Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Various Campylobacter-Specific Quantitative PCR (qPCR) Assays for Detection and Enumeration of Campylobacteraceae in Irrigation Water and Wastewater via a Miniaturized Most-Probable-Number–qPCR Assay

ABSTRACT Campylobacter spp. are the leading cause of bacterial gastroenteritis worldwide, and water is increasingly seen as a risk factor in transmission. Here we describe a most-probable-number (MPN)–quantitative PCR (qPCR) assay in which water samples are centrifuged and aliquoted into microtiter plates and the bacteria are enumerated by qPCR. We observed that commonly used Campylobacter molecular assays produced vastly different detection rates. In irrigation water samples, detection rates varied depending upon the PCR assay and culture method used, as follows: 0% by the de Boer Lv1-16S qPCR assay, 2.5% by the Van Dyke 16S and Jensen glyA qPCR assays, and 75% by the Linton 16S endpoint PCR when cultured at 37°C. Primer/probe specificity was the major confounder, with Arcobacter spp. routinely yielding false-positive results. The primers and PCR conditions described by Van Dyke et al. (M. I. Van Dyke, V. K. Morton, N. L. McLellan, and P. M. Huck, J Appl Microbiol 109:1053–1066, 2010, http://dx.doi.org/10.1111/j.1365-2672.2010.04730.x) proved to be the most sensitive and specific for Campylobacter detection in water. Campylobacter occurrence in irrigation water was found to be very low (<2 MPN/300 ml) when this Campylobacter-specific qPCR was used, with the most commonly detected species being C. jejuni, C. coli, and C. lari. Campylobacters in raw sewage were present at ∼102/100 ml, with incubation at 42°C required for reducing microbial growth competition from arcobacters. Overall, when Campylobacter prevalence and/or concentration in water is reported using molecular methods, considerable validation is recommended when adapting methods largely developed for clinical applications. Furthermore, combining MPN methods with molecular biology-based detection algorithms allows for the detection and quantification of Campylobacter spp. in environmental samples and is potentially suited to quantitative microbial risk assessment for improved public health disease prevention related to food and water exposures. IMPORTANCE The results of this study demonstrate the importance of assay validation upon data interpretation of environmental monitoring for Campylobacter when using molecular biology-based assays. Previous studies describing Campylobacter prevalence in Canada utilized primers that we have determined to be nonspecific due to their cross-amplification of Arcobacter spp. As such, Campylobacter prevalence may have been vastly overestimated in other studies. Additionally, the development of a quantitative assay described in this study will allow accurate determination of Campylobacter concentrations in environmental water samples, allowing more informed decisions to be made about water usage based on quantitative microbial risk assessment.
Navigation of the autonomous mobile robot using laser range finder based on the non quantity map

In this research, we propose a method of mobile robot navigation system with a simple environmental data expression, graph-map. In general, autonomous mobile robot has to estimate its position. Usually it is necessary for a robot to correct cumulative error with landmark. For this purpose, it requires complex preparation before the robot being navigated. Our navigation system does not need special equipment and only requires easy environmental map. In this paper, we verified the effectiveness of the system by the experiment, using a robot.
Optical and thin film properties of mixed oxides deposited by pulsed reactive magnetron sputtering

Reactive magnetron sputtering was used to deposit optical thin films. In order to obtain high deposition rates, metallic targets were used. For the creation of mixed oxides bipolar pulsed sputtering was applied to two different targets. A new process control setup was developed to monitor the oxidation state of both targets individually. Two different elemental targets are co-sputtered in oxygen-argon atmosphere within the lambda-probe stabilized transition mode. The composition is controlled by optical emission spectroscopy. Thus different mixtures are accessible without changing target material. Varied mixtures in the system hafnia-silica have been prepared. The optical properties (refractive indices, absorption, surface roughness, density) as well as mechanical behavior (film stress, hardness) of the mixtures are compared to pure oxide materials. By mixing the oxides thin film quality can be improved beyond the properties of the single materials.
Genome-wide analysis of transcription factors during somatic embryogenesis in banana (Musa spp.) cv. Grand Naine

