Miracle-dz/UniFAR-FTUs huggingface dataset:
Incidence and persistence of zoonotic bacterial and protozoan pathogens in a beef cattle feedlot runoff control vegetative treatment system.

Determining the survival of zoonotic pathogens in livestock manure and runoff is critical for understanding the environmental and public health risks associated with these wastes. The occurrence and persistence of the bacterial pathogens Escherichia coli O157:H7 and Campylobacter spp. in a passive beef cattle feedlot runoff control-vegetative treatment system were examined over a 26-mo period. Incidence of the protozoans Cryptosporidium spp. and Giardia spp. was also assessed. The control system utilizes a shallow basin to collect liquid runoff and accumulate eroded solids from the pen surfaces; when an adequate liquid volume is attained, the liquid is discharged from the basin onto a 4.5-ha vegetative treatment area (VTA) of bromegrass which is harvested as hay. Basin discharge transported E. coli O157, Campylobacter spp. , and generic E. coli into the VTA soil, but without additional discharge from the basin, the pathogen prevalences decreased over time. Similarly, the VTA soil concentrations of generic E. coli initially decreased rapidly, but lower residual populations persisted. Isolation of Cryptosporidium oocysts and Giardia cysts from VTA samples was infrequent, indicating differences in sedimentation and/or transport in comparison to bacteria. Isolation of generic E. coli from freshly cut hay from VTA regions that received basin discharge (12 of 30 vs. 1 of 30 control samples) provided evidence for the risk of contamination; however, neither E. coli O157 or Campylobacter spp. were recovered from the hay following baling. This work indicates that the runoff control system is effective for reducing environmental risk by containing and removing pathogens from feedlot runoff.
Symmetry Partition Sort

In this paper, we propose a useful replacement for quicksort‐style utility functions. The replacement is called Symmetry Partition Sort, the principle of which is similar to that of Proportion Extend Sort. The main characteristic of the new algorithm is that it always places partially sorted inputs (used as a basis for proportional extensions) at each end of an array when entering the partitioning routine. This is advantageous in speeding up the processing for partitioning. The library function we developed based on the new algorithm is more attractive than the Psort library function introduced in 2004 because of its simple implementation mechanism, clearer source code, and faster operation with a performance guarantee of O(n log n). Increased robustness and adaptivity also make it highly competitive as a library function. Copyright © 2007 John Wiley & Sons, Ltd.
Massive MU-MIMO downlink TDD systems with linear precoding and downlink pilots

We consider a massive MU-MIMO downlink time-division duplex system where a base station (BS) equipped with many antennas serves several single-antenna users in the same time-frequency resource. We assume that the BS uses linear precoding for the transmission. To reliably decode the signals transmitted from the BS, each user should have an estimate of its channel. In this work, we consider an efficient channel estimation scheme to acquire CSI at each user, called beamforming training scheme. With the beamforming training scheme, the BS precodes the pilot sequences and forwards to all users. Then, based on the received pilots, each user uses minimum mean-square error channel estimation to estimate the effective channel gains. The channel estimation overhead of this scheme does not depend on the number of BS antennas, and is only proportional to the number of users. We then derive a lower bound on the capacity for maximum-ratio transmission and zero-forcing precoding techniques which enables us to evaluate the spectral efficiency taking into account the spectral efficiency loss associated with the transmission of the downlink pilots. Comparing with previous work where each user uses only the statistical channel properties to decode the transmitted signals, we see that the proposed beamforming training scheme is preferable for moderate and low-mobility environments.
Assessing Yellow Fever Risk in the Ecuadorian Amazon

