Miracle-dz/UniFAR-FTUs huggingface dataset:
Skeleton-based automatic parallelization of image processing algorithms for GPUs

Graphics Processing Units (GPUs) are becoming increasingly important in high performance computing. To maintain high quality solutions, programmers have to efficiently parallelize and map their algorithms. This task is far from trivial, leading to the necessity to automate this process. In this paper, we present a technique to automatically parallelize and map sequential code on a GPU, without the need for code-annotations. This technique is based on skeletonization and is targeted at image processing algorithms. Skeletonization separates the structure of a parallel computation from the algorithm's functionality, enabling efficient implementations without requiring architecture knowledge from the programmer. We define a number of skeleton classes, each enabling GPU specific parallelization techniques and optimizations, including automatic thread creation, on-chip memory usage and memory coalescing. Recently, similar skeletonization techniques have been applied to GPUs. Our work uses domain specific skeletons and a finer-grained classification of algorithms. Comparing skeleton-based parallelization to existing GPU code generators in general, we potentially achieve a higher hardware efficiency by enabling algorithm restructuring through skeletons. In a set of benchmarks, we show that the presented skeleton-based approach generates highly optimized code, achieving high data throughput. Additionally, we show that the automatically generated code performs close or equal to manually mapped and optimized code. We conclude that skeleton-based parallelization for GPUs is promising, but we do believe that future research must focus on the identification of a finer-grained and complete classification.
Independent Versus Coupled Inactivation in Sodium Channels

The voltage sensor of the sodium channel is mainly comprised of four positively charged S4 segments. Depolarization causes an outward movement of S4 segments, and this movement is coupled with opening of the channel. A mutation that substitutes a cysteine for the outermost arginine in the S4 segment of the second domain (D2:R1C) results in a channel with biophysical properties similar to those of wild-type channels. Chemical modification of this cysteine with methanethiosulfonate-ethyltrimethylammonium (MTSET) causes a hyperpolarizing shift of both the peak current–voltage relationship and the kinetics of activation, whereas the time constant of inactivation is not changed substantially. A conventional steady state inactivation protocol surprisingly produces an increase of the peak current at −20 mV when the 300-ms prepulse is depolarized from −190 to −110 mV. Further depolarization reduces the current, as expected for steady state inactivation. Recovery from inactivation in modified channels is also nonmonotonic at voltages more hyperpolarized than −100 mV. At −180 mV, for example, the amplitude of the recovering current is briefly almost twice as large as it was before the channels inactivated. These data can be explained readily if MTSET modification not only shifts the movement of D2/S4 to more hyperpolarized potentials, but also makes the movement sluggish. This behavior allows inactivation to have faster kinetics than activation, as in the HERG potassium channel. Because of the unique properties of the modified mutant, we were able to estimate the voltage dependence and kinetics of the movement of this single S4 segment. The data suggest that movement of modified D2/S4 is a first-order process and that rate constants for outward and inward movement are each exponential functions of membrane potential. Our results show that D2/S4 is intimately involved with activation but plays little role in either inactivation or recovery from inactivation.
Multi-class brain segmentation using atlas propagation and EM-based refinement

In recent years, multi-atlas segmentation has emerged as one of the most accurate techniques for the segmentation of brain magnetic resonance (MR) images, especially when combined with intensity-based refinement techniques such as graph-cut or expectation-maximization (EM) optimization. However, most of the work so far has focused on intensity-based refinement strategies for individual anatomical structures such as the hippocampus. In this work we extend a previously proposed framework for labeling whole brain scans by incorporating a global and stationary Markov random field that ensures the consistency of the neighbourhood relations between structures with an a-priori defined model. In particular we improve the segmentation result of a locally weighted multi-atlas fusion method for 41 different structures simultaneously by applying a subsequent EM optimization step. We evaluate the proposed approach on 30 manually annotated brain MR images and observe an improvement of label overlaps to a manual reference by up to 6%. We also achieved a considerably improved group separation when the proposed segmentation framework is applied to a volumetric analysis of 404 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort.
Clinical Insights into Pragmatic Theory: Frontal Lobe Deficits and Sarcasm

