Miracle-dz/UniFAR-FTUs huggingface dataset:
Perspectives on the basic reproductive ratio

The basic reproductive ratio, R0, is defined as the expected number of secondary infections arising from a single individual during his or her entire infectious period, in a population of susceptibles. This concept is fundamental to the study of epidemiology and within-host pathogen dynamics. Most importantly, R0 often serves as a threshold parameter that predicts whether an infection will spread. Related parameters which share this threshold behaviour, however, may or may not give the true value of R0. In this paper we give a brief overview of common methods of formulating R0 and surrogate threshold parameters from deterministic, non-structured models. We also review common means of estimating R0 from epidemiological data. Finally, we survey the recent use of R0 in assessing emerging diseases, such as severe acute respiratory syndrome and avian influenza, a number of recent livestock diseases, and vector-borne diseases malaria, dengue and West Nile virus.
Community-based targeted case finding for tuberculosis and HIV in household contacts of patients with tuberculosis in South Africa.

RATIONALE South Africa has a high prevalence of tuberculosis (TB) and HIV-coinfected adults in whom TB is often diagnosed late in the course of disease. OBJECTIVES Improved case-finding approaches for TB and HIV are needed to reduce mortality and prevent transmission. METHODS We identified newly diagnosed index TB cases in a rural district and enrolled their households in a TB-HIV contact-tracing study. A group of randomly selected control households were enrolled to determine community prevalence of undetected TB and HIV. Field teams screened participants for TB symptoms, collected sputum specimens for smear microscopy and culture, provided HIV counseling and testing, and collected blood for CD4 testing. Participants were referred to public clinics for TB treatment and antiretroviral therapy. MEASUREMENTS AND MAIN RESULTS We evaluated 2,843 household contacts of 727 index patients with TB and 983 randomly selected control household members. The prevalence of TB in household contacts was 6,075 per 100,000 (95% confidence interval, 5,789-6,360 per 100,000), whereas the prevalence detected in randomly selected households was 407 per 100,000 (95% confidence interval, 0-912 per 100,000; prevalence difference, 5,668 per 100,000; P < 0.001). TB detected among contacts was less likely to be smear-positive than in the index patients (6% vs. 22%; P < 0.001). Most contacts with culture-confirmed TB were asymptomatic. At least one case of undiagnosed TB was found in 141 (19%) of 727 contact versus 4 (1%) of 312 control households. HIV testing was positive in 166 (11%) of 1,568 contacts tested versus 76 (14%) of 521 control participants tested (odds ratio, 1.48; P = 0.02). CONCLUSIONS Active case finding in TB contact households should be considered to improve TB and HIV case detection in high-prevalence settings, but sensitive diagnostic tools are necessary.
Non-stationary job search when jobs are not forever: A structural estimation

This paper considers a job search model where the environment is not stationary along the unemployment spell and where jobs do not last forever. Under this circumstance, reservation wages can be lower than without separations, as in a stationary environment, but they can also be initially higher because of the non-stationarity of the model. Moreover, the time-dependence of reservation wages is stronger than with no separations. The model is estimated structurally using Spanish data for the period 1985-1996. The main finding is that, although the decrease in reservation wages is the main determinant of the change in the exit rate from unemployment for the first four months, later on the only effect comes from the job offer arrival rate, given that acceptance probabilities are roughly equal to one.
Discordance between changes in the gut microbiota and pathogenicity in a mouse model of spontaneous colitis

Under conventional conditions, mice deficient in core 1-derived O-glycans (TM-IEC C1galt1−/−), which have a defective mucus layer, experienced spontaneous inflammation of the colon. Analysis of fecal bacterial populations by pyrosequencing of 16S rRNA gene showed that disease in conventional TM-IEC C1galt1−/− was associated with shifts in the microbiota manifested by increases in Lactobacillus and Clostridium species, and decreases in unclassified Ruminococcaceae and Lachnospiraceae. Under germ-free (GF) conditions, TM-IEC C1galt1−/− presented decreased goblet cells, but did not develop inflammation. Monoassociation of GF TM-IEC C1galt1−/− revealed that bacterial species differ significantly in their ability to induce inflammatory changes. Bacteroides thetaiotaomicron caused inflammation, while Lactobacillus johnsonii (enriched during colitis) did not. These observations demonstrate that not all microbiota shifts that correlate with disease contribute to pathogenesis.
An Association Between the Kinship and Fertility of Human Couples

