The assessment of benchmarks executed on bare-metal and using para-virtualization

A full assessment of para-­virtualization is important, because without knowledge about the various overheads, users can not understand whether using virtualization is a good idea or not. In this paper we are very interested in assessing the overheads of running various benchmarks on bare-­‐metal, as well as on para-­‐virtualization. The idea is to see what the overheads of para-­‐ virtualization are, as well as looking at the overheads of turning on monitoring and logging. The knowledge from assessing various benchmarks on these different systems will help a range of users understand the use of virtualization systems. In this paper we assess the overheads of using Xen, VMware, KVM and Citrix, see Table 1. These different virtualization systems are used extensively by cloud-­‐users. We are using various Netlib1 benchmarks, which have been developed by the University of Tennessee at Knoxville (UTK), and Oak Ridge National Laboratory (ORNL). In order to assess these virtualization systems, we run the benchmarks on bare-­‐metal, then on the para-­‐virtualization, and finally we turn on monitoring and logging. The later is important as users are interested in Service Level Agreements (SLAs) used by the Cloud providers, and the use of logging is a means of assessing the services bought and used from commercial providers. In this paper we assess the virtualization systems on three different systems. We use the Thamesblue supercomputer, the Hactar cluster and IBM JS20 blade server (see Table 2), which are all servers available at the University of Reading. A functional virtualization system is multi-­‐layered and is driven by the privileged components. Virtualization systems can host multiple guest operating systems, which run on its own domain, and the system schedules virtual CPUs and memory within each Virtual Machines (VM) to make the best use of the available resources. The guest-­‐operating system schedules each application accordingly. You can deploy virtualization as full virtualization or para-­‐virtualization. Full virtualization provides a total abstraction of the underlying physical system and creates a new virtual system, where the guest operating systems can run. No modifications are needed in the guest OS or application, e.g. the guest OS or application is not aware of the virtualized environment and runs normally. Para-­‐virualization requires user modification of the guest operating systems, which runs on the virtual machines, e.g. these guest operating systems are aware that they are running on a virtual machine, and provide near-­‐native performance. You can deploy both para-­‐virtualization and full virtualization across various virtualized systems. Para-­‐virtualization is an OS-­‐assisted virtualization; where some modifications are made in the guest operating system to enable better performance. In this kind of virtualization, the guest operating system is aware of the fact that it is running on the virtualized hardware and not on the bare hardware. In para-­‐virtualization, the device drivers in the guest operating system coordinate the device drivers of host operating system and reduce the performance overheads. The use of para-­‐virtualization [0] is intended to avoid the bottleneck associated with slow hardware interrupts that exist when full virtualization is employed. It has revealed [0] that para-­‐ virtualization does not impose significant performance overhead in high performance computing, and this in turn this has implications for the use of cloud computing for hosting HPC applications. The “apparent” improvement in virtualization has led us to formulate the hypothesis that certain classes of HPC applications should be able to execute in a cloud environment, with minimal performance degradation. In order to support this hypothesis, first it is necessary to define exactly what is meant by a “class” of application, and secondly it will be necessary to observe application performance, both within a virtual machine and when executing on bare hardware. A further potential complication is associated with the need for Cloud service providers to support Service Level Agreements (SLA), so that system utilisation can be audited.

Case studies to demonstrate the range of applications of the Southampton Hand Assessment Procedure

The Southampton Hand Assessment Procedure (SHAP) was devised to assess quantitatively the functional range of injured and healthy adult hands. It was designed to be a practical tool for use in a busy clinical setting; thus, it was made simple to use and easy to interpret. This paper describes four examples of its use: before and after a surgical procedure, to observe the impact of an injury, use with prostheses, and during recovery following a fracture. The cases show that the SHAP is capable of monitoring progress and recovery, identifying functional abilities in prosthetic hands and comparing the capabilities of different groups of injuries.

Assessment of cognitive symptoms in prodromal and early Huntington disease

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess cognitive symptoms in prHD and early HD individuals.