The validity of psycholinguistic theories of sarcasm was explored by examining subjects with mainly frontal lobe (FL) damage and concomitant concreteness of thought. The majority of FL subjects could interpret consistent verbal exchanges but not literally contradictory (sarcastic) verbal exchanges which implied that the literal meaning of a sarcastic comment needs to be rejected in order for the inference to be detected. Subsidiary analyses confirmed that failure on sarcasm tasks was associated with poor conceptual skills. Ability to process attitude was not associated with success at recognizing sarcasm. This suggested that attitude is not pivotal to the detection of sarcastic inference.
15-Year Follow-Up of Recurrent “Hypoglycemia” in Preterm Infants

BACKGROUND: Observational study of 543 infants who weighed <1850 g, published in 1988 reported seriously impaired motor and cognitive development at 18 months in those with recurrent, asymptomatic hypoglycemia (plasma glucose level ≤2.5 mmol/L on ≥3 days). No study has yet replicated this observation. AIM: To quantify disability in a similar cohort of children followed up throughout childhood. POPULATION: All children born at <32 weeks’ gestation in the north of England in 1990–1991 and had laboratory blood glucose levels measured daily for the first 10 days of life. RESULTS: Forty-seven index children of the 566 who survived to 2 years had a blood glucose level of ≤2.5 mmol/L on ≥3 days. All of these children and hypoglycemia-free controls, matched for hospital of care, gestation, and birth weight, were assessed at age 2. No differences in developmental progress or physical disability were detected. The families were seen again when the children were 15 years old, and 38 of the index children (81%) and matched controls agreed to detailed psychometric assessment. Findings in the 2 groups were nearly identical (mean full-scale IQ: 80.7 vs 81.2). Findings in the 21 children with a level of ≤2.5 mmol/L on ≥4 days, 7 children with a level this low on 5 days, and 11 children with a level of <2.0 mmol/L on 3 different days did not alter these conclusions. CONCLUSIONS: This study found no evidence to support the belief that recurrent low blood glucose levels (≤2.5 mmol/L) in the first 10 days of life usually pose a hazard to preterm infants.
Biocompatibility and Toxicity of Poly(vinyl alcohol)/N,O-Carboxymethyl Chitosan Scaffold

The in vivo biocompatibility and toxicity of PVA/NOCC scaffold were tested by comparing them with those of a biocompatible inert material HAM in a rat model. On Day 5, changes in the blood parameters of the PVA/NOCC-implanted rats were significantly higher than those of the control. The levels of potassium, creatinine, total protein, A/G, hemoglobulin, erythrocytes, WBC, and platelets were not significantly altered in the HAM-implanted rats, when compared with those in the control. On Day 10, an increase in potassium, urea, and GGT levels and a decrease in ALP, platelet, and eosinophil levels were noted in the PVA/NOCC-implanted rats, when compared with control. These changes were almost similar to those noted in the HAM-implanted rats, except for the unaltered potassium and increased neutrophil levels. On Day 15, the total protein, A/G, lymphocyte, monocyte, and eosinophil levels remained unaltered in the PVA/NOCC-implanted rats, whereas urea, A/G, WBC, lymphocyte, and monocyte levels remained unchanged in the HAM-implanted rats. Histology and immunohistochemistry analyses revealed inflammatory infiltration in the PVA/NOCC-implanted rats, but not in the HAM-implanted rats. Although a low toxic tissue response was observed in the PVA/NOCC-implanted rats, further studies are necessary to justify the use of this material in tissue engineering applications.
Simulating ENSO SSTAs from TAO/TRITON Winds: The Impacts of 20 Years of Buoy Observations in the Pacific Waveguide and Comparison with Reanalysis Products

AbstractThe fundamental importance of near-equatorial zonal wind stress in the evolution of the tropical Pacific Ocean’s seasonal cycle and El Nino–Southern Oscillation (ENSO) events is well known. It has been two decades since the TAO/TRITON buoy array was deployed, in part to provide accurate surface wind observations across the Pacific waveguide. It is timely to revisit the impact of TAO/TRITON winds on our ability to simulate and thereby understand the evolution of sea surface temperature (SST) in this region. This work shows that forced ocean model simulations of SST anomalies (SSTAs) during the periods with a reasonably high buoy data return rate can reproduce the major elements of SSTA variability during ENSO events using a wind stress field computed from TAO/TRITON observations only. This demonstrates that the buoy array usefully fulfills its waveguide-wind-measurement purpose. Comparison of several reanalysis wind fields commonly used in recent ENSO studies with the TAO/TRITON observations reveal.
Effect of Surrogate Aggregates on the Thermal Conductivity of Concrete at Ambient and Elevated Temperatures