Previous studies have reported that related human couples tend to produce more children than unrelated couples but have been unable to determine whether this difference is biological or stems from socioeconomic variables. Our results, drawn from all known couples of the Icelandic population born between 1800 and 1965, show a significant positive association between kinship and fertility, with the greatest reproductive success observed for couples related at the level of third and fourth cousins. Owing to the relative socioeconomic homogeneity of Icelanders, and the observation of highly significant differences in the fertility of couples separated by very fine intervals of kinship, we conclude that this association is likely to have a biological basis.
Simultaneous mobility in MIPv6

Mobile IP for IPv6 (MIPv6) includes a procedure for route optimization, which allows packets from the correspondent host to go directly to the mobile host. However, the way route optimization is implemented makes it vulnerable to problems with simultaneous mobility, which can occur when two mobile hosts are communicating with each other. In this paper, we suggest ways to change MIPv6 to reduce its vulnerability to the simultaneous mobility problem.
Experimental study of active vibration control for flexible beam by using a Stewart platform manipulator

Experiments of active vibration control for flexible beam are studied, with a Stewart platform manipulator (SPM) employed as an active equipment at the bottom of the beam. The dynamic modal of the rigid-flexible coupling system composed of the upper platform of the SPM and the flexible beam is built, and an auto disturbances rejection controller (ADRC) is designed. Then based on the dSPACE real-time simulation system, the control test system for the beam is built, on which the auto disturbances rejection control experiments are carried out. Experimental results show the rate of amplitude attenuation using ADRC is almost 10 times faster than the free attenuation. For comparison purpose, a classic LQG controller is applied in another experiment on the same test system. The results of the two experiments show that ADRC has a better performance than LQG controller for the nonlinear system. At the same time, the results verify the effectiveness of the control conducted by SPM at the bottom of the beam.
A simulation software of forest fires based on two-level cellular automata

A software system for the simulation of small-scale fires in Mediterranean landscapes is presented. The software uses a model of fire spreading deriving from the classical Rothermel’s Rate-Of-Spread theory. It exports this method, based on American forests peculiarities, using Valette’s classes of inflammability, tested for Mediterranean coverage. The forest is modeled as a two-layer cellular automata: the upper layer representing the crowns of the trees and the lower one the surface coverage. Slope, air temperature and moisture data are introduced through coefficients like in Rothermel’s model; wind effects are based on Alexander’s ellipse theory. The software has been developed to supply fire-operators with a real-time tool: the simulator automatically retrieves GIS coverage and digital terrain model data, shows on the screen all the active operators by GPS positioning, saves and re-runs any step of the simulation to test different fire management actions.
High-Performance Solvers for Large-Scale Dense

We introduce a new collection of solvers – subsequently called EleMRRR – for large-scale dense Hermitian eigenproblems. EleMRRR solves various types of problems: generalized, standard, and tridiagonal eigenproblems. Among these, the last is of particular importance as it is a solver on its own right, as well as the computational kernel for the first two; we present a fast and scalable tridiagonal solver based on the Algorithm ofMultiple Relatively Robust Representations – referred to as PMRRR. Like the other EleMRRR solvers, PMRRR is part of the freely available Elemental library, and is designed to fully support both message-passing (MPI) and multithreading parallelism (SMP). As a result, the solvers can equally be used in pure MPI or in hybrid MPI-SMP fashion. We conducted a thorough performance study of EleMRRR and ScaLAPACK’s solvers on two supercomputers. Such a study, performed with up to 8,192 cores, provides precise guidelines to assemble the fastest solver within the ScaLAPACK framework; it also indicates that EleMRRR outperforms even the fastest solvers built from ScaLAPACK’s components.
Electroencephalography/magnetoencephalography study of cortical activities preceding prosaccades and antisaccades