Assessment of day-to-day functioning in prodromal and early Huntington disease

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess functional impact in day-to-day activities in prHD and early HD individuals.

Assessment of depression, anxiety and apathy in prodromal and early Huntington disease

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess Depression, Anxiety and Apathy in prHD and early HD individuals.

Health-related quality of life in Huntington’s Disease patients: a comparison of proxy assessment and patient self-rating using the disease-specific Huntington’s Disease health-related quality of life questionnaire (HDQoL)

Huntington’s disease (HD) is a fatal, neurodegenerative disease for which there is no known cure. Proxy evaluation is relevant for HD as its manifestation might limit the ability of persons to report their health-related quality of life (HrQoL). This study explored patient–proxy ratings of HrQoL of persons at different stages of HD, and examined factors that may affect proxy ratings. A total of 105 patient–proxy pairs completed the Huntington’s disease health-related quality of life questionnaire (HDQoL) and other established HrQoL measures (EQ-5D and SF-12v2). Proxy–patient agreement was assessed in terms of absolute level (mean ratings) and intraclass correlation. Proxies’ ratings were at a similar level to patients’ self-ratings on an overall Summary Score and on most of the six Specific Scales of the HDQoL. On the Specific Hopes and Worries Scale, proxies on average rated HrQoL as better than patients’ self-ratings, while on both the Specific Cognitive Scale and Specific Physical and Functional Scale proxies tended to rate HrQoL more poorly than patients themselves. The patient’s disease stage and mental wellbeing (SF-12 Mental Component scale) were the two factors that primarily affected proxy assessment. Proxy scores were strongly correlated with patients’ self-ratings of HrQoL, on the Summary Scale and all Specific Scales. The patient–proxy correlation was lower for patients at moderate stages of HD compared to patients at early and advanced stages. The proxy report version of the HDQoL is a useful complementary tool to self-assessment, and a promising alternative when individual patients with advanced HD are unable to self-report.

Prediction and functional analysis of native disorder in proteins from the Three Kingdoms of Life

An automatic method for recognizing natively disordered regions from amino acid sequence is described and benchmarked against predictors that were assessed at the latest critical assessment of techniques for protein structure prediction (CASP) experiment. The method attains a Wilcoxon score of 90.0, which represents a statistically significant improvement on the methods evaluated on the same targets at CASP. The classifier, DISOPRED2, was used to estimate the frequency of native disorder in several representative genomes from the three kingdoms of life. Putative, long (>30 residue) disordered segments are found to occur in 2.0% of archaean, 4.2% of eubacterial and 33.0% of eukaryotic proteins. The function of proteins with long predicted regions of disorder was investigated using the gene ontology annotations supplied with the Saccharomyces genome database. The analysis of the yeast proteome suggests that proteins containing disorder are often located in the cell nucleus and are involved in the regulation of transcription and cell signalling. The results also indicate that native disorder is associated with the molecular functions of kinase activity and nucleic acid binding.

Improving assessment and modelling of climate change impacts on global terrestrial biodiversity.

Understanding how species and ecosystems respond to climate change has become a major focus of ecology and conservation biology. Modelling approaches provide important tools for making future projections, but current models of the climate-biosphere interface remain overly simplistic, undermining the credibility of projections. We identify five ways in which substantial advances could be made in the next few years: (i) improving the accessibility and efficiency of biodiversity monitoring data, (ii) quantifying the main determinants of the sensitivity of species to climate change, (iii) incorporating community dynamics into projections of biodiversity responses, (iv) accounting for the influence of evolutionary processes on the response of species to climate change, and (v) improving the biophysical rule sets that define functional groupings of species in global models.

