Miracle-dz/UniFAR-FTUs huggingface dataset:
Rate and cost of adaptation in the Drosophila genome

Recent studies have consistently inferred high rates of adaptive molecular evolution between Drosophila species. At the same time, the Drosophila genome evolves under different rates of recombination, which results in partial genetic linkage between alleles at neighboring genomic loci. Here we analyze how linkage correlations affect adaptive evolution. We develop a new inference method for adaptation that takes into account the effect on an allele at a focal site caused by neighboring deleterious alleles (background selection) and by neighboring adaptive substitutions (hitchhiking). Using complete genome sequence data and fine-scale recombination maps, we infer a highly heterogeneous scenario of adaptation in Drosophila. In high-recombining regions, about 50% of all amino acid substitutions are adaptive, together with about 20% of all substitutions in proximal intergenic regions. In low-recombining regions, only a small fraction of the amino acid substitutions are adaptive, while hitchhiking accounts for the majority of these changes. Hitchhiking of deleterious alleles generates a substantial collateral cost of adaptation, leading to a fitness decline of about 30/2N per gene and per million years in the lowest-recombining regions. Our results show how recombination shapes rate and efficacy of the adaptive dynamics in eukaryotic genomes. Author Summary Because recombination takes place at a limited rate, alleles at neighboring sites in a genome can remain genetically linked over evolutionary periods. In this paper, we show that evolutionary forces generated by genetic linkage have drastic consequences for the adaptive dynamics in low-recombining parts of the Drosophila genome. Our study is based on a new method to analyze allele frequencies that is applicable to genome data at both high and low rates of recombination. We show that genes in low-recombining regions of the Drosophila genome incur a substantial cost of adaptation, because deleterious alleles get fixed more frequently than under high recombination. This cost reduces rate and power of the adaptive process. Our results suggest that the Drosophila genome has evolved to minimize this cost by placing genes under high adaptive pressure in high-recombining regions.
Cerebral Blood Flow during Rest Associates with General Intelligence and Creativity

Recently, much scientific attention has been focused on resting brain activity and its investigation through such methods as the analysis of functional connectivity during rest (the temporal correlation of brain activities in different regions). However, investigation of the magnitude of brain activity during rest has focused on the relative decrease of brain activity during a task, rather than on the absolute resting brain activity. It is thus necessary to investigate the association between cognitive factors and measures of absolute resting brain activity, such as cerebral blood flow (CBF), during rest (rest-CBF). In this study, we examined this association using multiple regression analyses. Rest-CBF was the dependent variable and the independent variables included two essential components of cognitive functions, psychometric general intelligence and creativity. CBF was measured using arterial spin labeling and there were three analyses for rest-CBF; namely mean gray matter rest-CBF, mean white matter rest-CBF, and regional rest-CBF. The results showed that mean gray and white matter rest-CBF were significantly and positively correlated with individual psychometric intelligence. Furthermore, mean white matter rest-CBF was significantly and positively correlated with creativity. After correcting the effect of mean gray matter rest-CBF the significant and positive correlation between regional rest-CBF in the perisylvian anatomical cluster that includes the left superior temporal gyrus and insula and individual psychometric intelligence was found. Also, regional rest-CBF in the precuneus was significantly and negatively correlated with individual creativity. Significance of these results of regional rest-CBF did not change when the effect of regional gray matter density was corrected. The findings showed mean and regional rest-CBF in healthy young subjects to be correlated with cognitive functions. The findings also suggest that, even in young cognitively intact subjects, resting brain activity (possibly underlain by default cognitive activity or metabolic demand from developed brain structures) is associated with cognitive functions.
Policy Based Security Middleware as a Service

Cloud computing is amongst the major topics researched in Computer Science. Cloud computing security is at the heart of the topic. The reason behind this is that, as a technology, cloud computing is a great alternative that allows companies to outsource the management of their computing resources. However, due to the security issues, the cloud technology is not reaching its full potential. In this paper we present a system that allows the enforcement of privacy, accountability, integrity, and availability in each one of cloud computing levels using software policies. We present and describe the architecture of the Policy-Based Security Middleware as a Service.
Efficacy and Safety of A Liposome-Based Vaccine against Protein Tau, Assessed in Tau.P301L Mice That Model Tauopathy

