Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation.Peer reviewe

Pre-hospital CPR and early REBOA in trauma patients-results from the ABOTrauma Registry

Publisher Copyright: © 2020 The Author(s).Background: Severely injured trauma patients suffering from traumatic cardiac arrest (TCA) and requiring cardiopulmonary resuscitation (CPR) rarely survive. The role of resuscitative endovascular balloon occlusion of the aorta (REBOA) performed early after hospital admission in patients with TCA is not well-defined. As the use of REBOA increases, there is great interest in knowing if there is a survival benefit related to the early use of REBOA after TCA. Using data from the ABOTrauma Registry, we aimed to study the role of REBOA used early after hospital admission in trauma patients who required pre-hospital CPR. Methods: Retrospective and prospective data on the use of REBOA were collected from the ABOTrauma Registry from 11 centers in seven countries globally between 2014 and 2019. In all patients with pre-hospital TCA, the predicted probability of survival, calculated with the Revised Injury Severity Classification II (RISC II), was compared with the observed survival rate. Results: Of 213 patients in the ABOTrauma Registry, 26 patients (12.2%) who had received pre-hospital CPR were identified. The median (range) Injury Severity Score (ISS) was 45.5 (25-75). Fourteen patients (54%) had been admitted to the hospital with ongoing CPR. Nine patients (35%) died within the first 24 h, while seventeen patients (65%) survived post 24 h. The survival rate to hospital discharge was 27% (n = 7). The predicted mortality using the RISC II was 0.977 (25 out of 26). The observed mortality (19 out of 26) was significantly lower than the predicted mortality (p = 0.049). Patients not responding to REBOA were more likely to die. Only one (10%) out of 10 non-responders survived. The survival rate in the 16 patients responding to REBOA was 37.5% (n = 6). REBOA with a median (range) duration of 45 (8-70) minutes significantly increases blood pressure from the median (range) 56.5 (0-147) to 90 (0-200) mmHg. Conclusions: Mortality in patients suffering from TCA and receiving REBOA early after hospital admission is significantly lower than predicted by the RISC II. REBOA may improve survival after TCA. The use of REBOA in these patients should be further investigated.Peer reviewe

The analysis of predictability of alpha-decay half-life formulae and the alpha partial half-lives of some exotic nuclei

The predictabilities of the three alpha-decay half-life formulae, the Royer GLDM, the Viola-Seaborg and the Sobiczewski-Parkhomenko formulae, have been evaluated by developing a method based on the ansatz of standard experimental benchmarking. The coefficients of each formula were re-derived using the reliable data of the alpha-standards nuclei. The modified formulae that resulted were used to evaluate the accuracies of the formulae towards the prediction of half-lives of a set of nuclides with well-studied alpha- spectroscopic data as well as a set of exotic alpha-emitters. Further, a simple linear optimization of the modified formulae allowed adjustments for the insufficient statistics of the primary data set without changing the modified formulae. While the three modified formulae showed equivalent results for all the medium heavy nuclei except the odd-odd, the modified GLDM showed relatively the best figures of merit for the odd-odd and superheavy nuclides.Comment: 16 pages, 4 tables, 2 figure

Identification and quantification of microplastics in wastewater using focal plane array-based reflectance micro-FT-IR imaging

Microplastics (<5 mm) have been documented in environmental samples on a global scale. While these pollutants may enter aquatic environments via wastewater treatment facilities, the abundance of microplastics in these matrices has not been investigated. Although efficient methods for the analysis of microplastics in sediment samples and marine organisms have been published, no methods have been developed for detecting these pollutants within organic-rich wastewater samples. In addition, there is no standardized method for analyzing microplastics isolated from environmental samples. In many cases, part of the identification protocol relies on visual selection before analysis, which is open to bias. In order to address this, a new method for the analysis of microplastics in wastewater was developed. A pretreatment step using 30% hydrogen peroxide (H2O2) was employed to remove biogenic material, and focal plane array (FPA)-based reflectance micro-Fourier-transform (FT-IR) imaging was shown to successfully image and identify different microplastic types (polyethylene, polypropylene, nylon-6, polyvinyl chloride, polystyrene). Microplastic-spiked wastewater samples were used to validate the methodology, resulting in a robust protocol which was nonselective and reproducible (the overall success identification rate was 98.33%). The use of FPA-based micro-FT-IR spectroscopy also provides a considerable reduction in analysis time compared with previous methods, since samples that could take several days to be mapped using a single-element detector can now be imaged in less than 9 h (circular filter with a diameter of 47 mm). This method for identifying and quantifying microplastics in wastewater is likely to provide an essential tool for further research into the pathways by which microplastics enter the environment.This work is funded by a NERC (Natural Environment Research Council) CASE studentship (NE/K007521/1) with contribution from industrial partner Fera Science Ltd., United Kingdom. The authors would like to thank Peter Vale, from Severn Trent Water Ltd, for providing access to and additionally Ashley Howkins (Brunel University London) for providing travel and assistance with the sampling of the Severn Trent wastewater treatment plant in Derbyshire, UK. We are grateful to Emma Bradley and Chris Sinclair for providing helpful suggestions for our research

Genetic analysis of D-xylose metabolism by endophytic yeast strains of Rhodotorula graminis and Rhodotorula mucilaginosa

