Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation-tolerant OpenMP tasking on tightly-coupled processor clusters

We present a variation-tolerant tasking technique for tightly-coupled shared memory processor clusters that relies upon modeling advance across the hardware/software interface. This is implemented as an extension to the OpenMP 3.0 tasking programming model. Using the notion of Task-Level Vulnerability (TLV) proposed here, we capture dynamic variations caused by circuit-level variability as a high-level software knowledge. This is accomplished through a variation-aware hardware/software codesign where: (i) Hardware features variability monitors in conjunction with online per-core characterization of TLV metadata; (ii) Software supports a Task-level Errant Instruction Management (TEIM) technique to utilize TLV metadata in the runtime OpenMP task scheduler. This method greatly reduces the number of recovery cycles compared to the baseline scheduler of OpenMP [22], consequently instruction per cycle (IPC) of a 16-core processor cluster is increased up to 1.51× (1.17× on average). We evaluate the effectiveness of our approach with various number of cores (4,8,12,16), and across a wide temperature range(ΔT=90°C).
Total eclipse of the heart: the AM CVn Gaia14aae/ASSASN-14cn

We report the discovery and characterization of a deeply eclipsing AM CVn-system, Gaia14aae (=ASSASN-14cn). Gaia14aae was identified independently by the All-Sky Automated Survey for Supernovae (ASAS-SN; Shappee et al.) and by the Gaia Science Alerts project, during two separate outbursts. A third outburst is seen in archival Pan-STARRS-1 (PS1; Schlafly et al.; Tonry et al.; Magnier et al.) and ASAS-SN data. Spectroscopy reveals a hot, hydrogen-deficient spectrum with clear double-peaked emission lines, consistent with an accreting double-degenerate classification. We use follow-up photometry to constrain the orbital parameters of the system. We find an orbital period of 49.71 min, which places Gaia14aae at the long period extremum of the outbursting AM CVn period distribution. Gaia14aae is dominated by the light from its accreting white dwarf (WD). Assuming an orbital inclination of 90° for the binary system, the contact phases of the WD lead to lower limits of 0.78 and 0.015 M⊙ on the masses of the accretor and donor, respectively, and a lower limit on the mass ratio of 0.019. Gaia14aae is only the third eclipsing AM CVn star known, and the first in which the WD is totally eclipsed. Using a helium WD model, we estimate the accretor's effective temperature to be 12 900 ± 200 K. The three outburst events occurred within four months of each other, while no other outburst activity is seen in the previous 8 yr of Catalina Real-time Transient Survey (CRTS; Drake et al.), Pan-STARRS-1 and ASAS-SN data. This suggests that these events might be rebrightenings of the first outburst rather than individual events.
Developing IDEAS: supporting children with autism within a participatory design team

IDEAS (Interface Design Experience for the Autistic Spectrum) is a method for involving children with Autism Spectrum Disorders (ASD) in the technology design process. This paper extends the IDEAS method to enable use with a design team, providing specific added support for communication and collaboration difficulties that may arise. A study to trial this extended method was conducted with two design teams, each involving three children with ASD, in a series of six, weekly design sessions focused on designing a math game. The findings from this study reveal that the children were able to successfully participate in the sessions and collaborate with other children. The findings also highlight the positive experience that involvement in such a process can offer this population.
Residual Stresses and Their Redistribution During Annealing of a Girth-Butt Welded Thin-Walled Pipe

The redistribution of calculated welding stresses during different post weld heat treatments (PWHT) is numerically investigated for a girth-butt welded thin-walled pipe made of a micro-alloyed carbon manganese steel. A finite element analysis with assumed rotational symmetry is performed. The influence of creep, relaxation and phase transformations is included. The amount of stress reduction is found to be mainly controlled by the holding temperature. Most of this reduction was observed to occur during the end of the heating period where the transient stresses followed the fall of the yield stress with temperature.
Composite Synchronization in Parallel Discrete-Event Simulation

