Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

Detecting genetic signatures of selection is of great interest for many research issues. Common approaches to separate selective from neutral processes focus on the variance of FST across loci, as does the original Lewontin and Krakauer (LK) test. Modern developments aim to minimize the false positive rate and to increase the power, by accounting for complex demographic structures. Another stimulating goal is to develop straightforward parametric and computationally tractable tests to deal with massive SNP data sets. Here, we propose an extension of the original LK statistic (TLK), named TF–LK, that uses a phylogenetic estimation of the population's kinship (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{\mathcal{F}}\) \end{document}) matrix, thus accounting for historical branching and heterogeneity of genetic drift. Using forward simulations of single-nucleotide polymorphisms (SNPs) data under neutrality and selection, we confirm the relative robustness of the LK statistic (TLK) to complex demographic history but we show that TF–LK is more powerful in most cases. This new statistic outperforms also a multinomial-Dirichlet-based model [estimation with Markov chain Monte Carlo (MCMC)], when historical branching occurs. Overall, TF–LK detects 15–35% more selected SNPs than TLK for low type I errors (P < 0.001). Also, simulations show that TLK and TF–LK follow a chi-square distribution provided the ancestral allele frequencies are not too extreme, suggesting the possible use of the chi-square distribution for evaluating significance. The empirical distribution of TF–LK can be derived using simulations conditioned on the estimated \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{\mathcal{F}}\) \end{document} matrix. We apply this new test to pig breeds SNP data and pinpoint outliers using TF–LK, otherwise undetected using the less powerful TLK statistic. This new test represents one solution for compromise between advanced SNP genetic data acquisition and outlier analyses.
Identification of Influenza A/H7N9 Virus Infection-Related Human Genes Based on Shortest Paths in a Virus-Human Protein Interaction Network

The recently emerging Influenza A/H7N9 virus is reported to be able to infect humans and cause mortality. However, viral and host factors associated with the infection are poorly understood. It is suggested by the “guilt by association” rule that interacting proteins share the same or similar functions and hence may be involved in the same pathway. In this study, we developed a computational method to identify Influenza A/H7N9 virus infection-related human genes based on this rule from the shortest paths in a virus-human protein interaction network. Finally, we screened out the most significant 20 human genes, which could be the potential infection related genes, providing guidelines for further experimental validation. Analysis of the 20 genes showed that they were enriched in protein binding, saccharide or polysaccharide metabolism related pathways and oxidative phosphorylation pathways. We also compared the results with those from human rhinovirus (HRV) and respiratory syncytial virus (RSV) by the same method. It was indicated that saccharide or polysaccharide metabolism related pathways might be especially associated with the H7N9 infection. These results could shed some light on the understanding of the virus infection mechanism, providing basis for future experimental biology studies and for the development of effective strategies for H7N9 clinical therapies.
GUIDE2ux: a GUI design environment for enhancing the user experience.

For the design and development of graphical user interfaces, designers have to take various guidelines, standards and target platform characteristics into account. This is often a hard and time consuming activity because guidelines are spread over multiple documents using different styles, and furthermore it requires considerable effort to verify whether a design will work well on the targeted device. We propose GUIDE2ux, a design environment that (1) identifies and shows usability problems automatically and (2) facilitates designers to verify their designs on the target device easily. With GUIDE2ux, we make design standards more accessible for designers and help them to improve and test the user experience of their designs.
Estimating Mean Time to Failure in Digital Systems Using Manufacturing Defective Part Level

Companies spend a great deal of resources testing their circuits and systems to ensure that very few defective parts reach their customers. Unfortunately, some defective parts always escape the testing process, and the number of these escapes is identified as the defective part level. However, while defective part level is an invaluable metric for both industry and its customers, another important metric is MTTF (mean time to failure) for those defective parts. Specifically, the shorter the time to failure, the more vital it is that that part be screened out as defective during the testing process. In this paper we present preliminary work for predicting MTTF from data obtained during manufacture testing.
Direction of arrival estimation using nonlinear function of sum and difference beam

In this paper, a high resolution direction of arrival (DOA) estimation algorithm is proposed that based on the usage of nonlinear function of sum and difference beam. The generalized expression of this technique for different scenarios was derived in details. Unlike the conventional high resolution algorithm such as the MVDR, the MUSIC, and the ESPRIT, the proposed algorithm keeps the high resolution ability under low Signal-to-Noise Ratio (SNR) conditions. In addition, the proposed algorithm is suitable for real-time applications in that it has low computation complexity. Simulation results verified the validity of the proposed algorithm.
Structure preserving model reduction of large-scale second-order linear dynamical systems