Two novel endophytic yeast strains, WP1 and PTD3, isolated from within the stems of poplar (Populus) trees, were genetically characterized with respect to their xylose metabolism genes. These two strains, belonging to the species Rhodotorula graminis and R. mucilaginosa, respectively, utilize both hexose and pentose sugars, including the common plant pentose sugar, D-xylose. The xylose reductase (XYL1) and xylitol dehydrogenase (XYL2) genes were cloned and characterized. The derived amino acid sequences of xylose reductase (XR) and xylose dehydrogenase (XDH) were 32%∼41% homologous to those of Pichia stipitis and Candida. spp., two species known to utilize xylose. The derived XR and XDH sequences of WP1 and PTD3 had higher homology (73% and 69% identity) with each other. WP1 and PTD3 were grown in single sugar and mixed sugar media to analyze the XYL1 and XYL2 gene regulation mechanisms. Our results revealed that for both strains, the gene expression is induced by D-xylose, and that in PTD3 the expression was not repressed by glucose in the presence of xylose

The Rise and Fall of Hypertension: Lessons Learned from Eastern Europe

Hypertension is a progressive cardiovascular syndrome that arises from many differing, but interrelated, etiologies. Hypertension is the most prevalent cardiovascular disorder, affecting 20% to 50% of the adult population in developed countries. Arterial hypertension is a major risk factor for cardiovascular diseases and death. Epidemiologic data have shown that control of hypertension is achieved in only a small percentage of hypertensive patients. Findings from the World Health Organization project Monitoring Trends and Determinants in Cardiovascular Diseases (MONICA) showed a remarkably high prevalence (about 65%) of hypertension in Eastern Europeans. There is virtually no difference however, between the success rate in controlling hypertension when comparing Eastern and Western European populations. Diagnosing hypertension depends on both population awareness of the dangers of hypertension and medical interventions aimed at the detecting elevated blood pressure, even in asymptomatic patients. Medical compliance with guidelines for the treatment of hypertension is variable throughout Eastern Europe. Prevalence of hypertension increases with age, and the management of hypertension in elderly is a significant problem. The treatment of hypertension demands a comprehensive approach to the patient with regard to cardiovascular risk and individualization of hypertensive therapy

Quantification of sodium present in dry aggregates and anodes

In aluminum industry, it is important to determine the concentration of contaminants present in anode raw materials as rapidly as possible in order to adjust the anode recipe. Sodium, which is an impurity coming largely from anode butts, significantly influences the anode reactivity, and an increase in its concentration increases the anode consumption. A simple and inexpensive method was developed to quantify the sodium content in dry aggregates and anodes without grinding the samples. The method is based on potentiometric principles using a sodium-ion specific electrode. A sample can be analyzed easily within thirty minutes. In order to prevent the rapid degradation of the specific electrode due to experimental conditions, sodium is extracted from samples by electrophoresis prior to the test. The comparison shows that the measured sodium concentrations obtained are similar to the results determined by other test methods

Summary of cerebrospinal fluid routine parameters in neurodegenerative diseases

In neurodegenerative diseases, cerebrospinal fluid analysis (CSF) is predominantly performed to exclude inflammatory diseases and to perform a risk assessment in dementive disorders by measurement of tau proteins and amyloid beta peptides. However, large scale data on basic findings of CSF routine parameters are generally lacking. The objective of the study was to define a normal reference spectrum of routine CSF parameters in neurodegenerative diseases. Routine CSF parameters (white cell count, lactate and albumin concentrations, CSF/serum quotients of albumin (Qalb), IgG, IgA, IgM, and oligoclonal IgG bands (OCB)) were retrospectively analyzed in an academic research setting. A total of 765 patients (Alzheimer’s disease (AD), Parkinson’s disease (PD), Parkinson’s disease dementia (PDD), vascular dementia (VD), frontotemporal lobar degeneration (FTLD), progressive supranuclear palsy (PSP), multisystem atrophy (MSA), motor neuron diseases (MND), spinocerebellar ataxia (SCA), Huntington’s disease (HD)) and non-demented control groups including a group of patients with muscular disorders (MD). The main outcome measures included statistical analyses of routine CSF parameters. Mildly elevated Qalb were found in a small percentage of nearly all subgroups and in a higher proportion of patients with PSP, MSA, VD, PDD, and MND. With the exception of 1 MND patient, no intrathecal Ig synthesis was observed. Isolated OCBs in CSF were sometimes found in patients with neurodegenerative diseases without elevated cell counts; lactate levels were always normal. A slightly elevated Qalb was observed in a subgroup of patients with neurodegenerative diseases and does not exclude the diagnosis. Extensive elevation of routine parameters is not characteristic and should encourage a re-evaluation of the clinical diagnosis

Tizanidine does not affect the linear relation of stretch duration to the long latency M2 response of m. flexor carpi radialis

The long latency M2 electromyographic response of a suddenly stretched active muscle is stretch duration dependent of which the nature is unclear. We investigated the influence of the group II afferent blocker tizanidine on M2 response characteristics of the m. flexor carpi radialis (FCR). M2 response magnitude and eliciting probability in a group of subjects receiving 4 mg of tizanidine orally were found to be significantly depressed by tizanidine while tizanidine did not affect the significant linear relation of the M2 response to stretch duration. The effect of tizanidine on the M2 response of FCR is supportive of a group II afferent contribution to a compound response of which the stretch duration dependency originates from a different mechanism, e.g., rebound Ia firing