This paper considers a technique for composing global (barrier-style) and local (channel scanning) synchronization protocols within a single parallel discrete-event simulation. Composition is attractive because it allows one to tailor the synchronization mechanism to the model being simulated. We first motivate the problem by showing the large performance gap that can be introduced by a mismatch of model and synchronization method. Our solution calls for each channel between submodels to be classified as synchronous or asynchronous. We mathematically formulate the problem of optimally classifying channels and show that, in principle, the optimal classification can be obtained in time proportional to max{C/spl times/log C, V/spl times/N}, where C is the number of channels, V the number of unique minimal delays on those channels, and N is the number of submodels. We then demonstrate an implementation which finds an optimal solution at runtime and consider its performance on network topologies, including one of the global Internet at the autonomous system level. We find that the automated method effectively determines channel assignments that maximize performance.
Study of trabecular bone microstructure using spatial autocorrelation analysis

The spatial autocorrelation analysis method represents a powerful, new approach to quantitative characterization of structurally quasi-periodic anisotropic materials such as trabecular bone (TB). The method is applicable to grayscale images and thus does not require any preprocessing, such as segmentation which is difficult to achieve in the limited resolution regime of in vivo imaging. The 3D autocorrelation function (ACF) can be efficiently calculated using the Fourier transform. The resulting trabecular thickness and spacing measurements are robust to the presence of noise and produce values within the expected range as determined by other methods from μCT and μMRI datasets. TB features found from the ACF are shown to correlate well with those determined by the Fuzzy Distance transform (FDT) in the transverse plane, i.e. the plane orthogonal to bone’s major axis. The method is further shown to be applicable to in-vivo μMRI data. Using the ACF, we examine data acquired in a previous study aimed at evaluating the structural implications of male hypogonadism characterized by testosterone deficiency and reduced bone mass. Specifically, we consider the hypothesis that eugonadal and hypogonadal men differ in the anisotropy of their trabecular networks. The analysis indicates a significant difference in trabecular bone thickness and longitudinal spacing between the control group and the testosterone deficient group. We conclude that spatial autocorrelation analysis is able to characterize the 3D structure and anisotropy of trabecular bone and provides new insight into the structural changes associated with osteoporotic trabecular bone loss.
Amyloid-Associated Nucleic Acid Hybridisation

Nucleic acids promote amyloid formation in diseases including Alzheimer's and Creutzfeldt-Jakob disease. However, it remains unclear whether the close interactions between amyloid and nucleic acid allow nucleic acid secondary structure to play a role in modulating amyloid structure and function. Here we have used a simplified system of short basic peptides with alternating hydrophobic and hydrophilic amino acid residues to study nucleic acid - amyloid interactions. Employing biophysical techniques including X-ray fibre diffraction, circular dichroism spectroscopy and electron microscopy we show that the polymerized charges of nucleic acids concentrate and enhance the formation of amyloid from short basic peptides, many of which would not otherwise form fibres. In turn, the amyloid component binds nucleic acids and promotes their hybridisation at concentrations below their solution K d, as shown by time-resolved FRET studies. The self-reinforcing interactions between peptides and nucleic acids lead to the formation of amyloid nucleic acid (ANA) fibres whose properties are distinct from their component polymers. In addition to their importance in disease and potential in engineering, ANA fibres formed from prebiotically-produced peptides and nucleic acids may have played a role in early evolution, constituting the first entities subject to Darwinian evolution.
Multi-Phase Process Mining : Aggregating Instance Graphs into EPCs and Petri Nets

The goal of process mining is to automatically generate a process model from an event log, e.g., automatically constructing an EPC based on the transaction logs in SAP. Currently available process mining techniques typically try to generate a complete process model from the data acquired in a single step. In this paper, we propose a multistep approach. First models are generated for each individual process instance (this can be done in many steps). In the final step however, these instance models are aggregated to obtain an overall model for the entire data set. In this paper, we focus on that final step, i.e., aggregating instance graphs. The work is motivated by recent tools and techniques to generate instance models. For example, widely used tools such as ARIS PPM and InConcert generate instance models that can be interpreted by our process mining tool. The result of our multi-step approach can be represented in different types of process models. In this paper, we show a translation from aggregated instance graphs to Petri nets using Event-driven Process Chains (EPCs) as an intermediate step.
Effects of Soluble Cerous Compound as a Surface Modifier on the Properties of Isotactic Polypropylene/Hollow Glass Beads Composites

