Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of stimulus novelty and negativity on BOLD activity in the amygdala, hippocampus, and bed nucleus of the stria terminalis

Abstract The amygdala responds to stimulus novelty, which may correspond to an evaluation of novel stimuli for potential threat, and trait anxiety may modulate this response. The bed nucleus of the stria terminalis (BNST) may also be sensitive to novelty as it responds to both uncertainty and threat. If so, a BNST novelty response may also be affected by trait anxiety and interact with stimulus negativity. We presented participants with novel and repeated negative and neutral images while measuring brain activity via fMRI, and assessed participants’ self-reported trait anxiety. We expected to replicate past findings of novelty responses in the hippocampus and amygdala that are independent of stimulus negativity. We also expected BNST novelty-sensitivity and that trait anxiety would predict greater sensitivity to both novelty and negativity in the amygdala and BNST, but not the hippocampus. Our a priori analyses replicated past findings of a novelty response that was independent of valence in the hippocampus and amygdala. The BNST exhibited a novelty response for negative, but not neutral, images. Trait anxiety did not modulate the response to novelty or negativity in any of the ROIs investigated. Our findings suggest that the BNST plays a role in the detection of novelty. Key words: novelty; bed nucleus of the stria terminalis; BNST; amygdale; fMRI; BST
Respiratory Kinetics of Marine Bacteria Exposed to Decreasing Oxygen Concentrations

ABSTRACT During aerobic respiration, microorganisms consume oxygen (O2) through the use of different types of terminal oxidases which have a wide range of affinities for O2. The Km values for O2 of these enzymes have been determined to be in the range of 3 to 200 nmol liter−1. In this study, we examined the time course of development of aerobic respiratory kinetics of four marine bacterial species (Dinoroseobacter shibae, Roseobacter denitrificans, Idiomarina loihiensis, and Marinobacter daepoensis) during exposure to decreasing O2 concentrations. The genomes of all four species have genes for both high-affinity and low-affinity terminal oxidases. The respiration rate of the bacteria was measured by the use of extremely sensitive optical trace O2 sensors (range, 1 to 1,000 nmol liter−1). Three of the four isolates exhibited apparent Km values of 30 to 60 nmol liter−1 when exposed to submicromolar O2 concentrations, but a decrease to values below 10 nmol liter−1 was observed when the respiration rate per cell was lowered and the cell size was decreased due to starvation. The fourth isolate did not reach a low respiration rate per cell during starvation and exhibited apparent Km values of about 20 nmol liter−1 throughout the experiment. The results clearly demonstrate not only that enzyme kinetics may limit O2 uptake but also that even individual cells may be diffusion limited and that this diffusion limitation is the most pronounced at high respiration rates. A decrease in cell size by starvation, due to limiting organic carbon, and thereby more efficient diffusion uptake may also contribute to lower apparent Km values.
Parallel Simulated Annealing using Speculative Computation

A parallel simulated annealing algorithm that is problem-independent, maintains the serial decision sequence, and obtains speedup which can exceed log/sub 2/P on P processors is discussed. The algorithm achieves parallelism by using the concurrency technique of speculative computation. Implementation of the parallel algorithm on a hypercube multiprocessor and application to a task assignment problem are described. The simulated annealing solutions are shown to be, on average, 28% better than the solutions produced by a random task assignment algorithm and 2% better than the solutions produced by a heuristic. >
Predicting Sexual Behaviors Among Homeless Young Adults: Ecological Momentary Assessment Study

