Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiological characteristics and molecular typing of Salmonella enterica serovar Typhi during a waterborne outbreak in Eastern Anatolia

Abstract In this study, we aimed to study the molecular and epidemiological characteristics of Salmonella enterica serovar Typhi (S. typhi) outbreak in Eastern Anatolia. Six hundred and thirty-seven patients from the same county with clinical diagnosis of typhoid fever were investigated with conventional methods from stool, urine and blood specimens. Antibiotic susceptibility tests and identifications were performed for positive specimens. Clonal relationships between the isolates were investigated using pulsed field gel electrophoresis (PFGE) method. A questionnaire was completed for the water consumption habits of patients. Of 91 culture positive specimens, 76 were blood, 13 were stool and 2 were urine. The isolates were resistant to ampicillin, ampicillin/sulbactam, chloramphenicol, cefuroxime, amikacin, gentamicin and trimethoprim–sulfamethoxazole. Although there was a single band difference in some isolates, PFGE results indicated that this was an outbreak caused by single strain according to the Tenover criteria. This outbreak thought to be associated with the consumption of tap water contaminated with sewage represents a breakdown of the basic public health and civil engineering infrastructure. Appropriate public health measures should be taken in order to avoid such outbreaks in the future.
Overexpression of HER2 (erbB2) in Human Breast Epithelial Cells Unmasks Transforming Growth Factor β-induced Cell Motility*

We have examined overexpression of the human epidermal growth factor receptor 2 (HER2) to determine if it modifies the anti-proliferative effect of transforming growth factor (TGF)-β against MCF-10A human mammary epithelial cells. Exogenous TGF-β inhibited cell proliferation and induced Smad-dependent transcriptional reporter activity in both MCF-10A/HER2 and MCF-10A/vector control cells. Ligand-induced reporter activity was 7-fold higher in HER2-overexpressing cells. In wound closure and transwell assays, TGF-β induced motility of HER2-transduced, but not control cells. The HER2-blocking antibody trastuzumab (Herceptin) prevented TGF-β-induced cell motility. Expression of a constitutively active TGF-β type I receptor (ALK5T204D) induced motility of MCF-10A/HER2 but not MCF-10A/vector cells. TGF-β-induced motility was blocked by coincubation with either the phosphatidylinositol 3-kinase inhibitor LY294002, the mitogen-activated protein kinase (MAPK) inhibitor U0126, the p38 MAPK inhibitor SB202190, and an integrin β1 blocking antibody. Rac1 activity was higher in HER2-overexpressing cells, where both Rac1 and Pak1 proteins were constitutively associated with HER2. Both exogenous TGF-β and transduction with constitutively active ALK5 enhanced this association. TGF-β induced actin stress fibers as well as lamellipodia within the leading edge of wounds. Herceptin blocked basal and TGF-β-stimulated Rac1 activity but did not repress TGF-β-stimulated transcriptional reporter activity. These data suggest that 1) overexpression of HER2 in nontumorigenic mammary epithelial is permissive for the ability of TGF-β to induce cell motility and Rac1 activity, and 2) HER2 and TGF-β signaling cooperate in the induction of cellular events associated with tumor progression.
Face tracking with an Adaptive Adaboost-based Particle Filter

A novel algorithm, termed a Boosted Adaptive Particle Filter (AAPF), for integrated face detection and face tracking is proposed. The proposed algorithm is based on the synthesis of an adaptive particle filtering algorithm and the AdaBoost face detection algorithm. An Adaptive Particle Filter (AAPF), based on a new sampling technique, is proposed. The APF is shown to yield more accurate estimates of the proposal distribution than the standard Particle Filter thus enabling more accurate tracking in video sequences. In the proposed AAPF algorithm, the AdaBoost algorithm is used to detect faces in input image frames, the APF algorithm incorporate the detection result of AdaBoost algorithm to improve the proposal distribution of the particles. Experimental results show that the proposed AAPF algorithm provides a means for robust face detection and accurate face tracking under various tracking scenarios.
Nanoscale measurements of the mechanical properties of lipid bilayers

