Miracle-dz/UniFAR-FTUs huggingface dataset:
Can a Reasonable Time Limit Improve the Effective Usage of a Computerized Decision Aid?

This study examines the impact of a reasonable time limit on the effective usage of a computerized decision aid. Using current decision making models, a theoretical argument about decision aid usage is developed. This argument is then investigated via two lab experiments. The first experiment determines a reasonable time limit for the task used in the study. The second experiment investigates users’ behavior and heart rate variability under this time limit. The results of our study indicate that the reasonable time limit determined in the first study improved effective utilization of the computerized decision aid. The analysis of heart rate variability provides evidence that the given time constraint improved users’ cognitive coherence.
Earth rotation monitoring, UT1 determination and prediction

Monitoring the Earth's rotation angle is essential in various domains linked to reference systems such as space navigation, precise orbit determinations of artificial Earth satellites including the Global Navigation Satellite Systems (GNSS), positional astronomy and for geophysical studies on time scales ranging from a few hours to decades. Universal Time UT1 is based on the rotation of the Earth on its axis. Historically it was related to mean solar time on the meridian of Greenwich, sometimes known as Greenwich Mean Time. Monitoring Earth orientation, and in particular UT1, is the primary task of the International Earth Rotation and Reference Systems Service (IERS). The Earth Orientation Center is responsible for monitoring Earth orientation parameters (EOPs) including long-term consistency and leap second announcements. The Rapid Service/Prediction Center is in charge of the rapid, near real-time solution and predictions. These two complementary services of the IERS provide Earth orientation information from results derived predominantly from Very Long Baseline Interferometry with valuable input from GNSS observations and global atmospheric angular momentum for both the combination and prediction of EOPs.
Distributions of Irritative Zones Are Related to Individual Alterations of Resting-State Networks in Focal Epilepsy

Alterations in the connectivity patterns of the fMRI-based resting-state networks (RSNs) have been reported in several types of epilepsies. Evidence pointed out these alterations might be associated with the genesis and propagation of interictal epileptiform discharges (IEDs). IEDs also evoke blood-oxygen-level dependent (BOLD) responses, which have been used to delineate irritative zones during preoperative work-up. Therefore, one may expect a relationship between the topology of the IED-evoked BOLD response network and the altered spatial patterns of the RSNs. In this study, we used EEG recordings and fMRI data obtained simultaneously from a chronic model of focal epilepsy in Wistar rats to verify our hypothesis. We found that IED-evoked BOLD response networks comprise both cortical and subcortical structures with a rat-dependent topology. In all rats, IEDs evoke both activation and deactivation types of BOLD responses. Using a Granger causality method, we found that in many cases areas with BOLD deactivation have directed influences on areas with activation (p<0.05). We were able to predict topological properties (i.e., focal/diffused, unilateral/bilateral) of the IED-evoked BOLD response network by performing hierarchical clustering analysis on major spatial features of the RSNs. All these results suggest that IEDs and disruptions in the RSNs found previously in humans may be different manifestations of the same transient events, probably reflecting altered consciousness. In our opinion, the shutdown of specific nodes of the default mode network may cause uncontrollable excitability in other functionally connected brain areas. We conclude that IED-evoked BOLD responses (i.e., activation and deactivation) and alterations of RSNs are intrinsically related, and speculate that an understanding of their interplay is necessary to discriminate focal epileptogenesis and network propagation phenomena across different brain modules via hub-based connectivity.
Biological properties of extracellular vesicles and their physiological functions

In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.
Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean

