Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae)

Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD) were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation.
Comprehensive Modeling of Corneal Alkali Injury in the Rat Eye

ABSTRACT Purpose: To characterize the molecular, clinical, and histopathological profiles in the rat cornea after alkali injury over a 21-day period. Methods: Alkali injury was induced in one eye of male Lewis rats. Corneal opacity and corneal neovascularization were assessed daily. Real-time qRT-PCR analysis and immunohistochemical staining were conducted to examine inflammation, neovascularization, and fibrosis. Results: We found that within 2 hours of chemical exposure, corneal opacification rapidly developed with an acute increase in various cytokine expressions, while several cytokines demonstrated a secondary peak by day 7. Early neutrophil infiltration peaked at day 1 post-injury while macrophage infiltration peaked at day 7. Throughout the time course of the study, corneal opacity persisted and neovascularization, lymphangiogenesis, and fibrosis progressed. Conclusions: This study highlights the molecular, clinical, and histopathological changes throughout the progression of alkali injury in the rat cornea. These profiles will assist in the development of new strategies and therapies for ocular alkali injury.
Across-ear stimulus-specific adaptation in the auditory cortex

The ability to detect unexpected or deviant events in natural scenes is critical for survival. In the auditory system, neurons from the midbrain to cortex adapt quickly to repeated stimuli but this adaptation does not fully generalize to other rare stimuli, a phenomenon called stimulus-specific adaptation (SSA). Most studies of SSA were conducted with pure tones of different frequencies, and it is by now well-established that SSA to tone frequency is strong and robust in auditory cortex. Here we tested SSA in the auditory cortex to the ear of stimulation using broadband noise. We show that cortical neurons adapt specifically to the ear of stimulation, and that the contrast between the responses to stimulation of the same ear when rare and when common depends on the binaural interaction class of the neurons.
Clonal Comparison of Staphylococcus aureus Isolates from Healthy Pig Farmers, Human Controls, and Pigs

Pig farming is a risk factor for increased nasal Staphylococcus aureus colonization. Using sequence typing and phylogenetic comparisons, we showed that overcolonization of farmers was caused by a few bacterial strains that were not present in nonfarmers but often caused swine infections. This finding suggests a high rate of strain exchange between pigs and farmers.
Nonappearance of vortices in fast mechanical expansions of liquid He=4 through the lambda transition

A new experiment has been performed to study the formation of topological defects (quantized vortices) during rapid quenches of liquid He-4 through the superfluid transition, with particular care taken to minimize vortex creation via conventional hydrodynamic flow processes. It is found that the generated vortices, if any, are being produced at densities at least 2 orders of magnitude less than might be expected on the basis of the Kibble-Zurek mechanism.
A Generic Large Scale Simulator for Ubiquitous Computing

The complexity associated to gathering and processing contextual data makes testing mobile context-aware applications and services difficult. Furthermore, the lack of standard data sets and simulation tools makes the evaluation of machine learning algorithms in context-aware settings an even harder task. To ease the situation, we introduce a generic simulator that has been designed with the above mentioned purposes in mind. The simulator has also proven to be a good demonstration tool for mobile services and applications that are aimed at groups. The simulator is highly customizable and it can output context information of individual entities both through an interactive GUI and as data streams consisting of comma separated values. To support a wide range of tasks and scenarios, we have separated the three main information sources: behavior of agents, the scenario being simulated and the used context variable. The simulator has been implemented using Java, and the data streams have been made available through a Web service interface
Production–perception entrainment in speech rhythm

The article reports favorable initial results to the hypoth esis that rhythm perception can be seen as a listener–speake r entrainment process. The data comes from an experiment in which subjects had to detect a click in test sentences. Each sentence contained one click that was associated to one of th syllables of two consecutive stress groups defined by durati on criteria. Reaction time (RT) to click detection is assumed t o reflect the degree of listener-speaker entrainment: faster de ction meaning stronger entrainment. Results show that the closer t the phrasally stressed syllable the click is the faster the R T is. The crucial result concerning our working hypothesis, thou gh, is that RT slows down after the stress group boundary, resumi ng its decrease trend afterwards. Multiple linear regression analysis performed on different acoustical parameters of the te st sentences shows that duration and F0 explain around 50% of RT variance. We interpreted these results as a positive prel iminary corroboration of the entrainment hypothesis by showi ng that boundaries in the spoken utterances seem to trigger a re set in entrainment activity and that duration seems to be the mai n acoustical feature driving listeners’ behavior.
Image denoising using dual tree statistical models for complex wavelet transform coefficient magnitudes

