Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing an outbreak of vancomycin-resistant enterococci using hidden Markov models

Background. Antibiotic-resistant nosocomial pathogens can arise in epidemic clusters or sporadically. Genotyping is commonly used to distinguish epidemic from sporadic vancomycin-resistant enterococci (VRE). We compare this to a statistical method to determine the transmission characteristics of VRE. Methods and findings. A structured continuous-time hidden Markov model (HMM) was developed. The hidden states were the number of VRE-colonized patients (both detected and undetected). The input for this study was weekly point-prevalence data; 157 weeks of VRE prevalence. We estimated two parameters: one to quantify the cross-transmission of VRE and the other to quantify the level of VRE colonization from sporadic sources. We compared the results to those obtained by concomitant genotyping and phenotyping. We estimated that 89% of transmissions were due to ward cross-transmission while 11% were sporadic. Genotyping found that 90% had identical glycopeptide resistance genes and 84% were identical or nearly identical on pulsed-field gel electrophoresis (PFGE). There was some evidence, based on model selection criteria, that the cross-transmission parameter changed throughout the study period. The model that allowed for a change in transmission just prior to the outbreak and again at the peak of the outbreak was superior to other models. This model estimated that cross-transmission increased at week 120 and declined after week 135, coinciding with environmental decontamination. Significance. We found that HMMs can be applied to serial prevalence data to estimate the characteristics of acquisition of nosocomial pathogens and distinguish between epidemic and sporadic acquisition. This model was able to estimate transmission parameters despite imperfect detection of the organism. The results of this model were validated against PFGE and glycopeptide resistance genotype data and produced very similar results. Additionally, HMMs can provide information about unobserved events such as undetected colonization.
Linear threaded algebraic space-time constellations

Space-time (ST) constellations that are linear over the field of complex numbers are considered. Relevant design criteria for these constellations are summarized and some fundamental limits to their achievable performances are established. The fundamental tradeoff between rate and diversity is investigated under different constraints on the peak power, receiver complexity, and rate scaling with the signal-to-noise ratio (SNR). A new family of constellations that achieve optimal or near-optimal performance with respect to the different criteria is presented. The proposed constellations belong to the threaded algebraic ST (TAST) signaling framework, and achieve the optimal minimum squared Euclidean distance and the optimal delay. For systems with one receive antenna, these constellations also achieve the optimal peak-to-average power ratio for quadrature amplitude modulation (QAM) and phase-shift keying (PSK) input constellations, as well as optimal coding gains in certain scenarios. The framework is general for any number of transmit and receive antennas and allows for realizing the optimal tradeoff between rate and diversity under different constraints. Simulation results demonstrate the performance gains offered by the proposed designs in average power and peak power limited systems.
Metabolite and Lipid Profiling of Biobank Plasma Samples Collected Prior to Onset of Rheumatoid Arthritis

Objective The early diagnosis of rheumatoid arthritis (RA) is desirable to install treatment to prevent disease progression and joint destruction. Autoantibodies and immunological markers pre-date the onset of symptoms by years albeit not all patients will present these factors, even at disease onset. Additional biomarkers would be of high value to improve early diagnosis and understanding of the process, leading to disease development. Methods Plasma samples donated before the onset of RA were identified in the Biobank of Northern Sweden, a collection within national health survey programs. Thirty samples from pre-symptomatic individuals and nineteen from controls were subjected to liquid chromatography-mass spectrometry (LCMS) metabolite and lipid profiling. Lipid and metabolite profiles discriminating samples from pre-symptomatic individuals from controls were identified after univariate and multivariate OPLS-DA based analyses. Results The OPLS-DA models including pre-symptomatic individuals and controls identified profiles differentiating between the groups that was characterized by lower levels of acyl-carnitines and fatty acids, with higher levels of lysophospatidylcholines (LPCs) and metabolites from tryptophan metabolism in pre-symptomatic individuals compared with controls. Lipid profiling showed that the majority of phospholipids and sphingomyelins were at higher levels in pre-symptomatic individuals in comparison with controls. Conclusions Our LCMS based approach demonstrated that there are changes in small molecule and lipid profiles detectable in plasma samples collected from the pre-symptomatic individuals who subsequently developed RA, which point to an up-regulation of levels of lysophospatidylcholines, and of tryptophan metabolism, perturbation of fatty acid beta-oxidation and increased oxidative stress in pre-symptomatic individuals’ years before onset of symptoms.
Fake News: Evidence from Financial Markets

