The accuracy of diagnostic ultrasound imaging for musculoskeletal soft tissue pathology of the extremities: A comprehensive review of the literature

Musculoskeletal diagnostic ultrasound imaging (MSK-DUSI) has been growing outside the traditional radiology speciality. Increased use of this technology has been reported in several healthcare settings, however an apparent gap in the knowledge of the accuracy of this diagnostic technology indicated a review was warranted. We undertook a structured review of the literature to assess the accuracy of MSK-DUSI for the diagnosis of musculoskeletal soft tissue pathology of the extremities. An electronic search of the National Library of Medicine’s PubMed database (1972 to mid-2014) was conducted. All relevant systematic reviews of diagnostic studies, all diagnostic studies published after the date of the latest systematic reviews and relevant diagnostic studies outside the scope the systematic reviews that directly compared the accuracy of MSK-DUSI (the index test) to an appropriate reference standard for the target condition were included. A fundamental appraisal of the methodological quality of studies was completed. The individual sensitivity, specificity and likelihood ratio data were extracted and entered into diagnostic accuracy tables. A total of 207 individual studies were included. The results show that MSK-DUSI has acceptable diagnostic accuracy for a wide spectrum of musculoskeletal conditions of the extremities. However, there is a lack of high quality prospective experimental studies in this area and as such clinicians should interpret the results with some caution due to the potential for overestimation of diagnostic accuracy

Liver concentrations of flame retardants in Eurasian otters (Lutra lutra) collected from Scotland between 2013 and 2015: a Predatory Bird Monitoring Scheme (PBMS) report

The Predatory Bird Monitoring Scheme (PBMS; http://pbms.ceh.ac.uk/) is the umbrella project that encompasses the Centre for Ecology & Hydrology’s National Capability contaminant monitoring and surveillance work on avian predators. By monitoring sentinel vertebrate species, the PBMS aims to detect and quantify current and emerging chemical threats to the environment and in particular to vertebrate wildlife. The current study presents the results of a study in which the concentrations of polybrominated diphenyl ethers (PBDEs) were determined in the livers of a small sample of Eurasian otters (Lutra lutra) that died in Scotland between 2013 and 2015. The principle aim of this work was to determine the current concentrations of PBDEs that are accumulated by otters in Scotland and whether these concentrations are likely to cause adverse effects in those individuals analysed. The otters that were analysed included adult and sub-adult, males and females although there were insufficient sample numbers to test for differences among these demographic groups. Liver tissue was analysed using Gas Chromatograph – Mass Spectrometry (GC-MS). PBDEs were detected in all otter livers analysed, with congeners BDE47, BDE153 and BDE100 dominant in the congener profile. The toxicological consequences of exposure to PBDEs in otters are uncertain given the lack of established links between liver PBDE concentrations and health effects in this species but concentrations were lower than those associated with adverse effects in mink. The general low levels of PBDEs suggests that there is little evidence to date of toxicologically significant contamination of Scottish otters with these compounds. There is clear evidence that Scottish otters have significantly lower residues of the less-brominated PBDEs than those previously measured in otters from England and Wales. However, these results may not be representative of otters from throughout Scotland as the present sample came predominantly from the Inner Hebrides

Evaluation of methods for detecting human reads in microbial sequencing datasets

Sequencing data from host-associated microbes can often be contaminated by the body of the investigator or research subject. Human DNA is typically removed from microbial reads either by subtractive alignment (dropping all reads that map to the human genome) or by using a read classification tool to predict those of human origin, and then discarding them. To inform best practice guidelines, we benchmarked eight alignment-based and two classification-based methods of human read detection using simulated data from 10 clinically prevalent bacteria and three viruses, into which contaminating human reads had been added. While the majority of methods successfully detected >99 % of the human reads, they were distinguishable by variance. The most precise methods, with negligible variance, were Bowtie2 and SNAP, both of which misidentified few, if any, bacterial reads (and no viral reads) as human. While correctly detecting a similar number of human reads, methods based on taxonomic classification, such as Kraken2 and Centrifuge, could misclassify bacterial reads as human, although the extent of this was species-specific. Among the most sensitive methods of human read detection was BWA, although this also made the greatest number of false positive classifications. Across all methods, the set of human reads not identified as such, although often representing 300 bp) bacterial reads, the highest performing approaches were classification-based, using Kraken2 or Centrifuge. For shorter (c. 150 bp) bacterial reads, combining multiple methods of human read detection maximized the recovery of human reads from contaminated short read datasets without being compromised by false positives. A particularly high-performance approach with shorter bacterial reads was a two-stage classification using Bowtie2 followed by SNAP. Using this approach, we re-examined 11 577 publicly archived bacterial read sets for hitherto undetected human contamination. We were able to extract a sufficient number of reads to call known human SNPs, including those with clinical significance, in 6 % of the samples. These results show that phenotypically distinct human sequence is detectable in publicly archived microbial read datasets