Wavelet shrinkage is a standard technique for denoising natural images. Originally proposed for univariate shrinkage in the Discrete Wavelet Transform (DWT) domain, it has since been optimised through the exploitation of translationally invariant wavelet decompositions such as the Dual-Tree Complex Wavelet Transform (DT-CWT) alongside bivariate analysis techniques that condition the shrinkage on spatially related coefficients across neighbouring scales. These more recent techniques have denoised the real and imaginary components of the DT-CWT coefficients separately. Processing real and imaginary components separately has been found to lead to an increase in the phase noise of the transform which in turn affects denoising performance. On this basis, the work presented in this paper offers improved denoising performance through modelling the bivariate distribution of the coefficient magnitudes. The results were compared to the current state of the art non-local means denoising technique BM3D, showing clear subjective improvements, through the retention of high frequency structural and textural information. The paper also compares objective measures, using both PSNR and the more perceptually valid structural similarity measure (SSIM). Whereas PSNR results were slightly below those for BM3D, those for SSIM showed closer correlation with subjective assessment, indicating improvements over BM3D for most noise levels on the images tested.
Numbers in Space: Differences between Concrete and Abstract Situations

Numbers might be understood by grounding in spatial orientation, where small numbers are represented as low or to the left and large numbers are represented as high or to the right. We presented numbers in concrete (seven shoes in a shoe shop) or abstract (29 – 7) contexts and asked participants to make relative magnitude judgments. Following the judgment a target letter was presented at the top or bottom (Experiments 1–3) or left or right (Experiment 4) of the visual field. Participants were better at identifying letters at congruent than incongruent locations, but this effect was obtained only when numbers were presented in concrete contexts. We conclude that spatial grounding might have a smaller role for numbers in abstract than in concrete context.
Reviewing the Health of Software Ecosystems - A Conceptual Framework Proposal

The health of a software ecosystem is an indication of how well the ecosystem is functioning. The measurement of health can point to issues that need to be addressed in the ecosystem and areas for the ecosystem to improve. However, the software ecosystem field lacks an applicable way to measure and evaluate health. In this work, we review the literature related to the concept of software ecosystem health and the literature that inspired the software ecosystem health literature (a total of 23 papers) and (i) identify that the main source of inspiration is the health of business ecosystems while also influenced by theories from natural ecosystems and open source, (ii) identify two areas where software ecosystems differ from business and natural ecosystems, and (iii) propose a conceptual framework for defining and measuring the health of software ecosystems.
Summary of Weld Residual Stress Analyses for Dissimilar Metal Weld Nozzles

