Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmid-containing strains of Streptococcus mutans cluster within family and racial cohorts: implications for natural transmission

The transmission of mutans streptococci is thought to occur along familial lines based on investigations which have shown common strains within family units by using phenotypic typing methods, such as bacteriocin production and immunity profiles and serotyping. Difficulties in implementing these typing methods, coupled with conflicting interpretations of results between laboratories, led us to study the conservation of Streptococcus mutans strains within a mother-child cohort by using a genotypic marker, plasmid DNA. Plasmids (all 5.6 kilobases in size) were observed at an overall frequency of 3.3%, with a significantly different frequency in whites (1.5%) compared with blacks (6.6%). Plasmid-containing strains were significantly clustered in mother-child pairs compared with nonrelated individuals (58 versus 3.3%; P less than 0.001). Moreover, the different plasmid groups (I and II) were highly conserved within racial boundaries (P = 0.007). In those instances in which we were able to characterize distinct strains by either biotype or plasmid profile, we found that mothers harbored a more heterogeneous population of mutans streptococci than did their children. This suggested, among other possibilities, that children acquire additional strains as they approach adulthood. Alternatively, we may have been unable to detect more heterogeneity of strains in children because of quantitative differences of strains in saliva. We present collective data which show that strains of S. mutans are highly conserved within not only mothers and their children but also racial groups, suggesting vertical transmission of this organism within human populations. Moreover, we show that levels of S. mutans found in the saliva of the mother correlated with levels found in her child, demonstrating a quantitative relationship within mother-child pairs.
Nonrigid registration using free-form deformations: application to breast MR images

In this paper the authors present a new approach for the nonrigid registration of contrast-enhanced breast MRI. A hierarchical transformation model of the motion of the breast has been developed. The global motion of the breast is modeled by an affine transformation while the local breast motion is described by a free-form deformation (FFD) based on B-splines. Normalized mutual information is used as a voxel-based similarity measure which is insensitive to intensity changes as a result of the contrast enhancement. Registration is achieved by minimizing a cost function, which represents a combination of the cost associated with the smoothness of the transformation and the cost associated with the image similarity. The algorithm has been applied to the fully automated registration of three-dimensional (3-D) breast MRI in volunteers and patients. In particular, the authors have compared the results of the proposed nonrigid registration algorithm to those obtained using rigid and affine registration techniques. The results clearly indicate that the nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms.
From an Asynchronous Intermittent Rotating Star to an Eventual Leader

Considering an asynchronous system made up of n processes and where up to t of them can crash, finding the weakest assumption that such a system has to satisfy for a common leader to be eventually elected is one of the holy grail quests of fault-tolerant asynchronous computing. This paper is a step in that direction. It has two contributions. Considering a simple and general asynchronous system model where processes generate asynchronous pulses during which they send and receive messages, it first introduces an additional assumption that allows to elect an eventual leader in all the runs that satisfy that assumption. That assumption is captured by the notion of asynchronous intermittent rotating t-star. An x-star is made up of one process p (the center of the star) plus a sequence of sets of x processes (the successive points of the star), which satisfies some properties. Intuitively, the intermittent rotating t-star assumption means that there are a process p, a subset of pulse numbers pn, and associated sets of processes Q(pn) such that each process of Q(pn) receives from p a message sent in pulse pn in a timely manner or among the first (n-t) messages tagged pn it ever receives. The t-star is called rotating because the set Q(pn) is allowed to change with pn; it is intermittent because it can disappear during finite periods; it is asynchronous because the points of a star are not required to be simultaneously at the same pulse. (This assumption combines and generalizes several synchrony and time-free assumptions that have been previously proposed to elect an eventual leader, e.g., eventual t-source, eventual t-moving source, and message pattern assumption.) The second contribution of the paper is an algorithm that eventually elects a common leader in the systems that satisfy the asynchronous intermittent rotating t-star assumption. This algorithm enjoys, among others, two noteworthy properties. First, from a design point of view, it is simple. Second, from a cost point of view, only the pulse numbers increase without bound. This means that, even in infinite executions, be links timely or not (or have the corresponding sender crashed or not), all the other local variables (including the timers) and message fields have a finite domain.
Dysregulation of DNA methylation induced by past arsenic treatment causes persistent genomic instability in mammalian cells

