Miracle-dz/UniFAR-FTUs huggingface dataset:
Landscape genetics, historical isolation and cross‐Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae)

Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape–Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross‐Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio‐genetic patterns. Individual‐based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron–Paute deflection. F‐statistics derived from BC suggested an east‐to‐west dispersal history. Population‐based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross‐Andean dispersal in the AHZ. Along the cline, gene flow measured as FST was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross‐Andean divergence took place during the Quaternary. Significant historical isolation (RST > FST) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.
The effect of adult criminals' spillovers on the likelihood of youths becoming criminals

We use a unique data set at the individual level to estimate an empirical model explaining the probability of young individuals to become criminals as a function of the presence of adult criminals in their neighborhoods, an a complete set of control variables, including census sector fixed effects. We use the census of criminals captured in Medellin between 2000 and 2010 to construct our peer´s variables, and find a strong and robust positive effect of the presence of adult criminal neighbors on the probability of becoming criminal. The result is robust across different specifications of the presence of criminals, and with respect to the probability of committing different types of crimes, even controlling for contextual and group effects. Both modeling peer effects as the sum of friends´ efforts and modeling them as deviations from the means, affect the likelihood to become criminal, although with differential importance by type of crime.
The sensitivity of beta to the time horizon when log prices follow an Ornstein–Uhlenbeck process

This paper provides a new theoretical approach to investigate the sensitivity of the familiar beta of the capital asset pricing model to the length of the return measurement interval; a phenomenon known as the intervalling effect. By setting the problem in a continuous time setting, and using exact results, we are able to generalize existing results in the literature. We derive an expression for beta as a function of the time horizon h, conditional on current time t. We show that beta is monotonic in h and derive conditions for it to be increasing or decreasing.
Computing the Pseudo-Inverse of a Graph's Laplacian Using GPUs

Many applications in network analysis require the computation of the network's Laplacian pseudo-inverse - e.g., Topological centrality in social networks or estimating commute times in electrical networks. As large graphs become ubiquitous, the traditional approaches - with quadratic or cubic complexity in the number of vertices - do not scale. To alleviate this performance issue, a divide-and-conquer approach has been recently developed. In this work, we take one step further in improving the performance of computing the pseudo-inverse of Laplacian by parallelization. Specifically, we propose a parallel, GPU-based version of this new divide-and-conquer method. Furthermore, we implement this solution in Mat lab, a native environment for such computations, recently enhanced with the ability to harness the computational capabilites of GPUs. We find that using GPUs through Mat lab, we achieve speed-ups of up to 320x compared with the sequential divide-and-conquer solution. We further compare this GPU-enabled version with three other parallel solutions: a parallel CPU implementation and CUDA-based implementation of the divide-and-conquer algorithm, as well as a GPU-based implementation that uses cuBLAS to compute the pseudo-inverse in the traditional way. We find that the GPU-based implementation outperforms the CPU parallel version significantly. Furthermore, our results demonstrate that a best GPU-based implementation does not exist: depending on the size and structure of the graph, the relative performance of the three GPU-based versions can differ significantly. We conclude that GPUs can be successfully used to improve the performance of the pseudo-inverse of a graph's Laplacian, but choosing the best performing solution remains challenging due to the non-trivial correlation between the achieved performance and the characteristics of the input graph. Our future work attempts to expose and exploit this correlation.
Adaptive control for nonlinear systems based on quasi-ARX neural network

When a linear model is used for controlling nonlinear systems solely, it can't satisfy accuracy requirement. Whereas, although a neural network can deal with the accuracy problem, it may lead to instability. In this paper, an adaptive controller is proposed for nonlinear dynamical systems based on linear model and quasi-ARX neural network model. A switching algorithm is designed between the linear and nonlinear models. Theory analysis and simulations are given to show the effectiveness of the proposed method both on stability and accuracy.
Robustness to Adversarial Examples through an Ensemble of Specialists

We are proposing to use an ensemble of diverse specialists, where speciality is defined according to the confusion matrix. Indeed, we observed that for adversarial instances originating from a given class, labeling tend to be done into a small subset of (incorrect) classes. Therefore, we argue that an ensemble of specialists should be better able to identify and reject fooling instances, with a high entropy (i.e., disagreement) over the decisions in the presence of adversaries. Experimental results obtained confirm that interpretation, opening a way to make the system more robust to adversarial examples through a rejection mechanism, rather than trying to classify them properly at any cost.
A Fast RPC System for Virtual Machines