Lipid bilayers form the basis of the membranes that serve as a barrier between a cell and its physiological environment. Their physical properties make them ideally suited for this role: they are extremely soft with respect to bending but essentially incompressible under lateral tension, and they are quite permeable to water but essentially impermeable to ions which allows the rapid establishment of the osmotic gradients. The function of membrane proteins, which are vital for tasks ranging from signal transduction to energy conversion, depends on their interactions with the lipid environment. Because of the complexity of natural membranes, model systems consisting of simpler lipid mixtures have become indispensable tools in the study of membrane biophysics. The objective of the work reported here is to develop a deeper understanding of the underlying physics of lipid bilayers through nanoscale measurements of the mechanical properties of mixed lipid systems including cholesterol, a key ingredient of cell membranes. Atomic force microscopy (AFM) has been used extensively to measure the topographical and elastic properties of supported lipid bilayers displaying complex phase behaviour and containing mixtures of important PC, PE lipids and cholesterol. Phase transformations have been investigated varying the membrane temperature, and the effects of cholesterol in controlling membrane fluidity, phase, and energetics have been studied. Elastic modulus measurements were correlated with phase behaviour observations. To aid in the nanoscale probing of lipid bilayers, AFM probes with a high aspect ratio and tip radii of $sim$4~nm were fabricated and characterised. These probes were used to investigate the phase boundary in binary and ternary lipid systems, leading to the discovery of a raised region at the boundary which has implications for the localisation of reconstituted proteins as well as the role of natural domains or lipid rafts. The electrical properties of the probes were examined to assess their potential application for combined structural and electrical measurements in liquid. A novel technique was developed to aid in the study of the physical properties of lipid bilayers. Membrane budding was induced above microfabricated substrates through osmotic pressure. Modification of the adhesion energy of the bilayer through biotin-avidin linking was successful in modulating budding behaviour of liquid disordered bilayers. The free energy of the system was modelled to allow quantitative information to be extracted from the data.
Malate-Mediated Carbon Catabolite Repression in Bacillus subtilis Involves the HPrK/CcpA Pathway

ABSTRACT Most organisms can choose their preferred carbon source from a mixture of nutrients. This process is called carbon catabolite repression. The Gram-positive bacterium Bacillus subtilis uses glucose as the preferred source of carbon and energy. Glucose-mediated catabolite repression is caused by binding of the CcpA transcription factor to the promoter regions of catabolic operons. CcpA binds DNA upon interaction with its cofactors HPr(Ser-P) and Crh(Ser-P). The formation of the cofactors is catalyzed by the metabolite-activated HPr kinase/phosphorylase. Recently, it has been shown that malate is a second preferred carbon source for B. subtilis that also causes catabolite repression. In this work, we addressed the mechanism by which malate causes catabolite repression. Genetic analyses revealed that malate-dependent catabolite repression requires CcpA and its cofactors. Moreover, we demonstrate that HPr(Ser-P) is present in malate-grown cells and that CcpA and HPr interact in vivo in the presence of glucose or malate but not in the absence of a repressing carbon source. The formation of the cofactor HPr(Ser-P) could be attributed to the concentrations of ATP and fructose 1,6-bisphosphate in cells growing with malate. Both metabolites are available at concentrations that are sufficient to stimulate HPr kinase activity. The adaptation of cells to environmental changes requires dynamic metabolic and regulatory adjustments. The repression strength of target promoters was similar to that observed in steady-state growth conditions, although it took somewhat longer to reach the second steady-state of expression when cells were shifted to malate.
A Cartesian Adaptive Level Set Method for Two-Phase Flows

Abstract : Simulations of flows involving free surfaces have become ubiquitous in the literature. The evolution of both simulation methods and computer speed have allowed the investigation of many problems of increasing complexity and engineering relevance. For 2D simulations, it is reasonably common to use grid resolutions of 512 x 512 or larger. See for example the 2D planar breaking wave simulations of Chen et al. (1999), or the axisymmetric drop breakup simulations of Han and TryggvasonCorp Source (1999a, 1999b). Many such free surface problems are fundamentally three dimensional and the absence of three-dimensional effects such as the pinch-off of stretched filaments by surface tension makes it difficult to make valid physical conclusions or use 2D results to develop models. Achieving similar grid resolution in 3D, however, is outside the computational reach of most research centers.
A new global river network database for macroscale hydrologic modeling