Cerous trinitrate hexahydrate was used as a surface modifier to treat hollow glass beads via a process of chemical deposition, and its effects on the strength, rheological, optical, and thermal properties of isotactic polypropylene/hollow glass beads(iPP/HGB) composites were assessed. The strength test results showed that the tensile strength and impact strength of iPP/HGB composites were obviously improved when HGB were modified, the optimum weight concentration of this modifier was 1.2 wt%. Moreover, dynamic rheological measurements showed that the complex viscosity and storage and loss moduli of the iPP/HGB composites were also increased when the HGB were treated. Additionally, the influences of this modifier on the structure and thermal properties, including the crystallizing and melting behaviors, of the composites were studied by means of X-ray diffraction, polarized optical microscopy, and differential scanning calorimetry. The results showed that the modifier had a nucleating effect on the matrix and promoted the formation of β-crystals of isotactic polypropylene.
Partitioned cross-validation

Partitioned cross-validation is proposed as a method for overcoming the large amounts of across sample variability to which ordinary cross-validation is subject. The price for cutting down on the sample noise is that a type of bias is intriduced. A theory is presented for optimal trade-off of this variance and bias. Comparison with other bandwidth selection methods is given.
Novel Bioactivation Mechanism of Reactive Metabolite Formation from Phenyl Methyl-Isoxazoles

Recently, we described a series of phenyl methyl-isoxazole derivatives as novel, potent, and selective inhibitors of the voltage-gated sodium channel type 1.7 (Bioorg Med Chem Lett 21:3871–3876, 2011). The lead compound, 2-chloro-6-fluorobenzyl [3-(2,6-dichlorophenyl)-5-methylisoxazol-4-yl]carbamate, showed unprecedented GSH and cysteine reactivity associated with NADPH-dependent metabolism in trapping studies using human liver microsomes. Additional trapping experiments with close analogs and mass spectra and NMR analyses suggested that the conjugates were attached directly to the 5′-methyl on the isoxazole moiety. We propose a mechanism of bioactivation via an initial oxidation of the 5′-methyl generating a stabilized enimine intermediate and a subsequent GSH attack on the 5′-methylene. Efforts to ameliorate reactive metabolite generation were undertaken to minimize the potential risk of toxicity. Formation of reactive metabolites could be significantly reduced or prevented by removing the 5′-methyl, by N-methylation of the carbamate; by replacing the nitrogen with a carbon or removing the nitrogen to obtain a carboxylate; or by inserting an isomeric 5′-methyl isoxazole. The effectiveness of these various chemical modifications in reducing GSH adduct formation is in line with the proposed mechanism. In conclusion, we have identified a novel mechanism of bioactivation of phenyl 5-methyl-isoxazol-4-yl-amines. The reactivity was attenuated by several modifications aimed to prevent the emergence of an enimine intermediate. Whether 5′-methyl isoxazoles should be considered a structural alert for potential formation of reactive metabolites is dependent on their context, i.e., 4′-nitrogen.
Studies on the stretching behaviour of medium gauge high impact polystyrene sheets during positive thermoforming

High impact polystyrene sheets (HIPS) of 1.5 mm and 2.5 mm thicknesses were thermoformed on moulds of different parameters at sheet heating temperatures of 130℃ and 140℃. Formability studies indicated no difference in wall thickness distribution at different sheet temperatures. Due to non-uniform stretching of the sheet, wall thickness distribution along the slant length was found to have three regions. In the regions near the mould corner and clamp point, wall thickness was found to decrease with increase in distance from the corner, in these zones. The decrease near the corner was much greater and sharper than that near the clamp point. The decrease in both regions was found to increase at higher depths of draw and decrease at higher draft angles. In the intermediate portion of the slant length, no significant variation in wall thickness was observed.
Investigation of the performance of articular cartilage and synthetic biomaterials in multi-directional sliding motion as in orthopedic implants

Investigation of the performance of articular cartilage and synthetic biomaterials in multi-directional sliding motion as in orthopedic implants " (2006). Retrospective Theses and Dissertations. Paper 3021. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion.
Hypoxia-Inducible Factor-Dependent Expression of Angiopoietin-Like 4 by Conjunctival Epithelial Cells Promotes the Angiogenic Phenotype of Pterygia