Second-order linear dynamical systems appear in many physical systems of interests such as electrical, mechanical, electromechanically coupled, and thermomechanically coupled systems. When continuous systems of these types are discretized by a numerical method they lead to a large-scale system of equations which one must solve to obtain either the transient or steadystate behavior. In many cases one is interested in specific behavior, for example the response output of a scalar quantity of the system with respect to a scalar input quantity. This system can be characterized by the time-invariant single-input single-output second-order system of equations,
Rejection and Dating-app Experiences in Those with a History of Self-harm

Background: Rejection is an adverse experience that may help explain the heightened risk of self-harm and suicide amongst many societal groups. The aim of this systematic review was to determine the relationship between rejection experiences and self-harm and suicidal ideation. Methods: The databases PsychINFO, CINAHL, Medline and Web of Science were searched from inception until May 2017 using key search terms. Quantitative studies were included if they had: i) mean sample age over 18, ii) in the English language, iii) and had a measure of self-harm or suicidal behaviour and a measure of rejection. The results were synthesised narratively. Results: Eighteen studies were identified for the review. Fifteen out of the eighteen studies found a significant positive association between rejection and self-harm. This association was identified within several marginalised groups known to be at risk of selfharm, including those from lesbian, gay or bisexual sexuality or those who identify as transgender. However, heterogeneity between the measures of self-harm, suicidal behaviour and rejection, as well as the lack of longitudinal analyses made it difficult to draw firm conclusions. Conclusion: Perceived rejection may leave some individuals at risk of self-harm and might account for the elevated risk in marginalised societal groups. Interventions focused on modifying rejection experiences may help reduce the risk of self-harm in this population.
Small insect measurements using a custom MEMS force sensor

A multi-axis sensor with micro-Newton force resolution has been designed and fabricated for the purpose of studying the biomechanics of insect locomotion. The sensor comprises a rigid central plate supported at each corner by thin beams with piezoresistive transducers sensitive to both normal and in plane forces. The sensor is configured to measure the instantaneous ground reaction force components produced by insects as large as cockroaches when they step onto the sensor plate during walking or running. This paper describes the results of analytical modeling and finite element simulations used to characterize the performance and mechanical behavior of the sensor microstructure.
New design error modeling and metrics for design validation

When simulation is used for design verification, a subset of simulation input patterns is used, since exhaustive simulation is usually not practical. This produces uncertainty as to how much of the design has been verified. To provide a measure of the simulation pattern coverage based on design error modeling, a new simulation coverage metric is introduced. This measure is useful for obtaining insight into the actual level of design validation, since it provides more realistic results than those which are presently available. <<ETX>>
Social Dysfunction and Diet Outcomes in People with Psychosis

This analysis aimed to examine the association of social dysfunction with food security status, fruit intake, vegetable intake, meal frequency and breakfast consumption in people with psychosis from the Hunter New England (HNE) catchment site of the Survey of High Impact Psychosis (SHIP). Social dysfunction and dietary information were collected using standardised tools. Independent binary logistic regressions were used to examine the association between social dysfunction and food security status, fruit intake, vegetable intake, meal frequency and breakfast consumption. Although social dysfunction did not have a statistically significant association with most diet variables, participants with obvious to severe social dysfunction were 0.872 (95% CI (0.778, 0.976)) less likely to eat breakfast than those with no social dysfunction p < 0.05. Participants with social dysfunction were therefore, 13% less likely to have breakfast. This paper highlights high rates of social dysfunction, significant food insecurity, and intakes of fruits and vegetables below recommendations in people with psychosis. In light of this, a greater focus needs to be given to dietary behaviours and social dysfunction in lifestyle interventions delivered to people with psychosis. Well-designed observational research is also needed to further examine the relationship between social dysfunction and dietary behaviour in people with psychosis.
A Conceptual Design Model for High Performance Hotspot Network Infrastructure (GRID WLAN).

The emergence of wireless networking technologies for large enterprises, operators (service providers), small-medium organizations, has made hotspot solutions for metropolitan area networks (MAN), last mile wireless connectivity, mobile broadband solutions, IP-based cellular phones (VOIP) and other event-based wireless solutions in very high demand. Wireless radio gateways (routers and access points) with its wide-spread deployment has made Wi-Fi an integral part of today’s hotspot access technology in organizational models. Despite its role in affecting performance for mobility market segments, previous research has focused on media access control (MAC) protocol techniques , carrier sense multiple access with collision avoidance (CSMA/CA), fair scheduling, and other traffic improvement methodologies without detailed consideration for virtual switch partitioning for load balancing, reliable fragmentation capacities, buffer size dependencies, load effects, queuing disciplines as well as hotspot access control framework. This paper proposes a conceptual high performance hotspot solution (GRID WLAN) and through simulations with OPNET modeler, presents efficient performance metrics for its deployment. Considering the GRID WLAN access points in context, the results shows that with the design model, a careful selection of buffer sizes, fragmentation threshold, network management framework with network load intensity will guarantee an efficient hotspot solution.
Influence of low-and high-protein diets on glucose homeostasis in the rat

