UPC++ v1.0 Programmer’s Guide, Revision 2020.3.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

Functional environmental genomics of a municipal landfill soil.

We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects

Reliability and Interpretability of Sonographic Measurements of Palmar Dupuytren Nodules

Purpose: In the future, it is expected that treatment of Dupuytren disease (DD) may shift toward control of early disease. Ultrasound might be an accurate method to measure the outcome of such treatment. The aim of this study was to assess the reliability of sonographic measurement of palmar nodules. Methods: Fifty patients with nodules characteristic for early disease were assessed with ultrasound by 2 observers. Four different aspects of DD nodules were measured in the transversal and sagittal planes, width, depth, circumference, and area. The intra- and interobserver reliabilities were calculated using the intraclass correlation coefficient (ICC). The standard error of measurement (SEM) and the smallest detectable change (SDC) were also calculated for each aspect. Results: The intraobserver reliability was good (ICC, 0.724 [0.562–0.833] to 0.886 [0.808–0.934]), except for width in the sagittal direction (ICC, 0.671 [0.484–0.799]). The interobserver reliability was moderate (ICC, 0.385 [0.126–0.596] to 0.757 [0.538–0.869]). The intraobserver ICCs of area were highest (transverse, 0.847 [0.744–0.893]; sagittal, 0.886 [0.808–0.934]). The SEM and SDC of area were 6.1 and 16.9 mm2 in the transverse and 8.0 and 22.2 mm2 in the sagittal plane. Conclusions: The intraobserver reliability of sonographic assessment of DD nodules is good. The measurement of area is the most reliable and is, therefore, recommended for future studies. However, even single-observer measurements have a clear dispersion, and a change beyond 16.9 (61%) and 22.2 mm2 (79%) has to be observed in the transverse and sagittal planes, respectively, before it can be considered as regression or progression. Clinical relevance: Repeated ultrasonographic measurements in DD should ideally be done by a single observer, using area of the nodule in the sagittal plane. Change beyond 16.9 (transverse) and 22.2 (sagittal) mm2 can be considered as a real change in nodule size

Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta

<p>Abstract</p> <p>Background</p> <p>Metallothionein (<it>mt</it>) transcription is elevated in heavy metal tolerant field populations of <it>Orchesella cincta </it>(Collembola). This suggests that natural selection acts on transcriptional regulation of <it>mt </it>in springtails at sites where cadmium (Cd) levels in soil reach toxic values This study investigates the nature and the evolutionary origin of polymorphisms in the metallothionein promoter (<it>pmt</it>) and their functional significance for <it>mt </it>expression.</p> <p>Results</p> <p>We sequenced approximately 1600 bp upstream the <it>mt </it>coding region by genome walking. Nine <it>pmt </it>alleles were discovered in NW-European populations. They differ in the number of some indels, consensus transcription factor binding sites and core promoter elements. Extensive recombination events between some of the alleles can be inferred from the alignment. A deviation from neutral expectations was detected in a cadmium tolerant population, pointing towards balancing selection on some promoter stretches. Luciferase constructs were made from the most abundant alleles, and responses to Cd, paraquat (oxidative stress inducer) and moulting hormone were studied in cell lines. By using paraquat we were able to dissect the effect of oxidative stress from the Cd specific effect, and extensive differences in <it>mt </it>induction levels between these two stressors were observed.</p> <p>Conclusion</p> <p>The <it>pmt </it>alleles evolved by a number of recombination events, and exhibited differential inducibilities by Cd, paraquat and molting hormone. In a tolerant population from a metal contaminated site, promoter allele frequencies differed significantly from a reference site and nucleotide polymorphisms in some promoter stretches deviated from neutral expectations, revealing a signature of balancing selection. Our results suggest that the structural differences in the <it>Orchesella cincta </it>metallothionein promoter alleles contribute to the metallothionein -over-expresser phenotype in cadmium tolerant populations.</p

Exploring DNA methylation patterns in copper exposed Folsomia candida and Enchytraeus crypticus

Accumulating evidence shows that epigenetics-mediated phenotypic plasticity plays a role in an organism’s ability to deal with environmental stress. However, to date, the role of epigenetic modifications in response to stress is hardly investigated in soil invertebrates. The main objective of this proof of principle study was to explore whether total cytosine and locus-specific CpG methylation are present in two important ecotoxicological model organisms, the springtail Folsomia candida and the potworm Enchytraeus crypticus, and if so, whether methylation patterns might change with increased toxicant exposure. LC-MS/MS analyses and bisulfite sequencing were performed to identify the CpG methylation state of the organisms. We show here, for the first time, a total level of 1.4% 5-methyl cytosine methylation in the genome of E. crypticus, and an absence of both total cytosine and locus-specific CpG methylation in F. candida. In E. crypticus, methylation of CpG sites was observed in the coding sequence (CDS) of the housekeeping gene Elongation Factor 1α, while the CDS of the stress inducible Heat Shock Protein 70 gene almost lacked methylation. This confirms previous observations that DNA methylation differs between housekeeping and stress-inducible genes in invertebrates. DNA methylation patterns in E. crypticus were not affected by exposure to copper (II) sulfate pentahydrate (CuSO4·5H2O) mixed in with LUFA 2.2 soil at sublethal effect concentrations that decreased reproduction by 10%, 20% and 50%. Although, differences in CpG methylation patterns between specific loci suggest a functional role for DNA methylation in E. crypticus, genome-wide bisulfite sequencing is needed to verify whether environmental stress affects this epigenetic hallmark

UPC++ v1.0 Programmer’s Guide, Revision 2019.9.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

Voeren van Texelaar x Flevolander vleeslammeren

In een voederproef werd de invloed van het niveau en de duur van een energiebeperking op de groei, voederconversie en slachtkwaliteit onderzocht

UPC++ v1.0 Specification, Revision 2019.9.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. We are revising the library under the auspices of the DOE’s Exascale Computing Project, to meet the needs of applications requiring PGAS support. UPC++ is intended for implementing elaborate distributed data structures where communication is irregular or fine-grained. The UPC++ interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and similar to those used in conventional C++. The UPC++ programmer can expect communication to run at close to hardware speeds. The key facilities in UPC++ are global pointers, that enable the programmer to express ownership information for improving locality, one-sided communication, both put/get and RPC, futures and continuations. Futures capture data readiness state, which is useful in making scheduling decisions, and continuations provide for completion handling via callbacks. Together, these enable the programmer to chain together a DAG of operations to execute asynchronously as high-latency dependencies become satisfied

Intensief mesten Flevolander vleeslammeren alleen mogelijk bij relatief lage karkasgewichten

Bij deze voederproef was de vraag of met een vergaande energiebeperking de ram- en ooilammeren op resp. 36 en 40 kg afgeleverd kunnen worden met een 2°-vetbedekking