Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Regions Conserved in Lineage II Escherichia coli O157:H7 Strains

ABSTRACT Populations of the food- and waterborne pathogen Escherichia coli O157:H7 are comprised of two major lineages. Recent studies have shown that specific genotypes within these lineages differ substantially in the frequencies with which they are associated with human clinical disease. While the nucleotide sequences of the genomes of lineage I strains E. coli O157 Sakai and EDL9333 have been determined, much less is known about the genomes of lineage II strains. In this study, suppression subtractive hybridization (SSH) was used to identify genomic features that define lineage II populations. Three SSH experiments were performed, yielding 1,085 genomic fragments consisting of 811 contigs. Bacteriophage sequences were identified in 11.3% of the contigs, 9% showed insertions and 2.3% deletions with respect to E. coli O157:H7 Sakai, and 23.2% did not have significant identity to annotated sequences in GenBank. In order to test for the presence of these novel loci in lineage I and II strains, 27 PCR primer sets were designed based on sequences from these contigs. All but two of these PCR targets were found in the majority (51.9% to 100%) of 27 lineage II strains but in no more than one (<6%) of the 17 lineage I strains. Several of these linage II-related fragments contain insertions/deletions that may play an important role in virulence. These lineage II-related loci were also shown to be useful markers for genotyping of E. coli O157:H7 strains isolated from human and animal sources.
Trusted Terminal Design of Distributed Environment

In the distributed environment, one important security issue is how to apply further security control to the object that is released to other terminals. The appearance of trusted computing technology has provided an effective solution for this issue in the distributed environment. At the same time, through combining trusted computing technology with the strong isolation and sharing characteristic provided by virtual machine technology has further increased the security and the flexibility of distributed access control. Therefore, this paper uses trusted computing technology to improve the security of the terminal in carrying out the distributed access control, designs a trusted terminal architecture that bases on the trusted computing technology and the virtual machine technology as well as a enhanced mode that suits in distributed access control, and on this basis, analyzes the security of system design.
Quantization of Discrete Probability Distributions

We study the problem of quantization of discrete probability distributions, arising in universal coding, as well as other applications. We show, that in many situations this problem can be reduced to the covering problem for the unit simplex. This setting yields precise asymptotic characterization in the high-rate regime. We also describe a simple and asymptotically optimal algorithm for solving this problem. Performance of this algorithm is studied and compared with several known solutions.
Delay sensitive routing in PNNI-based ATM networks

We propose an enhanced path selection algorithm for ATM networks that implement the private network-node interface (PNNI) v1.0 standard. Our enhancement stems from the fact that we consider delay in determining the appropriate route for an ATM call. The paper presents two new path selection algorithms based on two different delay accumulation methods, namely the simple (additive) method, and the asymptotic method. The delay based path selection algorithm is achieved by adopting a constrained shortest path algorithm which optimizes two metrics simultaneously in contrast to Dijkstra's algorithm that optimizes only one. The execution times of these two algorithms are also compared and quantified based on the results of an experimental study. Using an analytical model we demonstrate the performance gain by adopting a delay-based routing procedure in simple network configurations in terms of the number of crankbacks. Our network configurations and traffic loading patterns showed that up to 36% less crankbacks can be obtained when adopting a delay-sensitive routing scheme as opposed to a simple shortest-path algorithm.
PIKACHU: How to Rebalance Load in Optimizing MapReduce On Heterogeneous Clusters

For power, cost, and pricing reasons, datacenters are evolving towards heterogeneous hardware. However, MapReduce implementations, which power a representative class of datacenter applications, were originally designed for homogeneous clusters and performed poorly on heterogeneous clusters. The natural solution, rebalancing load among the reducers running on heterogeneous nodes has been explored in Tarazu, but shown to be only mildly effective. In this paper, we revisit the key design challenge in this important optimization for MapReduce on heterogeneous clusters and make three contributions. (1) We show that Tarazu estimates the target load distribution too early into MapReduce job execution, which results in the rebalanced load far from the optimal. (2) We articulate the delicate tradeoff between the estimation accuracy versus wasted work from delayed load adjustment, and propose a load rebalancing scheme that strikes a balance between the tradeoff. (3)We implement our design in the PIKACHU task scheduler, which outperforms Hadoop by up to 42% and Tarazu by up to 23%.
American Urban High School Reform: Talent Development - The Philadelphia Story

America's urban public schools' success or failure will ultimately reflect the will and commitment of educators and policy makers to address historical injustices and educational segregation that mirrors that of society. Urban public schools are a microcosm of American society, which is validated by research, observations, or/and participation in the process of educating twenty-first century urban youth at all levels of schooling. As both an extension and complement to the perspectives on urban education presented in an earlier issue of this journal by Fuhrman (2002), one can posit that large, comprehensive urban public high schools present an extraordinary set of unique challenges to achieving a measure of success in America's educational system.
Acquisition of Body and Object Representation Based on Motion Learning and Planning Framework

