Miracle-dz/UniFAR-FTUs huggingface dataset:
Adapting Data Representations for Optimizing Data-Intensive Applications

Author(s): Kusum, Amlan | Advisor(s): Gupta, Rajiv | Abstract: The need for efficiently managing Big Data has grown due the large sizes of data sets encountered by real-world Big Data applications. For example, large-scale graph analytics involves processing of graphs that have billions of nodes or edges. Because of the compute- and data-intensive nature of data analytics, programmers face multiple challenges in trying to achieve efficiency. This dissertation presents two novel approaches for handling data to scale up the performance of Big Data applications.The first approach supports multiple in-memory physical representations (data structures) for data and dynamically selects, or switches to, the best representation for the given data/workload characteristics. For example, in a graph processing application, where the graph evolves over time, our approach switches to the best data structure as the characteristics of the graph (e.g., graph density) change over time. Similarly, in a key-value store, upon changes in relative frequencies of different types of queries over time, we switch to a more efficient data structure for that query load. Our programming and compiler support produces adaptive applications that automatically switch data structures on-the-fly with little overhead and without the developer worrying about safety. Our evaluation shows running that our adaptive applications enjoy average speedups of 1.6x for graph applications and average throughput increase of 1.4x for a key-value store, compared to their non-adaptive versions. The second approach employs data transformations to create alternate data representations to accelerate shared memory and out-of-core applications. A large input graph is transformed into smaller graphs using a sequence of data transformations. Execution time reductions are achieved using a processing model that effectively runs the original iterative algorithm in two phases: first, using the reduced input graph to reduce execution time; and second, using the original input graph along with the results from the first phase for computing precise results. In the context of out-of-core applications this model is used to reduce I/O cost by creating a smaller graph that can be held in memory during the first phase. For parallel graph applications, our approach yields speedups of up to 2.14x and 1.81x for in-memory and out-of-core processing respectively, compared to applications running on untransformed data.
Physical vapor deposition of metal nanoparticles on chemically modified graphene: observations on metal-graphene interactions.

The growth of metallic nanoparticles formed on chemically modified graphene (CMG) by physical vapor deposition is investigated. Fine control over the size (down to ∼1.5 nm for Au) and coverage (up to 5 × 10(4) μm(-2) for Au) of nanoparticles can be achieved. Analysis of the particle size distributions gives evidence for Au nanocluster diffusion at room temperature, while particle size statistics differ clearly between metal deposited on single- and multilayer regions. The morphology of the nanoparticles varies markedly for different metals (Ag, Au, Fe, Pd, Pt, Ti), from a uniform thin film for Ti to a droplet-like growth for Ag. A simple model explains these morphologies, based only on consideration of 1) the different energy barriers to surface diffusion of metal adatoms on graphene, and 2) the ratio of the bulk cohesive energy of the metal to the metal-graphene binding energy. Understanding these interactions is important for controlling nanoparticle and thin-film growth on graphene, and for understanding the resultant charge transfer between metal and graphene.
Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology

The impact of natural killer (NK) cell alloreactivity on hematopoietic stem cell transplantation (HSCT) outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR)/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS) technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19) using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci) and a high percentage of mapping (mean 93% for all loci). Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in HSCT but also on the role of KIR+ NK cell populations in control of viral infections and diseases.
Automatic Detection Of Vocal Segments In Popular Songs

This paper presents a technique for the automatic classification of vocal and non-vocal regions in an acoustic musical signal. The proposed technique uses acoustic features which are suitable to distinguish vocal and non-vocal signals. We employ the Hidden Markov Model (HMM) classifier for vocal and non-vocal classification. In contrast to conventional HMM training methods which employ one model for each class, we create an HMM model space (multi-model HMMs) for segmentation with improved accuracy. In addition, we employ an automatic bootstrapping process which adapts the test song’s own models for better classification accuracy. Experimental evaluations conducted on a database of 20 popular music songs show the validity of the proposed approach.
Re-thinking residential mobility

