Chain Reduction for Binary and Zero-Suppressed Decision Diagrams

Chain reduction enables reduced ordered binary decision diagrams (BDDs) and zero-suppressed binary decision diagrams (ZDDs) to each take advantage of the others' ability to symbolically represent Boolean functions in compact form. For any Boolean function, its chain-reduced ZDD (CZDD) representation will be no larger than its ZDD representation, and at most twice the size of its BDD representation. The chain-reduced BDD (CBDD) of a function will be no larger than its BDD representation, and at most three times the size of its CZDD representation. Extensions to the standard algorithms for operating on BDDs and ZDDs enable them to operate on the chain-reduced versions. Experimental evaluations on representative benchmarks for encoding word lists, solving combinatorial problems, and operating on digital circuits indicate that chain reduction can provide significant benefits in terms of both memory and execution time

Highly accelerated simulations of glassy dynamics using GPUs: caveats on limited floating-point precision

Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD) simulations for system sizes ranging up to about 1 million particles. Particular emphasis is put on the numerical long-time stability in terms of energy and momentum conservation, and caveats on limited floating-point precision are issued. Strict energy conservation over 10^8 MD steps is obtained by double-single emulation of the floating-point arithmetic in accuracy-critical parts of the algorithm. For the slow dynamics of a supercooled binary Lennard-Jones mixture, we demonstrate that the use of single-floating point precision may result in quantitatively and even physically wrong results. For simulations of a Lennard-Jones fluid, the described implementation shows speedup factors of up to 80 compared to a serial implementation for the CPU, and a single GPU was found to compare with a parallelised MD simulation using 64 distributed cores.Comment: 12 pages, 7 figures, to appear in Comp. Phys. Comm., HALMD package licensed under the GPL, see http://research.colberg.org/projects/halm

A Retrospective on DOSE: An Interpretive Approach to Structure Editor Generation

DOSE is unique among structu.re editor generators in its interpretive approach. This approach leads to very fast turn-around time for changes and provides multi-language facilities for no additional effort or cost. This article compares the interpretive approach to the compilation approach of other structu.re editor generators. It describes some of the design and implementation decisions made and remade during this project and the lessons learned. It emphasizes the advantages and disadvantages of DOSE with respect to other structure editing systems

Knockout of the Carbohydrate Responsive Element Binding Protein Enhances Proliferation and Tumorigenesis in Renal Tubules of Mice

Glycogen-storing so-called clear cell kidney tubules (CCTs), precursor lesions of renal cell carcinoma, have been described in diabetic rats and in humans. The lesions show upregulation of the Akt/mTOR-pathway and the related transcription factor carbohydrate responsive element binding protein (ChREBP), which is supposedly pro-oncogenic. We investigated the effect of ChREBP-knockout on nephrocarcinogenesis in streptozotocin-induced diabetic and normoglycemic mice. Diabetic, but not non-diabetic mice, showed CCTs at 3, 6 and 12 months of age. Glycogenosis was confirmed by periodic acid schiff reaction and transmission electron microscopy. CCTs in ChREBP-knockout mice consisted of larger cells and occurred more frequently compared to wildtype mice. Progression towards kidney tumors was observed in both diabetic groups but occurred earlier in ChREBP-knockout mice. Proliferative activity assessed by BrdU-labeling was lower in 1-week-old but higher in 12-month-old diabetic ChREBP-knockout mice. Surprisingly, renal neoplasms occurred spontaneously in non-diabetic ChREBP-knockout, but not non-diabetic wildtype mice, indicating an unexpected tumor-suppressive function of ChREBP. Immunohistochemistry showed upregulated glycolysis and lipogenesis, along with activated Akt/mTOR-signaling in tumors of ChREBP-knockout groups. Immunohistochemistry of human clear cell renal cell carcinomas revealed reduced ChREBP expression compared to normal kidney tissue. However, the molecular mechanisms by which loss of ChREBP might facilitate tumorigenesis require further investigation

New relative intensity ambulatory accelerometer thresholds for elderly men and women: the Generation 100 study

BACKGROUND: Public health initiatives world-wide recommend increasing physical activity (PA) to improve health. However, the dose and the intensity of PA producing the most benefit are still debated. Accurate assessment of PA is necessary in order to 1) investigate the dose–response relationship between PA and health, 2) shape the most beneficial public health initiatives and 3) test the effectiveness of such initiatives. Actigraph accelerometer is widely used to objectively assess PA, and the raw data is given in counts per unit time. Count-thresholds for low, moderate and vigorous PA are mostly based on absolute intensity. This leads to largely inadequate PA intensity assessment in a large proportion of the elderly, who due to their declining maximal oxygen uptake (VO(2max)) cannot reach the moderate/vigorous intensity as defined in absolute terms. To resolve this issue, here we report relative Actigraph intensity-thresholds for the elderly. METHODS: Submaximal-oxygen-uptake, VO(2max) and maximal heart rate (HR(max)) were measured in 111 70–77 year olds, while wearing an Actigraph-GT3X+. Relationship between VO(2max) percentage (%), counts-per-minute (CPM) and gender (for both the vertical-axis (VA) and vector-magnitude (VM)) and VO(2max)% and HR(max)% was established using a mixed-regression-model. VM-and VA-models were tested against each other to see which model predicts intensity of PA better. RESULTS: VO(2max) and gender significantly affected number of CPM at different PA intensities (p < 0.05). Therefore, intensity-thresholds were created for both men and women of ranging VO(2max) values (low, medium, high). VM-model was found to be a better predictor of PA-intensity than VA-model (p < 0.05). Established thresholds for moderate intensity (46−63 % of VO(2max)) ranged from 669–3367 and 834–4048 CPM and vigorous intensity (64−90 % of VO(2max)) from 1625–4868 and 2012-5423CPM, for women and men, respectively. Lastly, we used this evidence to derive a formula that predicts customized relative intensity of PA (either VO(2max)% or HR(max)%) using counts-per-minute values as input. CONCLUSION: Intensity-thresholds depend on VO(2max), gender and Actigraph-axis. PA intensity-thresholds that take all these factors into account allow for more accurate relative intensity PA assessment in the elderly and will be useful in future PA research. TRIAL REGISTRATION: (ClinicalTrials.gov Identifier: NCT02017847, registered 17. December 2013