1. The influence of the protein content of the diet on glucose homeostasis was studied in the rat. Rats of 28 d of age received ad lib. a control diet containing (g/kg) 150 protein (Pl5), or a diet containing 50 protein (P5) or 450 protein (P45). Since P5 rats spontaneously reduced their food intake, a fourth group of rats (P25) received the same amount of energy as P5 rats and the same amount of protein as P15 rats. 2. After 12-13 weeks on these diets, plasma glucose and insulin levels were similar in fed P45, P25 and control PI5 rats, but were lower in P5 rats. In fasted animals, plasma glucose and insulin levels were also decreased in P5 rats, whereas plasma glucose levels were increased in both P45 and P25 animals. 3. During an oral glucose tolerance test, the glucose rise was only slightly larger in P5 than in PI5 rats in spite of a considerably smaller increase in insulin levels. P45 rats displayed a normal tolerance to glucose with a normal insulin response, whereas tolerance to glucose was slightly poorer in P25 rats in spite of a normal insulin response. 4. Pancreatic insulin stores were lower in P5 than in control PI5 rats, not only because of the smaller size of their pancreas, but also because of a decrease in the insulin concentration in the gland. A much smaller decrease was also observed in P25 rats, whereas insulin reserves were not altered in P45 rats. 5. It is concluded that the changes in glucose homeostasis observed in protein+nergy malnutrition (P5 rats) are due to protein deprivation rather than to energy deprivation. A high-protein diet has little influence on glucose homeostasis in the rat.
Personal DLP for Facebook

Data Loss Prevention (DLP) is a well-established security and privacy concept in enterprise environments: Enterprise DLP tools scan outgoing messages and stop unintended information flows. It may catch malicious insiders, but the main use case is avoiding data leaks due to human errors. Good DLP tools prevent careless employees from doing something they would probably regret if made aware of. Individuals using online social networks are in a very similar situation: Often they share the wrong information with the wrong people, unaware of the risks and often even unaware of the technical meaning of what they are doing. Personal DLP, introduced in this paper, extends the notion of DLP to individual users. It makes the individual users aware of risks and mistakes, and it does so based on rules explicitly set by each user, and rules derived from that users' past behavior and individual settings. Personal DLP raises awareness by explaining the risks, but the final decision is always with the user.
The Anatomy of a Collaborative Image Search System

“An image tells more than a thousand words”. Yet, while text searching on the Internet has become indispensable, with fast and scalable techniques, searching for images has not. The purpose of this paper is to design an infrastructure for an Internet-based Collaborative Image Search System (hereafter also called CISS ), using existing Information Retrieval techniques and adjusting them to work play nice with multimedia. For this purpose I will use relevance feedback, distributed indexing and distributed computing using Hadoop and HBase
Dynamics simulation on object handling tasks by using a myoelectric upper limb prosthesis with bimanual coordination

We have proposed the upper limb prosthesis control system which helps an amputee perform a two-handed task with the healthy arm and the prosthesis in our previous work. Our first focus was on motion generation of the prosthesis. However, ideal motion of the prosthesis does not guarantee success of a two-hand task because of interaction between the prosthesis and the handled object. In this paper, we demonstrated dynamics simulation of lifting-up-a-box tasks with the healthy arm and the prosthesis in order to evaluate effect of interaction between objects such as contact and friction on task performance. We prepared the five boxes with different size in order to consider training error and generalization error of the neural network based motion generation. We showed that lifting-up-a-box tasks with different boxes can be successfully completed on the dynamics simulation considering contact and friction by using our proposed prosthesis control system.
ARUBAS: An Association Rule Based Similarity Framework for Associative Classifiers

This article introduces ARUBAS, a new framework to build associative classifiers. In contrast with many existing associative classifiers, it uses class association rules to transform the feature space and uses instance-based reasoning to classify new instances. The framework allows the researcher to use any association rule mining algorithm to produce the class association rules. Every aspect of the framework is extensively introduced and discussed and five different fitness measures used for classification purposes are defined. The empirical results determine which fitness measure is the best and compares the framework with other classifiers. These results show that the ARUBAS framework is able to produce associative classifiers which are competitive with other classification techniques. More specifically, with ARUBAS-Scheffer-phi5 we have introduced a parameter-free algorithm which is competitive with classification techniques such as C4.5, RIPPER and CBA.
Asymptotic optimal tradeoff inMonteCarlo simulation of security prices