Transcription factors BABY BOOM (BBM), WUSCHEL (WUS), BSD, LEAFY COTYLEDON (LEC), LEAFY COTYLEDON LIKE (LIL), VIVIPAROUS1 (VP1), CUP SHAPED COTYLEDONS (CUC), BOLITA (BOL), and AGAMOUS LIKE (AGL) play a crucial role in somatic embryogenesis. In this study, we identified eighteen genes of these nine transcription factors families from the banana genome database. All genes were analyzed for their structural features, subcellular, and chromosomal localization. Protein sequence analysis indicated the presence of characteristic conserved domains in these transcription factors. Phylogenetic analysis revealed close evolutionary relationship among most transcription factors of various monocots. The expression patterns of eighteen genes in embryogenic callus containing somatic embryos (precisely isolated by Laser Capture Microdissection), non-embryogenic callus, and cell suspension cultures of banana cultivar Grand Naine were analyzed. The application of 2, 4-dichlorophenoxyacetic acid (2, 4-D) in the callus induction medium enhanced the expression of MaBBM1, MaBBM2, MaWUS2, and MaVP1 in the embryogenic callus. It suggested 2, 4-D acts as an inducer for the expression of these genes. The higher expression of MaBBM2 and MaWUS2 in embryogenic cell suspension (ECS) as compared to non-embryogenic cells suspension (NECS), suggested that these genes may play a crucial role in banana somatic embryogenesis. MaVP1 showed higher expression in both ECS and NECS, whereas MaLEC2 expression was significantly higher in NECS. It suggests that MaLEC2 has a role in the development of non-embryogenic cells. We postulate that MaBBM2 and MaWUS2 can be served as promising molecular markers for the embryogencity in banana.
Carbon Replicas of Porous Concrete Obtained by Chemical Vapor Deposition—Some Aspects of the Synthesis Mechanism

In this contribution, the template assisted synthesis of porous carbons by chemical vapor deposition in porous concrete templates has been described for the first time. Porous concrete made templates can be obtained in almost any geometrical shape and are therefore attractive templates to prepare porous carbon monoliths. The carbon deposition process in porous concrete follows a three-stage-course consisting in an initial period, a period of fast carbon deposition and a period of slow carbon deposition. The carbon growth within the template pores occurs obviously plug-like from the inner to the outer sphere. Any continuous covering of the template pore walls by carbon could not be observed. In difference to porous concrete, the carbon deposition in silica gel is strongly accompanied by mass transfer limitations. For porous concrete, such strong effect has not been observed obviously due to its hierarchical pore system. The template materials have been loaded with carbon by chemical vapor deposition in a flow reactor. The process of the template pore filling has been characterized by the time dependence of the template mass gain. The materials have been characterized by means of X-ray tomography and nitrogen adsorption at 77 K, respectively.
Learning Rules from Multiple Instance Data: Issues and Algorithms

In a multiple-instance representation, each learning example is represented by a “bag” of fixed-length “feature vectors”. Such a representation, lying somewhere between propositional and first-order representation, offers a tradeoff between the two. This paper proposes a generic extension to propositional rule learners to handle multiple-instance data. It describes NAIVE-RIPPERMI, an implementation of this extension on the rule learning algorithm RIPPER. It then explains several pitfalls encountered by this naive extension during induction. It goes on to describe algorithmic modifications and a new multipleinstance coverage measure which are shown to avoid these pitfalls. Experimental results show the benefits of this approach for solving propositionalized relational problems in terms of speed and accuracy. keywords: Multiple-instance learning problem, rule learning, propositionalization, relational learning, mutagenesis learning task
Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics.
Family Violence and Football: The Effect of Unexpected Emotional Cues on Violent Behavior

We study the link between family violence and the emotional cues associated with wins and losses by professional football teams. We hypothesize that the risk of violence is affected by the “gain-loss” utility of game outcomes around a rationally expected reference point. Our empirical analysis uses police reports of violent incidents on Sundays during the professional football season. Controlling for the pregame point spread and the size of the local viewing audience, we find that upset losses (defeats when the home team was predicted to win by four or more points) lead to a 10% increase in the rate of at-home violence by men against their wives and girlfriends. In contrast, losses when the game was expected to be close have small and insignificant effects. Upset wins (victories when the home team was predicted to lose) also have little impact on violence, consistent with asymmetry in the gain-loss utility function. The rise in violence after an upset loss is concentrated in a narrow time window near the end of the game and is larger for more important games. We find no evidence for reference point updating based on the halftime score.
Spatial Heterogeneity of Autoinducer Regulation Systems