Flaw indications have been found in some dissimilar metal nozzle to stainless steel piping welds in pressurized water reactors (PWR) throughout the world. The nozzle welds usually involve welding ferritic (often A508) nozzles to 304/316 stainless steel pipe using Alloy 182/82 weld metal. Due to an unexpected aging issue with the weld metal, the weld becomes susceptible to a form of corrosion cracking referred to as primary water stress corrosion cracking (PWSCC). It can occur if the temperature is high enough (usually >300C) and the water chemistry in the PWR is typical of operating plants. This paper represents one of a series of papers which examine the propensity for cracking in a particular operating PWR in the UK. This paper represents an examination of the weld residual stress distributions which occur in four different size nozzles in the plant. Companion papers in this conference examine crack growth and PWSCC mitigation efforts related to this plant. British Energy (BE) has developed a work program to assess the possible impact of PWSCC on dissimilar metal welds in the primary circuit of the Sizewell ‘B’ pressurized water reactor. This effort has included the design and manufacture of representative PWR safety/relief valve nozzle welds both with and without a full structural weld overlay, multiple residual stress measurements on both mock-ups using the deep hole and incremental deep hole methods, and a number of finite element weld residual stress simulations of both the mock-ups and equivalent plant welds. This work is summarized in companion papers [1–3]. Here, the detailed weld residual stress predictions for these nozzles are summarized. The weld residual stresses in a PWR spray nozzle, safety/relief nozzle, surge nozzle, and finally a steam generator hot-leg nozzle are predicted here using an axis-symmetric computational weld solution process. The residual stresses are documented and these feed into a natural crack growth analysis provided in a companion PVP 2010-25162 paper [1]. The solutions are made using several different constitutive models: kinematic hardening, isotropic hardening, and a mixed hardening model. Discussion will be provided as to the appropriateness of the constitutive model for multi-pass DM weld modeling. In addition, the effect of including or neglecting the post-weld heat treatment process, which typically occurs after the buttering process in a DM weld, is presented. During operation the DM welds in a PWR experience temperatures in excess of 300°C. The coefficient of thermal expansion (CTE) mismatch between the three materials, particularly the higher CTE in the stainless steel, affects the stresses at operating temperature. The K-weld geometry used in the steam generator nozzles in this plant combines with CTE mis-match effects to result in service stresses somewhat different from V-weld groove cases.Copyright © 2010 by ASME
Experimental Investigation of Large Time–Bandwidth Product Photonic Hilbert Transformer Based on Compact Bragg Grating

We propose and experimentally demonstrate an integrated photonic Hilbert transformer (PHT) with substantial time bandwidth product (TBP). Due to the current substrate material and fabrication technique, PHT devices find it challenging to achieve ultrawide operative bandwidth while maintaining the minimum bandwidth level presented as the narrow central notch in frequency response. This implies that the TBP value is restricted. Here, we investigate the synthesized refractive index profile in compact Bragg grating design for theoretical simulation and the linearity-enhanced direct UV grating writing fabrication for experimental implementation. The fabricated device could process microwave photonic signals as Hilbert transformation between 50 GHz and 3 THz, with the TBP above 60, which is the largest experimental data to the best of our knowledge. This technique allows the PHT with improved spectral performance to be suitable for analog all-optical signal processing.
FDI Inflows, Price and Exchange Rate Volatility: New Empirical Evidence from Latin America

This paper investigates the impact of price and real exchange rate volatility on Foreign Direct Investment (FDI) inflows in a panel of 10 Latin American and Caribbean countries, observed between 1990 and 2012. Both price and exchange rate volatility series are estimated through the Generalized Autoregressive Conditional Heteroscedasticity model (GARCH). Our results obtained, employing the Fixed Effects estimator, confirm the theory of hysteresis and option value, in so far as a statistically significant negative effect of exchange rate volatility on FDI is found. Price volatility, instead, turns out to be positive but insignificant. Moreover, we show that human capital and trade openness are key for attracting foreign capital. From the policy perspective, our analysis suggests the importance of stabilization policies as well as the policy of government credibility in promoting trade openness and human capital formation.
Filling holes on the surface of 3D point clouds based on tangent plane of hole boundary points

Filling the holes of a triangular mesh has been studied for many years in the field of geometric modeling. This research is one of the reconstructing steps of a triangular mesh (or called refinement of a mesh) in order to improve the quality of a 3D triangular surface. With the same idea of hole filling in a mesh, filling in the holes of a 3D point cloud is still a challenge to the researchers. This paper describes a method for filling holes in an elevation surface of 3D point clouds structured in a 3D grid. The novelty of the method is processed directly on the 3D point clouds consisting of two steps. In the first step, we determine the boundary of hole. In the second step, we fill the holes based on the computation of tangent plane for each boundary point. Following clock-wise direction on the hole boundary, we compute and insert missing points on each tangent plane. This process is repeated and refined ring by ring from the hole boundary to the inside of the hole. The obtained results show that the processing time of algorithm is very fast, the output surfaces preserve their initial shapes and local curvatures.
Exploration of Preterm Birth Rates Using the Public Health Exposome Database and Computational Analysis Methods

Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother’s age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques) representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%). Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births.
Belief Propagation by Message Passing in Junction Trees: Computing Each Message Faster Using GPU Parallelization

