correction per mm bone resected was 2.99 degrees in the posterior view and 1.84 in the Harris heel view. A 60 degree cut is not advised because it is not possible for many of the iterations due to limitations of the calcaneal or peroneal tuberosity. This study provides insight into the amount needed to resect to correct the deformity, but the optimal position varies between the patients