Despite nutrient-depleted conditions, coral reef waters harbor abundant and diverse microbes; as major agents of microbial mortality, viruses are likely to influence microbial processes in these ecosystems. However, little is known about marine viruses in these rapidly changing ecosystems. Here we examined spatial and short-term temporal variability in marine viral abundance (VA) and viral lytic activity across various reef habitats surrounding Moorea Island (French Polynesia) in the South Pacific. Water samples were collected along four regional cross-reef transects and during a time-series in Opunohu Bay. Results revealed high VA (range: 5.6 × 106–3.6 × 107 viruses ml-1) and lytic viral production (range: 1.5 × 109–9.2 × 1010 viruses l-1 d-1). Flow cytometry revealed that viral assemblages were composed of three subsets that each displayed distinct spatiotemporal relationships with nutrient concentrations and autotrophic and heterotrophic microbial abundances. The results highlight dynamic shifts in viral community structure and imply that each of these three subsets is ecologically important and likely to infect distinct microbial hosts in reef waters. Based on viral-reduction approach, we estimate that lytic viruses were responsible for the removal of ca. 24–367% of bacterial standing stock d-1 and the release of ca. 1.0–62 μg of organic carbon l-1 d-1 in reef waters. Overall, this work demonstrates the highly dynamic distribution of viruses and their critical roles in controlling microbial mortality and nutrient cycling in coral reef water ecosystems.
Brief Online Mindfulness Training

Background. Online training is feasible, but the impact of brief mindfulness training on health professionals needs to be better understood. Methods. We analyzed data from health professionals and trainees who completed self-reflection exercises embedded in online mindfulness training between May 2014 and September, 2015; their changes in mindfulness were measured using standardized scales. Results. Participants included nurses (34%), physicians (24%), social workers and psychologists (10%), dietitians (8%), and others (25%); 85% were women, and 20% were trainees. The most popular module was Introduction to Mindfulness (n = 161), followed by Mindfulness in Daily Life (n = 146), and Mindful Breathing and Walking (n = 129); most (68%) participants who took 1 module took all 3 modules. There were no differences in participation in any module by gender, trainee status, or profession. Completing modules was associated with small but significant improvements on the Cognitive and Affective Mindfulness Scale–Revised, the Mindful Attention Awareness Scale, and the Five Facet Mindfulness Questionnaire (P < 0.001 for all). Conclusion. Online training reaches diverse health professionals and is associated with immediate improvements in mindfulness. Additional research is warranted to compare the long-term cost-effectiveness of different doses of online and in-person mindfulness training on clinician burnout and quality of care.
Comparison of Two Toric IOLs with Different Haptic Design: Optical Quality after 1 Year

Background The purpose of this prospective, randomised study was to interocularly compare the visual performance after implantation of two different toric IOLs with different haptic design. Methods 59 subjects with corneal astigmatism greater than 1.25 diopter (D) were implanted with an AT TORBI 709M IOL (Carl Zeiss Meditec AG) in one eye and with a Tecnis toric aspheric IOL (Abbot Medical Optics) in the other eye. Observation procedure was performed 12 months postoperatively. Main outcome measures included uncorrected distance visual acuity (UDVA), manifest refraction, IOL rotation, and IOL position. Results Mean UCDVA was 0.04 ± 0.14 logMAR for AT TORBI eyes and 0.06 ± 0.15 logMAR for Tecnis eyes (p = 0.3). The postoperative spherical equivalent values were significantly lower in the AT TORBI group. Mean toric IOL axis rotation was 3.0 ± 2.26 degrees for AT TORBI eyes and 3.27 ± 2.37 for Tecnis eyes (p = 0.5). The mean vertical IOL tilt and vertical decentration values measured with the Visante OCT were significantly larger in the AT TORBI group (p < 0.05). Conclusions Both the Tecnis and the AT TORBI toric IOLs successfully reduced ocular astigmatism. Emmetropia could be better achieved with the AT TORBI IOL, whereas the Tecnis showed better positional stability. This trial is registered with ICMJE NCT03371576.
Insights into thermal stress in Japanese quail (Coturnix coturnix): dynamics of immunoendocrine and biochemical responses during and after chronic exposure

