Miracle-dz/UniFAR-FTUs huggingface dataset:
MPI-hybrid Parallelism for Volume Rendering on Large, Multi-core Systems

This work studies the performance and scalability characteristics of "hybrid" parallel programming and execution as applied to raycasting volume rendering — a staple visualization algorithm — on a large, multi-core platform. Historically, the Message Passing Interface (MPI) has become the de-facto standard for parallel programming and execution on modern parallel systems. As the computing industry trends towards multi-core processors, with fourand six-core chips common today and 128-core chips coming soon, we wish to better understand how algorithmic and parallel programming choices impact performance and scalability on large, distributed-memory multi-core systems. Our findings indicate that the hybrid-parallel implementation, at levels of concurrency ranging from 1,728 to 216,000, performs better, uses a smaller absolute memory footprint, and consumes less communication bandwidth than the traditional, MPI-only implementation.
Study of the Nankai seismogenic fault using dynamic wave propagation modelling of digital rock from the Nobeoka Fault

To understand the characteristics of the Nankai seismogenic fault in the plate convergent margin, we calculated the P- and S-wave velocities (VP and VS) of digital rock models constructed from core samples of an ancient plate boundary fault at Nobeoka, Kyushu Island, Japan. We first constructed 3D digital rock models from microcomputed tomography images and identified their heterogeneous textures such as cracks and veins. We replaced the cracks and veins with air, water, quartz, calcite and other materials with different bulk and shear moduli. Using the Rotated Staggered Grid Finite-Difference Method, we performed dynamic wave propagation simulations and quantified the effective VP, VS and the ratio of VP to VS (VP/VS) of the 3D digital rock models with different crack-filling minerals. Our results demonstrate that the water-saturated cracks considerably decreased the seismic velocity and increased VP/VS. The VP/VS of the quartz-filled rock model was lower than that in the water-saturated case and in the calcite-filled rock model. By comparing the elastic properties derived from the digital rock models with the seismic velocities (e.g. VP and VP/VS) around the seismogenic fault estimated from field seismic data, we characterised the evolution process of the deep seismogenic fault. The high VP/VS and low VP observed at the transition from aseismic to coseismic regimes in the Nankai Trough can be explained by open cracks (or fractures), while the low VP/VS and high VP observed at the deeper coseismic fault zone suggests quartz-filled cracks. The quartz-rich fault zone characterised as low VP/VS and high VP in this study could partially relate to the coseismic behaviour as suggested by previous studies, because quartz exhibits slip-weakening behaviour (i.e. unstable coseismic slip). We quantified effective VP, VS and the ratio of VP to VS of the 3D digital rock models with different crack-filling minerals. By comparing the elastic properties derived from the digital rock models with the seismic velocities around the Nankai seismogenic fault, we characterised the evolution process of the seismogenic fault.
Molecular Engineering of Ghfp, the Gonococcal Orthologue of Neisseria meningitidis Factor H Binding Protein

ABSTRACT Knowledge of the sequences and structures of proteins produced by microbial pathogens is continuously increasing. Besides offering the possibility of unraveling the mechanisms of pathogenesis at the molecular level, structural information provides new tools for vaccine development, such as the opportunity to improve viral and bacterial vaccine candidates by rational design. Structure-based rational design of antigens can optimize the epitope repertoire in terms of accessibility, stability, and variability. In the present study, we used epitope mapping information on the well-characterized antigen of Neisseria meningitidis factor H binding protein (fHbp) to engineer its gonococcal homologue, Ghfp. Meningococcal fHbp is typically classified in three distinct antigenic variants. We introduced epitopes of fHbp variant 1 onto the surface of Ghfp, which is naturally able to protect against meningococcal strains expressing fHbp of variants 2 and 3. Heterologous epitopes were successfully transplanted, as engineered Ghfp induced functional antibodies against all three fHbp variants. These results confirm that structural vaccinology represents a successful strategy for modulating immune responses, and it is a powerful tool for investigating the extension and localization of immunodominant epitopes.
Real time fault injection using logic emulators

A hardware based approach to Fault Emulation independent of the logic emulation system in use has been developed and is presented in this paper. Fault injection into a targeted circuit is made possible with the introduction of additional logic. The stuck-at-fault model is simulated with the method described here, which may also be used for multiple faults and bridging faults. This discussion will focus only on SSF. Using a commercial emulator, speeds for combinational circuits of several MHz were reached allowing for system testing at real time speed.
A novel control technique for Power Factor Correction in SEPIC converter utilizing input/output voltage waveforms sampling

