Brachial plexus injury mimicking a spinal-cord injury.

Objective High-energy impact to the head, neck, and shoulder can result in cervical spine as well as brachial plexus injuries. Because cervical spine injuries are more common, this tends to be the initial focus for management. We present a case in which the initial magnetic resonance imaging (MRI) was somewhat misleading and a detailed neurological exam lead to the correct diagnosis.Clinical presentation A 19-year-old man presented to the hospital following a shoulder injury during football practice. The patient immediately complained of significant pain in his neck, shoulder, and right arm and the inability to move his right arm. He was stabilized in the field for a presumed cervical-spine injury and transported to the emergency department.Intervention Initial radiographic assessment (C-spine CT, right shoulder x-ray) showed no bony abnormality. MRI of the cervical-spine showed T2 signal change and cord swelling thought to be consistent with a cord contusion. With adequate pain control, a detailed neurological examination was possible and was consistent with an upper brachial plexus avulsion injury that was confirmed by CT myelogram. The patient failed to make significant neurological recovery and he underwent spinal accessory nerve grafting to the suprascapular nerve to restore shoulder abduction and external rotation, while the phrenic nerve was grafted to the musculocutaneous nerve to restore elbow flexion.Conclusion Cervical spinal-cord injuries and brachial plexus injuries can occur by the same high energy mechanisms and can occur simultaneously. As in this case, MRI findings can be misleading and a detailed physical examination is the key to diagnosis. However, this can be difficult in polytrauma patients with upper extremity injuries, head injuries or concomitant spinal-cord injury. Finally, prompt diagnosis and early surgical renerveration have been associated with better long-term recovery with certain types of injury

Peripheral Innate Immune Activation Correlates With Disease Severity in GRN Haploinsufficiency.

Objective: To investigate associations between peripheral innate immune activation and frontotemporal lobar degeneration (FTLD) in progranulin gene (GRN) haploinsufficiency. Methods: In this cross-sectional study, ELISA was used to measure six markers of innate immunity (sCD163, CCL18, LBP, sCD14, IL-18, and CRP) in plasma from 30 GRN mutation carriers (17 asymptomatic, 13 symptomatic) and 29 controls. Voxel based morphometry was used to model associations between marker levels and brain atrophy in mutation carriers relative to controls. Linear regression was used to model relationships between plasma marker levels with mean frontal white matter integrity [fractional anisotropy (FA)] and the FTLD modified Clinical Dementia Rating Scale sum of boxes score (FTLD-CDR SB). Results: Plasma sCD163 was higher in symptomatic GRN carriers [mean 321 ng/ml (SD 125)] compared to controls [mean 248 ng/ml (SD 58); p < 0.05]. Plasma CCL18 was higher in symptomatic GRN carriers [mean 56.9 pg/ml (SD 19)] compared to controls [mean 40.5 pg/ml (SD 14); p < 0.05]. Elevation of plasma LBP was associated with white matter atrophy in the right frontal pole and left inferior frontal gyrus (p FWE corrected <0.05) in all mutation carriers relative to controls. Plasma LBP levels inversely correlated with bilateral frontal white matter FA (R2 = 0.59, p = 0.009) in mutation carriers. Elevation in plasma was positively correlated with CDR-FTLD SB (b = 2.27 CDR units/μg LBP/ml plasma, R2 = 0.76, p = 0.003) in symptomatic carriers. Conclusion: FTLD-GRN is associated with elevations in peripheral biomarkers of macrophage-mediated innate immunity, including sCD163 and CCL18. Clinical disease severity and white matter integrity are correlated with blood LBP, suggesting a role for peripheral immune activation in FTLD-GRN

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format

BOSC 2019, the 20th annual Bioinformatics Open Source Conference.

