Kerncraft: A Tool for Analytic Performance Modeling of Loop Kernels

Achieving optimal program performance requires deep insight into the interaction between hardware and software. For software developers without an in-depth background in computer architecture, understanding and fully utilizing modern architectures is close to impossible. Analytic loop performance modeling is a useful way to understand the relevant bottlenecks of code execution based on simple machine models. The Roofline Model and the Execution-Cache-Memory (ECM) model are proven approaches to performance modeling of loop nests. In comparison to the Roofline model, the ECM model can also describes the single-core performance and saturation behavior on a multicore chip. We give an introduction to the Roofline and ECM models, and to stencil performance modeling using layer conditions (LC). We then present Kerncraft, a tool that can automatically construct Roofline and ECM models for loop nests by performing the required code, data transfer, and LC analysis. The layer condition analysis allows to predict optimal spatial blocking factors for loop nests. Together with the models it enables an ab-initio estimate of the potential benefits of loop blocking optimizations and of useful block sizes. In cases where LC analysis is not easily possible, Kerncraft supports a cache simulator as a fallback option. Using a 25-point long-range stencil we demonstrate the usefulness and predictive power of the Kerncraft tool.Comment: 22 pages, 5 figure

On the "Fake" Inferred Entanglement Associated with the Maximum Entropy Inference of Quantum States

The inference of entangled quantum states by recourse to the maximum entropy principle is considered in connection with the recently pointed out problem of fake inferred entanglement [R. Horodecki, {\it et al.}, Phys. Rev. A {\it 59} (1999) 1799]. We show that there are operators $\hat A$, both diagonal and non diagonal in the Bell basis, such that when the expectation value $$ is taken as prior information the problem of fake entanglement is not solved by adding a new constraint associated with the mean value of $\hat A^2$ (unlike what happens when the partial information is given by the expectation value of a Bell operator). The fake entanglement generated by the maximum entropy principle is also studied quantitatively by comparing the entanglement of formation of the inferred state with that of the original one.Comment: 25 Revtex pages, 5 Postscript figures, submitted to J. Phys. A (Math. Gen.

New DRIE-Patterned Electrets for Vibration Energy Harvesting

This paper is about a new manufacturing process aimed at developing stable SiO2/Si3N4 patterned electrets using a Deep Reactive Ion Etching (DRIE) step for an application in electret-based Vibration Energy Harvesters (e-VEH). This process consists in forming continuous layers of SiO2/Si3N4 electrets in order to limit surface conduction phenomena and is a new way to see the problem of electret patterning. Experimental results prove that patterned electrets charged by a positive corona discharge show excellent stability with high surface charge densities that may reach 5mC/m^2 on 1.1\mu m-thick layers, even with fine patterning and harsh temperature conditions (up to 250{\deg}C). This paves the way to new e-VEH designs and manufacturing processes.Comment: Proc. European Energy Conference, 201

Stroke types, risk factors, quality of care and outcomes at a Referral Hospital in Western Kenya

Background: The prevalence of stroke is increasing in sub-Saharan Africa due to increases in size of  aging population and stroke risk factors.We assessed risk factors, quality of care and outcomes of stroke to identify modifiable risk factors and areas of care that need improvement for better outcomes.Objectives: To describe the stroke types, risk factors, outcomes and stroke quality of care in a large academic medical centre hospital.Design: Hospital based retrospective study.Setting: Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya.Subjects: All patients >18 years admitted with a diagnosis of stroke as per the WHO definition and with a supporting brain imaging (CT scan/ MRI )were included in the study. Data abstracted from the files included demographic details, stroke subtype, stroke risk factors, inpatient stroke care quality  indicators(based on US Joint Commission stroke quality indicator definitions) and in hospital stroke  outcomes. Descriptive statistics was used to summarise the data.Results: A total of 155 patients had stroke between January 2010 and December 2014 of whom 42% were male, the median age was 61 (IQR: 49-72) years. Majority (73%) had hypertension. The prevalence of diabetes was 4%. Left hemiplegia/hemiparesis was the predominant presentation (50%). Haemorrhagic strokes were frequent (52%) with anterior circulation stroke comprising 97% of all strokes. Assessment of quality of care indicators showed that overall, 84% of the patients had a brain CT scan on day one of admission,93% had a GCS documented at admission, 32% were on statins and 3% were screened for dysphagia before oral intake. Among patients with ischaemic strokes; none underwent thrombolysis, 24% received DVT prophylaxis, 54% received statins, and 73% received anti-thrombotic therapy by hospital day two. In hospital mortalityoccurred in 43(27%)with a higher rate among haemorrhagic strokes (31%) compared to ischaemic stroke (24%)(p=0.364).Conclusion: Haemorrhagic stroke was the most common type of stroke admitted, hypertension was the predominant risk factor and most strokes involved the anterior circulation. In-hospital mortality was 27%.There were several opportunities to improve evidence-based quality of care indicators