Despite the advances in high performance interdomain communications for virtual machines (VM), data intensive applications developed for VMs based on the traditional remote procedure call (RPC) mechanism still suffer from performance degradation due to the inherent inefficiency of data serialization/deserilization operations. This paper presents VMRPC, a lightweight RPC framework specifically designed for VMs that leverages the heap and stack sharing mechanism to circumvent unnecessary data copy and serialization/deserilization. Our evaluation shows that the performance of VMRPC is an order of magnitude better than traditional RPC systems and existing alternative interdomain communication optimization systems. The evaluation on a VMRPC-enhanced networked file system across a varied range of benchmarks further reveals the competitiveness of VMRPC in IO-intensive applications.
Cognitive aging explains age-related differences in face-based recognition of basic emotions except for anger and disgust

ABSTRACT This study aimed at a detailed understanding of the possible dissociable influences of cognitive aging on the recognition of facial expressions of basic emotions (happiness, surprise, fear, anger, disgust, and sadness). The participants were 36 older and 36 young adults. They viewed 96 pictures of facial expressions and were asked to choose one emotion that best described each. Four cognitive tasks measuring the speed of processing and fluid intelligence were also administered, the scores of which were used to compute a composite measure of general cognitive ability. A series of hierarchical regression analyses revealed that age-related deficits in identifying happiness, surprise, fear, and sadness were statistically explained by general cognitive ability, while the differences in anger and disgust were not. This provides clear evidence that age-related cognitive impairment remarkably and differentially affects the recognition of basic emotions, contrary to the common view that cognitive aging has a uniformly minor effect.
The Truth is in There : Rule Extraction from Opaque Models Using Genetic Programming

A common problem when using complicated models for prediction and classification is that the complexity of the model entails that it is hard, or impossible, to interpret. For some scenarios this might not be a limitation, since the priority is the accuracy of the model. In other situations the limitations might be severe, since additional aspects are important to consider; e.g. comprehensibility or scalability of the model. In this study we show how the gap between accuracy and other aspects can be bridged by using a rule extraction method (termed G-REX) based on genetic programming. The extraction method is evaluated against the five criteria accuracy, comprehensibility, fidelity, scalability and generality. It is also shown how G-REX can create novel representation languages; here regression trees and fuzzy rules. The problem used is a data-mining problem from the marketing domain where the impact of advertising is predicted from investment plans. Several experiments, covering both regression and classification tasks, are evaluated. Results show that G-REX in general is capable of extracting both accurate and comprehensible representations, thus allowing high performance also in domains where comprehensibility is of essence.
Design for happiness: A telehomecare product case

In this paper a design approach is introduced for designing products to increase happiness. Happiness reflects the degree to which people’s concerns are fulfilled. Based on this fact, a framework of all human concerns was created. After that, the framework was applied to a telehomecare case. Telehomecare products release the pressure on healthcare by increasing the ability of people to manage on their own at home. When people become ill, their everyday life may change dramatically. People are no longer able to meet with specific concerns. In this study the unmet concerns of ill people coming from this change in their life were mapped on available telehomecare products, showing the gaps in the current assortment of telehomecare products. These gaps were used as starting point in developing product concepts.
Arabidopsis GLUTATHIONE REDUCTASE1 Plays a Crucial Role in Leaf Responses to Intracellular Hydrogen Peroxide and in Ensuring Appropriate Gene Expression through Both Salicylic Acid and Jasmonic Acid Signaling Pathways1[C][W][OA]

Glutathione is a major cellular thiol that is maintained in the reduced state by glutathione reductase (GR), which is encoded by two genes in Arabidopsis (Arabidopsis thaliana; GR1 and GR2). This study addressed the role of GR1 in hydrogen peroxide (H2O2) responses through a combined genetic, transcriptomic, and redox profiling approach. To identify the potential role of changes in glutathione status in H2O2 signaling, gr1 mutants, which show a constitutive increase in oxidized glutathione (GSSG), were compared with a catalase-deficient background (cat2), in which GSSG accumulation is conditionally driven by H2O2. Parallel transcriptomics analysis of gr1 and cat2 identified overlapping gene expression profiles that in both lines were dependent on growth daylength. Overlapping genes included phytohormone-associated genes, in particular implicating glutathione oxidation state in the regulation of jasmonic acid signaling. Direct analysis of H2O2-glutathione interactions in cat2 gr1 double mutants established that GR1-dependent glutathione status is required for multiple responses to increased H2O2 availability, including limitation of lesion formation, accumulation of salicylic acid, induction of pathogenesis-related genes, and signaling through jasmonic acid pathways. Modulation of these responses in cat2 gr1 was linked to dramatic GSSG accumulation and modified expression of specific glutaredoxins and glutathione S-transferases, but there is little or no evidence of generalized oxidative stress or changes in thioredoxin-associated gene expression. We conclude that GR1 plays a crucial role in daylength-dependent redox signaling and that this function cannot be replaced by the second Arabidopsis GR gene or by thiol systems such as the thioredoxin system.
A Comparative Study of Multicast Protocols: Top, Bottom, or In the Middle?