Vision information processing is important for robots that act in human-interactive environments. In this paper, we propose to acquire visual representation of robot body and object that is suitable for motion learning in a bottom-up manner. An advantage of the proposed framework is that it does not require specific hand-coding depending on the visual properties of objects or the robot. A subtraction technique and SOM are used to compose the state space based on the image with extracted robot body and objects. Motion of the robot is planned based on reachable set. The task of moving an object to a target position is divided into two phases, one to reach a position that is suitable for starting pushing motion and the other to push the object to the target. The proposed method is verified by experiment of pushing manipulation of an object with a robot arm.
Improved Algorithms for Elliptic Curve Arithmetic in Gf(2 N ) Improved Algorithms for Elliptic Curve Arithmetic in Gf (2 N )

This paper describes three contributions for eecient implementation of elliptic curve cryptosystems in GF(2 n). The rst is a new method for doubling an elliptic curve point, which is simpler to implement than the fastest known method, due to Schroeppel, and which favors sparse elliptic curve coeecients. The second is a generalized and improved version of the Guajardo and Paar's formulas for computing repeated doubling points. The third contribution consists of a new kind of projective coordinates that provides the fastest known arithmetic on elliptic curves. The algorithms resulting from this new formulation lead to a running time improvement for computing a scalar multiplication of about 17% over previous projective coordinate methods.
Physicochemical Property Space of Hepatobiliary Transport and Computational Models for Predicting Rat Biliary Excretion

Biliary excretion (BE) is a major elimination pathway, and its prediction is particularly important for optimization of systemic and/or target-site exposure of new molecular entities. The objective is to characterize the physicochemical space associated with hepatobiliary transport and rat BE and to develop in silico models. BE of 123 in-house compounds was obtained using the bile-duct cannulated rat model. Human and rat hepatic uptake transporters (hOATP1B1, hOATP1B3, hOATP2B1, and rOatp1b2) substrates (n = 183) were identified using transfected cells. Furthermore, the datasets were extended by adding BE of 163 compounds and 97 organic anion transporting polypeptide (OATP) substrates from the literature. Approximately 60% of compounds showing percentage of BE (%BE) ≥ 10 are anions, with mean BE of anions (36%) more than 3-fold higher than that of nonacids (11%). Compounds with %BE ≥ 10 are found to have high molecular mass, large polar surface area, more rotatable bonds, and high H-bond count, whereas the lipophilicity and passive membrane permeability are lower compared with compounds with %BE < 10. According to statistical analysis and principal component analysis, hOATPs and rOatp1b2 substrates showed physicochemical characteristics that were similar to those of the %BE ≥ 10 dataset. We further build categorical in silico models to predict rat BE, and the models (gradient boosting machine and scoring function) developed showed 80% predictability in identifying the rat BE bins (%BE ≥ 10 or < 10). In conclusion, the significant overlap of the property space of OATP substrates and rat BE suggests a predominant role of sinusoidal uptake transporters in biliary elimination. Categorical in silico models to predict rat BE were developed, and successful predictions were achieved.
Comparative Genomic Analysis of Chlamydia trachomatis Oculotropic and Genitotropic Strains

ABSTRACT Chlamydia trachomatis infection is an important cause of preventable blindness and sexually transmitted disease (STD) in humans. C. trachomatis exists as multiple serovariants that exhibit distinct organotropism for the eye or urogenital tract. We previously reported tissue-tropic correlations with the presence or absence of a functional tryptophan synthase and a putative GTPase-inactivating domain of the chlamydial toxin gene. This suggested that these genes may be the primary factors responsible for chlamydial disease organotropism. To test this hypothesis, the genome of an oculotropic trachoma isolate (A/HAR-13) was sequenced and compared to the genome of a genitotropic (D/UW-3) isolate. Remarkably, the genomes share 99.6% identity, supporting the conclusion that a functional tryptophan synthase enzyme and toxin might be the principal virulence factors underlying disease organotropism. Tarp (translocated actin-recruiting phosphoprotein) was identified to have variable numbers of repeat units within the N and C portions of the protein. A correlation exists between lymphogranuloma venereum serovars and the number of N-terminal repeats. Single-nucleotide polymorphism (SNP) analysis between the two genomes highlighted the minimal genetic variation. A disproportionate number of SNPs were observed within some members of the polymorphic membrane protein (pmp) autotransporter gene family that corresponded to predicted T-cell epitopes that bind HLA class I and II alleles. These results implicate Pmps as novel immune targets, which could advance future chlamydial vaccine strategies. Lastly, a novel target for PCR diagnostics was discovered that can discriminate between ocular and genital strains. This discovery will enhance epidemiological investigations in nations where both trachoma and chlamydial STD are endemic.
Context Availability , Contextual Constraint and Abstractness

