Execution of the SimSET Monte Carlo PET/SPECT Simulator in the Condor Distributed Computing Environment

SimSET is a package for simulation of emission tomography data sets. Condor is a popular distributed computing environment. Simple C/C++ applications and shell scripts are presented which allow the execution of SimSET on the Condor environment. This is accomplished without any modification to SimSET by executing multiple instances and using its combinebin utility. This enables research facilities without dedicated parallel computing systems to utilize the idle cycles of desktop workstations to greatly reduce the run times of their SimSET simulations. The necessary steps to implement this approach in other environments are presented along with sample results

Numerical Simulations of Void Linkage in Model Materials using a Nonlocal Ductile Damage Approximation

Experiments on the growth and linkage of 10 μm diameter holes laser drilled in high precision patterns into Al-plates were modelled with finite elements. The simulations used geometries identical to those of the experiments and incorporated ductile damage by element removal under the control of a ductile damage indicator based on the micromechanical studies of Rice and Tracey. A regularization of the problem was achieved through an integral-type nonlocal model based on the smoothing of the rate of a damage indicator D over a characteristic length L. The simulation does not predict the experimentally observed damage acceleration either in the case where no damage is included or when only a local damage model is used. However, the full three-dimensional simulations based on the nonlocal damage methodology do predict both the failure path and the failure strain at void linkage for almost all configurations studied. For the cases considered the critical parameter controlling the local deformations at void linkage was found to be the ratio between hole diameter and hole spacing

Grid computing in image analysis

Diagnostic surgical pathology or tissue–based diagnosis still remains the most reliable and specific diagnostic medical procedure. The development of whole slide scanners permits the creation of virtual slides and to work on so-called virtual microscopes. In addition to interactive work on virtual slides approaches have been reported that introduce automated virtual microscopy, which is composed of several tools focusing on quite different tasks. These include evaluation of image quality and image standardization, analysis of potential useful thresholds for object detection and identification (segmentation), dynamic segmentation procedures, adjustable magnification to optimize feature extraction, and texture analysis including image transformation and evaluation of elementary primitives

Risk and clinical-outcome indicators of delirium in an emergency department intermediate care unit (EDIMCU) : an observational prospective study

We are thankful to the staff at the EDIMCU of Hospital de Braga.Background Identification of delirium in emergency departments (ED) is often underestimated; within EDs, studies on delirium assessment and relation with patient outcome in Intermediate Care Units (IMCU) appear missing in European hospital settings. Here we aimed to determine delirium prevalence in an EDIMCU (Hospital de Braga, Braga, Portugal) and assessed routine biochemical parameters that might be delirium indicators. Methods The study was prospective and observational. Sedation level was assessed via the Richmond Agitation-Sedation Scale and delirium status by the Confusion Assessment Method for the ICU. Information collected included age and gender, admission type, Charlson Comorbidity Index combined condition score (Charlson score), systemic inflammatory response syndrome criteria (SIRS), biochemical parameters (blood concentration of urea nitrogen, creatinine, hemoglobin, sodium and potassium, arterial blood gases, and other parameters as needed depending on clinical diagnosis) and EDIMCU length of stay (LOS). Statistical analyses were performed as appropriate to determine if baseline features differed between the ‘Delirium’ and ‘No Delirium’ groups. Multivariate logistic regression was performed to assess the effect of delirium on the 1-month outcome. Results Inclusion and exclusion criteria were met in 283 patients; 238 were evaluated at 1-month for outcome follow-up after EDIMCU discharge (“good” recovery without complications requiring hospitalization or institutionalization; “poor” institutionalization in permanent care-units/assisted-living or death). Delirium was diagnosed in 20.1% patients and was significantly associated with longer EDIMCU LOS. At admission, Delirium patients were significantly older and had significantly higher blood urea, creatinine and osmolarity levels and significantly lower hemoglobin levels, when compared with No Delirium patients. Delirium was an independent predictor of increased EDIMCU LOS (odds ratio 3.65, 95% CI 1.97-6.75) and poor outcome at 1-month after discharge (odds ratio 3.51, CI 1.84-6.70), adjusted for age, gender, admission type, presence of SIRS criteria, Charlson score and osmolarity at admission. Conclusions In an EDIMCU setting, delirium was associated with longer LOS and poor outcome at1-month post-discharge. Altogether, findings support the need for delirium screening and management in emergency settings.NCS is supported by the post-doctoral fellowship UMINHO/BPD/013/2011 by the European Commission (FP7) “SwitchBox” Project (Contract HEALTH-F2-2010-259772)

