Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of an automatic system classifying hepatic lesions on multi-phase computer tomography images

In this paper, we propose to assess the results obtained by our automatic system for classifying hepatic lesions. Our database contains 107 multi-phase liver nodules from 7 different diagnosis types. As multi-phase scans are not commonly found in Computer Aided Diagnosis systems, an analysis of the potential improvement introduced by working on multiphase versus single portal phase CT acquisitions is made, as well as the comparison of our tool classification results to the ones obtained by two radiologists. Experimental results led to the validation of the method.
Uncertain Databases in Collaborative Data Management

We discuss an approach to collaborative data management based on uncertain databases. Note that, in a collaborative data management system, users may have contradicting opinions about the correct values of data items. In our approach, we propose to store all conflicting data versions in parallel and to resolve conflicts based on user ratings. We show that such a collaborative data management system can be nicely represented in an uncertain database using U-relations.
Aerobic Heterotrophic Bacterial Populations of Sewage and Activated Sludge

The nature and behavior of the microbial population developed on a synthetic waste containing salts and sorbitol are compared to that of a treatment-plant activated sludge. The population of the adapted sludge developed on the synthetic waste consisted approximately of only six kinds of bacteria. Experiments with radioactive sorbitol indicate that the microbial population developed on the synthetic waste showed the effects of repression by glucose on the metabolism of sorbitol; in contrast, the activated sludge from a plant treating primarily domestic waste was able to attack both substrates immediately and simultaneously.
Autoregressive product of multi-frame predictions can improve the accuracy of hybrid models

We describe a simple but effective way of using multi-frame targets to improve the accuracy of Artificial Neural NetworkHidden Markov Model (ANN-HMM) hybrid systems. In this approach a Deep Neural Network (DNN) is trained to predict the forced-alignment state of multiple frames using a separate softmax unit for each of the frames. This is in contrast to the usual method of training a DNN to predict only the state of the central frame. By itself this is not sufficient to improve accuracy of the system significantly. However, if we average the predictions for each frame from the different contexts it is associated with we achieve state of the art results on TIMIT using a fully connected Deep Neural Network without convolutional architectures or dropout training. On a 14 hour subset of Wall Street Journal (WSJ) using a context dependent DNN-HMM system it leads to a relative improvement of 6.4% on the dev set (testdev93) and 9.3% on test set (test-eval92).
Modeling loop reorganization free energies of acetylcholinesterase: A comparison of explicit and implicit solvent models

The treatment of hydration effects in protein dynamics simulations varies in model complexity and spans the range from the computationally intensive microscopic evaluation to simple dielectric screening of charge‐charge interactions. This paper compares different solvent models applied to the problem of estimating the free‐energy difference between two loop conformations in acetylcholinesterase. Molecular dynamics (MD) simulations were used to sample potential energy surfaces of the two basins with solvent treated by means of explicit and implicit methods. Implicit solvent methods studied include the generalized Born (GB) model, atomic solvation potential (ASP), and the distance‐dependent dieletric constant. By using the linear response approximation (LRA), the explicit solvent calculations determined a free‐energy difference that is in excellent agreement with the experimental estimate, while rescoring the protein conformations with GB or the Poisson equation showed inconsistent and inferior results. While the approach of rescoring conformations from explicit water simulations with implicit solvent models is popular among many applications, it perturbs the energy landscape by changing the solvent contribution to microstates without conformational relaxation, thus leading to non‐optimal solvation free energies. Calculations applying MD with a GB solvent model produced results of comparable accuracy as observed with LRA, yet the electrostatic free‐energy terms were significantly different due to optimization on a potential energy surface favored by an implicit solvent reaction field. The simpler methods of ASP and the distance‐dependent scaling of the dielectric constant both produced considerable distortions in the protein internal free‐energy terms and are consequently unreliable. Proteins 2004. Published 2004 Wiley‐Liss, Inc.
Physical map of the genome of Treponema pallidum subsp. pallidum (Nichols)