While researchers are increasingly re-conceptualizing international migration, far less attention has been devoted to re-thinking short-distance residential mobility and immobility. In this paper we harness the life course approach to propose a new conceptual framework for residential mobility research. We contend that residential mobility and immobility should be re-conceptualized as relational practices that link lives through time and space while connecting people to structural conditions. Re-thinking and re-assessing residential mobility by exploiting new developments in longitudinal analysis will allow geographers to understand, critique and address pressing societal challenges.
Advantages of indium–tin oxide‐coated glass slides in correlative scanning electron microscopy applications of uncoated cultured cells

A method of direct visualization by correlative scanning electron microscopy (SEM) and fluorescence light microscopy of cell structures of tissue cultured cells grown on conductive glass slides is described. We show that by growing cells on indium–tin oxide (ITO)‐coated glass slides, secondary electron (SE) and backscatter electron (BSE) images of uncoated cells can be obtained in high‐vacuum SEM without charging artefacts. Interestingly, we observed that BSE imaging is influenced by both accelerating voltage and ITO coating thickness. By combining SE and BSE imaging with fluorescence light microscopy imaging, we were able to reveal detailed features of actin cytoskeletal and mitochondrial structures in mouse embryonic fibroblasts. We propose that the application of ITO glass as a substrate for cell culture can easily be extended and offers new opportunities for correlative light and electron microscopy studies of adherently growing cells.
Application of Fluorescence Two-Dimensional Difference In-Gel Electrophoresis as a Proteomic Biomarker Discovery Tool in Muscular Dystrophy Research

In this article, we illustrate the application of difference in-gel electrophoresis for the proteomic analysis of dystrophic skeletal muscle. The mdx diaphragm was used as a tissue model of dystrophinopathy. Two-dimensional gel electrophoresis is a widely employed protein separation method in proteomic investigations. Although two-dimensional gels usually underestimate the cellular presence of very high molecular mass proteins, integral membrane proteins and low copy number proteins, this method is extremely powerful in the comprehensive analysis of contractile proteins, metabolic enzymes, structural proteins and molecular chaperones. This gives rise to two-dimensional gel electrophoretic separation as the method of choice for studying contractile tissues in health and disease. For comparative studies, fluorescence difference in-gel electrophoresis has been shown to provide an excellent biomarker discovery tool. Since aged diaphragm fibres from the mdx mouse model of Duchenne muscular dystrophy closely resemble the human pathology, we have carried out a mass spectrometry-based comparison of the naturally aged diaphragm versus the senescent dystrophic diaphragm. The proteomic comparison of wild type versus mdx diaphragm resulted in the identification of 84 altered protein species. Novel molecular insights into dystrophic changes suggest increased cellular stress, impaired calcium buffering, cytostructural alterations and disturbances of mitochondrial metabolism in dystrophin-deficient muscle tissue.
Comparative Morphological Analysis of the Immature Stages of the Grass Blue Butterflies Zizeeria and Zizina (Lepidoptera: Lycaenidae)

The pale grass blue butterfly has been used to assess the biological effects of the Fukushima nuclear accident. Zizeeria and Zizina are two closely related genera of grass blue butterflies that are widely distributed in tropical to temperate Asia, Australia, and Africa, making them suitable environmental indicators for these areas. However, the morphological features of the immature stages have been examined only in fragmentary fashion. Here, we reared Zizeeria maha argia, Zizeeria maha okinawana, Zizeeria karsandra karsandra, Zizina emelina emelina, Zizina otis labradus, and Zizina otis riukuensis using a standard rearing method that was developed for Zizeeria maha, and comparatively identified morphological traits to effectively classify the immature stages of species or subspecies. Morphological information on these and other subspecies including Zizeeria knysna knysna and Zizina otis antanossa from Africa was also collected from literature. The subspecies were all reared successfully. The subspecies all had dorsal nectary and tentacle organs with similar morphology. For the subspecies of Zizeeria maha, only minor morphological differences were noted. Similarly, the subspecies of Zizina otis shared many traits. Most importantly, Zizeeria and Zizina differed in the shape of the sensory hairs that accompany the dorsal nectary organ; Zizeeriahad pointed hairs, and Zizina had blunt or rounded hairs. However, Zizina emelina exhibited several intermediate features between these two genera. Overall, the morphological traits did not completely reflect the conventional systematic relationships. This comparative study describes the efficient rearing of the grass blue butterflies and provides a morphological basis for the use of these species as environmental indicators.
Thread-based benchmarking deployment