Separating heart and brain: on the reduction of physiological noise from multichannel functional near-infrared spectroscopy (fNIRS) signals

Objective. Functional near-infrared spectroscopy (fNIRS) is an emerging technique for the in vivo assessment of functional activity of the cerebral cortex as well as in the field of brain–computer interface (BCI) research. A common challenge for the utilization of fNIRS in these areas is a stable and reliable investigation of the spatio-temporal hemodynamic patterns. However, the recorded patterns may be influenced and superimposed by signals generated from physiological processes, resulting in an inaccurate estimation of the cortical activity. Up to now only a few studies have investigated these influences, and still less has been attempted to remove/reduce these influences. The present study aims to gain insights into the reduction of physiological rhythms in hemodynamic signals (oxygenated hemoglobin (oxy-Hb), deoxygenated hemoglobin (deoxy-Hb)). Approach. We introduce the use of three different signal processing approaches (spatial filtering, a common average reference (CAR) method; independent component analysis (ICA); and transfer function (TF) models) to reduce the influence of respiratory and blood pressure (BP) rhythms on the hemodynamic responses. Main results. All approaches produce large reductions in BP and respiration influences on the oxy-Hb signals and, therefore, improve the contrast-to-noise ratio (CNR). In contrast, for deoxy-Hb signals CAR and ICA did not improve the CNR. However, for the TF approach, a CNR-improvement in deoxy-Hb can also be found. Significance. The present study investigates the application of different signal processing approaches to reduce the influences of physiological rhythms on the hemodynamic responses. In addition to the identification of the best signal processing method, we also show the importance of noise reduction in fNIRS data.

Automatic spiral analysis for objective assessment of motor symptoms in Parkinson's disease

Objective: To develop a method for objective quantification of PD motor symptoms related to Off episodes and peak dose dyskinesias, using spiral data gathered by using a touch screen telemetry device. The aim was to objectively characterize predominant motor phenotypes (bradykinesia and dyskinesia), to help in automating the process of visual interpretation of movement anomalies in spirals as rated by movement disorder specialists. Background: A retrospective analysis was conducted on recordings from 65 patients with advanced idiopathic PD from nine different clinics in Sweden, recruited from January 2006 until August 2010. In addition to the patient group, 10 healthy elderly subjects were recruited. Upper limb movement data were collected using a touch screen telemetry device from home environments of the subjects. Measurements with the device were performed four times per day during week-long test periods. On each test occasion, the subjects were asked to trace pre-drawn Archimedean spirals, using the dominant hand. The pre-drawn spiral was shown on the screen of the device. The spiral test was repeated three times per test occasion and they were instructed to complete it within 10 seconds. The device had a sampling rate of 10Hz and measured both position and time-stamps (in milliseconds) of the pen tip. Methods: Four independent raters (FB, DH, AJ and DN) used a web interface that animated the spiral drawings and allowed them to observe different kinematic features during the drawing process and to rate task performance. Initially, a number of kinematic features were assessed including ‘impairment’, ‘speed’, ‘irregularity’ and ‘hesitation’ followed by marking the predominant motor phenotype on a 3-category scale: tremor, bradykinesia and/or choreatic dyskinesia. There were only 2 test occasions for which all the four raters either classified them as tremor or could not identify the motor phenotype. Therefore, the two main motor phenotype categories were bradykinesia and dyskinesia. ‘Impairment’ was rated on a scale from 0 (no impairment) to 10 (extremely severe) whereas ‘speed’, ‘irregularity’ and ‘hesitation’ were rated on a scale from 0 (normal) to 4 (extremely severe). The proposed data-driven method consisted of the following steps. Initially, 28 spatiotemporal features were extracted from the time series signals before being presented to a Multilayer Perceptron (MLP) classifier. The features were based on different kinematic quantities of spirals including radius, angle, speed and velocity with the aim of measuring the severity of involuntary symptoms and discriminate between PD-specific (bradykinesia) and/or treatment-induced symptoms (dyskinesia). A Principal Component Analysis was applied on the features to reduce their dimensions where 4 relevant principal components (PCs) were retained and used as inputs to the MLP classifier. Finally, the MLP classifier mapped these components to the corresponding visually assessed motor phenotype scores for automating the process of scoring the bradykinesia and dyskinesia in PD patients whilst they draw spirals using the touch screen device. For motor phenotype (bradykinesia vs. dyskinesia) classification, the stratified 10-fold cross validation technique was employed. Results: There were good agreements between the four raters when rating the individual kinematic features with intra-class correlation coefficient (ICC) of 0.88 for ‘impairment’, 0.74 for ‘speed’, 0.70 for ‘irregularity’, and moderate agreements when rating ‘hesitation’ with an ICC of 0.49. When assessing the two main motor phenotype categories (bradykinesia or dyskinesia) in animated spirals the agreements between the four raters ranged from fair to moderate. There were good correlations between mean ratings of the four raters on individual kinematic features and computed scores. The MLP classifier classified the motor phenotype that is bradykinesia or dyskinesia with an accuracy of 85% in relation to visual classifications of the four movement disorder specialists. The test-retest reliability of the four PCs across the three spiral test trials was good with Cronbach’s Alpha coefficients of 0.80, 0.82, 0.54 and 0.49, respectively. These results indicate that the computed scores are stable and consistent over time. Significant differences were found between the two groups (patients and healthy elderly subjects) in all the PCs, except for the PC3. Conclusions: The proposed method automatically assessed the severity of unwanted symptoms and could reasonably well discriminate between PD-specific and/or treatment-induced motor symptoms, in relation to visual assessments of movement disorder specialists. The objective assessments could provide a time-effect summary score that could be useful for improving decision-making during symptom evaluation of individualized treatment when the goal is to maximize functional On time for patients while minimizing their Off episodes and troublesome dyskinesias.