Background Homeless youth continue to be disproportionately affected by HIV compared with their housed peers, with prevalence rates as high as 13%. Yet, HIV prevention in this high-risk population has been only marginally effective. Objective The aim of this study was to use ecological momentary assessments to examine real-time factors to determine the predictors of sexual activity among homeless youth. Methods Youth experiencing homelessness aged between 18 and 24 years were recruited from a drop-in center in Houston, Texas, between August 2015 and May 2016. All the participants received a study-issued mobile phone that prompted brief ecological momentary assessments (EMAs) 5 times a day for 21 days. EMA items assessed near real-time sexual behaviors, cognitions, stress, affect, environmental factors, and environmental circumstances. Results Participants (N=66) were predominantly male (41/66, 64%) and black (43/66, 66%) with a median age of 20 years. The mean number of EMAs completed by each participant was 45 out of 105 possible observations. During the study, 70% (46/66) of participants were sexually active and reported condomless sex in 102 of the 137 cases of sexual intercourse (74.5%). In total, 82% (38/46) of the youth who reported having sex during the 3 weeks of data collection also reported engaging in high-risk sexual activities, including having condomless sex (24/46, 53%), having multiple sexual partners on the same day (12/46, 26%), trading sex (7/46, 16%), and sharing needles while injecting drugs (1/46, 3%). Of those, 71% (27/38) were engaged in multiple sexual risk behaviors. The predictive model was based on observations from 66 subjects who reported 137 cases of sexual intercourse over 811 days; sexual orientation, race, mental health, drug use, and sexual urge were included as predictors in the parsimonious generalized linear mixed model selected on the basis of the Akaike information criterion. The estimated odds ratios (ORs) were notable for same-day drug use (OR 8.80, 95% CI 4.48-17.31; P<.001) and sexual urge (OR 4.23, 95% CI 1.60-11.28; P=.004). The performance of the risk estimator was satisfactory, as indicated by the value of 0.834 for the area under the receiver operating characteristic curve. Conclusions Real-time EMA data can be used to predict sexual intercourse among a sample of high-risk, predominately unsheltered homeless youth. Sexual urge and drug use accounts for increased odds of engaging in sexual activity on any given day. Interventions targeting sexual urge and drug use may help predict sexual activity among a population at high risk of HIV.
Příprava a charakterizace strukturovaných povrchů na bázi křemíku

The goal of this work was the development and optimization of a novel process for the pre-paration of structured silicon-based surfaces using anizotropic etching in a temperature gradient. These surfaces were further characterized using surface displaying methods atomic force microscopy (AFM) and scanning electron microscopy (SEM). The effects of etching solvent composition, etch time, etching solvent volume, temperature, temperature gradient and surface purity were studied. The experimental results show that by choosing optimal etching parameters and when using modified machine made for Si wafer etching one can prepare differently structured surfaces which differ in homogenous coverage of etched area and in size of structural elements.
Results from the Canadian Nosocomial Infection Surveillance Program on Carbapenemase-Producing Enterobacteriaceae, 2010 to 2014

ABSTRACT Carbapenemase-producing Enterobacteriaceae (CPE) are increasing globally; here we report on the investigation of CPE in Canada over a 5-year period. Participating acute care facilities across Canada submitted carbapenem-nonsusceptible Enterobacteriaceae from 1 January 2010 to 31 December 2014 to the National Microbiology Laboratory. All CPE were characterized by antimicrobial susceptibilities, pulsed-field gel electrophoresis, multilocus sequence typing, and plasmid restriction fragment length polymorphism analysis and had patient data collected using a standard questionnaire. The 5-year incidence rate of CPE was 0.09 per 10,000 patient days and 0.07 per 1,000 admissions. There were a total of 261 CPE isolated from 238 patients in 58 hospitals during the study period. blaKPC-3 (64.8%) and blaNDM-1 (17.6%) represented the highest proportion of carbapenemase genes detected in Canadian isolates. Patients who had a history of medical attention during international travel accounted for 21% of CPE cases. The hospital 30-day all-cause mortality rate for the 5-year surveillance period was 17.1 per 100 CPE cases. No significant increase in the occurrence of CPE was observed from 2010 to 2014. Nosocomial transmission of CPE, as well as international health care, is driving its persistence within Canada.
Estimation of Discharge From Three Braided Rivers Using Synthetic Aperture Radar Satellite Imagery: Potential Application to Ungaged Basins

Analysis of 41 ERS 1 synthetic aperture radar images and simultaneous ground measurements of discharge for three large braided rivers indicates that the area of active flow on braided river floodplains is primarily a function of discharge. A power law correlation is found between satellite-derived effective width We and discharge Q, where We is the water surface area within a braided reach divided by the reach length. Synthetic values of We and Q generated from a cellular automata model of stream braiding display a similar power law correlation. Power functions that are fit through plots of We and Q represent satellite-derived rating curves that can subsequently be used to estimate instantaneous river discharge from space, with errors ranging from tens to hundreds of cubic meters per second. For ungaged rivers, changes in relative discharge can be determined from satellite data alone to determine the shape and timing of annual flows in glacierized basins. Absolute discharge can probably be estimated within a factor of 2. More accurate estimates will require either (1) one or more ground measurements of discharge acquired simultaneously with a satellite image acquisition, or (2) successful parameterization of known morphologic controls such as total sinuosity 5;P, valley slope, bank material and stability, and braid channel hydraulic geometry. Values of total sinuosity 5;P derived from satellite imagery and field measurements from two rivers of braid channel width, depth, velocity, water surface slope, and bed material grain size indicate that while the shape of satellite-derived We-Q rating curves may be influenced by all of these variables, the sensitivity of flow area to changing discharge is most dependent upon the degree of braiding. Efforts to monitor river discharge from space will be most successful for intensely braided rivers with high values of total sinuosity. Subsampling of existing daily discharge records from the Iskut River suggests that satellite return times of about 1 week are sufficient for approximating the shape and timing of the seasonal hydrograph in large, glacierized basins. Although errors are large, the presented technique represents the only currently available way to estimate discharge in ungauged braided rivers.
Modeling Trans-Device Content Experience and Knowledge Development for Detection of TV Audiences