Abstract Avian require comfortable temperatures for optimal development and heat stress is a high concern in warm weather countries. We aimed to assess the dynamics of immunoendocrine and biochemical variables responses of birds exposed to a heat stressor applied during daylight hours, during the chronic stress and the recovery periods. We hypothesize that variables involved in the birds response will be differentially and gradually modified during those periods. Female quail (n = 210) were housed in six rearing boxes. At 29 days of age, the temperature in three boxes was increased from 24 to 34 °C during the light period throughout the nine days (Stress Treatment). The other three boxes remained at 24 °C and were used as controls. The subsequent 12 days were considered as recovery period. Different sets of 12 birds/treatment were blood-sampled at 29 (basal), 32, 35, 38 (stress), 41, 44, 47, and 50 (recovery) days of age, respectively. Immunoendocrine (corticosterone, lymphoproliferation, heterophil/lymphocyte ratio (H/L), and antibody response) and biochemical (glucose, total proteins, globulins, and albumin) variables were assessed. During stress, progressive corticosterone and H/L increments, and antibody titers and lymphoproliferation decreases were detected. No clear pattern of changes was found in biochemical variables. During recovery, while corticosterone and lymphoproliferation had recovered three days after the stressor ended, H/L and antibody responses required respectively nine and 12 days to recover to their basal levels, respectively. Findings suggest that immunity is already threatened when heat stress is sustained for three or more days. However, the system appears resilient, needing six to 12 days to recover to their basal responses.
Effect of Mild-to-Moderate Smoking on Viral Load, Cytokines, Oxidative Stress, and Cytochrome P450 Enzymes in HIV-Infected Individuals

Mild-to-moderate tobacco smoking is highly prevalent in HIV-infected individuals, and is known to exacerbate HIV pathogenesis. The objective of this study was to determine the specific effects of mild-to-moderate smoking on viral load, cytokine production, and oxidative stress and cytochrome P450 (CYP) pathways in HIV-infected individuals who have not yet received antiretroviral therapy (ART). Thirty-two human subjects were recruited and assigned to four different cohorts as follows: a) HIV negative non-smokers, b) HIV positive non-smokers, c) HIV negative mild-to-moderate smokers, and d) HIV positive mild-to-moderate smokers. Patients were recruited in Cameroon, Africa using strict selection criteria to exclude patients not yet eligible for ART and not receiving conventional or traditional medications. Those with active tuberculosis, hepatitis B or with a history of substance abuse were also excluded. Our results showed an increase in the viral load in the plasma of HIV positive patients who were mild-to-moderate smokers compared to individuals who did not smoke. Furthermore, although we did not observe significant changes in the levels of most pro-inflammatory cytokines, the cytokine IL-8 and MCP-1 showed a significant decrease in the plasma of HIV-infected patients and smokers compared with HIV negative non-smokers. Importantly, HIV-infected individuals and smokers showed a significant increase in oxidative stress compared with HIV negative non-smoker subjects in both plasma and monocytes. To examine the possible pathways involved in increased oxidative stress and viral load, we determined the mRNA levels of several antioxidant and cytochrome P450 enzymes in monocytes. The results showed that the levels of most antioxidants are unaltered, suggesting their inability to counter oxidative stress. While CYP2A6 was induced in smokers, CYP3A4 was induced in HIV and HIV positive smokers compared with HIV negative non-smokers. Overall, the findings suggest a possible association of oxidative stress and perhaps CYP pathway with smoking-mediated increased viral load in HIV positive individuals.
Interlaminar Fracture Behavior and Fiber Bridging of Glass-Epoxy Composite Under Mode I Static and Cyclic Loadings

Interlaminar fracture behavior of composite materials under static and cyclic loadings has been studied using a width tapered double cantilever beam specimen. The fracture energy is evaluated by compliance, beam and area methods. The comparison results show that the initial fracture energy could be evaluated either by beam or area method while the crack growth resistance could be calculated by compliance method. Increases in the criti cal load and fracture energy due to fiber bridging are predicted by a power function of fracture area. The interlaminar fatigue crack growth behavior is studied through the con stant cyclic strain energy release rate range test. A modification of Paris' power law is made to interpret fatigue crack growth under the influence of fiber bridging. The predicted fatigue life by the modified power law is reasonably close to the experimental data. Frac tography study shows that the interlaminar failure mechanism of a composite beam in volves fiber breakage, matrix tearing and transverse microcracking as well as the delamination of the layers.
Fast evaluation of 69 basal cell carcinomas with ex vivo fluorescence confocal microscopy: criteria description, histopathological correlation, and interobserver agreement.