Progressive aggregation of protein Tau into oligomers and fibrils correlates with cognitive decline and synaptic dysfunction, leading to neurodegeneration in vulnerable brain regions in Alzheimer's disease. The unmet need of effective therapy for Alzheimer's disease, combined with problematic pharmacological approaches, led the field to explore immunotherapy, first against amyloid peptides and recently against protein Tau. Here we adapted the liposome-based amyloid vaccine that proved safe and efficacious, and incorporated a synthetic phosphorylated peptide to mimic the important phospho-epitope of protein Tau at residues pS396/pS404. We demonstrate that the liposome-based vaccine elicited, rapidly and robustly, specific antisera in wild-type mice and in Tau.P301L mice. Long-term vaccination proved to be safe, because it improved the clinical condition and reduced indices of tauopathy in the brain of the Tau.P301L mice, while no signs of neuro-inflammation or other adverse neurological effects were observed. The data corroborate the hypothesis that liposomes carrying phosphorylated peptides of protein Tau have considerable potential as safe and effective treatment against tauopathies, including Alzheimer's disease.
Games for crowdsourcing mobile content: An analysis of contribution patterns

Crowdsourcing of mobile content through games is becoming a major way of populating information-rich online environments. A current research gap is that actual usage patterns of crowdsourcing games has been inadequately investigated. We address this gap by comparing content creation patterns in a game for crowdsourcing mobile content against a non-game version. Results show distinct differences in the types and distribution of content created.
AIC and BIC based approaches for SVM parameter value estimation with RBF kernels

We study the problem of selecting the best parameter values to use for a support vector machine (SVM) with RBF kernel. Our methods extend the well-known formulas for AIC and BIC, and we present two alternative approaches for calculating the necessary likelihood functions for these formulas. Our rst approach is based on using the distances of support vectors from the separating hyperplane. Our second approach estimates the probability that the SVM hyperplane coincides with the Bayes classier, by analysing the disposition of points in the kernel feature space. We experimentally compare our two approaches with several existing methods and show they are able to achieve good accuracy, whilst also having low running time.
Psychological and Neural Processing of Social Rejection and Inclusion in Major Depressive Disorder

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Splitting spacetime and cloning qubits: linking no‐go theorems across the ER=EPR duality

We analyze the no‐cloning theorem in quantum mechanics through the lens of the proposed ER=EPR (Einstein‐Rosen = Einstein‐Podolsky‐Rosen) duality between entanglement and wormholes. In particular, we find that the no‐cloning theorem is dual on the gravity side to the no‐go theorem for topology change, violating the axioms of which allows for wormhole stabilization and causality violation. Such a duality between important no‐go theorems elucidates the proposed connection between spacetime geometry and quantum entanglement.
LEVEL-0 STRUCTURE OF LEVEL-1 UQ (SL2)-MODULES AND MACDONALD POLYNOMIALS

The level-1 integrable highest weight modules of Uq(sl2) admit a level-0 action of the same algebra. This action is defined using the affine Hecke algebra and the basis of the level-1 module generated by components of vertex operators. Each level-1 module is a direct sum of finite-dimensional irreducible level-0 modules, whose highest weight vector is expressed in terms of Macdonald polynomials. This decomposition leads to the fermionic character formula for the level-1 modules.
SmartPad: a finger-sensing keypad for mobile interaction

This paper introduces SmartPad, a new input device for mobile computers that is an enhanced physical keypad by a finger position sensor. This input device acts as a normal keypad for mobile devices, such as cellular phones, and also recognizes finger position on the keypad be before the user presses the key. This feature is used to recognize finger gesture on the keypad, and can also be used to give preview information to the user before the user actually pressing the key. This previewable function helps users to predict the effect of the action, and it is also helpful when the key definitions are frequently changed according to the context, such as in the case of universal commanders.
Transverse Spin Physics at HERMES

Single-spin asymmetries in semi-inclusive pion production are measured by the HERMES experiment for the first time, with a transversely polarised hydrogen target. Two different sine-dependencies are extracted which can be related to the quark distributions transversity h_1(x) and the Sivers function f_1T^perp(x).
An Artificial Bee Colony (ABC) Algorithm for Efficient Partitioning of Social Networks

