sCore eindrapportage

In opdracht van Syntens heeft de Intelligent Systems groep van Wageningen UR Food & Biobased Research de sCore-applicatie gebouwd. De sCore-applicatie is een van de pijlers in het project “De Toekomst Bedrijven”. Dit is de eindrapportage van het sCore-project

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements

Person Detection in the Restaurant of the Future

Many computer vision techniques dealing with humans require that the location within an image of a person is known. In this research, we investigated into the subject of person detection in a real-world environment: the Restaurant of the Future. We evaluated several methods and selected one: person detection using face detection. In order to apply this we evaluated several known methods for face detection. Then we determined which aspects of the recordings from the Restaurant impacted the performance of the face detectors. All methods suffered strongly from the complex background in the Restaurant and the low quality of the recordings. The angled viewpoint had an impact on several of the methods while the video encoding used affected others. On the worst conditions, the Viola-Jones detector performed best. The analysis of the weaknesses of the face detectors will give future researchers a starting point in improving known or finding new methods.

Assessing the variation in workload among general practitioners in urban and rural areas: An analysis based on SMS time sampling data

Item does not contain fulltextObjective: An important reason why general practitioners (GPs) are less inclined to work in rural areas is a perception of a higher workload. This study assesses the differences in the workloads of GPs in rural and urban areas. We used two definitions of rurality, one based on the number of addresses per square kilometre, and a second defined by the expected decline in population. Methods: We collected time use data over 1 year by sending SMS text messages to Dutch GPs who each participated during a period of 1 week. This data was matched with those from GPs' registration and practice location. Data from 596 self-employed GPs were analysed using descriptive statistics and multiple regression analyses. Results: In group practices, the patient list size of rural GPs was, on average, 231 patients more than those of urban GPs. They worked 3.5 more hours per week, with 2.6 more hours directly related to patients. A small significant relation was found between degree of urbanisation and the dependent variables list size and working hours. Working in a depopulation area had no significant effect on the workload indicators. Furthermore, GPs in group practices worked significantly fewer hours, and had smaller list sizes, than GPs in single-handed practices. Conclusion: The results show that the assumption of a higher workload in rural practices does not completely match the objective workload of GPs in these areas. Rural GPs have a higher workload in certain cases, but the type of a practice seems a more important determinant

Going green: Optimizing GPUs for energy efficiency through model-steered auto-tuning

Graphics Processing Units (GPUs) have revolutionized the computing landscape over the past decade. However, the growing energy demands of data centres and computing facilities equipped with GPUs come with significant capital and environmental costs. The energy consumption of GPU applications greatly depend on how well they are optimized. Auto-tuning is an effective and commonly applied technique of finding the optimal combination of algorithm, application, and hardware parameters to optimize performance of a GPU application. In this paper, we introduce new energy monitoring and optimization capabilities in Kernel Tuner, a generic auto-tuning tool for GPU applications. These capabilities enable us to investigate the difference between tuning for execution time and various approaches to improve energy efficiency, and investigate the differences in tuning difficulty. Additionally, our model for GPU power consumption greatly reduces the large tuning search space by providing clock frequencies for which a GPU is likely most energy efficient

Urinary renin, but not angiotensinogen or aldosterone, reflects the renal renin-angiotensin-aldosterone system activity and the efficacy of renin-angiotensin-aldosterone system blockade in the kidney

Objective To study which renin-angiotensin-aldosterone system (RAAS) component best reflects renal RAAS activity. Methods and results We measured urinary and plasma renin, prorenin, angiotensinogen, aldosterone, albumin and creatinine in 101 diabetic and nondiabetic patients with or without hypertension. Plasma prorenin was elevated in diabetic patients. Urinary prorenin was undetectable. Urinary albumin and renin were higher in diabetic patients. Men had higher plasma renin/prorenin levels, and lower plasma angiotensinogen levels than women. Plasma creatinine and albumin were also higher in men. Urinary RAAS components showed no sexual dimorphism, whereas urinary creatinine and albumin were higher in men. Angiotensin-converting enzyme inhibitors and angiotensin II type 1 receptor blockers increased plasma renin and decreased plasma angiotensinogen, without altering plasma aldosterone. In contrast, in urine, these drugs decreased renin and aldosterone without affecting angiotensinogen. When analyzing all patients together, urinary angiotensinogen excretion closely mimicked that of albumin, whereas urinary angiotensinogen and albumin levels both were 0.05% or less of their concomitant plasma levels. This may reflect the identical glomerular filtration and tubular handling of both proteins, which have a comparable molecular weight. In contrast, urinary renin excretion did not correlate with urinary albumin excretion, and the urinary/plasma concentration ratio of renin was more than 200 times the ratio of albumin, despite its comparable molecular weight. Urinary aldosterone excretion closely followed urinary creatinine excretion. Conclusion The increased urinary renin levels in diabetes and the decreased urinary renin levels following RAAS blockade, occurring independently of changes in plasma renin, reflect the activated renal RAAS in diabetes and the success of RAAS blockade in the kidney, respectively. Urinary renin, therefore, more closely reflects renal RAAS activity than urinary angiotensinogen or aldosterone. J Hypertens 29: 2147-2155 (C) 2011 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins

Chromatin immunoprecipitation scanning identifies glucocorticoid receptor binding regions in the proximal promoter of a ubiquitously expressed glucocorticoid target gene in brain

While the actions of glucocorticoids on brain functions have been comprehensively studied, the underlying genomic mechanisms are poorly understood. In this study, we show that glucocorticoid‐induced leucine zipper (GILZ) mRNA is strongly and ubiquitously induced in rat brain. To decipher the molecular mechanisms underlying these genomic effects, it is of interest to identify the regulatory sites in the promoter region. Alignment of the rat GILZ promoter with the well‐characterized human promoter resulted in poor sequence homology. Consequently, we analyzed the rat 5′ flanking sequence by Matrix REDUCE and identified two high‐affinity glucocorticoid response elements (GRE) located 2 kb upstream of the transcription start site. These findings were corroborated using the glucocorticoid receptor (GR) expressing Ns‐1 PC12 rat cell‐line. In these cells, dexamethasone treatment leads to a progressive increase of GILZ mRNA expression levels via a GR‐dependent mechanism. Subsequently, using chromatin immunoprecipitation assays we show that the two high‐affinity GREs are located within the GR‐binding regions. Lastly, we demonstrate using multiple tissue in situ hybridization a marked increase in mRNA expression levels in spleen, thymus, heart, lung, liver, muscle, testis, kidney, colon, ileum, as well as in brain and conclude that the GILZ gene can be used to study glucocorticoid effects in many additional rodent tissues