A physical map of the chromosome of Treponema pallidum subsp. pallidum (Nichols), the causative agent of syphilis, was constructed from restriction fragments produced by NotI, SfiI, and SrfI. These rare-cutting restriction endonucleases cleaved the T. pallidum genome into 16, 8, and 15 fragments, respectively. Summation of the physical lengths of the fragments indicates that the chromosome of T. pallidum subsp. pallidum is approximately 1,030 to 1,080 kbp in size. The physical map was constructed by hybridizing a variety of probes to Southern blots of single and double digests of T. pallidum genomic DNA separated by contour-clamped homogeneous electric field electrophoresis. Probes included cosmid clones constructed from T. pallidum subsp. pallidum genomic DNA, restriction fragments excised from gels, and selected genes. Physical mapping confirmed that the chromosome of T. pallidum subsp. pallidum is circular, as the SfiI and SrfI maps formed complete circles. A total of 13 genes, including those encoding five membrane lipoproteins (tpn47, tpn41, tpn29-35, tpn17, and tpn15), a putative outer membrane porin (tpn50), the flagellar sheath and hook proteins (flaA and flgE), the cytoplasmic filament protein (cfpA), 16S rRNA (rrnA), a major sigma factor (rpoD), and a homolog of cysteinyl-tRNA synthetase (cysS), have been localized in the physical map as a first step toward studying the genetic organization of this noncultivable pathogen.
Linkage Disequilibrium Mapping of Arabidopsis CRY2 Flowering Time Alleles Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY576055, AY576271.

The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an ∼65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to <16 kb around CRY2, the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype. This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
Typical Enteroaggregative and Atypical Enteropathogenic Types of Escherichia coli Are the Most Prevalent Diarrhea-Associated Pathotypes among Brazilian Children

ABSTRACT A 1-year prospective study was carried out in two large urban centers of São Paulo State, Brazil, to determine the prevalences and roles of the different Escherichia coli pathotypes in children less than 5 years of age with diarrhea presenting to the emergency rooms of public hospitals or visiting private pediatricians' offices. Of the pathotypes sought, typical enteroaggregative and atypical enteropathogenic types of E. coli were isolated for 8.9% and 5.4% of 774 diarrhea cases, respectively, and were found to be dominant and significantly associated with diarrhea.
Intracellular Cl− Dependence of Na-H Exchange in Barnacle Muscle Fibers under Normotonic and Hypertonic Conditions

We previously showed that shrinking a barnacle muscle fiber (BMF) in a hypertonic solution (1,600 mosM/kg) stimulates an amiloride-sensitive Na-H exchanger. This activation is mediated by a G protein and requires intracellular Cl−. The purpose of the present study was to determine (a) whether Cl− plays a role in the activation of Na-H exchange under normotonic conditions (975 mosM/kg), (b) the dose dependence of [Cl−]i for activation of the exchanger under both normo- and hypertonic conditions, and (c) the relative order of the Cl−- and G-protein-dependent steps. We acid loaded BMFs by internally dialyzing them with a pH-6.5 dialysis fluid containing no Na+ and 0–194 mM Cl−. The artificial seawater bathing the BMF initially contained no Na+. After dialysis was halted, adding 50 mM Na+ to the artificial seawater caused an amiloride-sensitive pHi increase under both normo- and hypertonic conditions. The computed Na-H exchange flux (J Na-H) increased with increasing [Cl−]i under both normo- and hypertonic conditions, with similar apparent K m values (∼120 mM). However, the maximal J Na-H increased by nearly 90% under hypertonic conditions. Thus, activation of Na-H exchange at low pHi requires Cl− under both normo- and hypertonic conditions, but at any given [Cl−]i, J Na-H is greater under hyper- than normotonic conditions. We conclude that an increase in [Cl−]i is not the primary shrinkage signal, but may act as an auxiliary shrinkage signal. To determine whether the Cl−-dependent step is after the G-protein-dependent step, we predialyzed BMFs to a Cl−-free state, and then attempted to stimulate Na-H exchange by activating a G protein. We found that, even in the absence of Cl−, dialyzing with GTPγS or AlF3, or injecting cholera toxin, stimulates Na-H exchange. Because Na-H exchange activity was absent in control Cl−-depleted fibers, the Cl−-dependent step is at or before the G protein in the shrinkage signal-transduction pathway. The stimulation by AlF3 indicates that the G protein is a heterotrimeric G protein.
Development of HEMP Fiber Reinforced Polypropylene Composites

Nonwoven mats from hemp and polypropylene fibers in various proportions are produced and hot pressed to make composite material. The effect of hemp fiber content and anisotropy in the nonwoven mats resulting from the carding technology are examined on the basis of the three-point bending, tensile, and impact properties of the resultant composite materials. Because of the hydrophilic nature and poor dimensional stability of cellulosic fibers due to swelling, the effect of water sorption on mechanical performances is also investigated. Optimal mechanical properties are achieved in composites made from 40 to 50% of hemp fiber by weight. As expected, better mechanical properties are found in the specimens cut from the composite sheets parallel to the direction of carding. A strong decrease in three-point bending properties is noticed after immersing the composite samples in distilled water for 19 days, while the impact strength increased. Double carding of raw materials results in a decreased anisotropy in the composite material.
Estimating Lifetime of Notched Components Subjected to Variable Amplitude Fatigue Loading According to the Elastoplastic Theory of Critical Distances

