Miracle-dz/UniFAR-FTUs huggingface dataset:
Data transformation as a means towards dynamic data storage and polyglot persistence

Legacy applications have been built around the concept of storing their data in one relational data store. However, with the current differentiation in data store technologies as a consequence of the NoSQL paradigm, new and possibly more performant storage solutions are available to all applications. The concept of dynamic storage makes sure that application data are always stored in the most optimal data store at a given time to increase application performance. Additionally, polyglot persistence aims to push this performance even further by storing each different data type of an application in the data store technology best suited for it. To get legacy applications into dynamic storage and polyglot persistence, schema and data transformations between data store technologies are needed. This usually infers application redesigns as well to support the new data stores. This paper proposes such a transformation approach through a canonical model. It is based on the Lambda architecture to ensure no application downtime is needed during the transformation process, and after the transformation, the application can continue to query in the original query language, thus requiring no application code changes.
A Systematic Framework for Modernizing Legacy Application Systems

Researchers estimate that 180 - 200 billion lines of legacy code are still in use today. Legacy application system modernization is driven by an organization's desire to remain agile to changes, reduce operating costs and gain a clearer understanding of their application system infrastructure. In this paper we present a systematic modernization framework for legacy systems. Our framework considers the application code, information system and infrastructure as distinct entities which can be modernized independently. As a result, our approach can be applied sequentially to a single program module, or in parallel across multiple program modules. We validate our framework through an industrial case study involving a large, multinational financial services institution. Our case study results show that through modernization the organization reduced its cost to the sponsoring users by 80%, lines of code by 89%, operational complexity by 99%, and achieved an estimated 66% reduction in the man-hours required for time to market using the new application functions.
Comparison of multiple obesity indices for cardiovascular disease risk classification in South Asian adults: The CARRS Study

Background We comparatively assessed the performance of six simple obesity indices to identify adults with cardiovascular disease (CVD) risk factors in a diverse and contemporary South Asian population. Methods 8,892 participants aged 20–60 years in 2010–2011 were analyzed. Six obesity indices were examined: body mass index (BMI), waist circumference (WC), waist-height ratio (WHtR), waist-hip ratio (WHR), log of the sum of triceps and subscapular skin fold thickness (LTS), and percent body fat derived from bioelectric impedance analysis (BIA). We estimated models with obesity indices specified as deciles and as continuous linear variables to predict prevalent hypertension, diabetes, and high cholesterol and report associations (prevalence ratios, PRs), discrimination (area-under-the-curve, AUCs), and calibration (index χ2). We also examined a composite unhealthy cardiovascular profile score summarizing glucose, lipids, and blood pressure. Results No single obesity index consistently performed statistically significantly better than the others across the outcome models. Based on point estimates, WHtR trended towards best performance in classifying diabetes (PR = 1.58 [1.45–1.72], AUC = 0.77, men; PR = 1.59 [1.47–1.71], AUC = 0.80, women) and hypertension (PR = 1.34 [1.26,1.42], AUC = 0.70, men; PR = 1.41 [1.33,1.50], AUC = 0.78, women). WC (mean difference = 0.24 SD [0.21–0.27]) and WHtR (mean difference = 0.24 SD [0.21,0.28]) had the strongest associations with the composite unhealthy cardiovascular profile score in women but not in men. Conclusions WC and WHtR were the most useful indices for identifying South Asian adults with prevalent diabetes and hypertension. Collection of waist circumference data in South Asian health surveys will be informative for population-based CVD surveillance efforts.
Symbolic RTL simulation

Symbolic simulation is a promising formal verification technique combining the flexibility of conventional simulation with powerful symbolic methods. Unfortunately, existing symbolic simulators are restricted to gate level simulation or handle just a synthesizable subset of an HDL. Simulation of systems composed of design, testbench and correctness checkers, however, requires the complete set of HDL constructs. We present an approach that enables symbolic simulation of the complete set of RT-level Verilog constructs with full delay support. Additionally, we propose a flexible scheme for introducing symbolic variables and demonstrate how error traces can be simulated with this new scheme. Finally, we present some experimental results on an 8051 micro-controller design which prove the effectiveness of our approach.
Fibroblast Behavior on Tunable Gels With Decreasing Elasticity

