Exploring the Vision Processing Unit as Co-Processor for Inference

The success of the exascale supercomputer is largely debated to remain dependent on novel breakthroughs in technology that effectively reduce the power consumption and thermal dissipation requirements. In this work, we consider the integration of co-processors in high-performance computing (HPC) to enable low-power, seamless computation offloading of certain operations. In particular, we explore the so-called Vision Processing Unit (VPU), a highly-parallel vector processor with a power envelope of less than 1W. We evaluate this chip during inference using a pre-trained GoogLeNet convolutional network model and a large image dataset from the ImageNet ILSVRC challenge. Preliminary results indicate that a multi-VPU configuration provides similar performance compared to reference CPU and GPU implementations, while reducing the thermal-design power (TDP) up to 8x in comparison.The experimental results were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC Centre for High-Performance Com- puting (PDC-HPC). The work was funded by the European Commission through the SAGE project (Grant agreement no. 671500 / http://www.sagestorage.eu).Postprint (author's final draft

Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

peer-reviewedBackground: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.This research was part funded by the Irish Government under the National Development Plan 2000-2006. Support to BB under the Walsh Fellowship Programme of Teagasc is acknowledged

The TRiC/CCT chaperone is implicated in Alzheimer's disease based on patient GWAS and an RNAi screen in Aβ-expressing Caenorhabditis elegans.

The human Aβ peptide causes progressive paralysis when expressed in the muscles of the nematode worm, C. elegans. We have exploited this model of Aβ toxicity by carrying out an RNAi screen to identify genes whose reduced expression modifies the severity of this locomotor phenotype. Our initial finding was that none of the human orthologues of these worm genes is identical with the genome-wide significant GWAS genes reported to date (the "white zone"); moreover there was no identity between worm screen hits and the longer list of GWAS genes which included those with borderline levels of significance (the "grey zone"). This indicates that Aβ toxicity should not be considered as equivalent to sporadic AD. To increase the sensitivity of our analysis, we then considered the physical interactors (+1 interactome) of the products of the genes in both the worm and the white+grey zone lists. When we consider these worm and GWAS gene lists we find that 4 of the 60 worm genes have a +1 interactome overlap that is larger than expected by chance. Two of these genes form a chaperonin complex, the third is closely associated with this complex and the fourth gene codes for actin, the major substrate of the same chaperonin

(2R,5S)-2-Tri­chloro­methyl-3-oxa-1-aza­bi­cyclo­[3.3.0]­octane-4,8-dione

The crystal structure of the title bicyclic oxazolidindione, C7H6Cl3NO3, confirmed the absolute stereochemistry as 2R,5S

Muscle strength and areal bone mineral density at the hip in women: a cross-sectional study

BACKGROUND: Muscle strengthening exercises are promoted for building and maintaining a healthy skeleton. We aimed to investigate the relationship between muscle strength and areal bone mineral density (BMD) at the hip in women aged 26-97 years. METHODS: This cross-sectional study utilises data from 863 women assessed for the Geelong Osteoporosis Study. Measures of hip flexor and abductor strength were made using a hand-held dynamometer (Nicholas Manual Muscle Tester). The maximal measure from three trials on each leg was used for analyses. BMD was measured at the hip using dual energy x-ray absorptiometry (DXA; Lunar DPX-L). Total lean mass, body fat mass and appendicular lean mass were determined from whole body DXA scans. Linear regression techniques were used with muscle strength as the independent variable and BMD as the dependent variable. Models were adjusted for age and indices of body composition. RESULTS: Measures of age-adjusted hip flexor strength and hip abductor strength were positively associated with total hip BMD. For each standard deviation (SD) increase in hip flexor strength, the increase in mean total hip BMD (SD) was 10.4 % (p = 0.009). A similar pattern was observed for hip abductor strength, with an increase in mean total hip BMD of 22.8 % (p = 0.025). All associations between hip muscle strength and total hip BMD were independent of height, but were nullified after adjusting for appendicular lean mass or total lean mass. CONCLUSIONS: There was a positive association observed between muscle strength and BMD at the hip. However, this association was explained by measures of lean mass

Ultra-low-dose thoracic CT with model-based iterative reconstruction (MBIR) in cystic fibrosis patients undergoing treatment with cystic fibrosis transmembrane conductance regulators (CFTR)

