Genome information management and integrated data analysis with HaloLex

HaloLex is a software system for the central management, integration, curation, and web-based visualization of genomic and other -omics data for any given microorganism. The system has been employed for the manual curation of three haloarchaeal genomes, namely Halobacterium salinarum (strain R1), Natronomonas pharaonis, and Haloquadratum walsbyi. HaloLex, in particular, enables the integrated analysis of genome-wide proteomic results with the underlying genomic data. This has proven indispensable to generate reliable gene predictions for GC-rich genomes, which, due to their characteristically low abundance of stop codons, are known to be hard targets for standard gene finders, especially concerning start codon assignment. The proteomic identification of more than 600 N-terminal peptides has greatly increased the reliability of the start codon assignment for Halobacterium salinarum. Application of homology-based methods to the published genome of Haloarcula marismortui allowed to detect 47 previously unidentified genes (a problem that is particularly serious for short protein sequences) and to correct more than 300 start codon misassignments

Core-Collapse Simulations of Rotating Stars

We present the results from a series of two-dimensional core-collapse simulations using a rotating progenitor star. We find that the convection in these simulations is less vigorous because a) rotation weakens the core bounce which seeds the neutrino-driven convection and b) the angular momentum profile in the rotating core stabilizes against convection. The limited convection leads to explosions which occur later and are weaker than the explosions produced from the collapse of non-rotating cores. However, because the convection is constrained to the polar regions, when the explosion occurs, it is stronger along the polar axis. This asymmetric explosion can explain the polarization measurements of core-collapse supernovae. These asymmetries also provide a natural mechanism to mix the products of nucleosynthesis out into the helium and hydrogen layers of the star. We also discuss the role the collapse of these rotating stars play on the generation of magnetic fields and neutron star kicks. Given a range of progenitor rotation periods, we predict a range of supernova energies for the same progenitor mass. The critical mass for black hole formation also depends upon the rotation speed of the progenitor.Comment: 16 pages text + 13 figures, submitted to Ap

Instrumented gait analysis: a measure of gait improvement by a wheeled walker in hospitalized geriatric patients

Background In an increasing aging society, reduced mobility is one of the most important factors limiting activities of daily living and overall quality of life. The ability to walk independently contributes to the mobility, but is increasingly restricted by numerous diseases that impair gait and balance. The aim of this cross-sectional observation study was to examine whether spatio-temporal gait parameters derived from mobile instrumented gait analysis can be used to measure the gait stabilizing effects of a wheeled walker (WW) and whether these gait parameters may serve as surrogate marker in hospitalized patients with multifactorial gait and balance impairment. Methods One hundred six patients (ages 68–95) wearing inertial sensor equipped shoes passed an instrumented walkway with and without gait support from a WW. The walkway assessed the risk of falling associated gait parameters velocity, swing time, stride length, stride time- and double support time variability. Inertial sensor-equipped shoes measured heel strike and toe off angles, and foot clearance. Results The use of a WW improved the risk of spatio-temporal parameters velocity, swing time, stride length and the sagittal plane associated parameters heel strike and toe off angles in all patients. First-time users (FTUs) showed similar gait parameter improvement patterns as frequent WW users (FUs). However, FUs with higher levels of gait impairment improved more in velocity, stride length and toe off angle compared to the FTUs. Conclusion The impact of a WW can be quantified objectively by instrumented gait assessment. Thus, objective gait parameters may serve as surrogate markers for the use of walking aids in patients with gait and balance impairments

Significant improvement in neuropsychological functions after awake craniotomy in a patient with Oligodendroglioma: A case report

Objective: The goal of awake craniotomy in glioma patients is sparing of cognitive function. Previous investigations suggest that patients in the postoperative state may reach their preoperative level regarding domain-based criteria. Data on significant postoperative improvement beyond the preoperative level is sparse. This article examines the prospective neuropsychological assessment of a glioma patient who underwent awake craniotomy and has shown functional improvement exceeding preoperative levels. Methods: A 34-year-old patient with high premorbid cognitive function level who underwent awake craniotomy for left frontal oligodendroglioma was neuropsychologically assessed and took part in a fMRI-examination at 3 different time points. Results: Preoperative examination revealed severe isolated impairment of working memory, long-term narrative memory in free recall and recognition, and alertness with intact language production and comprehension. After transient global aphasia in the postoperative state, the follow-up examination showed significant improvement in memory and attention exceeding the preoperative level. Conclusions: Tumor location is an important factor in terms of surgical procedures. Cognitive impairment is, however, not always associated with a specific location. Mechanical pressure of the tumor might have led to the isolated consolidation deficit which fully recovered after tumor removal. Psychological disorders should be taken into account regarding prodromal symptoms of neurooncological diseases

Additional file 1: Table S1. of Instrumented gait analysis: a measure of gait improvement by a wheeled walker in hospitalized geriatric patients

Correlations analysis between gait parameter and clinical/functional assessments. (DOCX 19 kb