Coarse‐resolution (upscaled) river networks are critical inputs for runoff routing in macroscale hydrologic models. Recently, Wu et al. (2011) developed a hierarchical dominant river tracing (DRT) algorithm for automated extraction and spatial upscaling of river networks using fine‐scale hydrography inputs. We applied the DRT algorithms using combined HydroSHEDS and HYDRO1k global fine‐scale hydrography inputs and produced a new series of upscaled global river network data at multiple (1/16° to 2°) spatial resolutions. The new upscaled results are internally consistent and congruent with the baseline fine‐scale inputs and should facilitate improved regional to global scale hydrologic simulations.
THE RELATIVE BIOLOGICAL VALUE OF DL-METHIONINE AND METHIONINE HYDROXY ANALOGUE IN CHICK DIETS.

Abstract ALMOST all of the data presented in the literature indicate equal utilization of the d - and l - isomers of methionine. This subject was recently reviewed by Marrett et al. (1964). The relative utilization of dl -methionine and Methionine Hydroxy Analogue (MHA) is much more controversial than that of the activity of the d - and l - forms of methionine. Bird (1952) found MHA to be equal to dl -methionine in supporting performance of chicks when fed on an equimolar basis. Gordon and Sizer (1955) reported that MHA had equal activity to l -methionine and was more active than dl or d -methionine when added on an equimolar basis to a sulfur amino acid deficient chick diet. Sullivan and Bird (1957) compared MHA and dl -methionine on an equimolar basis in 12 and 14% protein chick diets and found the analogue failed by a wide margin to support performance equivalent to dl -methionine. The addition of either urea…
Evaluation of Large-Eddy Simulations via Observations of Nocturnal Marine Stratocumulus

Data from the first research flight (RF01) of the second Dynamics and Chemistry of Marine Stratocumulus (DYCOMS-II) field study are used to evaluate the fidelity with which large-eddy simulations (LESs) can represent the turbulent structure of stratocumulus-topped boundary layers. The initial data and forcings for this case placed it in an interesting part of parameter space, near the boundary where cloud-top mixing is thought to render the cloud layer unstable on the one hand, or tending toward a decoupled structure on the other hand. The basis of this evaluation consists of sixteen 4-h simulations from 10 modeling centers over grids whose vertical spacing wa s5ma t thecloud-top interface and whose horizontal spacing was 35 m. Extensive sensitivity studies of both the configuration of the case and the numerical setup also enhanced the analysis. Overall it was found that (i) if efforts are made to reduce spurious mixing at cloud top, either by refining the vertical grid or limiting the effects of the subgrid model in this region, then the observed turbulent and thermodynamic structure of the layer can be reproduced with some fidelity; (ii) the base, or native configuration of most simulations greatly overestimated mixing at cloud top, tending toward a decoupled layer in which cloud liquid water path and turbulent intensities were grossly underestimated; (iii) the sensitivity of the simulations to the representation of mixing at cloud top is, to a certain extent, amplified by particulars of this case. Overall the results suggest that the use of LESs to map out the behavior of the stratocumulus-topped boundary layer in this interesting region of parameter space requires a more compelling representation of processes at cloud top. In the absence of significant leaps in the understanding of subgrid-scale (SGS) physics, such a representation can only be achieved by a significant refinement in resolution—a refinement that, while conceivable given existing resources, is probably still beyond the reach of most centers.
Approches formelles de mise en oeuvre de politiques de contrôle d'accès pour des applications basées sur une architecture orientée services. (Formal approaches for enforcing access control policies in service oriented architecture based applications)