AIM: To assess the utility of a volumetric low-dose computed tomography (CT) thorax (LDCTT) protocol at a dose equivalent to a posteroanterior (PA) and lateral chest radiograph for surveillance of cystic fibrosis (CF) patients. MATERIALS AND METHODS: A prospective study was undertaken of 19 adult patients with CF that proceeded to LDCTT at 12 and 24 months following initiation of ivacaftor. A previously validated seven-section, low-dose axial CT protocol was used for the 12-month study. A volumetric LDCTT protocol was developed for the 24-month study and reconstructed with hybrid iterative reconstruction (LD-ASIR) and pure iterative reconstruction (model-based IR [LD-MBIR]). Radiation dose was recorded for each scan. Image quality was assessed quantitatively and qualitatively, and disease severity was assessed using a modified Bhalla score. Statistical analysis was performed and p-values of <0.05 were considered statistically significant. RESULTS: Volumetric LD-MBIR studies were acquired at a lower radiation dose than the seven-section studies (0.08 ± 0.01 versus 0.10 ± 0.02 mSv; p=0.02). LD-MBIR and seven-section ASIR images had significantly lower levels of image noise compared with LD-ASIR images (p<0.0001). Diagnostic acceptability scores and depiction of bronchovascular structures were found to be acceptable for axial and coronal LD-MBIR images. LD-MBIR images were superior to LD-ASIR images for all qualitative parameters assessed (p<0.0001). No significant change was observed in mean Bhalla score between 1-year and 2-year studies (p=0.84). CONCLUSIONS: The use of a volumetric LDCTT protocol (reconstructed with pure IR) enabled acquisition of diagnostic quality CT images, which were considered extremely useful for surveillance of CF patients, at a dose equivalent to a PA and lateral chest radiograph

Metabolic control analysis is helpful for informed genetic manipulation of oilseed rape (Brassica napus) to increase seed oil content

Top–down control analysis (TDCA) is a useful tool for quantifying constraints on metabolic pathways that might be overcome by biotechnological approaches. Previous studies on lipid accumulation in oilseed rape have suggested that diacylglycerol acyltransferase (DGAT), which catalyses the final step in seed oil biosynthesis, might be an effective target for enhancing seed oil content. Here, increased seed oil content, increased DGAT activity, and reduced substrate:product ratio are demonstrated, as well as reduced flux control by complex lipid assembly, as determined by TDCA in Brassica napus (canola) lines which overexpress the gene encoding type-1 DGAT. Lines overexpressing DGAT1 also exhibited considerably enhanced seed oil content under drought conditions. These results support the use of TDCA in guiding the rational selection of molecular targets for oilseed modification. The most effective lines had a seed oil increase of 14%. Moreover, overexpression of DGAT1 under drought conditions reduced this environmental penalty on seed oil content

Prophylactic treatment of migraine; the patient's view, a qualitative study

Contains fulltext : 109202.pdf (publisher's version ) (Open Access)BACKGROUND: Prophylactic treatment is an important but under-utilised option for the management of migraine. Patients and physicians appear to have reservations about initiating this treatment option. This paper explores the opinions, motives and expectations of patients regarding prophylactic migraine therapy. METHODS: A qualitative focus group study in general practice in the Netherlands with twenty patients recruited from urban and rural general practices. Three focus group meetings were held with 6-7 migraine patients per group (2 female and 1 male group). All participants were migraine patients according to the IHS (International Headache Society); 9 had experience with prophylactic medication. The focus group meetings were analysed using a general thematic analysis. RESULTS: For patients several distinguished factors count when making a decision on prophylactic treatment. The decision of a patient on prophylactic medication is depending on experience and perspectives, grouped into five categories, namely the context of being active or passive in taking the initiative to start prophylaxis; assessing the advantages and disadvantages of prophylaxis; satisfaction with current migraine treatment; the relationship with the physician and the feeling to be heard; and previous steps taken to prevent migraine. CONCLUSION: In addition to the functional impact of migraine, the decision to start prophylaxis is based on a complex of considerations from the patient's perspective (e.g. perceived burden of migraine, expected benefits or disadvantages, interaction with relatives, colleagues and physician). Therefore, when advising migraine patients about prophylaxis, their opinions should be taken into account. Patients need to be open to advice and information and intervention have to be offered at an appropriate moment in the course of migraine