The Bioinformatics Open Source Conference is a volunteer-organized meeting that covers open source software development and open science in bioinformatics. Launched in 2000, BOSC has been held every year since. BOSC 2019, the 20th annual BOSC, took place as one of the Communities of Special Interest (COSIs) at the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB 2019). The two-day meeting included a total of 46 talks and 55 posters, as well as eight Birds of a Feather interest groups. The keynote speaker was University of Cape Town professor Dr. Nicola Mulder, who spoke on "Building infrastructure for responsible open science in Africa". Immediately after BOSC 2019, about 50 people participated in the two-day CollaborationFest (CoFest for short), an open and free community-driven event at which participants work together to contribute to bioinformatics software, documentation, training materials, and use cases

Relative energetics and structural properties of zirconia using a self-consistent tight-binding model

We describe an empirical, self-consistent, orthogonal tight-binding model for zirconia, which allows for the polarizability of the anions at dipole and quadrupole levels and for crystal field splitting of the cation d orbitals. This is achieved by mixing the orbitals of different symmetry on a site with coupling coefficients driven by the Coulomb potentials up to octapole level. The additional forces on atoms due to the self-consistency and polarizabilities are exactly obtained by straightforward electrostatics, by analogy with the Hellmann-Feynman theorem as applied in first-principles calculations. The model correctly orders the zero temperature energies of all zirconia polymorphs. The Zr-O matrix elements of the Hamiltonian, which measure covalency, make a greater contribution than the polarizability to the energy differences between phases. Results for elastic constants of the cubic and tetragonal phases and phonon frequencies of the cubic phase are also presented and compared with some experimental data and first-principles calculations. We suggest that the model will be useful for studying finite temperature effects by means of molecular dynamics.Comment: to be published in Physical Review B (1 march 2000

Predicting enhanced absorption of light gases in polyethylene using simplified PC-SAFT and SAFT-VR

International audienceAbsorption of light gases in polyethylene (PE) is studied using two versions of the Statistical Associating Fluid Theory (SAFT): SAFT for chain molecules with attractive potentials of variable range (VR) and simplified perturbed-chain (PC) SAFT. Emphasis is placed on the light gases typically present during ethylene polymerisation in the gas-phase reactor (GPR) process. The two approaches are validated using experimental binary-mixture data for gas absorbed in PE, and predictions are made for mixtures of more components. For most cases studied both SAFT versions perform equally well. For the case of ternary mixtures of two gases with PE, it is predicted that the less-volatile of the two gases acts to enhance the absorption of the more-volatile gas, while the more-volatile gas inhibits the absorption of the less-volatile gas. This general behaviour is also predicted in mixtures containing more gases, such as typical reactor mixtures. The magnitude of the effect may vary considerably, depending on the relative proximity of the gas-mixture saturation pressure to the reactor pressure; for example it is predicted that the absorption of ethylene may be approximately doubled if diluent gases, propane or nitrogen, are partially or completely replaced by less-volatile butane or pentane for a reactor pressure similar to 2 MPa. In the case of a co-polymerisation reaction, it is predicted that increases in absorption of both co-monomers may be obtained in roughly equal proportion. Our findings cast light on the so-called co-monomer effect, in which substantial increases in the rate of ethylene polymerisation are observed in the presence of hexene co-monomer, while suggesting that the effect is more general and not restricted to co-monomer. For example, similar rate increases may be expected in the presence of, e.g., pentane instead of hexene, but without the change in the branch structure of the produced polymer that is inevitable when the amount of co-monomer is increased

Sense-making strategies in explorative intelligence analysis of network evolutions

Visualising how social networks evolve is important in intelligence analysis in order to detect and monitor issues, such as emerging crime patterns or rapidly growing groups of offenders. It remains an open research question how this type of information should be presented for visual exploration. To get a sense of how users work with different types of visualisations, we evaluate a matrix and a node-link diagram in a controlled thinking aloud study. We describe the sense-making strategies that users adopted during explorative and realistic tasks. Thereby, we focus on the user behaviour in switching between the two visualisations and propose a set of nine strategies. Based on a qualitative and quantitative content analysis we show which visualisation supports which strategy better. We find that the two visualisations clearly support intelligence tasks and that for some tasks the combined use is more advantageous than the use of an individual visualisation