Purpose Disappointing results from clinical studies assessing the efficacy of therapies targeting vascular endothelial growth factor (VEGF) for the treatment of pterygia suggest that other angiogenic mediators may also play a role in its development. We therefore explore the relative contribution of VEGF, hypoxia-inducible factor (HIF)-1α (the transcription factor that regulates VEGF expression in ocular neovascular disease), and a second HIF-regulated mediator, angiopoietin-like 4 (ANGPTL4), to the angiogenic phenotype of pterygia. Methods Expression of HIF-1α, VEGF, and ANGPTL4 were examined in surgically excised pterygia, and in immortalized human (ih) and primary rabbit (pr) conjunctival epithelial cells (CjECs). Endothelial cell (EC) tubule formation assays using media conditioned by ihCjECs in the presence or absence of inducers/inhibitors of HIF-1 or RNA interference (RNAi) targeting VEGF, ANGPTL4, or both were used to assess their relative contribution to the angiogenic potential of these cells. Results HIF-1α and VEGF expression were detected in 6/6 surgically excised pterygia and localized to CjECs. Accumulation of HIF-1α in was confirmed in ihCjECs and prCjECs, including stratified prCjECs grown on collagen vitrigel, and resulted in expression of VEGF and the promotion of EC tubule formation; the latter effect was partially blocked using RNAi targeting VEGF mRNA expression. We demonstrate expression of a second HIF-regulated angiogenic mediator, ANGPTL4, in CjECs in culture and in surgically excised pterygia. RNAi targeting ANGPTL4 inhibited EC tubule formation and was additive to RNAi targeting VEGF. Conclusions Our results support the development of therapies targeting both ANGPTL4 and VEGF for the treatment of patients with pterygia.
Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk

Background Defective cellular transport processes can lead to aberrant accumulation of trace elements, iron, small molecules and hormones in the cell, which in turn may promote the formation of reactive oxygen species, promoting DNA damage and aberrant expression of key regulatory cancer genes. As DNA damage and uncontrolled proliferation are hallmarks of cancer, including epithelial ovarian cancer (EOC), we hypothesized that inherited variation in the cellular transport genes contributes to EOC risk. Methods In total, DNA samples were obtained from 14,525 case subjects with invasive EOC and from 23,447 controls from 43 sites in the Ovarian Cancer Association Consortium (OCAC). Two hundred seventy nine SNPs, representing 131 genes, were genotyped using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). SNP analyses were conducted using unconditional logistic regression under a log-additive model, and the FDR q<0.2 was applied to adjust for multiple comparisons. Results The most significant evidence of an association for all invasive cancers combined and for the serous subtype was observed for SNP rs17216603 in the iron transporter gene HEPH (invasive: OR = 0.85, P = 0.00026; serous: OR = 0.81, P = 0.00020); this SNP was also associated with the borderline/low malignant potential (LMP) tumors (P = 0.021). Other genes significantly associated with EOC histological subtypes (p<0.05) included the UGT1A (endometrioid), SLC25A45 (mucinous), SLC39A11 (low malignant potential), and SERPINA7 (clear cell carcinoma). In addition, 1785 SNPs in six genes (HEPH, MGST1, SERPINA, SLC25A45, SLC39A11 and UGT1A) were imputed from the 1000 Genomes Project and examined for association with INV EOC in white-European subjects. The most significant imputed SNP was rs117729793 in SLC39A11 (per allele, OR = 2.55, 95% CI = 1.5-4.35, p = 5.66x10-4). Conclusion These results, generated on a large cohort of women, revealed associations between inherited cellular transport gene variants and risk of EOC histologic subtypes.
Ieee Transactions on Visualization and Computer Graphics 1 Directing Crowd Simulations Using Navigation Fields