We examine fake news in financial markets, a laboratory that offers an opportunity to quantify its direct and indirect impact. We study three experimental settings. The first is a unique dataset of unambiguous fake articles on financial news platforms prosecuted by the Securities and Exchange Commission. The second applies a linguistic algorithm to detect deception in expression on the universe of articles on these platforms, using the first sample to validate and calibrate the algorithm. The third is an event study exploiting the SEC investigation as a public shock to investor awareness of fake news. We find that trading activity and price volatility rise with fake news about the firms mentioned in the articles. Following public revelation of the existence of fake news, we find an immediate decrease in reaction to all news, including legitimate news, on these platforms, consistent with indirect spillover effects of fake news conjectured by theory. These findings are predominant among small firms with high retail ownership, and are stronger for more circulated articles. Our results are consistent with economic theory on media bias and its application to fake news.
An Empirical Evaluation of Security Indicators in Mobile Web Browsers

Mobile browsers are increasingly being relied upon to perform security sensitive operations. Like their desktop counterparts, these applications can enable SSL/TLS to provide strong security guarantees for communications over the web. However, the drastic reduction in screen size and the accompanying reorganization of screen real-estate significantly changes the use and consistency of the security indicators and certificate information that alert users of site identity and the presence of strong cryptographic algorithms. In this paper, we perform the first measurement of the state of critical security indicators in mobile browsers. We evaluate ten mobile and two tablet browsers, representing over 90% of the market share, against the recommended guidelines for web user interface to convey security set forth by the World Wide Web Consortium (W3C). While desktop browsers follow the majority of guidelines, our analysis shows that mobile browsers fall significantly short. We also observe notable inconsistencies across mobile browsers when such mechanisms actually are implemented. We show where and how these failures on mobile browsers eliminate clues previously designed for, and still present in, desktop browsers to detect attacks such as phishing and man-in-the-middle. Finally, we offer advice on where current standards are unclear or incomplete.
Time-frequency representations of the sternocleidomastoid muscle electromyographic signal recorded with concentric ring electrodes

The use of non-invasive methods for the study of respiratory muscle signals can provide clinical information for the evaluation of the respiratory muscle function. The aim of this study was to evaluate time-frequency characteristics of the electrical activity of the sternocleidomastoid muscle recorded superficially by means of concentric ring electrodes (CREs) in a bipolar configuration. The CREs enhance the spatial resolution, attenuate interferences, as the cardiac activity, and also simplify the orientation problem associated to the electrode location. Five healthy subjects underwent a respiratory load test in which an inspiratory load was imposed during the inspiratory phase. During the test, the electromyographic signal of the sternocleidomastoid muscle (EMGsc) and the inspiratory mouth pressure (Pmouth) were acquired. Time-frequency characteristics of the EMGsc signal were analyzed by means of eight time-frequency representations (TFRs): the spectrogram (SPEC), the Morlet scalogram (SCAL), the Wigner-Ville distribution (WVD), the Choi-Williams distribution (CHWD), two generalized exponential distributions (GED1 and GED2), the Born-Jordan distribution (BJD) and the Cone-Kernel distribution (CKD). The instantaneous central frequency of the EMGsc showed an increasing behavior during the inspiratory cycle and with the increase of the inspiratory load. The bilinear TFRs (WVD, CHWD, GEDs and BJD) were less sensitive to cardiac activity interference than classical TFRs (SPEC and SCAL). The GED2 was the TFR that shown the best results for the characterization of the instantaneous central frequency of the EMGsc.
Graded Functional Activation in the Visuospatial System with the Amount of Task Demand

Two studies examined how the amount and type of computational demand are related to fMRI-measured activation in three bilateral cortical regions involved in the Shepard-Metzler (1971) mental-rotation paradigm. The amount of demand for the computation of visuospatial coordinates was manipulated by presenting mental rotation problems with increasing angular disparity (0, 40, 80, or 120). Activation in both the left and right intraparietal sulcal regions increased linearly with angular disparity in two separate studies. Activation also occurred in the fusiform gyrus and inferior temporal regions, regions that are primarily associated with the processes of object and object-part identification. By contrast, the demand for object recognition and rotation processes was relatively low, and the demand for executing saccades was high in a control condition that required making a systematic visual scan of two grids. The grid-scanning condition resulted in relatively less activation in the parietal and inferior temporal regions but considerable activation in frontal areas that are associated with planning and executing saccades, including the precentral gyrus and sulcus into the posterior middle frontal region. These data suggest that the amount of activation in the various cortical regions that support visuospatial processing is related to the amount, as well as to the type, of computational demand.
Genetic analysis to determine the nature and magnitude of genetic variances and heritability estimates in maize (Zea mays L.)