Multi-host environments select for host-generalist conjugative plasmids

BACKGROUND: Conjugative plasmids play an important role in bacterial evolution by transferring ecologically important genes within and between species. A key limit on interspecific horizontal gene transfer is plasmid host range. Here, we experimentally test the effect of single and multi-host environments on the host-range evolution of a large conjugative mercury resistance plasmid, pQBR57. Specifically, pQBR57 was conjugated between strains of a single host species, either P. fluorescens or P. putida, or alternating between P. fluorescens and P. putida. Crucially, the bacterial hosts were not permitted to evolve allowing us to observe plasmid evolutionary responses in isolation. RESULTS: In all treatments plasmids evolved higher conjugation rates over time. Plasmids evolved in single-host environments adapted to their host bacterial species becoming less costly, but in the case of P. fluorescens-adapted plasmids, became costlier in P. putida, suggesting an evolutionary trade-off. When evolved in the multi-host environment plasmids adapted to P. fluorescens without a higher cost in P. putida. CONCLUSION: Whereas evolution in a single-host environment selected for host-specialist plasmids due to a fitness trade-off, this trade-off could be circumvented in the multi-host environment, leading to the evolution of host-generalist plasmids

Varespladib and cardiovascular events in patients with an acute coronary syndrome: the VISTA-16 randomized clinical trial

IMPORTANCE: Secretory phospholipase A2(sPLA2) generates bioactive phospholipid products implicated in atherosclerosis. The sPLA2inhibitor varespladib has favorable effects on lipid and inflammatory markers; however, its effect on cardiovascular outcomes is unknown. OBJECTIVE: To determine the effects of sPLA2inhibition with varespladib on cardiovascular outcomes. DESIGN, SETTING, AND PARTICIPANTS: A double-blind, randomized, multicenter trial at 362 academic and community hospitals in Europe, Australia, New Zealand, India, and North America of 5145 patients randomized within 96 hours of presentation of an acute coronary syndrome (ACS) to either varespladib (n = 2572) or placebo (n = 2573) with enrollment between June 1, 2010, and March 7, 2012 (study termination on March 9, 2012). INTERVENTIONS: Participants were randomized to receive varespladib (500 mg) or placebo daily for 16 weeks, in addition to atorvastatin and other established therapies. MAIN OUTCOMES AND MEASURES: The primary efficacy measurewas a composite of cardiovascular mortality, nonfatal myocardial infarction (MI), nonfatal stroke, or unstable angina with evidence of ischemia requiring hospitalization at 16 weeks. Six-month survival status was also evaluated. RESULTS: At a prespecified interim analysis, including 212 primary end point events, the independent data and safety monitoring board recommended termination of the trial for futility and possible harm. The primary end point occurred in 136 patients (6.1%) treated with varespladib compared with 109 patients (5.1%) treated with placebo (hazard ratio [HR], 1.25; 95%CI, 0.97-1.61; log-rank P = .08). Varespladib was associated with a greater risk of MI (78 [3.4%] vs 47 [2.2%]; HR, 1.66; 95%CI, 1.16-2.39; log-rank P = .005). The composite secondary end point of cardiovascular mortality, MI, and stroke was observed in 107 patients (4.6%) in the varespladib group and 79 patients (3.8%) in the placebo group (HR, 1.36; 95% CI, 1.02-1.82; P = .04). CONCLUSIONS AND RELEVANCE: In patients with recent ACS, varespladib did not reduce the risk of recurrent cardiovascular events and significantly increased the risk of MI. The sPLA2inhibition with varespladib may be harmful and is not a useful strategy to reduce adverse cardiovascular outcomes after ACS. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01130246. Copyright 2014 American Medical Association. All rights reserved

Bose-Einstein Correlations of Three Charged Pions in Hadronic Z^0 Decays

Bose-Einstein Correlations (BEC) of three identical charged pions were studied in 4 x 10^6 hadronic Z^0 decays recorded with the OPAL detector at LEP. The genuine three-pion correlations, corrected for the Coulomb effect, were separated from the known two-pion correlations by a new subtraction procedure. A significant genuine three-pion BEC enhancement near threshold was observed having an emitter source radius of r_3 = 0.580 +/- 0.004 (stat.) +/- 0.029 (syst.) fm and a strength of \lambda_3 = 0.504 +/- 0.010 (stat.) +/- 0.041 (syst.). The Coulomb correction was found to increase the \lambda_3 value by \~9% and to reduce r_3 by ~6%. The measured \lambda_3 corresponds to a value of 0.707 +/- 0.014 (stat.) +/- 0.078 (syst.) when one takes into account the three-pion sample purity. A relation between the two-pion and the three-pion source parameters is discussed.Comment: 19 pages, LaTeX, 5 eps figures included, accepted by Eur. Phys. J.