Compiling Bayesian networks (BNs) to junction trees and performing belief propagation over them is among the most prominent approaches to computing posteriors in BNs. However, belief propagation over junction tree is known to be computationally intensive in the general case. Its complexity may increase dramatically with the connectivity and state space cardinality of Bayesian network nodes. In this paper, we address this computational challenge using GPU parallelization. We develop data structures and algorithms that extend existing junction tree techniques, and specifically develop a novel approach to computing each belief propagation message in parallel. We implement our approach on an NVIDIA GPU and test it using BNs from several applications. Experimentally, we study how junction tree parameters affect parallelization opportunities and hence the performance of our algorithm. We achieve speedups ranging from 0.68 to 9.18 for the BNs studied.
A multi-class SVM classiﬁer ensemble for automatic hand washing quality assessment

Hand washing is a critical activity in preventing the spread of infection in health-care environments. Several guidelines recommended a hand washing protocol consisting of six steps that ensure that all areas of the hands are thoroughly cleaned. In this paper, we describe a novel approach that uses a computer vision system to monitor the user’s hands motions in order to ensure that the hand washing guidelines are followed. This work presents two main contributions: a description of a system which delivers robust segmentation of the hands using a combination of colour and motion analysis, and the implementation of a multi-class classiﬁcation of the hand gestures using a SVM ensemble. The system performance is analysed and compared with human performance, showing an accuracy close to that of human experts
Progress toward Understanding the Neurophysiological Basis of Predator‐Induced Morphology in Daphnia pulex

Previous studies have demonstrated that certain pesticides, including carbaryl and endosulfan, can modulate the expression of predator‐induced morphology in Daphnia. These pesticides affect the transmission of nervous impulses in vertebrates and invertebrates. The aim of this study was to determine the role of two neurotransmitter systems, excitatory cholinergic transmission and inhibitory γ‐aminobutyric acid (GABA)‐mediated transmission, in the regulation of inducible defenses of Daphnia. The effects of chemicals with four different modes of action on the expression of Chaoborus‐induced neckteeth in Daphnia pulex were measured. These chemicals included chemicals that could enhance transmission at cholinergic synapses (physostigmine, nicotine), inhibit cholinergic transmission (atropine), stimulate or enhance the effects of GABA (diazepam, muscimol, cis‐4‐aminocrotonic acid), or antagonise the action of GABA (picrotoxin, bicuculline, SR95531). The development of Chaoborus‐induced neckteeth in D. pulex was enhanced by physostigmine and picrotoxin and suppressed by atropine. It was proposed that these chemicals were acting on neurosecretory cells that release the hormones necessary to induce neckteeth development. The results also indicate mechanisms through which anthropogenic pollutants could influence the expression of inducible defenses, leading to inappropriate expression in environments with low predator intensity or to suppression in environments with high risks of predation.
Social jetlag affects subjective daytime sleepiness in school-aged children and adolescents: A study using the Japanese version of the Pediatric Daytime Sleepiness Scale (PDSS-J)

ABSTRACT The aim of this study was to elucidate the level of daytime sleepiness in Japanese school-aged children and adolescents, and to examine associated factors including sleep loss and social jetlag using the Japanese version of the Pediatric Daytime Sleepiness Scale (PDSS-J). After the linguistic validation of the PDSS-J with a multi-step translation methodology, consisting of forward translation, back translation, expert review and cognitive debriefing interviews, we conducted a psychometric validation for 492 students aged 11–16 years (46.7% boys) of public elementary school, junior high school and high school, using the PDSS-J, the Karolinska Sleepiness Scale (KSS), and bedtimes and wake-up times on school days and free days. Internal consistency (Cronbach’s alpha) of the PDSS-J was 0.77, and the test–retest reliability demonstrated by the intraclass coefficient was 0.88. Multivariate logistic regression analysis revealed that both short sleep duration and social jetlag were identified as factors associated with daytime sleepiness, after adjustment for age and sex. PDSS-J scores were significantly higher in the group with large social jetlag with or without sufficient sleep duration than in the group with sufficient sleep duration and small social jetlag. The PDSS-J is an important tool for assessing daytime sleepiness, given its ease of administration and robust psychometric properties. The impact of not only sleep loss but also social jetlag on daytime sleepiness among school-aged children and adolescents must be fully taken into account.