Multicast solutions have been evolving from "bottom" to "top", i.e., from IP layer (called IP multicast) to application layer (referred to as application layer multicast). Recently, there are some new proposals (named as overlay multicast) using certain "infrastructure" (composed of proxies) in the middle. Although it is well accepted that application layer multicast and overlay multicast are easier to deploy while sacrificing bandwidth efficiency compared with IP multicast, little research has been done to systematically evaluate and compare their performance. In this paper, we conduct a comparative study of different types of multicast routing protocols. We first present a qualitative comparison of three types of protocols, and then we provide a quantitative study of four representative protocols, namely, PIM-SSM, NARADA, NICE, and POM by extensive simulations. Our studies will help to answer some of the most important questions, such as which way to go: top, bottom, or in the middle?
Evaluation of an in Vitro Blood-Based Assay to Detect Production of Interferon-γ by Mycobacterium Bovis—Infected White-Tailed Deer (Odocoileus Virginianus)

Tuberculosis due to Mycobacterium bovis in captive Cervidae was identified as an important disease in the United States in 1990 and prompted the addition of captive Cervidae to the USDA Uniform Methods and Rules for eradication of bovine tuberculosis. As well, M. bovis infection was identified in free-ranging white-tailed deer in northeast Michigan in 1995. Tuberculosis in both captive and free-ranging Cervidae represents a serious challenge to the eradication of M. bovis infection from the United States. Currently, the only approved antemortem tests for tuberculosis in Cervidae are the intradermal tuberculin skin test and the blood tuberculosis test (BTB). At present, the BTB is not available in North America. Tuberculin skin testing of Cervidae is time-consuming and involves repeated animal handling and risk of injury to animals and humans. This study evaluated the potential of a new blood-based assay for tuberculosis in Cervidae that would decrease animal handling, stress, and losses due to injury. In addition, a blood-based assay could provide a more rapid diagnosis. Twenty 6–9-month-old white-tailed deer, male and female, were experimentally inoculated by instillation of 300 colony-forming units of M. bovis in the tonsillar crypts. Seven, age-matched uninfected deer served as controls. Blood was collected on days 90, 126, 158, 180, 210, 238, 263, and 307 after inoculation and was analyzed for the production of interferon-γ (IFN-γ) in response to incubation with M. bovis purified protein derivative (PPDb), M. avium PPDa, pokeweed mitogen (PWM), or media alone. Production of IFN-γ in response to PPDb was significantly greater (P < 0.05) at all time points in samples from M. bovis—infected deer as compared with uninfected control deer, whereas IFN-γ production to PWM did not differ significantly between infected and control deer. Measurement of IFN-γ production to PPDb may serve as a useful assay for the antemortem diagnosis of tuberculosis in Cervidae.
Motivational modulation of endogenous inputs to the superior colliculus

Proper initiation of saccadic eye movements depends on an intricate balance between exogenous and endogenous control mechanisms. The superior colliculus (SC) is a major site of signal integration that has been shown to drive the initiation of saccades in the brainstem. Previous work has shown that a winner-take-all mechanism implemented with a continuous attractor neural network (CANN) can explain and reproduce a multitude of behavioural findings, including the gap effect and the production of express saccades by K. Kopecz (1995) and by T.P. Trappenberg (2001). This investigation advances the CANN model of saccade initiation in several important ways in order to account for trial by trial adaptation of saccadic reaction times in a biologically plausible manner. A key hypothesis is that endogenous inputs to the intermediate layer of the SC can be adapted through motivationally-based feedback from other areas of the brain such as the basal ganglia or higher cortical areas.
WORD MORPHOLOGY ENHANCES READING FLUENCY IN CHILDREN WITH DEVELOPMENTAL DYSLEXIA