In this study, a simple and novel control technique for Power Factor Correction (PFC) is introduced, which is a SEPIC-based (Single-ended Primary-inductor Converter based) rectifier with high input power factor. Operation of the proposed method is based on sampling of input and output voltages in SEPIC rectifier. Using samples of input and output voltage, this control system makes the input current to follow a sinusoidal path. As a result, the line current's Total Harmonic Distortion (THD) is reduced and the input power factor is improved. This paper also compares the new method with the conventional control method for the power factor correction. In order to examine the proposed control technique comprehensively, computer simulations and experimental implementations were utilized to verify the feasibility and effectiveness of this novel control technique.
A Deep Primal-Dual Network for Guided Depth Super-Resolution

In this paper we present a novel method to increase the spatial resolution of depth images. We combine a deep fully convolutional network with a non-local variational method in a deep primal-dual network. The joint network computes a noise-free, high-resolution estimate from a noisy, low-resolution input depth map. Additionally, a high-resolution intensity image is used to guide the reconstruction in the network. By unrolling the optimization steps of a first-order primal-dual algorithm and formulating it as a network, we can train our joint method end-to-end. This not only enables us to learn the weights of the fully convolutional network, but also to optimize all parameters of the variational method and its optimization procedure. The training of such a deep network requires a large dataset for supervision. Therefore, we generate high-quality depth maps and corresponding color images with a physically based renderer. In an exhaustive evaluation we show that our method outperforms the state-of-the-art on multiple benchmarks.
Creating works-like prototypes of mechanical objects

Designers often create physical works-like prototypes early in the product development cycle to explore possible mechanical architectures for a design. Yet, creating functional prototypes requires time and expertise, which discourages rapid design iterations. Designers must carefully specify part and joint parameters to ensure that parts move and fit and together in the intended manner. We present an interactive system that streamlines the process by allowing users to annotate rough 3D models with high-level functional relationships (e.g., part A fits inside part B). Based on these relationships, our system optimizes the model geometry to produce a working design. We demonstrate the versatility of our system by using it to design a variety of works-like prototypes.
A population based case-control study of cataract and inhaled corticosteroids

Background/aims: Exposure to systemic corticosteroid use is known to be associated with a risk of cataract. Whether low doses of inhaled corticosteroids are associated with an increased risk of cataract is not known. This study was undertaken to quantify the risk of cataract associated with the use of inhaled corticosteroids and assess whether there is a dose-response relation. Methods: A population based case-control study based on the General Practice Research Database in the United Kingdom. 15 479 people with cataract and 15 479 controls were matched for age, sex, practice, and observation period. Results: The crude odds ratio for the association between any recorded exposure to inhaled corticosteroids and cataract was 1.58 (95% CI 1.46 to 1.71), reduced to 1.10 (95% CI 1.00 to 1.20) after adjustment for systemic corticosteroid exposure and consultation rate. There was a dose-response relation, the adjusted odds ratio rising from 0.99 (95% CI 0.87 to 1.13) at daily doses up to 400 μg to 1.69 (95% CI 1.17 to 2.43) for daily doses greater than 1600 μg. The association was also stronger with increasing duration of use. Conclusion: Higher doses and longer duration of exposure to inhaled corticosteroids are associated with an increased risk of cataract. The lowest doses compatible with good control of airways disease should be used. The risk of cataract associated with high doses of inhaled corticosteroids needs to be more widely appreciated.
Beacon Frame Spoofing Attack Detection in IEEE 802.11 Networks

A great variety of well-known attacks exist for the IEEE 802.11 protocol. The lack of mechanisms for management frame authentication and the complexity of the protocol itself have derived into a considerable number of denial of service and identity spoofing attacks. As most denial of service attacks are based on spoofing of MAC addresses, spoofed frame detection schemes have gained attentions. Currently the most efficient techniques to detect this kind of attacks are based on the creation of profiles for the wireless nodes and behavior based protocol anomaly detection. However, these techniques tend to generate too many of false positives. This is caused by the unstable nature of the wireless medium and also because of the difficulty to model the behaviour of the diverse implementations from different manufacturers. One way to reduce false positives is to combine different techniques to carry out the analysis. We propose a novel method that identifies the impersonation of certain management frames, which helps to reduce the number of false positives within other existing MAC spoofing detection techniques.
Policy Impact on the Chinese Stock Market: From the 1994 Bailout Policies to the 2015 Shanghai-Hong Kong Stock Connect

From the 1994 bailout policies to the 2015 Shanghai-Hong Kong Stock Connect, the policy impact on the Chinese stock market has changed over time. By May 2015, global investors can directly invest in a more legalized and normalized Chinese stock market, whereas they are still concerned about the policy-oriented market and its attendant risks. In this study, we employ the family of GARCH models to investigate the structural changes in risks with the implementation of a series of policies. Our results show that although many policies improve or stabilize the stock market, certain policies lead to substantial volatility. Among them, macro-control policies and transaction cost adjustments are a double-edged sword, which should be used with caution. Furthermore, with opening-up policies being launched recently, the Chinese stock market has entered a new stage in which it affects international capital markets. However, the increased risks, which may result in a sharp turnaround, cause worry.
Age of menarche and nutritional status of indigenous and non-indigenous adolescents in the Araucanía Region of Chile