The accurate assessment of the thermal conductivity of concretes is an important part of building design in terms of thermal efficiency and thermal performance of materials at various temperatures. We present an experimental assessment of the thermal conductivity of five thermally insulated concrete specimens made using lightweight aggregates and glass bubbles in place of normal aggregates. Four different measurement methods are used to assess the reliability of the thermal data and to evaluate the effects of the various sensor types. The concrete specimens are also assessed at every 100°C during heating to ~800°C. Normal concrete is shown to have a thermal conductivity of ~2.25 W m−1 K−1. The surrogate aggregates effectively reduce the conductivity to ~1.25 W m−1 K−1 at room temperature. The aggregate size is shown not to affect thermal conduction: fine and coarse aggregates each lead to similar results. Surface contact methods of assessment tend to underestimate thermal conductivity, presumably owing to high thermal resistance between the transducers and the specimens. Thermogravimetric analysis shows that the stages of mass loss of the cement paste correspond to the evolution of thermal conductivity upon heating.
Deciding What's News: A Study of CBS Evening News, NBC Nightly News, Newsweek, and Time . By Gans Herbert J.. (New York: Pantheon Books, 1979. Pp. xvii + 393. $12.95.)

politics. But the attempt to approach a theory of the legitimacy of administrative regulation misfires on the fact that the difficulties lie, not, as the author implies, within the boundaries of administrative law and regulation but within our own popular and political ambivalence toward the general form and structure of American government as a whole. The legitimacy of administrative law and regulation must be primarily dependent on the legitimacy of the larger whole of which they are part. Nevertheless the discussion of the five topics just above is sophisticated and illuminating in a much broader political sense than is common among most legal works. In a sense this segment of the book is an unusually competent explanation and justification of the need for and place of administrative law and regulation in our present version of a democratic society.
Code Switching and the Hispanic Consumer

This study examines the influence of acculturation and language on the emotional response of three print advertisements (English, Spanish, Code Switched) through an experimental methodology founded on the Revised Hierarchical and the Conceptual Feature Models. The advertising treatments and surveys were administered to a convenience sample of 272 respondents in a large southwestern metropolitan area from five local Hispanic churches. The Bidimensional Acculturation Scale for Hispanics was used to measure acculturation (Low, High, Bicultural). Emotional responses to the print advertisements were measured using the Emotional Quotient Scale and the condensed Reaction Profile. Results revealed some significant differences in advertising preferences. Results also suggested that a code-switched advertisement could be both culturally relevant and appropriate for reaching the majority of the Hispanic market. Implications, limitations, and recommendations for future research are discussed.
Numb Expression Contributes to the Maintenance of an Undifferentiated State in Human Epidermis

The epidermis is a stratified epithelium with a stem cell subpopulation in the basal layer that constantly replicates and periodically detaches from the base, undergoing a differentiation process that involves various developmental signals and regulatory pathways. During the last 10 years, a number of studies tried to elucidate the intricate scenario that maintains the epithelial shield during the entire life span. In our study, we investigated the role of Numb in the skin compartment and, in particular, its involvement in stem cell maintenance. Numb expression in the skin compartment was assessed by immunofluorescence and immunohistochemistry analysis. We evaluated Numb expression in primary epithelial cells at various differentiative stages. Moreover, we overexpressed Numb in the isolated population enriched for undifferentiated progenitors to establish its involvement in in vitro differentiation. We demonstrated that Numb in high-proliferating epithelial undifferentiated progenitors contributes to the maintenance of an undifferentiated state. This regulation involves the E3 ligases Itch binding. Moreover, the analysis of a cohort of cutaneous carcinomas showed that Numb is highly expressed in squamous cell carcinoma (SCC), where we observed a direct correlation between the expression of Numb and Ki-67. Our data indicate for the first time that Numb is involved in the maintenance of the undifferentiated proliferating stem cell pool in the epithelial basal layer and its expression could become a new marker in skin cancer.
The Association Between Poly-Substance Use, Coping, and Sex Trade Among Black South African Substance Users

The current study examined the relationship between poly-substance use and sex trade among 343 black South African substance users recruited from the Pretoria region between 2002 and (57% males; mean age 24 years). The assessment comprised a HIV-risk behavior interview, urinalysis to confirm self-report of drug use, and an HIV test. Logistic regression analyses indicated poly-substance use was positively associated with sex trade among persons using drugs to cope with stress. Results indicate the importance of considering coping strategies as modifiable psychosocial factor related to sexual risk-taking behaviors and substance use. The study's implications and limitations are discussed.
In Vivo Assembly of Overproduced DNA Polymerase III