Social networks clustering is an NP-hard problem because it is difficult to find the communities in a reasonable time; therefore, the solutions are based on heuristics. Social networks clustering aims to collect people with common interest in one group. Several approaches have been developed for clustering social networks. In this paper the researchers, introduce a new approach to cluster social networks based on Artificial Bee Colony optimization algorithm, which is a swarm based meta-heuristic algorithm. This approach aims to maximize the modularity, which is a measure that represents the quality of network partitioning. The researchers cluster some real known social networks with the proposed algorithm and compare it with the other approaches. Their algorithm increases the modularity and gives higher quality solutions than the previous approaches.
The Concept of Subjective Well-being in Housing Research

Abstract The aim of this article is to review the ways in which subjective well-being has been conceptualized within housing research, with a view to evaluating the use of the concept, the insights it has generated, the problems that have been experienced and the possible range of lessons that might be taken forward. The article begins with an analysis of the reasons why subjective well-being has become popular as a conceptual tool in many fields. The article continues with a discussion of the range of definitions that appear in the literature which leads into discussions of the research techniques and methodologies that have been used in empirical research. Empirical studies which focussed on the impact of physical housing conditions and tenure on subjective well-being are reviewed in order to evaluate what is known about the impact of housing on both personal and collective subjective well-being. This review highlights issues of status, reference groups and adaptation that are important insights from the subjective well-being approach that should set the agenda for further research in this area. The conclusion is that the relationship between housing and subjective well-being is a complex one that repays further study in order to understand the rich texture of the role of housing in people’s lives. The article concludes with suggestions for both conceptual and methodological approaches and the focus of future research.
Capturing the long-term impact of changes

Developers change source code to add new functionality, fix bugs, or refactor their code. Many of these changes have immediate impact on quality or stability. However, some impact of changes may become evident only in the long term. The goal of this thesis is to explore the long-term impact of changes by detecting dependencies between code changes and by measuring their influence on software quality, software maintainability, and development effort. Being able to identify the changes with the greatest long-term impact will strengthen our understanding of a project's history and thus shape future code changes and decisions.
Impact of Not Addressing Partially Cross-Classified Multilevel Structure in Testing Measurement Invariance: A Monte Carlo Study

In educational settings, researchers are likely to encounter multilevel data with cross-classified structure. However, due to the lack of familiarity and limitations of statistical software for cross-classified modeling, most researchers adopt less optimal approaches to analyze cross-classified multilevel data in testing measurement invariance. We conducted two Monte Carlo studies to investigate the performances of testing measurement invariance with cross-classified multilevel data when the noninvarinace is at the between-level: (a) the impact of ignoring crossed factor using conventional multilevel confirmatory factor analysis (MCFA) which assumes hierarchical multilevel data in testing measurement invariance and (b) the adequacy of the cross-classified multiple indicators multiple causes (MIMIC) models with cross-classified data. We considered two design factors, intraclass correlation (ICC) and magnitude of non-invariance. Generally, MCFA demonstrated very low statistical power to detect non-invariance. The low power was plausibly related to the underestimated factor loading differences and the underestimated ICC due to the redistribution of the variance component from the ignored crossed factor. The results demonstrated possible incorrect statistical inferences with conventional MCFA analyses that assume multilevel data as hierarchical structure for testing measurement invariance with cross-classified data (non-hierarchical structure). On the contrary, the cross-classified MIMIC model demonstrated acceptable performance with cross-classified data.
Monotone Iterative Technique for Fractional Evolution Equations in Banach Spaces

We investigate the initial value problem for a class of fractional evolution equations in a Banach space. Under some monotone conditions and noncompactness measure conditions of the nonlinearity, the well-known monotone iterative technique is then extended for fractional evolution equations which provides computable monotone sequences that converge to the extremal solutions in a sector generated by upper and lower solutions. An example to illustrate the applications of the main results is given.
Studying the effects of the rough sea surface on electromagnetic waves propagation

The electromagnetic waves (EWs) propagation on the rough sea surface simulated by the parabolic equation (PE) method is presented in this paper. The sea surface is simulated by the Elfouhaily spectrum and Longuet-Higgins model. In this sea surface propagation model, the relations between the effects of the rough sea surface on the EWs propagation and the wind speed, wind direction and the frequency of the EWs are studied. The simulation results of the rough sea surface model are compared with those of the Miller-Brown model. It demonstrates that, in a certain extent, the influence of the rough sea surface on the EWs propagation increases with the wind speed and the angle between the wind direction and the propagation direction, and decreases with the frequency of the EWs.
Incremental Maintenance of Minimal Bisimulation of Cyclic Graphs