Autoinducer signals enable coordinated behaviour of bacterial populations, a phenomenon originally described as quorum sensing. Autoinducer systems are often controlled by environmental substances as nutrients or secondary metabolites (signals) from neighbouring organisms. In cell aggregates and biofilms gradients of signals and environmental substances emerge. Mathematical modelling is used to analyse the functioning of the system. We find that the autoinducer regulation network generates spatially heterogeneous behaviour, up to a kind of multicellularity-like division of work, especially under nutrient-controlled conditions. A hybrid push/pull concept is proposed to explain the ecological function. The analysis allows to explain hitherto seemingly contradicting experimental findings.
Closed form frequency domain expressions for best achievable accuracy of spectral density estimation

The paper addresses the issue of quantifying the frequency domain accuracy of ARMA spectral estimates as dictated by the Cramer-Rao lower bound (CRLB). Classical work in this area has led to expressions that are asymptotically exact as both data length and model order tend to infinity, although they are commonly used in finite model order and finite data length settings as approximations. More recent work has established quantifications which, for AR models, are exact for finite model order. By employing new analysis methods based on rational orthonormal parameterisations, together with the ideas of reproducing kernel Hilbert spaces, the paper develops quantifications that extend the previous work by being exact for finite model order in all of the AR, MA and ARMA system cases. These quantifications, via their explicit dependence on poles and zeros of the underlying spectral factor, reveal certain fundamental aspects of the accuracy achievable by spectral estimates of ARMA processes.
Generation of pure single-photon states in commercial photonic-crystal fibers on telecommunication frequencies

A single-photon source is an essential part of many quantum information devices. The specific characteristics of such sources determine possibilities for their application [1]. Currently, the most promising trends are the following: 1) quantum memory devices and quantum calculation algorithms for searching in unordered databases; 2) quantum repeaters for building scalable quantum networks with high security; 3) applications for quantum metrology and quantum informatics. Spontaneous parametric down-conversion (SPDC) and spontaneous four-wave mixing (SFWM) are currently the most promising and advanced methods to generate single photons. In fact, SPDC and SFWM methods imply that there is the possibility of obtaining a two-photon state of light. The main advantages of these methods include the following: high stability of obtained states in time; the potential to generate spectrally limited pulses at room temperature; the possibility to adjust optical wavelength and spectrum width as well as the minute influence of multi-photon states. Basic disadvantages of the methods include the random nature of single-photon generation, which leads to the probability of obtaining a two-photon state, and a correlation between signal and idler photons. The correlation is caused by idiosyncracies of the two-photon generation process. Thus, mixed single-photon states are obtained for SPDS and SFWM methods. This means that there is a spatial, polarization and spectral correlation between the pair of photons. The elimination of all these types of correlation is necessary to obtain a “clean” single-photon state. A fundamental difficulty is the elimination of the spectral correlation between the signal and idler photons. This can be overcome by the proper selection of parameters for the nonlinear medium and the laser’s pump, such that the special matching conditions for the pump photon, signal and idler photons can be obtained. That is the essence of the problem for creating a single-photon source. Single-mode structures have several advantages over other media: generation in single spatial mode; suppression of lateral spatial modes; and high consistency with fiber-optical networks. Photonic crystal fibers (PCF) have the potential to provide the conditions with spectrally limited laser pulses [1, 2]. It should also be noted that the efficiency of single-photon states is strongly dependent upon the parameters of the nonlinear medium and pump pulses. This article provides the analysis of clean single-photon generation based on the SFWM method and femtosecond spectrally scanning laser for the commercial PCFs.
Evaluation of moving object segmentation comparing 6D-vision and monocular motion constraints

Detecting moving objects is a very important aspect of driver assistance systems (DAS). This paper handles this issue by using a vision based system mounted within the vehicle. The pipeline for both a stereoscopic and monocular approach are covered. Both approaches use image sequences and compare moving feature points over time. This sparse information is then segmented using the optimal graph-cut algorithm, by also incorporating the grey-scale images. This paper then evaluates and contrasts the two approaches to identify the accuracy and robustness of each approach. The two methods both work in real-time on normal PC hardware (Quad Core CPU).
Path planning for mobile vehicles within dynamic worlds using statistical data