The mechanisms by which arsenic‐induced genomic instability is initiated and maintained are poorly understood. To investigate potential epigenetic mechanisms, in this study we evaluated global DNA methylation levels in V79 cells and human HaCaT keratinocytes at several time points during expanded growth of cell cultures following removal of arsenite exposures. We have found altered genomic methylation patterns that persisted up to 40 cell generations in HaCaT cells after the treatments were withdrawn. Moreover, mRNA expression levels were evaluated by RT‐PCR for DNMT1, DNMT3A, DNMT3B, HMLH1, and HMSH2 genes, demonstrating that the down regulation of DNMT3A and DNMT3B genes, but not DNMT1, occurred in an arsenic dose‐dependent manner, and persisted for many cell generations following removal of the arsenite, offering a plausible mechanism of persistently genotoxic arsenic action. Analyses of promoter methylation status of the DNA mismatch repair genes HMLH1 and HMSH2 show that HMSH2, but not HMLH1, was epigenetically regulated by promoter hypermethylation changes following arsenic treatment. The results reported here demonstrate that arsenic exposure promptly induces genome‐wide global DNA hypomethylation, and some specific gene promoter methylation changes, that persist for many cell generations following withdrawal of arsenite, supporting the hypothesis that the cells undergo epigenetic reprogramming at both the gene and genome level that is durable over many cell generations in the absence of further arsenic treatment. These DNA methylation changes, in concert with other known epigenome alterations, are likely contributing to long‐lasting arsenic‐induced genomic instability that manifests in several ways, including aberrant chromosomal effects. Environ. Mol. Mutagen. 57:137–150, 2016. © 2015 Wiley Periodicals, Inc.
The Association between Conduct Problems and Bullying for Youth with and without Callous-Unemotional Traits

This Thesis is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Thesis in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rightsholder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself.
Calculating Probabilities Simplifies Word Learning

Children can use the statistical regularities of their environment to learn word meanings, a mechanism known as cross-situational learning. We take a computational approach to investigate how the information present during each observation in a cross-situational framework can affect the overall acquisition of word meanings. We do so by formulating various in-the-moment learning mechanisms that are sensitive to different statistics of the environment, such as counts and conditional probabilities. Each mechanism introduces a unique source of competition or mutual exclusivity bias to the model; the mechanism that maximally uses the model's knowledge of word meanings performs the best. Moreover, the gap between this mechanism and others is amplified in more challenging learning scenarios, such as learning from few examples.
Enhanced radar imaging via sparsity regularized 2D linear prediction

ISAR imaging based on the 2D linear prediction uses the l2 norm minimization of the prediction error to obtain 2D autoregressive (AR) model coefficients. However, this approach causes many spurious peaks in the resulting image. In this study, a new ISAR imaging method based on the 2D sparse AR modeling of backscattered data is proposed. The 2D model coefficients are obtained by the l2- norm minimization of the prediction error penalized by the l1 norm of the prediction coefficient vector. The resulting 2D prediction coefficient vector is sparse, and its use yields radar images with reduced side lobes compared to the classical l2- norm minimization.
Occlusal Caries: Biological Approach for Its Diagnosis and Management

The management of occlusal caries still remains a major challenge for researchers as well as for general practitioners. The present paper reviews and discusses the most up-to-date knowledge and evidence of the biological principles guiding diagnosis, risk assessment, and management of the caries process on occlusal surfaces. In addition, it considers the whole spectrum of the caries process on occlusal surfaces, ranging from the molecular ecology of occlusal biofilms to the management of deep occlusal caries lesions. Studies using molecular methods with focus on biofilms in relation to occlusal caries should explore the relationship between the function and the structural composition of these biofilms to understand the role of occlusal biofilms in caries development. State-of-the-art measures to evaluate risk for occlusal caries lesion activity, caries incidence, and progression should include the assessment of the occlusal biofilm and the stage of tooth eruption. Careful clinical examination of non-cavitated lesions, including assessment of the lesion activity status, remains the major tool to determine the immediate treatment need and to follow on the non-operative treatment outcome. Even medium occlusal caries lesions in the permanent dentition may be treated by non-invasive fissure sealing. By extending the criteria for non-invasive treatments, traditional restoration of occlusal surfaces can be postponed or even avoided, and the dental health in children and adolescents can be improved. Selective removal (incomplete) to soft dentin in deep carious lesions has greater success rates than stepwise excavation. Selective (complete) removal to firm dentin has a lower success rate due to increased pulp exposure.
Quantum Entanglement and Spin Control in Silicon Nanocrystal