Household audience ratings are the currency of the television broadcasting business. Information communication technology has rapidly changed television viewing since the beginning of this century, and the reproducibility of audience ratings as media indicators is beginning to be questioned. This is because television viewing through various devices must be considered, due to the decline of simultaneous viewing at a fixed time. This research applies artificial intelligence to explore several questions. What viewing features span media and devices? What are the viewer attitude models inherent in those features? What are the functions and rules driving the model? Can these be converted into knowledge, and can new hypotheses be obtained from this knowledge? For this, the technologies of natural language processing, neural network, and automated reasoning are applied. From data sequences including property amounts representing viewing attitudes, we visualize time-series feature patterns and extract a state space model driving these features and logical rules between the variables. This research is an example of the real-world application of a technical framework that combines symbolic inference and feature extraction, opening possibilities for more advanced reasoning.
Partial mutual information for simple model order determination in multivariate EEG signals and its application to transfer entropy

The context of this work is the analysis of depth electroencephalographic signals recorded with depth electrodes during seizures in patients with drug-resistant epilepsy. Usually, different phases are observed during the seizure process and we aim to determine how cerebral structures get involved during these phases, in particular whether some structures can “drive” other ones. To this end, we consider a pair of signals and use transfer entropy which needs beforehand to choose efficiently the size of two conditioning vectors built on the past values of these signals. In this contribution, we extend a partial mutual information based technique, first developed for monochannel prediction models, to the case of two channels. Experimental results on signals generated either by a linear autoregressive model or by a physiology-based model of coupled neuronal populations support the relevance of the proposed approach.
Towards Making Fault Injection on Abstract Models a More Accurate Tool for Predicting RT-Level Effects

Fault injection and fault simulation are a typical approach to analyze the effect of a fault on a hardware/software system. Often fault injection is done on abstract models of the system either to retrieve early results when no implementation is available, yet, or to speed-up the runtime intensive fault simulation on detailed models. The simulation results from the abstract model are typically inaccurate because details of the concrete hardware are missing.Here, we propose an approach to relate faults from an abstract untimed algorithmic model to their counterparts in the concrete register transfer models. This allows to understand which faults are covered on the concrete model and to speed up the fault simulation process.We use a mapping between both models' variables and mapped timing states for fault injection to corresponding variables on both models. After fault simulations the results are compared to check, whether a given fault produces the same behavior on both models. The results show that an injected fault to corresponding variables leads to the same behavior of both models for a large share of faults.
Channel prediction in point-to-point MIMO-systems

The present paper introduces three sophisticated techniques to predict the channel transfer functions in frequency division duplex MIMO-systems. In frequency division duplex systems it is beneficial to have the knowledge of the uplink channel and the downlink channel at both sides of the point-to-point transmission link. However, the base station can only estimate the uplink channel based on the transmission of a-priori known training signals from the mobile station. Due to the frequency selective behavior of the mobile radio channel, the channel state information of the uplink channel and the channel state information of the downlink channel are different. One possibility to obtain the channel state information of the downlink channel in the base station is to feed back this information from the mobile station. Unfortunately, this feedback decreases the spectral efficiency. The presented techniques to obtain the channel state information of the downlink channel in the base station are based on the physical path parameters and are based on filtering the previously estimated channel state information. The performance of the investigated techniques is evaluated by means of measurement results.
Secondhand Tobacco Smoke Exposure Associations With DNA Methylation of the Aryl Hydrocarbon Receptor Repressor