Clinical evaluation of enalapril maleate and furosemide usage in dogs with degenerative myxomatous mitral valve, CHF functional class Ib

A doença degenerativa mixomatosa da válvula mitral (DDMVM) é uma cardiopatia de alta incidência na clínica médica de pequenos animais, acometendo mormente cães idosos e raças de pequeno porte. Desta forma, foi realizada uma investigação científica objetivando avaliar clinicamente a utilização dos fármacos maleato de enalapril e furosemida em cães com a referida enfermidade na classe funcional Ib da ICC, antes e após a terapêutica implantada. Para isso, utilizaram-se 16 cães portadores da valvulopatia supracitada, distribuídos em dois grupos; com o primeiro recebendo furosemida (n=8) e o segundo maleato de enalapril (n=8), durante 56 dias. Os cães foram avaliados em quatro momentos (T0, T14, T28 e T56 dias) quanto aos sinais clínicos e parâmetros hematológicos e bioquímico-séricos, que incluíram concentrações séricas da enzima conversora da angiotensina (ECA) e aldosterona, como também avaliações radiográficas, eletrocardiográficas, ecodopplercardiográficas e da pressão arterial. Os resultados quanto aos parâmetros clínicos, avaliações hematológicas e bioquímicas séricas não revelaram alterações significativas em ambos os grupos, mas reduções significativas nos valores de ECA e aldosterona no grupo que recebeu o maleato de enalapril foram identificadas. Ao exame radiográfico observou-se reduções nos valores de VHS e na variável onda Pms do eletrocardiograma em ambos os grupos, mas sem alterações nos valores da pressão arterial. Por sua vez, o ecodopplercardiograma evidenciou diminuição significativa das variáveis DIVEd/s nos grupos estudados e na FEC% nos cães que receberam somente enalapril. Portanto, a análise dos resultados encontrados indicou que a monoterapia fundamentada no maleato de enalapril apresentou melhor eficiência no controle do quadro clínico em pacientes da classe funcional Ib da ICC.

Postural control and functional balance in individuals with diabetic peripheral neuropathy