Selective coherence control and electrically mediated exchange coupling of single electron spin between triplet and singlet states using numerically derived optimal control of proton pulses is demonstrated. We obtained spatial confinement below size of the Bohr radius for proton spin chain FWHM. Precise manipulation of individual spins and polarization of electron spin states are analyzed via proton induced emission and controlled population of energy shells in pure 29Si nanocrystal. Entangled quantum states of channeled proton trajectories are mapped in transverse and angular phase space of 29Si axial channel alignment in order to avoid transversal excitations. Proton density and proton energy as impact parameter functions are characterized in single particle density matrix via discretization of diagonal and nearest off-diagonal elements. We combined high field and low densities (1 MeV/92 nm) to create inseparable quantum state by superimposing the hyperpolarizationed proton spin chain with electron spin of 29Si. Quantum discretization of density of states (DOS) was performed by the Monte Carlo simulation method using numerical solutions of proton equations of motion. Distribution of gaussian coherent states is obtained by continuous modulation of individual spin phase and amplitude. Obtained results allow precise engineering and faithful mapping of spin states. This would provide the effective quantum key distribution (QKD) and transmission of quantum information over remote distances between quantum memory centers for scalable quantum communication network. Furthermore, obtained results give insights in application of channeled protons subatomic microscopy as a complete versatile scanning-probe system capable of both quantum engineering of charged particle states and characterization of quantum states below diffraction limit linear and in-depth resolution. PACS numbers: 03.65. Ud, 03.67. Bg, 61.85. +p, 67.30. hj
Variation in estrogen-related genes associated with cardiovascular phenotypes and circulating estradiol, testosterone, and dehydroepiandrosterone sulfate levels.

BACKGROUND Younger age at the onset of menopause and lower circulating levels of estrogen are risk factors for cardiovascular disease. Several studies have detected associations between variations in genes encoding estrogen receptors alpha (ESR1) and beta (ESR2), and enzyme aromatase (CYP19A1), which regulates the estrogen to testosterone ratio, and cardiovascular phenotypes in the Framingham Heart Study. To explore potential mechanisms by which these gene variants may contribute to cardiovascular disease, we tested the hypothesis that the polymorphisms were associated with endogenous steroid hormone levels. METHODS Multiple regression analysis was used to assess the relation between reported polymorphisms and total serum estradiol, testosterone, and dehydroepiandrosterone sulfate levels in 834 men and 687 women who attended the third and fourth Framingham Heart Study examination cycles. RESULTS In men, significant associations were detected between CYP19A1 polymorphisms and estradiol and testosterone levels, and the estradiol to testosterone ratio (P ranges 0.0005-0.01). Specifically, carriers of common haplotype rs700518[G]-(TTTA)(n) [L]-rs726547[C] had higher estradiol levels (5% per copy; P = 0.0004), lower testosterone levels (17% per copy; P = 0.036), and a higher estradiol to testosterone ratio (24% per copy; P < 0.0001) compared with the rs700518[A]-(TTTA)(n) [S]-rs726547[C] carriers. In addition, postmenopausal carriers of the ESR2 (CA)(n) long allele and rs1256031 [C] allele had moderately higher estradiol levels (P < or = 0.03). No significant associations with the ESR1 variants were detected. CONCLUSIONS Our findings suggest that variations in CYP19A1 correlate with steroid hormone levels in men. Knowledge that a specific carrier status may predispose to altered steroid hormone levels may lead to targeted intervention strategies to reduce health risks in genetically susceptible individuals.
A New Reliability Based Channel Allocation Model in Mobile Networks

The data transmission between mobile hosts and base stations (BSs) in Mobile networks are often vulnerable to failure. So, efficient link connectivity, in terms of the services of both base stations and communication channels of the network, is required in wireless mobile networks to achieve highly reliable data transmission. In addition, it is observed that the number of blocked hosts is increased due to insufficient number of channels during heavy load in the network. Under such scenario, the channels are allocated accordingly to offer a reliable communication at any given time. Therefore, a reliability-based channel allocation model with acceptable system performance is proposed as a MOO problem in this paper. Two conflicting parameters known as Resource Reuse factor (RRF) and the number of blocked calls are optimized under reliability constraint in this problem. The solution to such MOO problem is obtained through NSGA-II (Non dominated Sorting Genetic Algorithm). The effectiveness of the proposed model in this work is shown with a set of experimental results. Keywords—Base station, channel, GA, Pareto-optimal, reliability.
Dynamic Test Generation to Find Integer Bugs in x86 Binary Linux Programs

Recently, integer bugs, including integer overflow, width conversion, and signed/unsigned conversion errors, have risen to become a common root cause for serious security vulnerabilities. We introduce new methods for discovering integer bugs using dynamic test generation on x86 binaries, and we describe key design choices in efficient symbolic execution of such programs. We implemented our methods in a prototype tool SmartFuzz, which we use to analyze Linux x86 binary executables. We also created a reporting service, metafuzz.com, to aid in triaging and reporting bugs found by SmartFuzz and the black-box fuzz testing tool zzuf. We report on experiments applying these tools to a range of software applications, including the mplayer media player, the exiv2 image metadata library, and ImageMagick convert. We also report on our experience using SmartFuzz, zzuf, and metafuzz.com to perform testing at scale with the Amazon Elastic Compute Cloud (EC2). To date, the metafuzz.com site has recorded more than 2; 614 test runs, comprising 2; 361; 595 test cases. Our experiments found approximately 77 total distinct bugs in 864 compute hours, costing us an average of $2:24 per bug at current EC2 rates. We quantify the overlap in bugs found by the two tools, and we show that SmartFuzz finds bugs missed by zzuf, including one program where Smart-Fuzz finds bugs but zzuf does not.
Adaptive Multiwavelet-Based Watermarking Through JPW Masking