Introduction Cigarette smoking is inversely associated with DNA methylation of the aryl hydrocarbon receptor repressor (AHRR; cg05575921). However, the association between secondhand tobacco smoke (SHS) exposure and AHRR methylation is unknown. Methods DNA methylation of AHRR cg05575921 in CD14+ monocyte samples, from 495 never-smokers and 411 former smokers (having quit smoking ≥15 years) from the Multi-Ethnic Study of Atherosclerosis (MESA), was cross-sectionally compared with concomitantly ascertained self-reported SHS exposure, urine cotinine concentrations, and estimates of air pollutants at participants' homes. Linear regression was used to test for associations, and covariates included age, sex, race, education, study site, and previous smoking exposure (smoking status, time since quitting, and pack-years). Results Recent indoor SHS exposure (hours per week) was inversely associated with cg05575921 methylation (β ± SE = -0.009 ± 0.003, p = .007). The inverse effect direction was consistent (but did not reach significance) in the majority of stratified analyses (by smoking status, sex, and race). Categorical analysis revealed high levels of recent SHS exposure (≥10 hours per week) inversely associated with cg05575921 methylation (β ± SE = -0.28 ± 0.09, p = .003), which remained significant (p < .05) in the majority of stratified analyses. cg05575921 methylation did not significantly (p < .05) associate with low to moderate levels of recent SHS exposure (1-9 hours per week), urine cotinine concentrations, years spent living with people smoking, years spent indoors (not at home) with people smoking, or estimated levels of air pollutants. Conclusions High levels of recent indoor SHS exposure may be inversely associated with DNA methylation of AHRR in human monocytes. Implications DNA methylation is a biochemical alteration that can occur in response to cigarette smoking; however, little is known about the effect of SHS on human DNA methylation. In the present study, we evaluated the association between SHS exposure and DNA methylation in human monocytes, at a site (AHRR cg05575921) known to have methylation inversely associated with current and former cigarette smoking compared to never smoking. Results from this study suggest high levels of recent SHS exposure inversely associate with DNA methylation of AHRR cg05575921 in monocytes from nonsmokers, albeit with weaker effects than active cigarette smoking.
Trypanosoma cruzi Differentiates and Multiplies within Chimeric Parasitophorous Vacuoles in Macrophages Coinfected with Leishmania amazonensis

ABSTRACT The trypanosomatids Leishmania amazonensis and Trypanosoma cruzi are excellent models for the study of the cell biology of intracellular protozoan infections. After their uptake by mammalian cells, the parasitic protozoan flagellates L. amazonensis and T. cruzi lodge within acidified parasitophorous vacuoles (PVs). However, whereas L. amazonensis develops in spacious, phagolysosome-like PVs that may enclose numerous parasites, T. cruzi is transiently hosted within smaller vacuoles from which it soon escapes to the host cell cytosol. To investigate if parasite-specific vacuoles are required for the survival and differentiation of T. cruzi, we constructed chimeric vacuoles by infection of L. amazonensis amastigote-infected macrophages with T. cruzi epimastigotes (EPIs) or metacyclic trypomastigotes (MTs). These chimeric vacuoles, easily observed by microscopy, allowed the entry and fate of T. cruzi in L. amazonensis PVs to be dynamically recorded by multidimensional imaging of coinfected cells. We found that although T. cruzi EPIs remained motile and conserved their morphology in chimeric vacuoles, T. cruzi MTs differentiated into amastigote-like forms capable of multiplying. These results demonstrate that the large adaptive vacuoles of L. amazonensis are permissive to T. cruzi survival and differentiation and that noninfective EPIs are spared from destruction within the chimeric PVs. We conclude that T. cruzi differentiation can take place in Leishmania-containing vacuoles, suggesting this occurs prior to their escape into the host cell cytosol.
Implementing Contract-based Software Architectures in Java: The Structural, Behavioural, and Interaction Design Decisions

Architectural languages (ALs) have been so actively researched since the nineties and this leads to many ALs with different capabilities that have been proposed each day. However, most of the ALs ignore the specifications of the structural, behavioural, and interaction design decisions and do not support their analysis and development. The ALs that do support suffer from the process algebra based notation sets that practitioners do not prefer to work with. This issue is tackled in the paper by extending the Design-by-Contract based architectural language called XCD that supports the contractual specifications of the structural, behavioural, and interaction design decisions about software systems and their formal analysis. XCD is extended with a development support in Java so as to transform the contractual specifications in XCD into a complete Java program that considers all the structural, behavioural, and interaction decisions specified. So, practitioners will be able to specify non-algebraic, contractual specifications in XCD, formally analyse them, and produce the Java source-code that reflects the specified architecture completely and consistently. The produced Java code can also be tested for incompleteness and wrong use of component services automatically.