Cells sense and react to various extracellular matrix (ECM) cues including chemical and physical cues. Previous studies in our laboratory and others have used static substrates, where the elastic properties remain unchanged throughout the culture period, to examine the effects of mechanical stiffness on neuron and fibroblast behavior [1–4]. However, in vivo, the ECM is dynamic and alters due to pathological, developmental, and external factors [5]. To study the effects of dynamic ECM changes on cell behavior, we developed a DNA-crosslinked, polyacrylamide gel (DNA gel) that allows us to study how dynamic changes in ECM stiffness affect cell behavior [6, 7]. Copyright © 2011 by ASME
Controlling degradation in calcium phosphate cements

Calcium phosphate based cements can be moulded to irregular contours often encountered in medicine. Brushite cements are more soluble than hydroxyapatite (HA) in physiological conditions and as such can be more rapidly resorbed. The metastable nature of brushite means that it converts to HA following immersion in physiological conditions. This phase change reduces the resorption rate, resulting in long term stability. In this study, macropores were incorporated into brushite cement to accelerate degradation, preventing hydrolysis and long term stability. The incorporation of beads into the cement had no effect on the composition of the cement. By varying the proportion of beads in the cement, it was possible to control degradation and prevent the formation of HA within the cement. Interestingly, in the macroporous cement, after 14 days of aging, the only crystalline component was β-tricalcium phosphate, suggesting that an amorphous binding phase was formed following brushite dissolution; this phase may maintain the integrity of the cement.
Structural characterization of multimetallic nanoparticles

Mukundan, Vineetha Ph.D., Purdue University, December 2014. Structural Characterization of Multimetallic Nanoparticles. Major Professor: Oana Malis. Bimetallic and trimetallic alloy nanoparticles have enhanced catalytic activities due to their unique structural properties. Using in situ time-resolved synchrotronbased x-ray diffraction, we investigated the structural properties of nanoscale catalysts undergoing various heat treatments. Thermal treatment brings about changes in particle size, morphology, dispersion of metals on support, alloying, surface electronic properties, etc. First, the mechanisms of coalescence and grain growth in PtNiCo nanoparticles supported on planar silica on silicon were examined in detail in the temperature range 400 − 900◦C. The sintering process in PtNiCo nanoparticles was found to be accompanied by lattice contraction and L10 chemical ordering. The mass transport involved in sintering is attributed to grain boundary diffusion and its corresponding activation energy is estimated from the data analysis. Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles were also investigated in real time with in situ synchrotronbased x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. PdCu nanoparticles are interesting because they are found to be more efficient as catalysts in ethanol oxidation reaction (EOR) than monometallic Pd catalysts. The combination of metal support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. The composition of the as prepared Pd:Cu mixture in this study was 34% Pd and 66% Cu. At 300◦C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (>450◦C). The
Beyond pixels: exploring new representations and applications for motion analysis

The focus of motion analysis has been on estimating a flow vector for every pixel by matching intensities. In my thesis, I will explore motion representations beyond the pixel level and new applications to which these representations lead. I first focus on analyzing motion from video sequences. Traditional motion analysis suffers from the inappropriate modeling of the grouping relationship of pixels and from a lack of ground-truth data. Using layers as the interface for humans to interact with videos, we build a human-assisted motion annotation system to obtain ground-truth motion, missing in the literature, for natural video sequences. Furthermore, we show that with the layer representation, we can detect and magnify small motions to make them visible to human eyes. Then we move to a contour presentation to analyze the motion for textureless objects under occlusion. We demonstrate that simultaneous boundary grouping and motion analysis can solve challenging data, where the traditional pixel-wise motion analysis fails. In the second part of my thesis, I will show the benefits of matching local image structures instead of intensity values. We propose SIFT flow that establishes dense, semantically meaningful correspondence between two images across scenes by matching pixel-wise SIFT features. Using SIFT flow, we develop a new framework for image parsing by transferring the metadata information, such as annotation, motion and depth, from the images in a large database to an unknown query image. We demonstrate this framework using new applications such as predicting motion from a single image and motion synthesis via object transfer. Based on SIFT flow, we introduce a nonparametric scene parsing system using label transfer, with very promising experimental results suggesting that our system outperforms state-of-the-art techniques based on training classifiers. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Profile: Agincourt Health and Socio-demographic Surveillance System