In orthographies with regular letter-to-sound mapping, such as German or Italian, the reading of children with de velopmental dy slexia is extre mely slow and fragmented; accuracy is also impaired, but to a considerably lesser extent than in opaque orthographies, such as English (Wimmer 1993; Zoccolotti et al. 1999). Italian children with developm ental dyslexia are markedly sensitive to stimulus length effects - with long words yielding much longer reaction times than short words - and are much slower than typically developing readers at reading aloud words and nonwords (Spinelli, De Luca, Di Filippo, Martelli, and Zoccolotti 2005; Zoccolotti et al. 2005). A consistent pattern is found when children’s eye movements are recorded during reading. Develop mental dyslexics exhibit extremely fractionated text scanning, as the y proceed through stimulus display making a large number of very small amplitude saccades; in addition, they show longer fixation durations than typically developing readers. This pattern holds not only in reading passages of text (De Luca, Di Pace, Judica, Spinelli, and Zoccolotti 1999), but also in reading lists of single words and nonwords (De Luca, Borrelli, Judica, Spinelli, and Zoccolotti 2002; see also Hutzler and Wimmer 2004). The characteristic impairment of reading fluency in children with dyslexia may be interpreted as due to the limitations of their perceptual span (Martelli, Di Filippo, Spinelli, and Zoccolotti 2009), which causes difficulties in processing word stimuli as whole-units. Similarly to children at an early
B3IA: A control architecture for autonomous robot-assisted behavior intervention for children with Autism Spectrum Disorders

This paper describes a novel control architecture, B3IA, designed to address the challenges of developing autonomous robot systems for use as behavior intervention tools for children with autism spectrum disorders (ASD). Our goal is to create a system that can be easily adapted for use by non-roboticists engaged in ASD therapy. B3IA is a behavior-based architecture for control of socially assistive robots using human-robot interaction in the ASD context. We hypothesize that the organization of a robot control architecture is important to the success of a robot-assisted intervention, because the success of such intervention hinges on the behavior of the robot. We detail the organization of B3IA and present preliminary results from experiments that begin to experimentally test this hypothesis.
Long Journey Home: Family Reunification Experiences of the Disappeared Children of El Salvador

Established in 1994, Salvadoran Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos (Association for the Search of Disappeared Children) has located 384 children, often with the aid of DNA evidence, of the more than 500 who went missing or were abducted during El Salvador’s civil war. Families in other countries who were unaware of the forced separations adopted many of these children. Between 2005 and 2009, we conducted semi-structured interviews with twenty-six children, now young adults aged twenty-four to thirty-four years, who had been reunited with their biological families. We found that we could conceptually categorize the process of separation and reunification into six phases: pre-disappearance, disappearance, separation, searching, reunion, and reunification. While these young adults said that reunification was extremely important, they often found this stage psychologically challenging, given their new identities and their uncertainty about how they would reintegrate back—if at all—into their biological families. We call this process “ambiguous reunification. ”
Delay Distribution Analysis of the RTS/CTS mechanism of IEEE 802.11

A simple and accurate packet delay distribution analysis is presented for the RTS/CTS access scheme of the IEEE 802.11 distributed coordination function (DCF). The packet delay distribution is effectively studied by developing an analytical model that calculates the probability that a packet is successfully transmitted after experiencing a delay time equal to a given value. The model uses simple mathematical relations and provides accurate delay distribution curves. The accuracy of the analytical model is verified by simulations
Multiple inducers of the Drosophila heat shock locus 93D (hsr omega): inducer-specific patterns of the three transcripts

The Drosophila hsr omega locus produces one of the largest and most active heat shock puffs, yet it does not encode a heat shock protein. Instead, this locus produces a distinctive set of three transcripts, all from the same start site. The largest transcript, omega 1, is limited to the nucleus and appears to have a role there. A second nuclear transcript, omega 2, is produced by alternative termination and contains the sequence found in the 5' 20-25% of omega 1 (depending on the Drosophila species). The cytoplasmic transcript, omega 3, is produced by removal of a 700-bp intron from omega 2. All three hsr omega RNAs are produced constitutively and production is enhanced by heat shock. In addition to being a member of the set of heat shock puffs, the hsr omega puff is induced by agents that do not affect other heat shock loci, suggesting that hsr omega is more sensitive to environmental changes than other loci. We report here that agents that induce puffing of hsr omega loci in polytene nuclei also lead to an increase in hsr omega transcripts in diploid cells. We also show that the relative levels of omega 1 and omega 3 can be modulated independently by several agents. All drugs that inhibit translation, either initiation or elongation, stabilize the omega 3 transcript, which normally turns over within minutes in control cells. Drugs (such as benzamide and colchicine) that induce puffing of hsr omega, but not other heat shock loci, lead to large increases in omega 1. Although the constitutive level of omega 1 is relatively stable, the drug-induced excess is lost rapidly when the drug is withdrawn. The relative levels of hsr omega transcripts may reflect different states in cellular metabolism.