Abstract Background: Early onset of menarche has been linked to prevalence of obesity; however, this may differ for indigenous females. Objective: To analyse the relationship between age of menarche and nutritional status among indigenous and non-indigenous girls. Method: The design of this study was cross-sectional. Date of menarche was determined through interviews, and all responses were confirmed by the girls' mothers. A total of 8504 adolescents were screened for recent menarche. One hundred and thirty-one girls of Mapuche (indigenous) and 143 girls of Chilean–Spanish background were identified and evaluated by anthropometric measurements. Results: Median age of menarche was 150 months, interquartile range (IR) 143–157 in indigenous, and 145.5 months, IR 139–153 in non-indigenous girls (p = 0.04). The indigenous females showed a higher prevalence of overweight (36.4% vs 23.1%), although the frequency of obesity was similar (16.8% vs 16.3%). For indigenous girls, age of menarche was delayed by 2.69 months (confidence intervals (CI) –0.38 to 5.77). It was observed that girls with overweight experienced age of menarche 7.59 months earlier than those with normal weight, CI –10.78 to –4.41. In the analysis of obesity, the effect on age of menarche was similar, with onset 7.53 months earlier than for the normal weight, CI –11.34 to –3.72. Conclusion: Age of menarche is younger than has been previously reported and occurs earlier in girls with overweight and obesity, while being indigenous was not related.
Realistic team formation using navigation and homophily

This paper proposes an algorithm for selecting a team of experts from a social network, which is represented by a weighted undirected graph. Each node in the graph represents an individual who has one or more skills. We introduce the concept of realistic team formation and its associated constraints and assumptions. The main constraint is a local view of the network resulting in an absence of pre-computed network statistics. Nodes in the network are assumed to connect to people with whom they share common skills. Thus, this paper proposes a navigation based team formation algorithm that makes use of homophily to recruit candidates for the team. The objective is to create an effective team that can carry out a specific task. Since none of the related work has had a local view of the network, we use BfsRecruiter, a BFS based navigation algorithm as our baseline comparison. We implemented the proposed algorithm and ran many simulation experiments to measure the communication cost and effectiveness of the proposed algorithm.
Race Frontier: reproducing data races in parallel-program debugging

A data race is a typical case of unintended nondeterminism, which occurs when two or more processes concurrently access the same memory location, with at least one of the accesses being a write access. This paper presents a mechanism to debug data races in the execution of parallel programs. A RACE FRONTIER is a set of execution events, one event for each process, whose execution histories, including data races preceding them, can be reproduced. Data races can be debugged by first identifying a RACE FRONTIER and then reproducing all the events, including data-race events? up to the RACE FRONTIER. Reproducing and debugging data races up to a RACE FRONTIER will eventually result in an execution instance without any data races. This paper describes how to identify a RACE FRONTIER and how to reproduce the execution history of data races u~p to the RACE FRONTIER.
Application of trichloroacetic acid-acetone precipitation method for protein extraction in bone tissue.

OBJECTIVE To explore the feasibility and efficiency of extracting protein from bone tissue using trichloroacetic acid (TCA)-acetone precipitation method. METHODS Hydrochloric acid (HCL) decalcification method and TCA-acetone precipitation method were separately used for bone protein extraction. The efficiencies of these two methods were compared. RESULTS TCA-acetone precipitation method had significantly higher extraction efficiency. Compared with HCL decalcification method, it had less pollution from bone marrow hematopoietic tissue. Protein band distribution was similar between these two methods. CONCLUSION TCA-acetone precipitation method is useful for bone proteomics research.
An amplified assay for thiols based on reactivation of papain.

A sensitive spectrophotometric assay has been developed for thiol (sulfhydryl) groups using an inactive disulfide derivative of papain (papain-S-SCH3). The thiol-disulfide interchange reaction of a thiol with papain-S-SCH3 results in the stoichiometric formation of active papain (papain-SH). The reactivated papain catalyzes the hydrolysis of a chromogenic substrate, resulting in an amplified spectrophotometric signal proportional to the initial amount of thiol. A variety of thiols, e.g., cysteine, glutathione, penicillamine, cysteine methyl ester, and cysteamine, yield similar linear plots for the activity of papain vs the initial amount of thiol. An unknown concentration of a thiol is measured using a standard plot for the activity of papain vs the amount of thiol, obtained for the same thiol or for a similar thiol. Thiol groups on proteins and thiol groups of high values of pKa (2-mercaptoethanol, 3-mercaptopropanoic acid) can also be assayed using papain-S-SCH3 in the presence of excess cystamine. The assay is about 100-fold more sensitive than that using Ellman's reagent [5,5'-dithiobis(2-nitrobenzoic acid)]. A 0.4 microM solution of cysteine produces an absorbance change of 0.55 at 410 nm after 30 min in the assay, compared to a predicted change in absorbance of 0.0054 using Ellman's assay.
Overexpression of the MexEF-OprN Multidrug Efflux System Affects Cell-to-Cell Signaling in Pseudomonas aeruginosa