Information and knowledge are actually well and easily distributed thanks to electronic journals, news, mailing-lists and forums. It is however more difficult to deploy algorithmic and programming collaboration: the heterogeneity of the programming languages and the operating systems used by researchers constitutes a major problem to the design of a common testing platform. Current solutions exist to develop collaborative work. Generally, these solutions impose specific programming languages and/or operating systems to developers. Some others specific rules have to be respected. These heavy constrains slow down the usage of collaborative programming platforms. The OpenWatermark project proposes a modern architecture for cooperative programming exchanges that takes all these aspects into account. Developers work with their favorite programming languages and operating systems as long as the OpenWatermark platform supports them. In this paper, we will present the OpenWatermark platform (www.openwatermark.org) and its application to the benchmarking of image watermarking algorithms.
Vulnerabilities of network OS and mitigation with state-based permission system

The advancement of software defined networking SDN is redefining traditional computer networking architecture. The role of the control plane of SDN is of such importance that SDNs are referred to as network operating systems OSs. However, the robustness and security of the network OS has been overlooked. In this paper, we report three main issues pertaining to network OSs. First, we identified vulnerabilities that could be exploited by malicious or buggy applications running on network OSs. We also identified four major attack vectors that could undermine network OS operations: denial of service, global data manipulation, control plane poisoning, and system shell execution. Further, it was demonstrated that real-world attacks can be launched on commonly used network OSs without significant effort. Second, we present a method to address the attacks by analyzing network applications running on network OSs to identify their behavioral features, which enabled the extraction of a permission set for each network application. Based on this work, a permission-based malicious network application detector was introduced, which examines the permission set of each application and prevents it from executing without permission. Our system shows almost no performance overhead. Copyright © 2015 John Wiley & Sons, Ltd.
Theory and simulation of coupled grain boundary migration and grain rotation in low angle grain boundaries

Abstract Microstructure evolution due to coupled grain boundary migration and grain rotation in low angle grain boundaries is studied through a combination of molecular dynamics and phase field modeling. We have performed two dimensional molecular dynamics simulations on a bicrystal with a circular grain embedded in a larger grain. Both size and orientation of the embedded grain are observed to evolve with time. The shrinking embedded grain is observed to have two regimes: constant dislocation density on the grain boundary followed by constant rate of increase in dislocation density. Based on these observations from the molecular dynamics simulations, a theoretical formulation of the kinetics of coupled grain rotation is developed. The grain rotation rate is derived for the two regimes of constant dislocation density and constant rate of change of dislocation density on the grain boundary during evolution. The theoretical calculation of the grain rotation rate shows strong dependence on the grain size and compares very well with the molecular dynamics simulations. A multi-order parameter based phase field model with coupled grain rotation is developed using the theoretical formulation to model polycrystalline microstructure evolution.
Molybdenum Site Structure of MOSC Family Proteins

Mo K-edge X-ray absorption spectroscopy has been used to probe as-isolated structures of the MOSC family proteins pmARC-1 and HMCS-CT. The Mo K-edge near-edge spectrum of HMCS-CT is shifted ∼2.5 eV to lower energy compared to the pmARC-1 spectrum, which indicates that as-isolated HMCS-CT is in a more reduced state than pmARC-1. Extended X-ray absorption fine structure analysis indicates significant structural differences between pmARC-1 and HMCS-CT, with the former being a dioxo site and the latter possessing only a single terminal oxo ligand. The number of terminal oxo donors is consistent with pmARC-1 being in the MoVI oxidation state and HMCS-CT in the MoIV state. These structures are in accord with oxygen-atom-transfer reactivity for pmARC-1 and persulfide bond cleavage chemistry for HMCS-CT.
The effect of vitamin D on vaginal atrophy in postmenopausal women