This study reports results of a cross-sectional study based on interviews and seroepidemiological methods to identify risk factors for yellow fever infection among personnel of a military garrison in the Amazonian rainforest. Clinical symptoms and signs observed among yellow fever cases are also described. Humoral immune response to yellow fever, Mayaro, Venezuelan equine encephalitis, Oropouche, and dengue 2 infection was assessed by evaluating IgM and IgG specific antibodies. A yellow fever attack rate of 13% (44/341, with 3 fatal cases) was observed among military personnel. Signs of digestive track bleeding (14.6%) and hematuria (4.9%) were observed among the yellow fever cases. In 32.2% of the cases, we measured high levels of serum glutamic oxaloacetic transaminase and serum glutamic pyruvic transaminase with maximum levels of 6,830 and 3,500, respectively. Signs of bleeding or jaundice were observed in some cases, and high levels of transaminases were seen. The epidemiological and laboratory investigations demonstrated that the military personnel were affected by a yellow fever outbreak. The association between clearing the rainforest and also being at the detachments with yellow fever infection confirms that clearing is the main factor in the jungle model of transmission, which takes place deep in the Amazonian rainforest.
Robust ∞ H Fuzzy Output Feedback Control for Uncertain Discrete-time Nonlinear Systems

In this paper, a generalized non-quadratic Lyapunov function and non-parallel distributed compensation (non-PDC) law are proposed for robust ∞ H fuzzy control of discrete-time uncertain nonlinear systems. The focus is on designing a robust output feedback observer such that the observer error system is robustly asymptotically stable and has a guaranteed ∞ H performance. A new basisdependent idea is introduced to solve the fuzzy observer-based control problem, which is different from the quadratic framework that entails fixed matrices for the entire membership function, or the linearly basis-dependent framework that uses linear convex combinations of s matrices. This idea is realized by carefully selecting the structure of the matrices involved in the products with system matrices. Linear matrix inequality (LMI) conditions are obtained for the existence of observer and based on these the results are casted into a convex optimization problem, which can be readily solved via standard numerical software. The effectiveness and the superiority of the proposed approach are demonstrated by two examples borrowed from the literature.
Orphan Comparisons and Indirect Meta-analysis: A Case Study on Antidepressant Efficacy in Dysthymia Comparing Tricyclic Antidepressants, Selective Serotonin Reuptake Inhibitors, and Monoamine Oxidase Inhibitors by Using General Linear Models

Abstract: Direct comparisons of the efficacy of competing interventions are not always available in the literature. This situation leads to the presence of clinically relevant "orphan comparisons" of therapeutic interventions which have never been compared head-to-head. To overcome this limitation, simple methods for indirect meta-analysis have been suggested. Nevertheless, their results are prone to bias when more than 1 indirect comparison is tested because of the likely duplication of data for some comparisons. In contrast, general linear models can be used to extend simple indirect meta-analysis beyond 1 indirect comparison by fitting to incomplete data using maximum likelihood within the framework of multitreatment comparisons. This study presents a tutorial application of general linear models to the comparative efficacy of several antidepressants in dysthymia (tricyclic antidepressants, selective serotonin reuptake inhibitors, and monoamine oxidase inhibitors. Working with previously published data comparing the efficacy of antidepressants with placebo, it is shown that tricyclic antidepressants and selective serotonin reuptake inhibitors present similar efficacy (odds ratio = 1.19, P = 0.37; relative risk = 1.10, P = 0.24; risk difference = 0.03, P = 0.53), whereas monoamine oxidase inhibitors outperform both tricyclic antidepressants and selective serotonin reuptake inhibitors, at least for some effect scales (odds ratio = 1.57, P = 0.05; relative risk = 1.25, P = 0.05; risk difference = 0.09, P = 0.08). This finding, which is an instance of a relevant orphan comparison and could not be obtained otherwise, could motivate the conduct of clinical trials or focused systematic reviews to support or refute its importance through appropriate head-to-head comparisons.
The pharmacology of the ductus arteriosus.