Finite temperature effects in Coulomb blockade quantum dots and signatures of spectral scrambling

The conductance in Coulomb blockade quantum dots exhibits sharp peaks whose spacings fluctuate with the number of electrons. We derive the temperature-dependence of these fluctuations in the statistical regime and compare with recent experimental results. The scrambling due to Coulomb interactions of the single-particle spectrum with the addition of an electron to the dot is shown to affect the temperature-dependence of the peak spacing fluctuations. Spectral scrambling also leads to saturation in the temperature dependence of the peak-to-peak correlator, in agreement with recent experimental results. The signatures of scrambling are derived using discrete Gaussian processes, which generalize the Gaussian ensembles of random matrices to systems that depend on a discrete parameter -- in this case, the number of electrons in the dot.Comment: 14 pages, 4 eps figures included, RevTe

The role of interparticle heterogeneities in the selenization pathway of Cu Zn Sn S nanoparticle thin films a real time study

Real time energy dispersive X ray diffraction EDXRD analysis has been utilized to observe the selenization of Cu Zn Sn S nanoparticle films coated from three nanoparticle populations Cu and Sn rich particles roughly 5 nm in size, Zn rich nanoparticles ranging from 10 to 20 nm in diameter, and a mixture of both types of nanoparticles roughly 1 1 by mass , which corresponds to a synthesis recipe yielding CZTSSe solar cells with reported total area efficiencies as high as 7.9 . The EDXRD studies presented herein show that the formation of copper selenide intermediates during the selenization of mixed particle films can be primarily attributed to the small, Cu and Sn rich particles. Moreover, the formation of these copper selenide phases represents the first stage of the CZTSSe grain growth mechanism. The large, Zn rich particles subsequently contribute their composition to form micrometer sized CZTSSe grains. These findings enable further development of a previously proposed selenization pathway to account for the roles of interparticle heterogeneities, which in turn provides a valuable guide for future optimization of processes to synthesize high quality CZTSSe absorber layer

Confined granular packings: structure, stress, and forces

The structure and stresses of static granular packs in cylindrical containers are studied using large-scale discrete element molecular dynamics simulations in three dimensions. We generate packings by both pouring and sedimentation and examine how the final state depends on the method of construction. The vertical stress becomes depth-independent for deep piles and we compare these stress depth-profiles to the classical Janssen theory. The majority of the tangential forces for particle-wall contacts are found to be close to the Coulomb failure criterion, in agreement with the theory of Janssen, while particle-particle contacts in the bulk are far from the Coulomb criterion. In addition, we show that a linear hydrostatic-like region at the top of the packings unexplained by the Janssen theory arises because most of the particle-wall tangential forces in this region are far from the Coulomb yield criterion. The distributions of particle-particle and particle-wall contact forces $P(f)$ exhibit exponential-like decay at large forces in agreement with previous studies.Comment: 11 pages, 11 figures, submitted to PRE (v2) added new references, fixed typo

Magnetic Field Effects on Neutron Diffraction in the Antiferromagnetic Phase of UPt3UPt_3

We discuss possible magnetic structures in UPt$_3$ based on our analysis of elastic neutron-scattering experiments in high magnetic fields at temperatures $T<T_N$. The existing experimental data can be explained by a single-{\bf q} antiferromagnetic structure with three independent domains. For modest in-plane spin-orbit interactions, the Zeeman coupling between the antiferromagnetic order parameter and the magnetic field induces a rotation of the magnetic moments, but not an adjustment of the propagation vector of the magnetic order. A triple-{\bf q} magnetic structure is also consistent with neutron experiments, but in general leads to a non-uniform magnetization in the crystal. New experiments could decide between these structures.Comment: 5 figures included in the tex