A Neuropatia diabética periférica (NDP) cursa com redução somatossensitiva que pode levar a alterações no controle postural. O objetivo do estudo foi avaliar o controle postural na postura ereta, em diferentes condições, e o equilíbrio funcional em indivíduos com NDP, correlacionar os resultados obtidos na avaliação do controle postural com os valores do teste do equilíbrio funcional e comparar os resultados obtidos no grupo neuropata com o grupo controle, verificando as possíveis diferenças entre as condições de avaliação em ambos os grupos. Participaram do estudo 13 mulheres com NDP (GN) e 17 mulheres não diabéticas (GC). A avaliação do controle postural foi realizada por cinemetria nas condições: olhos abertos (OA), olhos fechados (OF) e semi tandem (ST). Após processamento no MATLAB, foram geradas as variáveis: amplitude média de oscilação (AMO) na direção ântero-posterior (AP) e médio-lateral (ML); e velocidade média de oscilação (VMO) na direção AP e ML. O equilíbrio funcional foi avaliado pelo Timed Up and Go Test. Houve diferença significante entre os grupos (p<0,005) na AMO-AP OA e OF, AMO-ML of e ST e VMO-ML ST. Houve diferença entre as condições OA e ST (p<0,005) e of e ST (p<0,005) para as variáveis AMO-ML e VMO-ML, com maior prejuízo para o GN, que também apresentou um menor equilíbrio funcional (p=0,001). A instabilidade ML foi correlacionada positivamente com o desequilíbrio funcional. Os resultados nos mostram uma alteração no sistema de controle postural na NDP, o que pode levar estes indivíduos a um maior risco a quedas e prejuízos funcionais.

Tradução, adaptação cultural e propriedades psicométricas da versão brasileira do Short-Form of the Mobility Assessment Tool (MAT-sf)

Objectives: to translate and assess the psychometric properties of the Brazilian short-form of the Mobility Assessment Tool (MAT-sf) in Brazilians community elderly. Methds: the 12 items MAT-sf went through the process of translation and back translation into Portuguese of the Brazil, considering the semantic and cultural adaptation. In a sample of 150 aged 65-74 years living in the community, the instrument's psychometric properties were evaluated by analysis of convergent and construct validity and test-retest reliability. The main outcomes measures used for validation included in the battery of tests of physical ability, self-repor measures of functional limitations, health, depression, cognitive and sex. The test-retest reliability of the instrument was assessed using the intra-class correlation coefficient (ICC), 40 subjects were reassessed after an interval of 14 days of assessment. Results: the concurrent validity for the MAT-sf was evidenced by significant correlations with SPPB (r = 0,53), number of functional limitations (r = -0,62) and depressive symptoms (r = -0,45). The construct validity of the instrument was measured by gradual and significant increase of the MAT-sf scores with high levels of physical performance and with positive self-reported health, also found that MAT-sf scores were statistically differents according to sex. The variation in MAT-sf scores (R2 = 0,41) was explained by SPPB, number of limitations for activities of daily life and depressive symptoms. High values for test-retest reliability was evidencend by ICC = 0,94, 95% CI = 0,90 0,97. Conclusions: the Brazilian version of the short-form of the Mobility Assessment Tool has values of validity and reliability to ensure its use in elderly populations living in communities

Clinical and pathological assessment of 82 patients with cardiovascular diseases undergoing autopsy at the Hospital das Clínicas of the Faculdade de Medicina de Botucatu from 1988 to 1993

OBJECTIVE: To evaluated the clinical diagnostic, efficiency for basic death causes in patients dying of circulatory disease and de relative frequency of those diseases. METHODS: Analysis of medical record data of 82 patients, ages from 16 to 84 years old (68 over 40 years old), whose died of circulatory disease and had undergone necropsy in the period from 1988 to 1993 years in the University Hospital of Medicine Faculty of Botucatu-UNESP, Br. RESULTS: The functional class of patients were III or IV, in 78%, and 81.7% needed urgent hospitalization. By the clinical judgment the death were by ischemic heart disease in 32 (21 acute myocardial infarction), Chagas'disease in 12, valvopathy in 11, cardiomyopathy in 7, heart failure with no specification of cardiopathy in 11 and other causes in 9. At the necropsy the death cause was ischemic heart disease in 34 patients, valvopathy in 10, Chagas'disease in 10, cardiomyopathy in 5, and heart failure with no specification of cardiopathy in 2.The concordance taxes were in thhe same order: 94,6%, 90,0%, 83.3%, 71.4% and 28.5%. CONCLUSION: There was a great efficiency of clinical diagnosis for death cause in a general university hospital. The ischemic heart disease were the main causes of death.