The ductus arteriosus is a shunt blood vessel of fetal life; it extends between the pulmonary artery and the aorta. It shunts deoxygenated blood from the main pulmonary artery to the descending aorta. Over half of the blood flow in the descending aorta is diverted to the umbilico-placental
Curvature-Based Equation of State for Microemulsion-Phase Behavior

An accurate description of the microemulsion-phase behavior is critical for many industrial applications, including surfactant flooding in enhanced oil recovery (EOR). Recent phase-behavior models have assumed constant-shaped micelles, typically spherical, using net-average curvature (NAC), which is not consistent with scattering and microscopy experiments that suggest changes in shapes of the continuous and discontinuous domains. On the basis of the strong evidence of varying micellar shape, principal micellar curves were used recently to model interfacial tensions (IFTs). Huh's scaling equation (Huh 1979) also was coupled to this IFT model to generate phase-behavior estimates, but without accounting for the micellar shape. In this paper, we present a novel microemulsion-phase-behavior equation of state (EoS) that accounts for changing micellar curvatures under the assumption of a general-prolate spheroidal geometry, instead of through Huh's equation. This new EoS improves phase-behavior-modeling capabilities and eliminates the use of NAC in favor of a more-physical definition of characteristic length. Our new EoS can be used to fit and predict microemulsion-phase behavior irrespective of IFT-data availability. For the cases considered, the new EoS agrees well with experimental data for scans in both salinity and composition. The model also predicts phase-behavior data for a wide range of temperature and pressure, and it is validated against dynamic scattering experiments to show the physical significance of the approach.
Modeling transcription factor complex binding to eukaryotic genomes

Author's declaration: aware of legal responsibility I hereby declare that I have written this dissertation myself and all the contents of the dissertation have been obtained by legal means. Abstract The binding of transcription factors (TFs) to their specific motifs in genomic regulatory elements of eukaryotic organisms is commonly studied in isolation. However , in order to elucidate the mechanisms of transcriptional regulation, it is essential to determine which TFs bind DNA cooperatively as dimers or higher order complexes , and to infer the precise nature of these interactions. So far, only a small number of such cooperative complexes are known. In this thesis, we present a method for predicting cell-type–specific TF-TF dimer-ization on DNA on a large scale. We applied it to DNase I hypersensitivity data, representing the universe of possible TF complexes by their corresponding motif complexes, and analyzed their occurrence at cell-type–specific DNase I hypersensi-tive sites. This way, we predicted 603 highly significant cell-type–specific TF dimers, the vast majority of which are novel. Our predictions included 69% (20/29) of the known dimeric complexes manually compiled from the existing biochemical literature. The predictions were also independently supported by evolutionary conservation , as well as quantitative variation in DNase I digestion patterns. Notably, the known and predicted TF dimers were almost always highly compact and rigidly spaced, suggesting that TFs dimerize in close proximity to their partners, which results in strict constraints on the structure of the DNA-bound complex. Applying our method to ChIP-seq data, we uncovered a general principle governing the structure of TF-TF-DNA ternary complexes, namely that the flexibility of the complex is correlated with, and most likely a consequence of, inter-motif spacing. To allow for a broad adoption of our method, we developed TACO, a software tool that takes as input any genome-wide set of regulatory elements and predicts cell-type–specific TF dimers based on enrichment of motif complexes. This is the first tool of such kind that can accommodate motif complexes composed of overlapping motifs, which are a characteristic feature of many known TF dimers. Our method comprehensively outperforms the existing approaches, iTFs and SpaMo, when benchmarked on a reference set of 29 known dimers. Finally, we propose MOCCA, a novel computational method to identify individual TF binding sites from genome sequence information and cell-type–specific experimental data, such as DNase-seq. We combine the strengths of its predecessors , CENTIPEDE and Wellington, while keeping the number of …
Comparison of the Added Value of Contrast-Enhanced 3D Fluid-Attenuated Inversion Recovery and Magnetization-Prepared Rapid Acquisition of Gradient Echo Sequences in Relation to Conventional Postcontrast T1-Weighted Images for the Evaluation of Leptomeningeal Diseases at 3T