Graph-structured databases have numerous recent applications including the Semantic Web, biological databases and XML, among many others. In this paper, we study the maintenance problem of a popular structural index, namely bisimulation , of a possibly cyclic data graph. To illustrate the design of our algorithm, ﬁrst, we present some challenges of bisimulation minimization of cyclic graphs. Second, in the context of database applications, it is natural to compute minimal bisimulation with merging algorithms. We present a maintenance algorithm for a minimal bisimulation of a cyclic graph in the style of merging algorithm. Third, we propose a feature-based optimization to prune the computation on non-bisimilar SCC s. The features are constructed and maintained more eﬃciently than bisimulation minimization. Finally, we present an experimental study that veriﬁes the scalability of our algorithm and shows that our features-based optimization pruned 50% unnecessary bisimulation computation on average. Our experiment shows that our algorithm introduces a capability to handle cyclic graphs explicitly.
Supporting coordinated adaptation in networked systems

Summary form only given. Our position is that the true potential of adaptation can only be realized if support is provided for more general solutions, including adaptations that span multiple hosts and multiple system components, and algorithmic adaptations that involve changing the underlying algorithms used by the system at runtime. Such a general solution must, however, address the difficult issues related to these types of adaptations. Adaptation by multiple related components, for example, must be coordinated so that these adaptations work together to implement consistent adaptation policies. Likewise, large-scale algorithmic adaptations need to be coordinated using graceful adaptation strategies in which as much normal processing as possible continues during the changeover. Here, we summarize our approach to addressing these problems in Cactus, a system for constructing highly-configurable distributed services and protocols.
Text-Level Structure of Research Papers: Implications for Text-Based Information Processing Systems

This paper discusses the implication of text-level structure for text-based information processing systems. In this paper, text-level structure of research papers is described with a set of typical functional components of research papers such as, background, purpose, methods, etc. and their order in a text. In order to suggest various applications, the experiments of retrieval and passage extraction were conducted using a manually structure-tagged fulltext database of research papers. As a result, we show that searching full-length texts using text-level structure achieved higher precision, compared to the searching without it. The paper also shows examples of extracted passages and suggests the application of text-level structure for text-based information systems, including passage extraction, browsing, and navigation within/across texts.
Internet Protocols for Network-Attached Peripherals

This paper presents our thesis that the advantages of the internet protocol framework make it the best choice for communications protocols to, and between, networkattached peripherals (NAPs). Moreover, the IP suite is more appropriate than the specialized protocol stacks being developed for commercial NAPs. The benets of using IP include support for heterogeneous network media, wide-area connectivity, and reduced research and development effort. We examine the issues for use of the internet protocols (TCP/UDP/IP) for NAPs, address commonly held concerns regarding its performance, and describe the Netstation project’s prototype implementations of IP peripherals.
Forwarding vs. Network Coding: Efficient Broadcasting in Multihop Wireless Networks

Broadcasting is used as a building block in many MANET (Mobile Ad hoc Network) routing protocols. In addition, broadcasting is a key primitive in ad hoc networks to support group-based applications. Efficiently supporting broadcasting in multihop wireless networks is therefore important. In this paper, we compare ef-ficient broadcasting protocols based on packet forwarding with those based on network coding. Using a number of network scenarios, we derive lower bounds for the required number of packet retransmissions at the MAC layer to support broadcast with and without applying network coding techniques. We compare these lower bounds with each other, as well as with protocols proposed for each approach. More specifically, we use SMF and PDP as sample forwarding-based broadcast protocols, and a simple XOR-based coding protocol over SMF and PDP as representative network coding solution. The results show that neither packet forwarding protocols nor network coding protocols achieve the theoretical lower bounds, in particular as the size of the network area (at constant density) increases. The comparison of the lower bounds also shows that network coding does have a potential performance advantage over packet forwarding solutions for broad-casting in multi-hop wireless networks, in particular for larger fixed density networks, justifying its inherent increased complexity.