This paper presents an efficient algorithm for the allocation of computing resources to the problem of Monte Carlo simulation of continuous-time security prices. The asymptotic optimal tradeoff m = c n between increasing n, the number of time intervals and, increasing m, the number of simulations, given a limited budget of computer time, is found for the discrete-time Euler scheme. The constant c is estimated by ĉ from the first round simulations. An efficient algorithm, based on the second round simulations according to the optimal tradeoff m = ĉ n, is provided for the desired security price.
INTERDISCIPLINARY INTEGRATION IN PROFESSIONAL EDUCATION Tools and Analysis from Cultural Historical Activity Theory

The purpose of this paper is to introduce readers of Issues in Integrative Studies to cultural historical activity theory (CHAT). CHAT represents a systems approach to understanding the sociocultural matrix in which knowledge is transmitted and transformed. Although it was developed in the context of early-childhood learning, CHAT is now invoked in a wide variety of educational and organizational settings. To ground an overview of this intricate theory, we begin the paper by summarizing our own recent study of an issue in integrative learning. That study addressed the challenges of cross-disciplinary integration for students in a professional graduate program of water resources science, policy, and management. In the paper's second major section, we present the origins and development of CHAT and current research based on it. In the final section, referring again to the water program study, we explain how CHAT's conceptual and descriptive tools could be employed to help students integrate knowledge across disciplines in the context of water-related social issues. We hope that this introduction to CHAT suggests to readers other applications of the theory in situations where the object is to understand dynamic connections among interlocked systems. The general relevance of CHAT to the integrative studies community may lie in its demonstrating the critical importance, to the productive growth of any collective endeavor, of identifying, engaging, and expanding beyond inevitable systemic contradictions.
Integrating Model Checking into Object-oriented Software Development Processes

A methodology for integrating model checking into object-oriented software development processes is defined, developed, and demonstrated. Model checking is applied to object-oriented analysis(OOA) models that have executable semantics specified as state machines rather than as programs in conventional programming languages. The complexity level of an OOA model yields a manageable state space for model checking. An automata based approach to model checking is used. The OOA models are automatically translated to automaton models. Predicates over the behaviors of the OOA models are mapped to predicates over the automaton models and evaluated by a model checker. Algorithms for translating OOA models to automaton models are given. Procedures for management of dynamic object instance sets and unbounded event queues are given. The algorithms and procedures have been implemented for OOA models constructed in the SES/Objectbench implementation of the Shlaer-Mellor method that provides executable semantics for a subset of Unified Modeling Language. Translation is to the S/R automaton language and the COSPAN system is used for model checking. The algorithms are readily adapted to other OOA models with executable semantics and other model checking systems. A simple example to demonstrate the capabilities is included in this paper. The companion paper[7] gives design rules for constructing OOA models which yield tractable automaton models upon translation and reports on application of the methodology to an OOA model of modest complexity, a minimal robot control system.
Assessing strategies to minimize unintended fitness consequences of aquaculture on wild populations

Artificial propagation programs focused on production, such as commercial aquaculture or forestry, entail strong domestication selection. Spillover from such programs can cause unintended fitness and demographic consequences for wild conspecifics. The range of possible management practices to minimize such consequences vary in their control of genetic and demographic processes. Here, we use a model of coupled genetic and demographic dynamics to evaluate alternative management approaches to minimizing unintended consequences of aquaculture escapees. We find that, if strong natural selection occurs between escape and reproduction, an extremely maladapted (i.e., nonlocal‐origin, highly domesticated) stock could have fitness consequences analogous to a weakly diverged cultured stock; otherwise, wild population fitness declines with increasing maladaptation in the cultured stock. Reducing escapees through low‐level leakage is more effective than reducing an analogous number of escapees from large, rare pulses. This result arises because low‐level leakage leads to the continual lowering of wild population fitness and subsequent increased proportional contribution of maladapted cultured escapees to the total population. Increased sterilization efficacy can cause rapid, nonlinear reductions in unintended fitness consequences. Finally, sensitivity to the stage of escape indicates a need for improved monitoring data on how the number of escapees varies across life cycle stages.
Delay-dependent L2-L∞ model reduction for polytopic systems with time-varying delay

This paper considers the L2-Linfin model reduction problems for polytopic system with time-varying delay. In terms of the solution of linear matrix inequalities (LMIs) and inverse constraints, sufficient conditions are presented to construct the reduced order models such that the L2-Linfin gain of the error system between the full order model and the reduced order one is less than a given scalar.