La securite des systemes d'information devient un enjeu preoccupant pour les organisations tant publiques que privees, car de tels systemes sont pour la plupart universellement accessibles a partir de navigateurs Web. Parmi tous les aspects lies a la securite des systemes d'information, c'est celui de la securite fonctionnelle qui est etudie dans cette these sous l'angle de la mise en œuvre de politiques de controle d'acces dans une architecture orientee services. L'element de base de la solution proposee est un modele generique qui introduit les concepts essentiels pour la conception de gestionnaires d'execution de politiques de controle d'acces et qui etablit une separation nette entre le systeme d'information et les mecanismes de controle d'acces. L'instanciation de ce modele conduit a un cadre d'applications qui comporte, entre autres, un filtre de controle d'acces dynamique. Cette these presente egalement deux methodes systematiques d'implementation de ce filtre a partir de politiques ecrites en ASTD, une notation graphique formelle basee sur les statecharts augmentes d'operateurs d'une algebre de processus. La notation ASTD est plus expressive que la norme RBAC et ses extensions, la solution actuellement privilegiee dans l'industrie. La premiere methode repose sur une transformation de politiques de controle d'acces, instanciees a partir de patrons de base exprimes en ASTD, en des processus BPEL. La deuxieme methode est basee sur une interpretation de specifications ASTD par des processus BPEL. Dans les deux cas, les processus BPEL s'executent dans un moteur d'execution BPEL et interagissent avec le systeme d'information. Ces deux methodes permettent une implementation automatique d'un cadre d'applications a partir de la specification de depart. Finalement, un prototype a ete realise pour chacune des deux methodes afin de montrer leur faisabilite au niveau fonctionnel et de comparer leurs performances au niveau systeme
Muscle denervation promotes opening of the permeability transition pore and increases the expression of cyclophilin D

Loss of neural input to skeletal muscle fibres induces atrophy and degeneration with evidence of mitochondria‐mediated cell death. However, the effect of denervation on the permeability transition pore (PTP), a mitochondrial protein complex implicated in cell death, is uncertain. In the present study, the impact of 21 days of denervation on the sensitivity of the PTP to Ca2+‐induced opening was studied in isolated muscle mitochondria. Muscle denervation increased the sensitivity to Ca2+‐induced opening of the PTP, as indicated by a significant decrease in calcium retention capacity (CRC: 111 ± 12 versus 475 ± 33 nmol (mg protein)−1 for denervated and sham, respectively). This phenomenon was partly attributable to in vivo mitochondrial and whole muscle Ca2+ overload. Cyclosporin A, which inhibits PTP opening by binding to cyclophilin D (CypD), was significantly more potent in mitochondria from denervated muscle and restored CRC to the level observed in mitochondria from sham‐operated muscles. In contrast, the CypD independent inhibitor trifluoperazine was equally effective at inhibiting PTP opening in sham and denervated animals and did not correct the difference in CRC between groups. This phenomenon was associated with a significant increase in the content of the PTP regulating protein CypD relative to several mitochondrial marker proteins. Together, these results indicate that Ca2+ overload in vivo and an altered expression of CypD could predispose mitochondria to permeability transition in denervated muscles.
The Existence of $\omega$-Chains for Transitive Mixed Linear Relations and Its Applications

We show that it is decidable whether a transitive mixed linear relation has an ω-chain. Using this result, we study a number of liveness verification problems for generalized timed automata within a unified framework. More precisely, we prove that (1) the mixed linear liveness problem for a timed automaton with dense clocks, reversal-bounded counters, and a free counter is decidable, and (2) the Presburger liveness problem for a timed automaton with discrete clocks, reversal-bounded counters, and a pushdown stack is decidable.
Use of Health Care Services for Psychological Distress by Immigrants in an Urban Multicultural Milieu

Objective: Research in the United States tends to attribute low rates of use of mental health services by immigrants to economic barriers. The purpose of our study was to examine this issue in the context of Canada's universal health care system. Methods: A survey of the catchment area of a comprehensive clinic in Montreal interviewed random samples of 924 Canadian-born individuals and 776 immigrants born in the Caribbean (n = 264), Vietnam (n = 234), or the Philippines (n = 278) to assess their health care use for somatic symptoms, psychological distress, and recent life events. Results: Overall rates of use of medical services in the past year were similar in immigrant (78.5%) and nonimmigrant (76.5%) groups. Rates of use of health care services for psychological distress were significantly lower among immigrants (5.5% compared with 14.7%, P < 0.001). This difference was attributable both to a lower rate of use of specialty mental health services by immigrants (2.5% compared with 11.7%, P < 0.001) and to differential use of medical services for psychological distress (3.5% compared with 5.8%, P = 0.02). When level of psychological distress was controlled, Vietnamese and Filipino immigrants were one-third as likely as Canadian-born residents to make use of mental health services. The lower rate of use by immigrants could not be explained by differences in sociodemographics, somatic or psychological symptoms, length of stay in Canada, or use of alternative sources of help. Conclusion: Immigrant status is associated with lower rates of use of mental health services, even with universal health insurance. This lower rate of use likely reflects cultural and linguistic barriers to care.
Comparative Study of Outlier Detection Algorithms