Background: Most of the women suffer from vaginal atrophy and dryness, and therefore, efficient and safe treatment is needed to improve vaginal lubrication. Vitamin D has several important functions which may be effective in proliferation and repair of the epithelial tissue. This study aimed to evaluate the effect of vitamin D vaginal suppositories on maturation index, pH, and dryness in postmenopausal women. Materials and Methods: Women were enrolled in this double-blind clinical trial, in whom menopause occurred at least one year ago. Those women who had an abnormal Papanicolaou smear, had undergone hormonal treatment, or have had vaginal infection in the previous year were excluded. Forty-four women who found eligible were randomized into two equal groups, the treatment and control groups, which received vitamin D and placebo vaginal suppository daily for 8 weeks, respectively. Vaginal pH and maturation value were measured at the beginning and end of the study. Pain, dryness, and paleness were assessed before treatment and at the end of the 2, 4, and 8 weeks of treatment. Results: In the treatment group, the number (Mean ± SD) of superficial cells increased (69.76 ± 12.4) and vaginal pH decreased (1.42 ± 0.67) significantly compared to the control group after 56 days. The mean pain significantly reduced after 8 weeks in the treatment group (1.23 ± 0.53) compared to the control group 1.95 ± 0.74 (P < 0.001). The mean of dryness and paleness reduced significantly in the treatment group versus control at 56 days. Conclusions: Vitamin D is effective in improving the maturation index and decreased the pH and dryness of the vaginal atrophy due to menopause.
Low-Density Parity-Check Codes for ATSC 3.0

In this paper, we introduce the overview and detailed structure of low-density parity-check (LDPC) codes, which are adopted for the physical layer standard of Advanced Television Systems Committee (ATSC) 3.0. As one of the features to mitigate channel errors efficiently, LDPC codes are used as a main part of forward error correction scheme within the bit interleaved coded modulation chain. This paper presents two different structures of LDPC codes in the ATSC 3.0 standard: 1) irregular repeat accumulate structure and 2) multi-edge type structure. After the detailed encoding methods for the two structures are introduced, the performance results including comparison studies with other broadcasting standards such as DVB-T2 and DVB-S2 are shown.
Multidimensional Analysis of System Logs in Large-scale Cluster Systems

It is effective to improve the reliability and availability of large-scale cluster systems through the analysis of failures. Existed failure analysis methods understand and analyze failures from one or few dimension. The analysis results are partial and with less precision because of the limitation of data source. This paper presents multidimensional analysis based on graph mining to analyze multi-source system logs, which is a promising failure analysis method to get more complete and precise failure knowledge.
Pallas: Self-Bootstrapping Fine-Grained Passive Indoor Localization Using WiFi Monitors

Passive indoor localization for smartphones requires no explicit cooperation of the smartphone and enables a new spectrum of applications such as passive user tracking, mobility monitoring, social pattern analysis, etc. However, existing passive localization methods either achieve coarse-grained localization accuracy or require expensive infrastructure support. In this paper, we present Pallas, a self-bootstrapping system for fine-grained passive indoor localization using non-intrusive WiFi monitors. Pallas uses off-the-shelf access point hardware to opportunistically capture WiFi packets to infer the location of smartphones in the indoor environment. The key novelty of Pallas lies in that the passive fingerprint database for localization is automatically constructed and updated without any active participation of WiFi devices or manual calibration. To achieve this, Pallas first identifies passive landmarks that are present in WiFi RSS traces. Given the knowledge of the indoor floor plan and the location of WiFi monitors, Pallas statistically maps the collected RSS traces to specific indoor pathways. With sufficient mapping opportunistically detected, Pallas is able to bootstrap a fine-grained passive fingerprint database and build Gaussian processes for localization automatically without requiring any additional calibration effort.
Control of Rheology, Strength and Fibre Bond of UHPC with Additions - Effect of Packing Density and Addition Type.

This contribution illustrates the effect of additions different in type and fineness and maximum packing density on the macroscopic properties, rheology and bond of steel fibres of UHPC. The results show that the properties of the UHPC investigated were decisively affected by the particle size distribution of the additions rather than the type of material. A new packing density test for fine materials (< 125 μm) was developed to provide calibrated input parameters for the calculation of the maximum packing density of UHPC with different additions. The rheological properties, and therefore fresh concrete workability, were affected by the maximum packing density of the UHPC bulk matrix. The bond strength of steel fibres in a straight pull-out test was affected by addition exchange too. Again, this is explained by packing density effects. Based on packing density calculations as well as SEM and EDX investigations, higher fibre bond strength is explained by a larger proportion of very fine particles in the matrix adjacent to the fibre ITZ which leads to a decrease in the maximum packing density of the fibre ITZ.