IMPORTANCE Fluorescence confocal microscopy (FCM) represents a first step toward a rapid "bedside pathology" in the Mohs surgery setting and in other fields of general pathology. OBJECTIVE To describe and validate FCM criteria for the main basal cell carcinoma (BCC) subtypes and to demonstrate the overall agreement with classic pathologic analysis of hematoxylin-eosin-stained samples. DESIGN A total of 69 BCCs from 66 patients were prospectively imaged using ex vivo FCM. Confocal mosaics were evaluated in real time and compared with classic pathologic analysis. SETTING Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain, between November 2010 and July 2011. PARTICIPANTS Patients with BCC attending the Mohs Surgery Unit. MAIN OUTCOMES AND MEASURES Presence or absence of BCC and histological subtype (superficial, nodular, and infiltrating) in the confocal mosaics. Eight criteria for BCC were described, evaluated, and validated. RESULTS Although there were minor differences among BCC subtypes, the most BCC-defining criteria were peripheral palisading, clefting, nuclear pleomorphism, and presence of stroma. These criteria were validated with independent observers (κ values >0.7 [corrected] for most criteria). CONCLUSIONS AND RELEVANCE We herein propose, describe, and validate FCM criteria for BCC diagnosis. Fluorescence confocal microscopy is an attractive alternative to histopathologic analysis of frozen sections during Mohs surgery because large areas of freshly excised tissue can be assessed in real time without the need for tissue processing while minimizing labor and costs.
Reallocating Time to Sleep, Sedentary Time, or Physical Activity: Associations with Waist Circumference and Body Mass Index in Breast Cancer Survivors

Background: Moderate-to-vigorous intensity physical activity (MVPA) is inversely associated with waist circumference and body mass index (BMI) among breast cancer survivors. Limited research has focused on behaviors that account for larger portions of the day [sleep, sedentary time, and light-intensity physical activity (LPA)]. We investigated the interdependent associations of self-reported sleep, objectively assessed prolonged and short bouts of sedentary time, total LPA, and total MVPA with waist circumference and BMI. Methods: A cross-sectional sample of breast cancer survivors (N = 256, mean age = 60 years; mean time since diagnosis = 3 years) wore an Actigraph GT3X+ accelerometer during waking hours for 7 days. Participants completed the Pittsburgh Sleep Quality Index and self-reported their waist circumference, height, and weight. An isotemporal substitution approach was used in linear regression models to explore the associations of reallocating time to sleep, sedentary and active behaviors on waist circumference, and BMI, after adjusting for potential confounders. Results: Reallocating 30 minutes to MVPA was significantly associated with lower waist circumference when allocated from sleep (−2.50 cm), prolonged sedentary time (−2.51 cm), or LPA (−2.71 cm). Reallocating 30 minutes of prolonged sedentary time to nonprolonged sedentary time was significantly associated with lower waist circumference (−0.94 cm). Similar results were observed for BMI. Conclusions: Reallocating 30 minutes to MVPA was associated with significantly lower waist circumference and BMI, as was reallocating 30 minutes of prolonged sedentary time to 30 minutes of nonprolonged sedentary time. Impact: Increasing MVPA levels and decreasing time spent in prolonged, unbroken sedentary bouts may be avenues for improving body composition in this population. Cancer Epidemiol Biomarkers Prev; 26(2); 254–60. ©2016 AACR.
Genetic Mutations Associated with Isoniazid Resistance in Mycobacterium tuberculosis: A Systematic Review