The genes for the polymerase core (αϵθ) of the DNA polymerase III holoenzyme map to widely separated loci on the Escherichia coli chromosome. To enable efficient overproduction and in vivo assembly of DNA polymerase III core, artificial operons containing the three structural genes, dnaE, dnaQ, and holE, were placed in an expression plasmid. The proteins α, αϵ and αϵθ were overexpressed and assembled in E. coli and purified to homogeneity. The three purified polymerases had a similar specific activity of about 6.0 × 106 units/mg in a gap-filling assay. Kinetics studies showed that neither ϵ nor θ influenced the Km of α for deoxynucleotide triphosphate and only slightly decreased the Km of α for DNA, although ϵ was absolutely required for maximal DNA synthesis. The rate of DNA synthesis by α-reconstituted holoenzyme using τ complex was about 5-fold less than that of αϵ or αϵθ-reconstituted holoenzyme as determined by a gel analysis. The processivity of α-reconstituted holoenzyme was very similar to that of αϵθ-reconstituted holoenzyme when τ complex was used as a clamp loader.
Electrostatic vibration energy harvester with combined effect of electrical nonlinearities and mechanical impact

This paper presents an advanced study including the design, characterization and theoretical analysis of a capacitive vibration energy harvester. Although based on a resonant electromechanical device, it is intended for operation in a wide frequency band due to the combination of stop-end effects and a strong biasing electrical field. The electrostatic transducer has an interdigited comb geometry with in-plane motion, and is obtained through a simple batch process using two masks. A continuous conditioning circuit is used for the characterization of the transducer. A nonlinear model of the coupled system ‘transduce-conditioning circuit’ is presented and analyzed employing two different semi-analytical techniques together with precise numerical modelling. Experimental results are in good agreement with results obtained from numerical modelling. With the 1 g amplitude of harmonic external acceleration at atmospheric pressure, the system transducer-conditioning circuit has a half-power bandwidth of more than 30% and converts more than 2 µW of the power of input mechanical vibrations over the range of 140 and 160 Hz. The harvester has also been characterized under stochastic noise-like input vibrations.
Genomic Variation in Natural Populations of Drosophila melanogaster

This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5′- and 3′-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species.
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays

Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high-density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.
Increased plasma concentration of ribavirin as a result of renal dysfunction in hepatitis C virus patients treated with telaprevir

vival of hepatocytes in cell culture and animal models and reinforces the antiapoptotic function of the receptor. Nevertheless, we previously demonstrated that during apoptosis Met is cleaved by caspases at another site located in the juxtamembrane region. This cleavage generates a 40-kDa fragment found in apoptotic murine hepatocytes in vivo. We recently showed that this fragment favors mitochondria permeabilization, leading to an acceleration of apoptosis, an opposite response when compared to the Cterminal cleavage. These novel data raise the question of whether Met caspase cleavages are inhibitors or activators of hepatocyte cell death. Interestingly, we previously demonstrated that these two cleavages of Met are sequential, with the C-terminal cleavage occurring before the juxtamembrane one. In light of the results of Zarnegar’s team, we can propose the following integrated model. In the early steps of apoptosis, the Met C-terminal caspase site could act as a “deathdefying domain” able to inhibit caspase 3 activity and to protect cells from apoptosis. In this context, the Met receptor is still inducible by its ligand and potentially able to promote survival (Fig. 1). In the later steps of apoptosis, when caspase activation reaches a higher level, Met is then cleaved at the juxtamembrane site leading to generation of a proapoptotic fragment able to promote mitochondrial permeabilization. At this stage, Met is not any longer inducible by its ligand. Therefore, Met could regulate survival/apoptosis balance through opposite functions according to the level of caspase activity. In human hepatocellular carcinoma (HCC) tissues, Met was found cleaved at the C-terminal site, suggesting an action of the Met “death-defying domain” in this pathological situation. Thus, the overexpression of Met often observed in HCC could directly inhibit caspase activity, contributing to apoptosis resistance. It would be now interesting to evaluate whether, in the opposite manner, the proapoptotic juxtamembrane cleavage of Met is inhibited in HCC.