The Agincourt health and socio-demographic surveillance system (HDSS), located in rural northeast South Africa close to the Mozambique border, was established in 1992 to support district health systems development led by the post-apartheid ministry of health. The HDSS (90 000 people), based on an annual update of resident status and vital events, now supports multiple investigations into the causes and consequences of complex health, population and social transitions. Observational work includes cohorts focusing on different stages along the life course, evaluation of national policy at population, household and individual levels and examination of household responses to shocks and stresses and the resulting pathways influencing health and well-being. Trials target children and adolescents, including promoting psycho-social well-being, preventing HIV transmission and reducing metabolic disease risk. Efforts to enhance the research platform include using automated measurement techniques to estimate cause of death by verbal autopsy, full ‘reconciliation’ of in- and out-migrations, follow-up of migrants departing the study area, recording of extra-household social connections and linkage of individual HDSS records with those from sub-district clinics. Fostering effective collaborations (including INDEPTH multi-centre work in adult health and ageing and migration and urbanization), ensuring cross-site compatibility of common variables and optimizing public access to HDSS data are priorities.
Identification and Characterization of Candidate Chemosensory Gene Families from Spodoptera exigua Developmental Transcriptomes

Insect chemosensory genes have been considered as potential molecular targets to develop alternative strategies for pest control. However, in Spodoptera exigua, a seriously polyphagous agricultural pest, only a small part of such genes have been identified and characterized to date. Here, using a bioinformatics screen a total of 79 chemosensory genes were identified from a public transcriptomic data of different developmental stages (eggs, 1st to 5th instar larvae, pupae, female and male adults), including 34 odorant binding proteins (OBPs), 20 chemosensory proteins (CSPs), 22 chemosensory receptors (10 odorant receptors (ORs), six gustatory receptors (GRs) and six ionotropic receptors (IRs)) and three sensory neuron membrane proteins (SNMPs). Notably, a new group of lepidopteran SNMPs (SNMP3 group) was found for the first time in S. exigua, and confirmed in four other moth species. Further, reverse transcription PCR (RT-PCR) and quantitative real time PCR (qPCR) were employed respectively to validate the sequences and determine the expression patterns of 69 identified chemosensory genes regarding to sexes, tissues and stages. Results showed that 67 of these genes could be detected and reconstructed in at least one tissue tested. Further, 60 chemosensory genes were expressed in adult antennae and 52 in larval heads with the antennae, whereas over half of the genes were also detected in non-olfactory tissues like egg and thorax. Particularly, S. exigua OBP2 showed a predominantly larval head-biased expression, and functional studies further indicated its potentially olfactory roles in guiding food searching of larvae. This work suggests functional diversities of S. exigua chemosensory genes and could greatly facilitate the understanding of olfactory system in S. exigua and other lepidopteran species.
Integrative Genomics: Quantifying Significance of Phenotype-Genotype Relationships from Multiple Sources of High-Throughput Data

Given recent advances in the generation of high-throughput data such as whole-genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent studies show that genome-wide association findings are likely to fall in loci with gene regulatory effects such as expression quantitative trait loci (eQTLs), demonstrating the utility of such integrative approaches. When genotype and gene expression data are available on the same individuals, we and others developed methods wherein top phenotype-associated genetic variants are prioritized if they are associated, as eQTLs, with gene expression traits that are themselves associated with the phenotype. Yet there has been no method to determine an overall p-value for the findings that arise specifically from the integrative nature of the approach. We propose a computationally feasible permutation method that accounts for the assimilative nature of the method and the correlation structure among gene expression traits and among genotypes. We apply the method to data from a study of cellular sensitivity to etoposide, one of the most widely used chemotherapeutic drugs. To our knowledge, this study is the first statistically sound quantification of the overall significance of the genotype-phenotype relationships resulting from applying an integrative approach. This method can be easily extended to cases in which gene expression data are replaced by other molecular phenotypes of interest, e.g., microRNA or proteomic data. This study has important implications for studies seeking to expand on genetic association studies by the use of omics data. Finally, we provide an R code to compute the empirical false discovery rate when p-values for the observed and simulated phenotypes are available.
Large Radiofrequency Ablation Lesions Can Be Created with a Retractable Infusion‐Needle Catheter

Background: Radiofrequency (RF) catheter ablation of ventricular tachycardia is sometimes limited by inadequate lesion depth. We report the use of a novel retractable needle‐tipped electrode catheter with intramyocardial (IM) saline infusion and IM RF energy delivery to create large myocardial ablation lesions.
Estimation of longitudinal and lateral vehicle velocities: An algebraic approach

This paper presents a new approach for estimating vehicle velocities at its gravity center. The proposed strategy relies on recent algebraic techniques for numerical differentiation and diagnosis. We do not use any tire model in order to obtain an estimation, which is robust with respect to model uncertainties (friction, .). All available measurements in a mass-production car are however exploited.
The proteome of cytosolic lipid droplets isolated from differentiated Caco-2/TC7 enterocytes reveals cell-specific characteristics