Background Tuberculosis (TB) incidence and mortality are declining worldwide; however, poor detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple, rapid molecular diagnostic tests have recently been developed to detect genetic mutations in Mycobacterium tuberculosis (Mtb) genes known to confer first-line drug resistance. Their utility, though, depends on the frequency and distribution of the resistance associated mutations in the pathogen population. Mutations associated with rifampicin resistance, one of the two first-line drugs, are well understood and appear to occur in a single gene region in >95% of phenotypically resistant isolates. Mutations associated with isoniazid, the other first-line drug, are more complex and occur in multiple Mtb genes. Objectives/Methodology A systematic review of all published studies from January 2000 through August 2013 was conducted to quantify the frequency of the most common mutations associated with isoniazid resistance, to describe the frequency at which these mutations co-occur, and to identify the regional differences in the distribution of these mutations. Mutation data from 118 publications were extracted and analyzed for 11,411 Mtb isolates from 49 countries. Principal Findings/Conclusions Globally, 64% of all observed phenotypic isoniazid resistance was associated with the katG315 mutation. The second most frequently observed mutation, inhA-15, was reported among 19% of phenotypically resistant isolates. These two mutations, katG315 and inhA-15, combined with ten of the most commonly occurring mutations in the inhA promoter and the ahpC-oxyR intergenic region explain 84% of global phenotypic isoniazid resistance. Regional variation in the frequency of individual mutations may limit the sensitivity of molecular diagnostic tests. Well-designed systematic surveys and whole genome sequencing are needed to identify mutation frequencies in geographic regions where rapid molecular tests are currently being deployed, providing a context for interpretation of test results and the opportunity for improving the next generation of diagnostics.
Realistic Evaluation of Semi-Supervised Learning Algorithms

Semi-supervised learning (SSL) provides a powerful framework for leveraging unlabeled data when labels are limited or expensive to obtain. SSL algorithms based on deep neural networks have recently proven successful on standard benchmark tasks. However, we argue that these benchmarks fail to address many issues that these algorithms would face in real-world applications. After creating a unified reimplementation of various widelyused SSL techniques, we test them in a suite of experiments designed to address these issues. We find that the performance of simple baselines which do not use unlabeled data is often underreported, that SSL methods differ in sensitivity to the amount of labeled and unlabeled data, and that performance can degrade substantially when the unlabeled dataset contains out-of-class examples. To help guide SSL research towards real-world applicability, we make our unified reimplemention and evaluation platform publicly available.
Gold Nanomaterial Uptake from Soil Is Not Increased by Arbuscular Mycorrhizal Colonization of Solanum Lycopersicum (Tomato)

Bioaccumulation of engineered nanomaterials (ENMs) by plants has been demonstrated in numerous studies over the past 5–10 years. However, the overwhelming majority of these studies were conducted using hydroponic systems and the degree to which the addition of the biological and chemical components present in the soil might fundamentally alter the potential of plant bioaccumulation of ENMs is unclear. Here, we used two genotypes of Solanum lycopersicum (tomato), reduced mycorrhizal colonization (rmc), a mutant which does not allow arbuscular mycorrhizal fungi (AMF) colonization, and its progenitor, 76R, to examine how colonization by AMF alters trends of gold ENM bioaccumulation from a natural soil. Gold was taken up and bioaccumulated by plants of both genotypes. Gold concentrations were significantly higher in the rmc treatment although this was likely attributable to the large differences in biomass between the 76R and rmc plants. Regardless, there was little evidence that AMF played a significant role in trafficking Au ENMs into the plants. Furthermore, despite very low NH4NO3 extractable Au concentrations, Au accumulated at the root-soil interface. Although this observation would seem to suggest that ENMs may have potential to influence this particularly biologically active and important soil compartment, we observed no evidence of this here, as the 76R plants developed a robust AMF symbiosis despite accumulation of Au ENMs at the rhizoplane.