This paper proposes a new path planning approach based on statistical information, like the occupancy probability of partly or completely dynamic obstacles and/or the statistical flow of dynamic obstacles. With this new approach it is possible to integrate the expected behavior of moving obstacles into the preplanning of paths without knowing the individual movement of these dynamic obstacles. As the preplanned paths coincide with the average movement pattern in the environment, the runtime planning is simplified. The authors propose an appropriate world model to represent the necessary statistical data, which can be obtained automatically. In addition, a path planning approach, suited for point-shaped and arbitrary-shaped vehicles, is sketched. These paths integrate geometrical detours to fit the planned movements into the statistical movement pattern of the dynamic obstacles. <<ETX>>
Structural And Magnetic Properties Of Mn-Doped SiC

Structural and magnetic properties of manganese (Mn)‐doped silicon carbide (SiC) are investigated. Two Mn‐doping methods of ‘thermal diffusion’ and ‘ion implantation’ are employed using 4H (hexagonal)‐ and 3C (cubic)‐SiC homoepitaxial wafer as the host material. In the case of 4H‐SiC doped using the thermal diffusion method, the extended X‐ray absorption fine structure (EXAFS) analysis suggests that most Mn atoms are incorporated on the interstitial site in the 4H‐SiC lattice, and a paramagnetic behavior is observed in the magnetization measurement. For the Mn‐implanted 3C‐SiC, on the other hand, we detect ferromagnetic behaviors and a Curie temperature is found to reach to 245 K.
Conventional Freezing, Straw, and Open-Pulled Straw Vitrification of Mouse Two Pronuclear (2-PN) Stage Embryos

Little is known on the cryopreservation of mouse pronuclear (PN) stage embryos. In the present experiment the mouse 2-PN stage embryos were cryopreserved by conventional freezing, straw, or open-pulled straw (OPS) vitrificaiton methods. The conventional freezing solution was 1.5 mol/L ethylene glycol (EG), and vitrification solutions were EFS30 (30% EG, Ficoll, and sucrose), EFS40 (40% EG, Ficoll, and sucrose), EDFS30 (15% EG, 15%dimethyl sulfoxide [DMSO], Ficoll, and sucrose), or EDFS40 (20% EG, 20%DMSO, Ficoll, and sucrose). The blastocyst rate of 2-PN stage embryos cryopreserved by conventional method (30.4%) was lower than those vitrified by straw method with EDFS (56.9% to 69.1%), by OPS method (66.0% to 85.7%), and that of control (80.8%) (P < 0.05). With a given vitrificaiton solution EFS30, EFS40, EDFS30, or EDFS40, the blastocyst rate of embryos vitrified by the OPS method (66.7%, 66.0%, 85.7%, or 76.9%) was higher than that of those vitrified by the straw method (46.8%, 43.8%, 69.1%, or 56.9%) (P < 0.05). When mouse 2-PN-stage embryos were vitrified with EDFS30 by straw or OPS method, the highest blastocyst rate was achieved (69.1% or 85.7%) and was similar to that of the control, respectively. The embryos transfer results revealed that the full-term development of blastocysts derived from 2-PN stage embryos vitrified by OPS method with EDFS30 (19.9%) was similar to that of the control (23.5%), and higher than that of those cryopreserved by conventional freezing (9.3%) (P < 0.05). The present research demonstrates that the OPS method, especially with EDFS30, is more effective in cryopreserving mouse 2-PN embryos.
Curve evolution implementation of the Mumford-Shah functional for image segmentation, denoising, interpolation, and magnification

In this work, we first address the problem of simultaneous image segmentation and smoothing by approaching the Mumford-Shah paradigm from a curve evolution perspective. In particular, we let a set of deformable contours define the boundaries between regions in an image where we model the data via piecewise smooth functions and employ a gradient flow to evolve these contours. Each gradient step involves solving an optimal estimation problem for the data within each region, connecting curve evolution and the Mumford-Shah functional with the theory of boundary-value stochastic processes. The resulting active contour model offers a tractable implementation of the original Mumford-Shah model (i.e., without resorting to elliptic approximations which have traditionally been favored for greater ease in implementation) to simultaneously segment and smoothly reconstruct the data within a given image in a coupled manner. Various implementations of this algorithm are introduced to increase its speed of convergence. We also outline a hierarchical implementation of this algorithm to handle important image features such as triple points and other multiple junctions. Next, by generalizing the data fidelity term of the original Mumford-Shah functional to incorporate a spatially varying penalty, we extend our method to problems in which data quality varies across the image and to images in which sets of pixel measurements are missing. This more general model leads us to a novel PDE-based approach for simultaneous image magnification, segmentation, and smoothing, thereby extending the traditional applications of the Mumford-Shah functional which only considers simultaneous segmentation and smoothing.