The present paper is concerned with the use of the elastoplastic theory of critical distances (TCD) to perform the fatigue assessment of notched components subjected to in-service variable amplitude (VA) fatigue loading. The elastoplastic TCD takes as its starting point the assumption that the detrimental effect of stress/strain concentrators of any kind can efficiently be taken into account by directly postprocessing the entire elastoplastic stress/strain field in the vicinity of the notch apex. Thanks to its specific features, the TCD can be formalized in different ways by simply changing size and geometrical features of the domain used to calculate the required effective stress. The so-called point method (PM) is the simplest form in which this theory can be applied. This formalization of the TCD postulates that the elastoplastic stress/strain state to be used to estimate fatigue damage has to be determined at a given distance from the tip of the notch being assessed. According to the TCD's philosophy, such a distance is treated as a fatigue property. Therefore, given the material, this critical length does not change as either the features of the assessed stress/strain concentrator or the profile of the investigated loading path vary. In the present study, the above design strategy is attempted to be used to estimate lifetime of notched component subjected to VA loading, the required critical distance being determined under constant amplitude (CA) loading. The accuracy and reliability of the devised approach were checked by using a number of experimental results generated by testing, under both concave upward and concave downward spectra, notched samples containing geometrical features having a different sharpness. Such a validation exercise allowed us to prove that the elastoplastic TCD, used in the form of the PM, is highly accurate in estimating fatigue damage also in notched components subjected to in-service VA loading.
Generating Counterexamples for Model Checking by Transformation

This volume contains the revised versions of papers presented at the Fourth International Workshop on Verification and Program Transformation (VPT 2016) on April 2, 2016 in Eindhoven, The Netherlands. The workshop is an event of the European Joint Conferences on Theory and Practice of Software (ETAPS 2016). The aim of the VPT workshops is to provide a forum where people from the area of program transformation and the area of program verification can fruitfully exchange ideas and gain a deeper understanding of the interactions between those two fields. The research papers which have been recently published in those fields, show that the interactions are very beneficial and, indeed, go both ways. In one direction, methods and tools developed in the field of program transformation, such as partial deduction, partial evaluation, fold/unfold transformations, and supercompilation, have all been applied with success for the verification of systems, and in particular, the verification of infinite state and parameterized systems. In the other direction, methods developed in program verification, such as model checking, abstract interpretation, SAT and SMT solving, and automated theorem proving, have been used to enhance program transformation techniques, thereby making these techniques more powerful and useful in practice.
The statistical adversary allows optimal money-making trading strategies

The distributional approach and competitive analysis have traditionally been used for the design and analysis of online algorithms. The former assumes a specific distribution of inputs, while the latter assumes inputs are chosen by an unrestricted adversary. This paper employs the statistical adversary (recently proposed by Raghavan) to analyze and design on-line algorithms for two-way cumncy trading. By statistical adversary, we mean an adversary that generates worst case input sequences, where each sequence must satisfy certain general statistical properties. The on-line algorithms presented in this paper have some very attractive properties. For instance, the algorithms are money-making. Although previous on-line algorithms are competitive, they can lose money even when the optimal off-line algorithm makes money. Against a weak statistical adversary, our methods yield an algorithm that outperforms the optimal off-line “buy-and-hold” strategy. Furthermore, it is guaranteed to make a substantial profit when it is known that the market is active and stable. In fact, our algorithm even makes money when the market exhibits a slightly unfavorable trend.
The design of a GUI paradigm based on tablets, two-hands, and transparency

An experimental GUI paradigm is presented which is based on the design goals of maximizing the amount of screen used for application data, reducing the amount that the UI diverts visual attentions from the application data, and increasing the quality of input. In pursuit of these goals, we integrated the non-standard UI technologies of multi-sensor tablets, toolglass, transparent UI components, and marking menus. We describe a working prototype of our new paradigm, the rationale behind it and our experiences introducing it into an existing application. Finally, we presents some ot the lessons learned: prototypes are useful to break the barriers imposed by conventional GUI design and some of their ideas can still be retrofitted seamlessly into products. Furthermore, the added functionality is not measured only in terms of user performance, but also by the quality of interaction, which allows artists to create new graphic vocabularies and graphic styles.
FPGA clock network architecture: flexibility vs. area and power