The F1 hybrids along with the parents were evaluated in field for genetic analysis to determine the nature and magnitude of genetic variances and heritability estimates a in maize (Zea mays L.) in 2012 using RCBD with three replications. Results analysis of variance showed, based upon the results of tests, simple genetic model was fully adequate for analyzing the data set for all traits except plant height. It was observed that a and b components which are due to additive and dominant gene effects, respectively, were significant for all studied characteristics. Estimates of genetic components of variance according to Hayman (1954) revealed that the value of D is less than H1 and H2 indicating that dominant genetic effects for traits such as the days taken to tasseling, plant height, HI and grain yield per plant were more important than additive genetic effects. Thus the selection in later generations may be more effective. However, the values of H1 and H2 were < D denoting that genes showing dominance effect for 100 grain weight, number of rows per ear and number of kernels per row were less important than additive genes. The 100 grain weight, number of rows per ear and number of kernels per row were under the control of additive type of gene action and so the selection in early generations will be more effective for these traits which is additively controlled.
Optimal throughput-delay scaling in wireless networks - part I: the fluid model

Gupta and Kumar (2000) introduced a random model to study throughput scaling in a wireless network with static nodes, and showed that the throughput per source-destination pair is Theta(1/radic(nlogn)). Grossglauser and Tse (2001) showed that when nodes are mobile it is possible to have a constant throughput scaling per source-destination pair. In most applications, delay is also a key metric of network performance. It is expected that high throughput is achieved at the cost of high delay and that one can be improved at the cost of the other. The focus of this paper is on studying this tradeoff for wireless networks in a general framework. Optimal throughput-delay scaling laws for static and mobile wireless networks are established. For static networks, it is shown that the optimal throughput-delay tradeoff is given by D(n)=Theta(nT(n)), where T(n) and D(n) are the throughput and delay scaling, respectively. For mobile networks, a simple proof of the throughput scaling of Theta(1) for the Grossglauser-Tse scheme is given and the associated delay scaling is shown to be Theta(nlogn). The optimal throughput-delay tradeoff for mobile networks is also established. To capture physical movement in the real world, a random-walk (RW) model for node mobility is assumed. It is shown that for throughput of Oscr(1/radic(nlogn)), which can also be achieved in static networks, the throughput-delay tradeoff is the same as in static networks, i.e., D(n)=Theta(nT(n)). Surprisingly, for almost any throughput of a higher order, the delay is shown to be Theta(nlogn), which is the delay for throughput of Theta(1). Our result, thus, suggests that the use of mobility to increase throughput, even slightly, in real-world networks would necessitate an abrupt and very large increase in delay.
Dynamic transcriptional profiling provides insights into tuberous root development in Rehmannia glutinosa

Rehmannia glutinosa, an herb of the Scrophulariaceae family, is widely cultivated in the Northern part of China. The tuberous root has well-known medicinal properties; however, yield and quality are threatened by abiotic and biotic stresses. Understanding the molecular process of tuberous root development may help identify novel targets for its control. In the present study, we used Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome that is relevant to tuberous root development. We then conducted RNA-seq quantification analysis to determine gene expression profiles of the adventitious root (AR), thickening adventitious root (TAR), and the developing tuberous root (DTR). Expression profiling identified a total of 6794 differentially expressed unigenes during root development. Bioinformatics analysis and gene expression profiling revealed changes in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone biosynthesis during root development. Moreover, we identified and allocated putative functions to the genes involved in tuberous root development, including genes related to major carbohydrate metabolism, hormone metabolism, and transcription regulation. The present study provides the initial description of gene expression profiles of AR, TAR, and DTR, which facilitates identification of genes of interest. Moreover, our work provides insights into the molecular mechanisms underlying tuberous root development and may assist in the design and development of improved breeding schemes for different R. glutinosa varieties through genetic manipulation.
A Finite Element Study of Micropipette Aspiration of Single Cells: Effect of Compressibility

Micropipette aspiration (MA) technique has been widely used to measure the viscoelastic properties of different cell types. Cells experience nonlinear large deformations during the aspiration procedure. Neo-Hookean viscohyperelastic (NHVH) incompressible and compressible models were used to simulate the creep behavior of cells in MA, particularly accounting for the effect of compressibility, bulk relaxation, and hardening phenomena under large strain. In order to find optimal material parameters, the models were fitted to the experimental data available for mesenchymal stem cells. Finally, through Neo-Hookean porohyperelastic (NHPH) material model for the cell, the influence of fluid flow on the aspiration length of the cell was studied. Based on the results, we suggest that the compressibility and bulk relaxation/fluid flow play a significant role in the deformation behavior of single cells and should be taken into account in the analysis of the mechanics of cells.
RAID10L: A high performance RAID10 storage architecture based on logging technique