In this paper, a multibit, multiplicative, spread spectrum watermarking using the discrete multiwavelet (including unbalanced and balanced multiwavelet) transform is presented. Performance improvement with respect to existing algorithm is obtained by means of a new just perceptual weighting (JPW) model. The new model incorporates various masking effects of human visual perception by taking into account the eye's sensitivity to noise changes depending on spatial frequency, luminance and texture of all the image subbands. In contrast to conventional JND threshold model, JPW describing minimum perceptual sensitivity weighting to noise changes, is fitter for nonadditive watermarking. Specifically, watermarking strength is adaptively adjusted to obtain minimum perceptual distortion by employing the JPW model. Correspondingly, an adaptive optimum decoding is derived using a statistic model based on generalized-Gaussian distribution (GGD) for multiwavelet coefficients of the cover-image. Furthermore, the impact of multiwavelet characteristics on proposed watermarking scheme is also analyzed. Finally, the experimental results show that proposed JPW model can improve the quality of the watermarked image and give more robustness of the watermark as compared with a variety of state-of-the-art algorithms.
Gaining Industrial Confidence for the Introduction of Domain-Specific Languages

Domain-Specific Languages (DSLs) receive attention as the possible next abstraction step in programming. Despite the benefits of using DSLs, in the industry there is also some reluctance against their introduction in product development. We address a number of issues that are important to gain industrial confidence for the introduction of DSLs. These include the available tools, the quality of generated code, and the incorporation in the industrial workflow. Our observations are based on an industrial study project at Philips Healthcare, especially concerning the development of a DSL for collision prevention. We also relate our experiences to the literature.
From Tags to Emotions: Ontology-driven Sentimental Analysis in the Social Semantic Web

Affective computing is receiving increasing attention in many sectors, ranging from advertisement to politics. This work, set in a Social Semantic Web framework, presents ArsEmotica, an application software for associating the predominant emotions to artistic resources of a social tagging platform. Our aim is to extract a rich emotional semantics (i.e. not limited to a positive or a negative reception) of tagged resources through an ontology driven approach. This is done by exploiting and combining available computational and sentiment lexicons with an ontology of emotional categories. The information sources we rely upon are the tags by which users annotated resources, that are available through the ArsMeteo platform, and the ontology OntoEmotion, that was enriched by means of our tool with over four hundred Italian emotional words referring to the about eighty-five emotional concepts of the ontology. Tags directly referring to ontological concepts are identified, while potentially affective tags, can be annotated by using the ontology thanks to the spontaneous intervention of the user, in a pure Web 2.0 approach. Finally, the tagged artworks are related with the emerging predominant emotions. Matteo Baldoni Dipartimento di Informatica, Universita degli Studi di Torino e-mail: baldoni@di.unito. it Cristina Baroglio Dipartimento di Informatica, Universita degli Studi di Torino e-mail: baroglio@di.unito. it Viviana Patti Dipartimento di Informatica, Universita degli Studi di Torino e-mail: patti@di.unito. it Paolo Rena Dipartimento di Informatica, Universita degli Studi di Torino e-mail: paolo.rena@gmail.com
Profile of CH 4 IR bands in ice mixtures

We studied the infrared spectral characteristics of frozen methane (CH4) in several astrophysically relevant ice mixtures, as deposited and after ion irradiation. We examined the profile (shape, width and peak position) of the CH 4 bands as a function of initial mixture, irradiation dose and warming up temperature, and compared our results with previously pub- lished laboratory and observational data. Finally, we present a list of spectra that may be used for direct comparison with present and future observations.
An Upper Bound of Singleton Type for Componentwise Products of Linear Codes

We give an upper bound that relates the dimensions of some given number of linear codes, with the minimum distance of their componentwise product. A typical result is as follows: given t linear codes C<sub>i</sub> of parameters [n,k<sub>i</sub>]<sub>q</sub> with full support, one can find codewords c<sub>i</sub> ∈ C<sub>i</sub> such that 1 ≤ w(c<sub>1</sub>*⋯*c<sub>t</sub>) ≤ max(t-1, n+t-(k<sub>1</sub>+⋯+k<sub>t</sub>)).