BACKGROUND AND PURPOSE: The usefulness of contrast-enhanced 3D T2-FLAIR MR imaging for the evaluation of leptomeningeal diseases has not been systematically investigated. The purpose of this study was to assess the value added by contrast-enhanced 3D T2-FLAIR and MPRAGE sequences to conventional postcontrast T1-weighted images in the evaluation of leptomeningeal diseases. We also undertook in vitro studies in attempts to understand the consequences of our patient study. MATERIALS AND METHODS: Twelve patients with confirmed leptomeningeal diseases underwent postcontrast T1-weighted, MPRAGE, and 3D T2-FLAIR imaging at 3T. Two radiologists independently assessed the presence of additional information on postcontrast 3D MR images compared with postcontrast T1-weighted images. The effect of different Gd concentrations and flow velocities on the signal intensity on 3D T2-FLAIR images was investigated in vitro. RESULTS: According to both reviewers, 3D T2-FLAIR images yielded significantly more information than did MPRAGE images (P < .05 and P < .01, respectively). In the in vitro study, 3D T2-FLAIR was more highly sensitive to low Gd concentrations and less sensitive to high Gd concentrations than were T1-weighted or MPRAGE sequences. On 3D T2-FLAIR sequences, at a flow velocity exceeding 1.0 cm/s, the signal intensity of blood-mimicking fluids at concentrations of 0 and 0.1 mmol/L was as low as at 1.3 mmol/L. CONCLUSIONS: For the depiction of leptomeningeal diseases, postcontrast 3D T2-FLAIR provides more additional information than postcontrast MPRAGE imaging. The superiority of the 3D T2-FLAIR sequence is associated with its high sensitivity to flow.
Antigen-Specific CD4+ T Cells Recognize Epitopes of Protective Antigen following Vaccination with an Anthrax Vaccine

ABSTRACT Detection of antigen-specific CD4+ T cells is facilitated by the use of fluorescently labeled soluble peptide-major histocompatibility complex (MHC) multimers which mirror the antigen specificity of T-cell receptor recognition. We have used soluble peptide-MHC class II tetramers containing peptides from the protective antigen (PA) of Bacillus anthracis to detect circulating T cells in peripheral blood of subjects vaccinated with an anthrax vaccine. PA-specific HLA class II-restricted T lymphocytes were isolated which displayed both TH1- and TH2-like characteristics, indicating heterogeneity of the lymphocyte lineage within the CD4+ response. Presentation of antigen to these T-cell clones by HLA-matched antigen-presenting cells exposed to the intact PA protein confirmed that the identified epitopes are indeed naturally processed by the human immune system. Specific tetramer-derived T-cell profiling may be useful for monitoring helper CD4+ T-cell responses to anthrax vaccination.
Optimal operator placement for distributed stream processing applications

Data Stream Processing (DSP) applications are widely used to timely extract information from distributed data sources, such as sensing devices, monitoring stations, and social networks. To successfully handle this ever increasing amount of data, recent trends investigate the possibility of exploiting decentralized computational resources (e.g., Fog computing) to define the applications placement. Several placement policies have been proposed in the literature, but they are based on different assumptions and optimization goals and, as such, they are not completely comparable to each other. In this paper we study the placement problem for distributed DSP applications. Our contributions are twofold. We provide a general formulation of the optimal DSP placement (for short, ODP) as an Integer Linear Programming problem which takes explicitly into account the heterogeneity of computing and networking resources and which encompasses - as special cases - the different solutions proposed in the literature. We present an ODP-based scheduler for the Apache Storm DSP framework. This allows us to compare some well-known centralized and decentralized placement solutions. We also extensively analyze the ODP scalability with respect to various parameter settings.
EARLY‐LIFE PREDICTORS OF INTERNALIZING SYMPTOM TRAJECTORIES IN CANADIAN CHILDREN

Previous research examining the development of anxious and depressive symptoms (i.e., internalizing symptoms) from childhood to adolescence has often assumed that trajectories of these symptoms do not vary across individuals. The purpose of this study was to identify distinct trajectories of internalizing symptoms from childhood to adolescence, and to identify risk factors for membership in these trajectory groups. In particular, we sought to identify risk factors associated with early appearing (i.e., child onset) symptoms versus symptoms that increase in adolescence (i.e., adolescent onset).
An Industry Perspective on Current and Future State of the Art in System-on-Chip (SoC) Technology