ABSTRACT Intrinsic and acquired antibiotic resistance of the nosocomial pathogen Pseudomonas aeruginosa is mediated mainly by the expression of several efflux pumps of broad substrate specificity. Here we report that nfxC type mutants, overexpressing the MexEF-OprN efflux system, produce lower levels of extracellular virulence factors than the susceptible wild type. These include pyocyanin, elastase, and rhamnolipids, three factors controlled by the las and rhl quorum-sensing systems of P. aeruginosa. In agreement with these observations are the decreased transcription of the elastase genelasB and the rhamnosyltransferase genesrhlAB measured in nfxC type mutants. Expression of the lasR and rhlR regulator genes was not affected in the nfxC type mutant. In contrast, transcription of the C4-homoserine lactone (C4-HSL) autoinducer synthase gene rhlI was reduced by 50% in the nfxC type mutant relative to that in the wild type. This correlates with a similar decrease in C4-HSL levels detected in supernatants of the nfxC type mutant. Transcription of an rhlAB-lacZ fusion could be partially restored by the addition of synthetic C4-HSL andPseudomonas quinolone signal (PQS). It is proposed that the MexEF-OprN efflux pump affects intracellular PQS levels.
Decision Analysis via Granulation Based on General Binary Relation

Decision theory considers how best to make decisions in the light of uncertainty about data. There are several methodologies that may be used to determine the best decision. In rough set theory, the classification of objects according to approximation operators can be fitted into the Bayesian decision-theoretic model, with respect to three regions (positive, negative, and boundary region). Granulation using equivalence classes is a restriction that limits the decision makers. In this paper, we introduce a generalization and modification of decision-theoretic rough set model by using granular computing on general binary relations. We obtain two new types of approximation that enable us to classify the objects into five regions instead of three regions. The classification of decision region into five areas will enlarge the range of choice for decision makers.
Using photonic crystal enhanced fluorescence on quartz substrates to improve the sensitivity of DNA microarrays

Gene expression analysis of low abundance genes remains difficult when DNA microarrays are performed on standard glass substrates. However, we have shown that by using photonic crystals (PC) made on quartz substrates, the fluorescence intensity of Cyanine-5 (Cy5) labeled microarray spots is greatly enhanced. In a 1-color microarray experiment studying gene expression of soybean cotyledon tissue, an average signal enhancement factor of 17.8× was observed on the PC. Furthermore, twice as many genes were detectable on these PCs as compared to glass. By improving the sensitivity of this fluorescent assay, low expression genes that were undetectable on glass were quantified on the PC.
Fluorescence visualization of the distribution of microfilaments in gonads and early embryos of the nematode Caenorhabditis elegans

Several intracellular motility events in the Caenorhabditis elegans zygote (pseudocleavage, the asymmetric meeting of the pronuclei, the segregation of germ line-specific granules, and the generation of an asymmetric spindle) appear to depend on microfilaments (MFs). To investigate how MFs participate in these manifestations of zygotic asymmetry, the distribution of MFs in oocytes and early embryos was examined, using both antibodies to actin and the F-actin-specific probe rhodamine-phalloidin. In early-stage zygotes, MFs are found in a uniform cortical meshwork of fine fibers and dots or foci. In later zygotes, concomitant with the intracellular movements that are thought to be MF mediated, MFs also become asymmetrically rearranged; as the zygote undergoes pseudocleavage and as the germ line granules become localized in the posterior half of the cell, the foci of actin become progressively more concentrated in the anterior hemisphere. The foci remain anterior as the spindle becomes asymmetric and the zygote undergoes its first mitosis, at which time fibers align circumferentially around the zygote where the cleavage furrow will form. A model for how the anterior foci of actin may participate in zygotic motility events is discussed. Phalloidin and anti-actin antibodies have also been used to visualize MFs in the somatic tissues of the adult gonad. The myoepithelial cells that surround maturing oocytes are visibly contractile and contain an unusual array of MF bundles; the MFs run roughly longitudinally from the loop of the gonad to the spermatheca. Myosin thick filaments are distributed along the MFs in a periodic manner suggestive of a sarcomere-like configuration. It is proposed that these actin and myosin filaments interact to cause sheath cell contraction and the movement of oocytes through the gonad.