This paper examines the tradeoffs between flexibility, area, and power dissipation of programmable clock networks for Field-Programmable Gate Arrays (FPGA's). The paper begins by describing a parameterized clock network model that describes a broad range of programmable clock network architectures. Specifically, the model supports architectures with multiple local and global clock domains and varying amounts of flexibility at various levels of the clock network. Using the model, the architectural parameters that control the flexibility of the clock network are varied to determine the cost of this flexibility in terms of area and power dissipation. From these experiments, the study finds that area and power costs are highest for networks with flexibility close to the logic blocks. Furthermore, it found that clock networks with local clock domains have little overhead and are significantly more efficient than clock networks without local clock domains for applications with multiple clocks.
Mining coherent patterns from heterogeneous microarray data

Microarray technology is a powerful tool for geneticists to monitor interactions among tens of thousands of genes simultaneously. There has been extensive research on coherent subspace clustering of gene expressions measured under consistent experimental settings. However, these methods assume that all experiments are run using the same batch of microarray chips with similar characteristics of noise. Algorithms developed under this assumption may not be applicable for analyzing data collected from heterogeneous settings, where the set of genes being monitored may be different and expression levels may be not directly comparable even for the same gene. In this paper, we propose a model, F-cluster, for mining subspace coherent patterns from heterogeneous gene expression data. We compare our model with previously proposed models. We analyze the search space of the problem and give a naïve solution for it.
Constrained Band Subset Selection for Hyperspectral Imagery

This letter extends the constrained band selection (CBS) technique to constrained band subset selection (CBSS) in a similar manner that constrained energy minimization has been extended to linearly constrained minimum variance. CBSS constrains multiple bands as a band subset as opposed to CBS constraining a single band as a singleton set. To achieve this goal, CBSS requires a strategy to search for an optimal band subset, while CBS does not. In this letter, two new sequential algorithms, referred to as sequential CBSS and successive CBSS, which do not exist in CBS are derived for CBSS to find desired band subsets and to avoid exhaustive search.
Discriminative Relational Representation Learning for RGB-D Action Recognition

This paper addresses the problem of recognizing human actions from RGB-D videos. A discriminative relational feature learning method is proposed for fusing heterogeneous RGB and depth modalities, and classifying the actions in RGB-D sequences. Our method factorizes the feature matrix of each modality, and enforces the same semantics for them in order to learn shared features from multimodal data. This allows us to capture the complex correlations between the two modalities. To improve the discriminative power of the relational features, we introduce a hinge loss to measure the classification accuracy when the features are employed for classification. This essentially performs supervised factorization, and learns discriminative features that are optimized for classification. We formulate the recognition task within a maximum margin framework, and solve the formulation using a coordinate descent algorithm. The proposed method is extensively evaluated on two public RGB-D action data sets. We demonstrate that the proposed method can learn extremely low-dimensional features with superior discriminative power, and outperforms the state-of-the-art methods. It also achieves high performance when one modality is missing in testing or training.
Damage Metric-Based Mapping Approaches for Developing Accelerated Thermal Cycling Guidelines for Electronic Packages

The accumulated equivalent inelastic strain per cycle and the maximum strain energy density over one cycle have been used as damage metrics to map the solder fatigue damage during Field-Cycling (FC) and Accelerated Thermal Cycling (ATC) simulations. The objective of this work is to develop accelerated thermal cycling guidelines for flip-chip on board and flip-chip chip-scale electronic packages used in, for example, automotive applications. The percentage contributions of plastic and creep strains to the total inelastic strain and contributions within the accelerated cycling are used as a basis for developing modified accelerated thermal cycles. Different temperature regimes are explored to match the contributions of plastic and creep strains to total inelastic strain during field-cycling and accelerated thermal cycling and to reduce the time required for accelerated thermal cycling. The process mechanics of component assembly, time-and temperature-dependent material behavior and critical geometric features of the assembly are taken into consideration while developing the comprehensive virtual accelerated thermal cycling methodology.
An FPGA-based system for the measurement of frequency noise and resolution of QCM sensors

The use of Quartz Crystal Oscillators (QCM) as high accuracy microbalance sensors is limited by the frequency noise present in the circuit. This work deals with the design and implementation of an FPGA-based system for the real-time meas- urement of the frequency noise and resolution of QCM sensors. This reconfigurable system integrates the frequency measurement and the mass resolution computation in a single FPGA chip. Parallel process- ing, pipeline stages and prediction techniques are combined in order to accelerate the computations maintaining a low hardware complexity. By this way, a reconfigurable and low cost QCM sensor sys- tem working as a standalone measurement platform with communication capabilities is obtained. The implemented system was validated with a Xilinx Virtex-4 FPGA and a QCM sensor operating in damping media for electrochemical applications.