A passive transmitter for quantum key distribution with coherent light

Signal state preparation in quantum key distribution schemes can be realized using either an active or a passive source. Passive sources might be valuable in some scenarios; for instance, in those experimental setups operating at high transmission rates, since no externally driven element is required. Typical passive transmitters involve parametric down-conversion. More recently, it has been shown that phase-randomized coherent pulses also allow passive generation of decoy states and Bennett-Brassard 1984 (BB84) polarization signals, though the combination of both setups in a single passive source is cumbersome. In this paper, we present a complete passive transmitter that prepares decoy-state BB84 signals using coherent light. Our method employs sum-frequency generation together with linear optical components and classical photodetectors. In the asymptotic limit of an infinite long experiment, the resulting secret key rate (per pulse) is comparable to the one delivered by an active decoy-state BB84 setup with an infinite number of decoy settings.Comment: 10 pages, 4 figures. arXiv admin note: substantial text overlap with arXiv:1009.383

Conditional q-Entropies and Quantum Separability: A Numerical Exploration

We revisit the relationship between quantum separability and the sign of the relative q-entropies of composite quantum systems. The q-entropies depend on the density matrix eigenvalues p_i through the quantity omega_q = sum_i p_i^q. Renyi's and Tsallis' measures constitute particular instances of these entropies. We perform a systematic numerical survey of the space of mixed states of two-qubit systems in order to determine, as a function of the degree of mixture, and for different values of the entropic parameter q, the volume in state space occupied by those states characterized by positive values of the relative entropy. Similar calculations are performed for qubit-qutrit systems and for composite systems described by Hilbert spaces of larger dimensionality. We pay particular attention to the limit case q --> infinity. Our numerical results indicate that, as the dimensionalities of both subsystems increase, composite quantum systems tend, as far as their relative q-entropies are concerned, to behave in a classical way

Genetics of Congenital Heart Disease

Congenital heart disease (CHD) is one of the most common birth defects. Studies in animal models and humans have indicated a genetic etiology for CHD. About 400 genes have been implicated in CHD, encompassing transcription factors, cell signaling molecules, and structural proteins that are important for heart development. Recent studies have shown genes encoding chromatin modifiers, cilia related proteins, and cilia-transduced cell signaling pathways play important roles in CHD pathogenesis. Elucidating the genetic etiology of CHD will help improve diagnosis and the development of new therapies to improve patient outcomes