A constraint-based theory of abstractness was investigated according to which abstractness of entities is a function of (i) perceptual observability and (ii) characteristics of contextual constraints. Participants performed ratings of context availability, imagery, and abstractness for 36 nouns that varied in abstractness and familiarity. The ratings were used to compare the predictions of abstractness ratings by context availability, dual coding theory and the constraint-based approach outlined in this paper. We found that only constraints explain variation of perceived abstractness for abstract concepts, whereas context availability and imagery are good predictors of the dichotomous distinction of concrete-abstract, and of variations of concreteness for concrete concepts only. A second study shows that introspection-based constraints are most critical for abstractness ratings. Implications are discussed.
Anesthetic Effects of a Mixture of Medetomidine, Midazolam and Butorphanol in Two Strains of Mice

The combination of ketamine and xylazine is a widely used anesthetic for laboratory animals. However, due to an abuse problem in Japan, ketamine has been specified as a narcotic since 2007. Instead of using ketamine, Kawai et al. reported an injectable formula with an equivalent effect to the mixture of ketamine and xylazine [11]. The mixture of 0.3 mg/kg body weight (b.w.) medetomidine (Med.), 4.0 mg/kg b.w. midazoram (Mid.), and 5.0 mg/kg b.w. butorphanol (But.) produced an anesthetic duration of around 40 min in outbred ICR mice. However, the anesthetic effect of the mixture for inbred mice strains remains unknown. Therefore, we examined anesthetic effects of the mixture of Med., Mid. , and But. in the BALB/c and C57BL/6J strains. After intraperitoneal injection into mice, right front paw, left hind paw, and tail pinch reflexes as well as corneal and righting reflexes were observed. Every 5 min, we scored each reflex category as 0 for reaction or 1 for no reaction. As long as the total score was at least 4 out of 5, we considered the mixture as putting a mouse in a surgical anesthetic state. The mixture produced an anesthetic duration of more than 45 min in both strains of mice. These results indicate that the mixture of Med., Mid. , and But. can be a useful and effective anesthesia for the BALB/c and C57BL/6J strains of inbred mice as well as outbred ICR mice.
Dynamic effects of a step‐wise increase in thermal conductivity and viscosity in the lowermost mantle

We present numerical models of mantle convection incorporating changes in viscosity and thermal conductivity at depth. Increasing the viscosity and/or thermal conductivity by a factor of 5 at depths below 2000 km increases the size and stability of thermal upwellings. Decreasing the thermal conductivity beneath 2000 km, in contrast, has comparatively little effect on thermal upwellings. Increases in viscosity and/or thermal conductivity close to a factor of 5 beneath 2000 km may tend to counteract the tendency of the post‐perovskite phase transition to decrease the size and stability of thermal upwellings. We also find that varying viscosity and thermal conductivity beneath 2000 km affects basal heat fluxes and mantle geotherms, which should have strong implications for the stability of the post‐perovskite phase change near the core‐mantle boundary (CMB).
Patients’ Experiences with and Attitudes towards a Diabetes Patient Web Portal

Objective A diabetes patient web portal allows patients to access their personal health record and may improve diabetes outcomes; however, patients’ adoption is slow. We aimed to get insight into patients’ experiences with a web portal to understand how the portal is being used, how patients perceive the content of the portal and to assess whether redesign of the portal might be needed. Materials and Methods A survey among 1500 patients with type 1 and type 2 diabetes with a login to a patient portal. Setting: 62 primary care practices and one outpatient hospital clinic, using a combined patient portal. We compared patients who requested a login but never used it or once (‘early quitters’) with patients who used it at least two times (‘persistent users’). Results 632 patients (42.1%) returned the questionnaire. Their mean age was 59.7 years, 63.1% was male and 81.8% had type 2 diabetes. 413 (65.3%) people were persistent users and 34.7% early quitters. In the multivariable analysis, insulin use (OR2.07; 95%CI[1.18–3.62]), experiencing more frequently hyperglycemic episodes (OR1.30;95%CI[1.14–1.49]) and better diabetes knowledge (OR1.02, 95%CI[1.01–1.03]) do increase the odds of being a persistent user. Persistent users perceived the usefulness of the patient portal significantly more favorable. However, they also more decisively declared that the patient portal is not helpful in supporting life style changes. Early quitters felt significantly more items not applicable in their situation compared to persistent users. Both persistent users (69.8%) and early quitters (58.8%) would prefer a reminder function for scheduled visits. About 60% of both groups wanted information about medication and side-effects in their portal. Conclusions The diabetes patient web portal might be improved significantly by taking into account the patients’ experiences and attitudes. We propose creating separate portals for patients on insulin or not.
Investigating Body Image Satisfaction among the Different Levels of Turkish Tennis Players as a Function of Gender