In fast-moving consumer electronics markets where product lifetimes may be measured in months rather than years, fast time-to-market development of the system-on-chip solutions that lie at the heart of these products has become critical to commercial success. New semiconductor process technologies have the potential to integrate ever greater functional complexity onto realistically priced silicon chips. Yet there still remains a significant design gap between what can theoretically be integrated onto silicon and what can be efficiently designed onto it. In addition, the advent of sub-100-nm process technologies has seen an end to the speed and power consumption scaling that the industry has been used to. This paper examines the current state of the art in SoC technology and identifies some of the challenges that lie ahead if the relentless progress of Moore's Law is to continue fuelling ever more advanced and affordable consumer electronics products. It also looks at the system-in-package solutions that are increasingly being used to achieve levels of functional integration that Moore's Law on its own cannot provide.
Formalizing a design technique for distributed programs

ADL-d is a graphical design technique for parallel and distributed software, in which communication modeling plays a central part. Recently the authors have used formal methods to define ADL-d's semantics. The original objective was to provide well-defined guidelines for future implementations of ADL-d's communication constructs, but, as it turned out, significant feedback resulted to the notation itself. They give an outline of the ADL-d notation and its intuitive semantics. They also introduce the formal semantics, and discuss what impact this formalization has had on the original notation.
Estimation of discrete curvature based on chain-code pairing and digital straightness

Estimation of discrete curvature is a challenging problem, since a mere replacement of functional derivatives by numerical differences fails to produce the desired result. Several algorithms have been proposed so far, which are mostly based on the concepts of real geometry and hence are computationally expensive. The existing measure of k-curvature, though easy to compute, is crippled with some unwanted syndromes arising out of improper consideration of chain codes. Hence, an improved algorithm for estimating k-curvature is proposed, which is marked by its inherent simplicity and computational attractiveness, and produces the expected estimate, whether the concerned point has an extreme (high or low) curvature or the concerned segment has a constant or changing curvature. Examples and experimental results demonstrate the fitness and effectiveness of the proposed technique for digital curves of arbitrary shapes.
Mineralisation density of human mandibular bone: quantitative backscattered electron image analysis

This study examined the tissue level mineralisation density distribution in mandibles from 88 adult humans. Mandibles (19–96 y) were sectioned vertically in midline (MID), mental foramen (MF), and third molar (M3) regions. Surgical fragments from M3 were obtained from individuals aged 16–38 y. All specimens were cleaned, embedded in PMMA, micromilled and examined by digital 20 kV backscattered electron (BSE) stereology. Quantitation was based on rescaling image histograms to the signal range between a monobrominated (0) and a monoiodinated (255) dimethacrylate resin standard. Mineralisation density increased with age (r=0.70; P<0.0001): the mean for 39 individuals aged between 16 and 50 y was significantly lower (P<0.0001) than for 35 individuals over 51 y (mean (±S.E.M.): 158.20 (1.63) and 174.71 (1.27) normalised grey level units respectively). There was good correlation in mean mineralisation density between different sites in the same mandible, but MID was significantly less highly mineralised than the other sites: MID 173.90, MF 177.34, M3 177.11 (P<0.002 and 0.01 for MF and M3 respectively; paired t test), as was the alveolar bone density when compared with the bone of the inferior cortex (e.g. MID: 171.13 (1.53) and 174.46 (1.14) P<0.0001). No sex difference was found. Partially dentate mandibles generally had regions of higher mineralisation than fully dentate and edentulous mandibles. The lowest density bone occurred at the alveolar crest anteriorly and superolingually at M3, matching sites of net resorption following tooth loss. Highest densities were found inferolingually at MID, inferiorly at MF and buccally at M3, matching the sites thought to experience the highest functional strains. This stresses the importance that local factors may have in the remodelling of the edentulous mandible. Morphology showed that there is a preponderance of highly mineralised cement lines, and of packets containing dead, mineralised, osteocytes.