CTEN/tensin 4 expression induces sensitivity to paclitaxel in prostate cancer

BACKGROUND Recently, we established paclitaxel-resistant prostate cancer cell lines (PC-3-TxR and DU145-TxR). To determine the mechanisms of paclitaxel resistance in PC-3-TxR cells, we compared the gene expression profiles between PC-3 and PC-3-TxR cells. Our results indicated that expression of the C-terminal tensin like protein (CTEN, tensin 4) gene was down-regulated by 10-fold in PC-3-TxR cells. We investigated the possibility that CTEN overexpression restores paclitaxel sensitivity. METHODS We investigated how knockdown and overexpression of CTEN in androgen-independent cell lines affect paclitaxel sensitivity by colony formation assay and growth inhibition assay. To determine the mechanisms by which CTEN affects paclitaxel sensitivity, we investigated the relationships between CTEN and F-actin or epidermal growth factor receptor (EGFR) in PC-3 cells. We also examined the association between expression of CTEN and grade of prostate cancer by immunohistochemistry using tissue microarray analysis. RESULTS Down-regulation of CTEN, which is located in the cytoskeleton, played an important role in paclitaxel resistance in PC-3-TxR cells. Knockdown of CTEN expression in PC-3 cells induced paclitaxel resistance. Overexpression of CTEN in PC-3-TxR and DU145-TxR cells restored paclitaxel sensitivity. CTEN expression was inversely correlated with F-actin and EGFR expression. Then knockdown of actin and EGFR in PC-3-TxR cells recovered paclitaxel sensitivity, indicating that CTEN down-regulation mediates paclitaxel resistance through elevation of EGFR and actin expression. Moreover, CTEN expression was inversely correlated with Gleason score. CONCLUSIONS These results strongly suggested that CTEN plays an important role in paclitaxel sensitivity and that CTEN expression level may be a prognostic predictive factor for PCa patients. Prostate 70: 48–60, 2010. © 2009 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64566/1/21037_ftp.pd

The Versatile Molecular Complex Component LC8 Promotes Several Distinct Steps of Flagellar Assembly

LC8 is present in various molecular complexes. However, its role in these complexes remains unclear. We discovered that although LC8 is a subunit of the radial spoke (RS) complex in Chlamydomonas flagella, it was undetectable in the RS precursor that is converted into the mature RS at the tip of elongating axonemes. Interestingly, LC8 dimers bound in tandem to the N-terminal region of a spoke phosphoprotein, RS protein 3 (RSP3), that docks RSs to axonemes. LC8 enhanced the binding of RSP3 N-terminal fragments to purified axonemes. Likewise, the N-terminal fragments extracted from axonemes contained LC8 and putative spoke-docking proteins. Lastly, perturbations of RSP3’s LC8-binding sites resulted in asynchronous flagella with hypophosphorylated RSP3 and defective associations between LC8, RSs, and axonemes. We propose that at the tip of flagella, an array of LC8 dimers binds to RSP3 in RS precursors, triggering phosphorylation, stalk base formation, and axoneme targeting. These multiple effects shed new light on fundamental questions about LC8-containing complexes and axoneme assembly

Cis‐acting allele specific expression (ASE) differences induced by alcohol and impacted by sex as well as parental genotype of origin

Background Alcohol use disorders (AUDs) are influenced by complex interactions between the genetics of the individual and their environment. We have previously identified hundreds of polygenic genetic variants between the selectively bred high and low alcohol drinking (HAD and LAD) rat lines. Here we report allele specific expression (ASE) differences, between the HAD2 and LAD2 rat lines. Methods The HAD2 and LAD2 rats which have been sequenced were reciprocally crossed to generate 10 litters of F1 progeny. For 5 of these litters, the sire was HAD2; and, for the other 5 litters, the sire was a LAD2. From these 10 litters, two males and two females were picked from each F1 litter (N = 40 total). The F1‐pups were divided, with balancing for sex and direction of cross, into an alcohol (15%) vs a water control group. Alcohol‐drinking started in the middle of adolescence (~PND 35) and lasted 9 weeks. At the end of these treatments, rats were euthanized, the nucleus accumbens was dissected, and RNA was processed for RNA‐sequencing and ASE analyses. Results Analyses revealed that adolescent ethanol drinking, individual ethanol drinking levels, parentage, and sex‐of‐animal affected ASEs of about 300 genes. The identified genes included those associated with ethanol metabolism (e.g., Aldh2); neuromodulatory function [e.g., Cckbr, Slc6a7, and Slc1a1]; ion channel activity (e.g., Kcnc3); as well as other synaptic and epigenetic function. Conclusion These data indicate that ethanol drinking differentially amplified paternal vs maternal allelic contribution to the transcriptome. We hypothesize that this was due, at least in part, to ethanol‐induced changes in cis‐regulation of polymorphisms previously identified between the HAD2 and LAD2 rat lines. This report highlights the complexity of gene‐by‐environment interactions mediating a genetic predisposition for, and/or the active development of, alcohol use disorders