As the dimension of the data is increasing day by day, outlier detection is emerging as one of the active area of research. Finding of the outliers from large data sets is the main problem. Outlier is considered as the pattern that is different from the rest of the patterns present in the data set. The detection of the outlier in the data set is an important process as it helps in acquiring the useful information that further helps in the data analysis. Various algorithms have been proposed till date for the detection of the outliers. This paper covers a study of various outlier detection algorithms like Statistical based outlier detection, Depth based outlier detection, Clustering based technique, Density based outlier detection etc. Comparison study of these outlier detection methods is done to find out which of the outlier detection algorithms are more applicable on high dimensional data.
Seleção Dinâmica de Objetos de Aprendizagem Baseados no Padrão SCORM no Ambiente Moodle

Este artigo descreve um modelo para selecao de Objetos de Aprendizagem (OA) em cursos a distância, baseado no paradigma de Sistemas Multiagentes, com o intuito de facilitar o uso de OAs de forma adaptativa em ambientes virtuais. O framework proposto estende o conceito de Objetos Inteligentes de Aprendizagem, atraves da utilizacao de uma arquitetura de agentes BDI, permitindo a comunicacao com os recursos instrucionais que constituem o OA de acordo com o padrao SCORM. Os elementos obtidos durante a interacao do aluno com o objeto sao usados no processo de raciocinio dos agentes, possibilitando o desenvolvimento de experiencias de aprendizagem dinâmicas aprimoradas. O LMS Moodle foi usado para validar o modelo proposto.
Laparoscopic resection of submucosal tumor on posterior wall of gastric fundus.

AIM Laparoscopic resection of tumors on the posterior wall of gastric fundus, especially when they are next to the esophagocardiac junction (ECJ), is both difficult and time-consuming. Furthermore, it can lead to inadvertent esophagus stenosis and injury to the spleen. In order to overcome these difficulties, laparoscopically extraluminal resection of gastric fundus was designed to manage submucosal tumors located on the posterior wall of gastric fundus and next to ECJ. METHODS From January 2001 to September 2003, laparoscopically extraluminal resection of gastric fundus was successfully carried out on 15 patients. There were 11 males and 4 females with an average age of 58 years (range, 38 to 78 years). The mean diameter of the tumors was 4.8 cm. The distance of the tumor border from ECJ was about 1.5-2.5 cm. The four-portal operation procedures were as follows: localization of the tumor, dissection of the omentum, mobilization of the gastric fundus and the upper polar of spleen, exposure of ECJ, and resection of the gastric fundus with Endo GIA. RESULTS The laparoscopic operation time averaged (66.2+/-10.4) min, the average amount of bleeding was (89.4+/-21.7) mL. The mean post-operative hospital stay was (5.3+/-1.1) d. Within 36 h post-operation, 73.3% of all the patients recovered their gastrointestinal function and began to eat something and to walk. In all the operations, no apparent tumor focus was left and no complication or conversion to open surgery occurred. CONCLUSION Our newly designed procedure, laparoscopically extraluminal resection of the gastric fundus, can avoid contamination of the abdominal cavity, injury to the spleen and esophageal stenosis. The procedure seems to be both safe and effective.
Head Injuries and Helmet Laws in Australia and New Zealand

%HI for accidents not involving motorvehicles Fig 2. Percentages of NZ cyclists wearing helmets (%helmet) & with head injury (%HI, from Robinson 2001) Head Injuries and Helmet Laws in Australia and New Zealand Victoria was the first Australian State to introduce bicycle helmet laws, on 1 July 1990. Over the next few years, all other States passed similar legislation, because of threats by the Federal Government to reduce road funding if States failed to comply with a 10-point road safety program including bicycle helmet laws. New Zealand (NZ) also introduced a bicycle helmet law in January 1994. [2] [3] [4] [5]