The temporal and spatial characteristics of brain activity preceding prosaccades and antisaccades were investigated using source reconstructions of 64-channel electroencephalography and 148-channel magnetoencephalography data. Stimulus-locked data showed early cuneus activity was stronger during antisaccades, and later occipital gyrus activity was stronger preceding prosaccades, which suggests a top-down influence on early visual processing. Response-locked data showed that supplementary eye field, prefrontal cortex, and medial frontal eye field activity was greater for antisaccades than for prosaccades prior to saccade generation. Lateral frontal eye field activity appeared to be inhibited prior to antisaccade response generation. The spatial and temporal resolution of combined electroencephalography/magnetoencephalography data allows the evaluation of specific cortical activities preceding saccades and for demonstration of how activities differ as a function of response contingencies.
Effects of Optical Combiner and IPD Change for Convergence on Near-Field Depth Perception in an Optical See-Through HMD

Many error sources have been explored in regards to the depth perception problem in augmented reality environments using optical see-through head-mounted displays (OST-HMDs). Nonetheless, two error sources are commonly neglected: the ray-shift phenomenon and the change in interpupillary distance (IPD). The first source of error arises from the difference in refraction for virtual and see-through optical paths caused by an optical combiner, which is required of OST-HMDs. The second occurs from the change in the viewer's IPD due to eye convergence. In this paper, we analyze the effects of these two error sources on near-field depth perception and propose methods to compensate for these two types of errors. Furthermore, we investigate their effectiveness through an experiment comparing the conditions with and without our error compensation methods applied. In our experiment, participants estimated the egocentric depth of a virtual and a physical object located at seven different near-field distances (40~200 cm) using a perceptual matching task. Although the experimental results showed different patterns depending on the target distance, the results demonstrated that the near-field depth perception error can be effectively reduced to a very small level (at most 1 percent error) by compensating for the two mentioned error sources.
Visual perception and visual cognition in healthy and pathological ageing

Our understanding of visual perception and visual cognition has advanced considerably over the last decades. The effects of ageing on visual perception and visual cognition are less well understood. This Research Topic features state-of-the-art approaches to determining the effects of ageing on visual perception, visual attention, visual memory and visually guided behaviour. Studies using methods that incorporate psychophysics, eye movements, electrophysiology, structural and functional neuroimaging, as well as computational modelling are included. In addition to the focus on how ageing effects normal vision, the topic also includes studies on the effects of pathological ageing in the retina (e.g., age-related macular degeneration) and the brain (e.g., neurodegenerative disorders) on vision and visual cognition.
Foreign exchange intervention in Colombia 1

This paper describes the Banco de la República’s FX intervention policy, with a focus on its objectives and main features. It then argues, based on a review of the literature on the effectiveness of sterilized intervention in Colombia, that this tool is not a useful way of coping with the challenges posed by medium-term external factors such as quantitative easing in advanced economies, reduced risk premiums in emerging economies or high international commodity prices. The impact of sterilized intervention on the exchange rate (if any) is of much shorter duration than are the effects of those external factors. Finally, the paper argues that if sterilized FX intervention is effective through the operation of the portfolio balance channel, it may also have an expansionary effect on credit supply and aggregate demand. In this case, the macroeconomic outcomes of intervention depend on the monetary policy response. This issue is studied with a small open economy DSGE model. In general, FX intervention creates more volatility of credit and consumption than occurs with more efficient allocation and under alternative monetary regimes without intervention. Furthermore, the more inclined the central bank is to meet an inflation target, the stronger its response to the expansionary effects of the intervention, and consequently the lower the impact of the intervention on the exchange rate.
Interaction of silicon and cadmium in Brassica juncea and Brassica napus