RAID10 storage system suffers the relatively poor write performance due to the write request must be served by both disks in a mirror set. To address this problem, in this paper we propose a novel RAID10 storage architecture, called RAID10L, which extends the data mirroring redundancy of RAID10 by incorporating a dedicated log disk. The goal of RAID10L is to significantly improve the write performance of RAID10 at some little expense of reliability. In RAID10L both read and write requests are processed in a balance scheme. For every write request, RAID10L keeps two copies of the write data: one in its normal place of data disk chosen by a write balance scheme and the other in the log disk by writing sequentially. The update to another data disk in a mirror set is delayed to the next quiet period between bursts of client activity. Reliability analysis shows that the reliability of RAID10L, in terms of MTTDL (mean time to data loss), is somewhat worse than RAID10 but much better than RAID5. On the other hand, our prototype implementation of RAID10L driven by Iometer benchmark shows that RAID10L outperforms RAID10 by up to 47.1% and RAID0 by 27.3% in terms of average response time. Driven by some real-life traces, RAID10L gains improvement up to 30.7% with an average of 27.7% than RAID10 in terms of average response time.
Impacts of regular and random noise on the behaviour, growth and development of larval Atlantic cod (Gadus morhua)

Anthropogenic noise impacts behaviour and physiology in many species, but responses could change with repeat exposures. As repeat exposures can vary in regularity, identifying regimes with less impact is important for regulation. We use a 16-day split-brood experiment to compare effects of regular and random acoustic noise (playbacks of recordings of ships), relative to ambient-noise controls, on behaviour, growth and development of larval Atlantic cod (Gadus morhua). Short-term noise caused startle responses in newly hatched fish, irrespective of rearing noise. Two days of both regular and random noise regimes reduced growth, while regular noise led to faster yolk sac use. After 16 days, growth in all three sound treatments converged, although fish exposed to regular noise had lower body width–length ratios. Larvae with lower body width–length ratios were easier to catch in a predator-avoidance experiment. Our results demonstrate that the timing of acoustic disturbances can impact survival-related measures during development. Much current work focuses on sound levels, but future studies should consider the role of noise regularity and its importance for noise management and mitigation measures.
LMI-Based Control for Grid-Connected Converters With LCL Filters Under Uncertain Parameters

This paper presents a linear matrix inequality-based procedure for the design of state feedback current controllers that are robust to uncertainties on grid inductance for grid-connected converters with LCL filters. The state feedback control law includes the filter state variables, the states of resonant controllers, and considers also the delay from digital control implementation. As the main contribution here, the proposed strategy allows to deal with resonant controllers of arbitrary dimension, and provides results complying with IEEE Standard 1547 requirements. The control synthesis condition takes into account the assignment of the closed-loop eigenvalues in a circular region with radius r, located inside the unit circle, and the control design relies only on the choice of the value of the radius in the interval 0 <; r ≤ 1, providing all the state feedback gains in a simple and efficient procedure.
A Novel Methodology for Vehicle Number Plate Recognition using Artificial Neural Network

Number plate recognition system is used for vehicle management, security, congestion control, access control and in the vehicle behavior monitoring system. This paper presents a real time number plate recognition system which is able to recognize the vehicle number plate in different illumination conditions, independent of orientation and scale of the plate. This research work begins by pre-processing, detecting plate region, segmentation, feature extraction and finally recognition of the character by using neural network. This system has been tested with other paper's data set that has different images with different illumination conditions and this system can recognize the number plates under different illumination conditions with a success rate of about 95%.
C-doped semi-insulating GaN HFETs on sapphire substrates with a high breakdown voltage and low specific on-resistance

High breakdown voltage (BV) AlGaN∕GaN heterojunction field effect transistors (HFETs) with a low specific on-resistance (ARDS(on)) were successfully fabricated using intentionally C-doped semi-insulating GaN buffers with a high resistivity on sapphire substrates. With the improvement of not only the resistivity of a C-doped GaN buffer but also the layout design near the gate feeding region, the fabricated devices exhibited a high BV of ∼1600V and low ARDS(on) of 3. 9mΩcm2. This result even reaches the 4H-SiC theoretical limit and the best ever reported for the high-power GaN-based HFETs realized on sapphire substrates to the best of our knowledge.