—We present a novel approach to direct and control virtual crowds using navigation fields. Our method guides one or more agents towards desired goals based on guidance fields. The system allows the user to specify these fields by either sketching paths directly in the scene via an intuitive authoring interface or by importing motion flow fields extracted from crowd video footage. We propose a novel formulation to blend input guidance fields to create singularity-free, goal-directed navigation fields. Our method can be easily combined with most current local collision-avoidance methods and we use two such methods as examples to highlight the potential of our approach. We illustrate its performance on several simulation scenarios.
Centrosome duplication proceeds during mimosine‐induced G1 cell cycle arrest

Centrosome duplication must remain coordinated with cell cycle progression to ensure the formation of a strictly bipolar mitotic spindle, but the mechanisms that regulate this coordination are poorly understood. Previous work has shown that prolonged S‐phase is permissive for centrosome duplication, but prolonging either G2 or M‐phase cannot support duplication. To examine whether G1 is permissive for centrosome duplication, we release serum‐starved G0 cells into mimosine, which delays the cell cycle in G1. We find that in mimosine, centrosome duplication does occur, albeit slowly compared with cells that progress into S‐phase; centrosome duplication in mimosine‐treated cells also proceeds in the absence of a rise in Cdk2 kinase activity normally associated with the G1/S transition. CHO cells arrested with mimosine can also assemble more than four centrioles (termed “centrosome amplification”), but the extent of centrosome amplification during prolonged G1 is decreased compared to cells that enter S‐phase and activate the Cdk2‐cyclin complex. Together, our results suggest a model, which predicts that entry into S‐phase and the rise in Cdk2 activity associated with this transition are not absolutely required to initiate centrosome duplication, but rather, serve to entrain the centrosome reproduction cycle with cell cycle progression. J. Cell. Physiol. 215: 182–191, 2008. © 2007 Wiley‐Liss, Inc.
A R T I C L E I N T R O D U C T I O N

Airway surface liquid (ASL) composition and volume are tightly regulated to maintain mucociliary clearance and healthy lung function. Contributions to the ASL composition and thickness come from both surface epithelia and submucosal glands, with the glands thought to be the predominant source of secreted fl uid and peptides for innate defense (Wang et al., 2001 ; Wine, 2006). Elec-trolyte transport across the surface epithelium, together with accompanying osmotic water fl ow, determines the height of the ASL (Tarran et al., 2001), and this in turn determines the effi ciency of mucociliary clearance. Several recent studies have implicated basal or constitutive CFTR activity in calcium-mediated gland secretion (Song et al., 2006 ; Ishibashi et al., 2008), modulation of ASL pH (Song et al., 2006), and surface epithelial electro-lyte transport (Wang et al., 2005). Evidence for constitutive activity of CFTR in airway epithelia has a long history: Smith and Welsh (1992) noted a substantial baseline (non-cAMP – stimulated) apical anion effl ux in their studies to evaluate the bi-carbonate permeability of CFTR. Since then, constitu-tive currents have been noted in human bronchial (Coakley et al., 2003) and nasal (Paradiso et al., 2003) epithelial cultures, as well as the serous cell model of Calu-3 cells (Krouse et al., 2004). These studies attributed the basal chloride currents to constitutive CFTR activity, due primarily to their absence in cystic fi brosis (CF) epithelia. After the discovery of the higher specifi city CFTR channel blockers CFI172 and GlyH-101 (Ma et al., 2002 ; Muanprasat et al., 2004), several studies have confi rmed that basal chloride currents were sensitive to these agents, reinforcing the hypothesis of constitutive CFTR activity. In addition, a role for basal anion secretion in maintaining the ASL pH was proposed by Song et al. (2006) SLC26A9 is a constitutively active, CFTR-regulated anion conductance in human bronchial epithelia Human bronchial epithelial (HBE) cells exhibit constitutive anion secretion that is absent in cells from cystic fi bro-sis (CF) patients. The identity of this conductance is unknown, but SLC26A9, a member of the SLC26 family of CF transmembrane conductance regulator (CFTR)-interacting transporters, is found in the human airway and exhibits chloride channel behavior. We sought differences in the properties of SLC26A9 and CFTR expressed in HEK 293 (HEK) cells as a fi ngerprint to identify HBE apical anion conductances. HEK cells expressing SLC26A9 displayed a constitutive chloride current that was inhibited by the CFTR blocker GlyH-101 …