The objective of this study was to determine the effect of silicon (Si) and cadmium (Cd) on root and shoot growth and Cd uptake in two hydroponically cultivated Brassica species (B. juncea (L.) Czern. cv. Vitasso and B. napus L. cv. Atlantic). Both species are potentially usable for phytoextraction. Inhibitory effects of Cd on root elongation were diminished by the impact of Si. Primary roots elongation in the presence of Cd + Si compared with Cd was stronger and the number of lateral roots was lower in B. juncea than in B. napus. Cd content per plant was higher in B. napus roots and shoots compared with B. juncea. Suberin lamellae were formed closer to the root apex in Cd + Si than in Cd treated plants and this effect was stronger in B. napus than in B. juncea. Accelerated maturation of endodermis was associated with reduced Cd uptake. Cd decreased the content of chlorophylls and carotenoids in both species, but Si addition positively influenced the content of photosynthetic pigments which was higher in B. napus than in B. juncea. Si enhanced more substantially translocation of Cd into the shoot of B. napus than of B. juncea. Based on our results B. napus seems to be more suitable for Cd phytoextraction than B. juncea because these plants produce more biomass and accumulate higher amount of Cd. The protective effect of Si on Cd treated Brassica plants could be attributed to more extensive development of suberin lamellae in endodermis.
Atmosphere sounding by GPS radio occultation: First results from CHAMP

The first radio occultation measurements of the CHAMP (CHAllenging Minisatellite Payload) satellite using Global Positioning System (GPS) signals have been performed on February 11, 2001. By the end of April 2001 more than 3000 occultations were recorded. Globally distributed vertical profiles of dry temperature and specific humidity are derived, of which a set of 438 vertical dry temperature profiles is compared with corresponding global weather analyses. The observed temperature bias is less than ∼1 K above the tropopause and even less than 0.5 K in the altitude interval from 12 to 20 km at latitudes >30°N. About 55% of the compared profiles reached the last kilometer above the Earth's surface. In spite of the activated anti‐spoofing mode of the GPS system the state‐of‐the‐art GPS flight receiver aboard CHAMP combined with favorable antenna characteristics allows for atmospheric sounding with high accuracy and vertical resolution.
Single-Carrier Space Time Transmission Diversity with Decision Feedback Equalization

In order to suppress inter-symbol interference (ISI), the Frequency domain decision feedback equalization (FD-DFE) algorithm is proposed in this paper for single carrier frequency domain equalization (SC-FDE) combined with Alamouti space time block coding (STBC) systems over frequency-selective channels. We use the cyclic prefix (CP) and two transmit antennas to achieve the significant diversity gain. The feedback equalization part is designed by Mean Square Error (MSE) criterion and the coefficients of filters are all in the frequency domain for the given channel frequency response. The outage and diversity analysis of system is also made to measure the equalization performance. Finally, the simulation results show that the proposed algorithm has better performance than the conventional liner equalization (LE) and hybrid structure decision feedback equalization (HDFE) schemes, and the computational complexity of our method is acceptable.
Control-based p-persistent adaptive communication protocol

An enhancement to the CSMA p-persistent protocol family is proposed, based on a fully decentralized control that adjusts the message transmission rate of each node to the estimated density of surrounding transmitting nodes. The system does not require enumeration of nodes nor control messages, the only input to the control coming from the physical medium occupation. Stability conditions are given in both cases of fixed and switching topologies. We show that good channel exploitation levels can be assured as well by suitably tuning the control parameters.
Predicting Availability of Mobile Peers in Large Peer-to-Peer Networks