Background information. Intestinal absorption of alimentary lipids is a complex process ensured by enterocytes and leading to TRL [TAG (triacylglycerol)‐rich lipoprotein] assembly and secretion. The accumulation of circulating intestine‐derived TRL is associated with atherosclerosis, stressing the importance of the control of postprandial hypertriglyceridaemia. During the postprandial period, TAGs are also transiently stored as CLDs (cytosolic lipid droplets) in enterocytes. As a first step for determining whether CLDs could play a role in the control of enterocyte TRL secretion, we analysed the protein endowment of CLDs isolated by sucrose‐gradient centrifugation from differentiated Caco‐2/TC7 enterocytes, the only human model able to secrete TRL in culture and to store transiently TAGs as CLDs when supplied with lipids. Cells were analysed after a 24 h incubation with lipid micelles and thus in a state of CLD‐associated TAG mobilization.
New high-thermal-conductivity composite material for high-precision space optics

This paper reports on the newly developed graphite-cyanate composite pipes for high-precision space optics such as the Solar-B optical telescope. Fundamental mechanical, thermal, and hygroscopic properties of unidirectional graphite- cyanate laminates were evaluated, first. The orientation of fibers in the pipe was designed to minimize longitudinal thermal deformation. Model pipes were fabricated based on the design, and have conducted a series of measurements to evaluate the thermal expansion behavior, the hygroscopic performance, the thermal conductivity, and the long-term stability. Excellent performance of the pipe was successfully verified and the material was found to be the most promising candidate for space optics structures.
Microbial Scout Hypothesis, Stochastic Exit from Dormancy, and the Nature of Slow Growers

ABSTRACT We recently proposed a scout model of the microbial life cycle (S. S. Epstein, Nature 457:1083, 2009), the central element of which is the hypothesis that dormant microbial cells wake up into active (so-called scout) cells stochastically, independently of environmental cues. Here, we check the principal prediction of this hypothesis: under growth-permissive conditions, dormant cells initiate growth at random time intervals and exhibit no species-specific lag phase. We show that a range of microorganisms, including environmental species, Escherichia coli, and Mycobacterium smegmatis, indeed wake up in a seemingly stochastic manner and independently of environmental conditions, even in the longest incubations conducted (months to years long). As is implicit in the model, most of the cultures we obtained after long incubations were not inherently slow growers. Of the environmental isolates that required ≥7 months to form visible growth, only 5% needed an equally long incubation upon subculturing, with the majority exhibiting regrowth within 24 to 48 h. This apparent change was not a result of adaptive mutation; rather, most microbial species that appear to be slow growers were in fact fast growers with a delayed initiation of division. Genuine slow growth thus appears to be less significant than previously believed. Random, low-frequency exit from the nongrowing state may be a key element of a general microbial survival strategy, and the phylogenetic breadth of the organisms exhibiting such exit indicates that it represents a general phenomenon. The stochasticity of awakening can also provide a parsimonious explanation to several microbiological observations, including the apparent randomness of latent infections and the existence of viable-but-nonculturable cells (VBNC).
Free Vibration Analysis of Spherical Caps Using a G.D.Q. Numerical Solution

In this paper we present the frequency evaluation of spherical shells by means of the generalized differential quadrature method (G.D.Q.M.), an effective numerical procedure which pertains to the class of generalized collocation methods. The shell theory used in this study is a first-order shear deformation theory with transverse shearing deformations and rotatory inertia included. The shell governing equations in terms of mid-surface displacements are obtained and, after expansion in partial Fourier series of the circumferential coordinate, solved with the G.D. Q.M. Several comparisons are made with available results, showing the reliability and modeling capability of the numerical scheme in argument.
Exploiting Passive Dynamics with Variable Stiffness Actuation in Robot Brachiation

This paper explores a passive control strategy with variable stiffness actuation for swing movements. We consider brachiation as an example of a highly dynamic task which re- quires exploitation of gravity in an efficient manner for successful task execution. First, we present our passive control strategy considering a pendulum with variable stiffness actuation. Then, we formulate the problem based an optimal control framework with temporal optimization in order to simultaneously find an appropriate stiffness profile and movement duration such that the resultant movement will be able to exploit the passive dynamics of the robot. Finally, numerical evaluations on a two- link brachiating robot with a variable stiffness actuator (VSA) model are provided to demonstrate the effectiveness of our approach under different task requirements, modelling errors and switching in the robot dynamics. In addition, we discuss the issue of task description in terms of the choice of cost function for successful task execution in optimal control.