The study designed to investigate the role of playing tennis on Turkish university students’ body image satisfaction as a function of gender. The present study also aimed to find out differences in body image satisfaction scores between different levels of tennis players. Data were obtained from 152 (77 men, 75 women) different levels of tennis players who are volunteer undergraduate university students from Middle East Technical University (METU) in Ankara, Turkey. In this study, data were gathered by administering two instruments, namely, Turkish version of Body Image Satisfaction Questionnaire and Demographic Information Form which was developed to collect personal information. A two-way ANOVA and 7X2 ANOVA were performed to analyze data. According to results there was no significant effect for gender on body image satisfaction scores. However, it can be stated that there was a significant difference between body image satisfaction scores and participants’ tennis ability levels.
A progressive flow auction approach for low-cost on-demand P2P media streaming

Realizing on-demand media streaming in a Peer-to-Peer (P2P) fashion is more challenging than in the case of live media streaming, since only peers with close-by media play progresses may help each other in obtaining the media content. The situation is further complicated if we wish to pursue low link cost in the transmission. In this paper, we present a new algorithmic perspective towards on-demand P2P streaming protocol design. While previous approaches employ streaming trees or passive neighbour reconciliation for media content distribution, we instead coordinate the streaming session as an auction where each peer participates locally by bidding for and selling media flows encoded with network coding. We show that this auction approach is promising in achieving low-cost on-demand streaming in a scalable fashion. It is amenable to asynchronous, distributed, and light-weight implementations, and is flexible enough to provide support for random-seek and pause functionalities.
Web-based Augmented Reality applied to upper limb simulation

Research in Virtual and Augmented Reality applied to biomedicine has been deeply investigated in recent years. The application to upper limb prosthesis is a wide field. Traditionally virtual upper limb prosthesis is a desktop application, used for training in rehabilitation centers. Thus, this article reports on the use of Augmented Reality (AR) in a web-application. The objective here is to create a home based training environment.
Nrc Publications Archive (nparc) Archives Des Publications Du Cnrc (nparc) Identification of Similarities among Ms/ms Spectra from Human Identification of Similarities among Ms/ms Spectra from Human Brain

L'accès à ce site Web et l'utilisation de son contenu sont assujettis aux conditions présentées dans le site Access and use of this website and the material on it are subject to the Terms and Conditions set forth at Abstract Human brain samples are used for an investigation of three spectra similarities that are useful within machine learning techniques such as supervised nearest neighbour approaches. Such bioinformatic pattern recognition of biological data leads to an MS/MS based methodology to both potentially increase peptide identification and to identify post-translational modifications without theoretical database search.
Carbon nanotube-anandamide complex exhibits sustained protective effects in an in vitro model of stroke

Introduction: The therapeutic potential of anandamide (AEA) for the neurological disorders may be negatively affected by its short half-life or poor solubility. The superior properties of carbon nanotubes (CNTs) for controlled drug delivery, prompted us to design AEA-CNTs complex and assess its effect in in vitro model of ischemic stroke. Methods: In this experimental study, a multi-walled CNTs (MWCNTs)-AEA complex was prepared using amino-functionalized COOH-MWCNTs and characterized by Fourier transform infrared spectroscopy and transmission electron microscopy. PC12 cells in the presence of AEA (0.5, 1, 2 μg/ml), acid- or amine-modified MWCNTs, or MWCNTs-AEA complex (2, 5, 8 μg/ml) were exposed to 1 and 3 h oxygen-glucose deprivation (OGD) followed by 24 h re-oxygenation. In vitro cytotoxicity and oxidative stress were evaluated using three-way ANOVA. Results: AEA immobilization on the aminated MWCNTs was confirmed. OGD significantly reduced cell viability (P 0.05). MWCNTs-AEA complex was effective at both time points (MDA and GSH: P<0.01, P<0.001, SOD: P<0.05, P<0.01, P<0.001). This nanostructure was more effective than AEA following longer exposure periods to OGD insult (P<0.05, P<0.01, P<0.001).
Synchronization versus staggering of price changes in Brazil

While several models assume that price changes are staggered over time, both theory and empirical evidence are ambiguous. This work attempts to identify the behavior of price setters by analyzing a large Brazilian data set. It is found an evidence of staggering, but the more aggregated the data are, the closer the price changes are to perfect synchronization. The Brazilian economy also presents a heterogeneous frequency and synchronization of price adjustments among product categories, which also vary with the inflation rate.