Cerebrovascular reactivity among native-raised high altitude residents: an fMRI study

Background: The impact of long term residence on high altitude (HA) on human brain has raised concern among researchers in recent years. This study investigated the cerebrovascular reactivity among native-born high altitude (HA) residents as compared to native sea level (SL) residents. The two groups were matched on the ancestral line, ages, gender ratios, and education levels. A visual cue guided maximum inspiration task with brief breath holding was performed by all the subjects while Blood-Oxygenation-Level-Dependent (BOLD) functional Magnetic Resonance Imaging (fMRI) data were acquired from them

Emotional well-being in children and adolescents treated with atomoxetine for attention-deficit/hyperactivity disorder: Findings from a patient, parent and physician perspective using items from the pediatric adverse event rating scale (PAERS)

<p>Abstract</p> <p>Background</p> <p>The objective of this analysis was to measure changes in items on the Pediatric Adverse Event Rating Scale (PAERS) that relate to emotional well-being of children and adolescents with Attention-Deficit/Hyperactivity Disorder (ADHD) during treatment with atomoxetine for up to 24 weeks from the perspective of the patient, the parent, and the physician.</p> <p>Methods</p> <p>Patients aged 6–17 years with ADHD were treated with atomoxetine (target dose 1.2 mg/kg/day). In the two studies on which this secondary analysis is based the PAERS was used to assess the tolerability of atomoxetine in children and adolescents. This scale has a total of 48 items. The ten items that reflect emotional well-being were selected to measure changes over time from a patient, parent, and physician perspective.</p> <p>Results</p> <p>421 patients were treated with atomoxetine. 355 patients completed the 8-week treatment period, and 260 patients completed the 24-week treatment period. The ten items that reflect emotional well-being were grouped in five dimensions: depressed mood, self-harm, irritability/agitation, drowsiness, and euphoria. The scores of these dimensions decreased over time, both from a patient as well as from a parent and physician perspective. Only the dimension self-harm was extremely low at baseline and stayed low over time. The mean scores for the ten items depended on the rater perspective.</p> <p>Conclusion</p> <p>The emotional well-being of children and adolescents with ADHD improved in terms of depressed mood, irritability/agitation, drowsiness, and euphoria during treatment with atomoxetine for up to 24 weeks.</p

Dating the Origin of Language Using Phonemic Diversity

Language is a key adaptation of our species, yet we do not know when it evolved. Here, we use data on language phonemic diversity to estimate a minimum date for the origin of language. We take advantage of the fact that phonemic diversity evolves slowly and use it as a clock to calculate how long the oldest African languages would have to have been around in order to accumulate the number of phonemes they possess today. We use a natural experiment, the colonization of Southeast Asia and Andaman Islands, to estimate the rate at which phonemic diversity increases through time. Using this rate, we estimate that present-day languages date back to the Middle Stone Age in Africa. Our analysis is consistent with the archaeological evidence suggesting that complex human behavior evolved during the Middle Stone Age in Africa, and does not support the view that language is a recent adaptation that has sparked the dispersal of humans out of Africa. While some of our assumptions require testing and our results rely at present on a single case-study, our analysis constitutes the first estimate of when language evolved that is directly based on linguistic data

Replication and active partition of integrative and conjugative elements (ICEs) of the SXT/R391 family : the line between ICEs and conjugative plasmids is getting thinner

Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a family of ICEs