Peer-to-peer (P2P) applications for mobile devices are becoming more and more popular because of increasing bandwidth, computational performance and storage capabilities. Such a mobile based distributed architecture offers significant advantages in several scenarios from the perspective of both users and network operators. In these situations, a certain redundancy must be built into the system because the availability of the nodes can vary greatly. The goal of this paper is to present a methodology to minimize the necessary redundancy by predicting the number of available nodes. The prediction is performed in two steps, first an estimation is done locally at the node level, then a centralized aggregation is executed. We propose a hypothesis which highlights the key advantages of our solution when compared to single step estimation. Finally we discuss about the correctness of the computed redundancy.
Bayesian Regression Methodology for Receiver Operating Characteristic Curve Analysis

The receiver operating characteristic (ROC) curve is a useful tool for assessing the accuracy of a discriminant analysis that yields continuous classi cation results. We consider data that include covariates in addition to the gold standard. We propose two Bayesian regression models for deriving an ROC curve. The full model contains all interaction terms between the gold standard and each covariate, along with interactions among covariates. The partial model omits gold standard and covariate interactions. Summary ROC measures are reported. Under the partial model the e ect of the choice of prior distributions of the regression coeÆcients is investigated. The methods are illustrated on the diagnosis of prostate cancer.
Adaptive trajectory following control of a fixed-wing UAV in presence of crosswind

An adaptive backstepping approach to obtain directional control of a fixed-wing UAV in presence of unknown crosswind is developed in this paper. The dynamics of the cross track error with respect to a desired trajectory is derived from the lateral airplane equations of motion. Adaptation laws are proposed to estimate the parameters of the unknown disturbances and are employed in closed-loop system. The stability analysis is proved using Lyapunov theory. In addition, several simulations taking into account unknown wind gusts are performed to analyze the behavior and the robustness of the control scheme. A test platform has been developed in order to validate the proposed control law.
A Target Repurposing Approach Identifies N-myristoyltransferase as a New Candidate Drug Target in Filarial Nematodes

Myristoylation is a lipid modification involving the addition of a 14-carbon unsaturated fatty acid, myristic acid, to the N-terminal glycine of a subset of proteins, a modification that promotes their binding to cell membranes for varied biological functions. The process is catalyzed by myristoyl-CoA:protein N-myristoyltransferase (NMT), an enzyme which has been validated as a drug target in human cancers, and for infectious diseases caused by fungi, viruses and protozoan parasites. We purified Caenorhabditis elegans and Brugia malayi NMTs as active recombinant proteins and carried out kinetic analyses with their essential fatty acid donor, myristoyl-CoA and peptide substrates. Biochemical and structural analyses both revealed that the nematode enzymes are canonical NMTs, sharing a high degree of conservation with protozoan NMT enzymes. Inhibitory compounds that target NMT in protozoan species inhibited the nematode NMTs with IC50 values of 2.5–10 nM, and were active against B. malayi microfilariae and adult worms at 12.5 µM and 50 µM respectively, and C. elegans (25 µM) in culture. RNA interference and gene deletion in C. elegans further showed that NMT is essential for nematode viability. The effects observed are likely due to disruption of the function of several downstream target proteins. Potential substrates of NMT in B. malayi are predicted using bioinformatic analysis. Our genetic and chemical studies highlight the importance of myristoylation in the synthesis of functional proteins in nematodes and have shown for the first time that NMT is required for viability in parasitic nematodes. These results suggest that targeting NMT could be a valid approach for the development of chemotherapeutic agents against nematode diseases including filariasis.
Catecholamine and cardiovascular response to electro-convulsion therapy in man.

Fourteen anaesthetized patients undergoing electro-convulsion therapy on one or more occasions were studied. Systolic and diastolic blood pressure, heart rate, and plasma adrenaline and noradrenaline levels were measured before, during and after the electric shock. With the electric shock, blood pressure and heart rate rose and adrenaline and noradrenaline levels in plasma increased steeply. These values returned to normal within 10 minutes. Asystole of about 2 seconds duration was common with application of the electric shock in patients not premedicated with atropine. With repeated electro-shocks, resting plasma noradrenaline levels decreased as did the noradrenaline response to the shock. Systolic arterial pressure was significantly correlated with circulating levels of noradrenaline in plasma.