Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporation , Relative Homoplasy , and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

Phylogenetic analysis of nucleotide and amino acid sequences requires the alignment of homologous sequences. The alignment procedure often requires the insertion of gaps, putatively corresponding to insertion or deletion events, which can be coded as phylogenetic characters. As a general class of phylogenetic characters, gaps have variously been suggested to be reliable (e.g., Lloyd and Calder, 1991; Van Dijk et al., 1999) or unreliable (e.g., Golenberg et al., 1993; Ford et al., 1995). This difference in opinion, coupled with the lack of a well-supported method for the coding of gaps, has led to a diversity of approaches by which gaps have been treated in, or excluded from, tree searches (González, 1996). In an earlier paper we presented two methods, termed simple and complex indel coding, in which all gaps (excluding leading and trailing gaps, which are generally artifacts) can be coded from aligned sequence-based matrices (Simmons and Ochoterena, 2000). Simple indel coding, which is used in this study, is implemented by coding all gaps that have different 5’ or 3’ termini as separate presence/absence characters. Whenever a gap is being coded and the region it spans is completely included within the span of another gap, those sequences having the longer gap (i.e., one that extends to or beyond both the 5’ and 3’ termini of the gap being coded) are scored as inapplicable for the gap character being coded. Some have suggested on theoretical and empirical grounds that longer gaps are better phylogenetic characters than shorter gaps. Lloyd and Calder (1991) argued that multiresidue gaps are reliable phylogenetic characters because indels are unlikely to be repeated in the exact same position with the same length and sequence (for insertions); indels of different lengths at the same position are recognized as separate events. Similarly, van Ham et al. (1994) suggested that, based on the relative levels of homoplasy in the intergenic spacer between trnL and trnF, gaps longer than two positions are reliable phylogenetic characters. In this paper we assess the relative levels of homoplasy of gap and base characters from a selection of 38 published sequence-based matrices. We determine the potential phylogenetic information included in gap characters and the extent to which inclusion of gap characters alters the gene tree topology and branch support values. We also test the assertion that longer gaps are better phylogenetic characters than shorter gaps.
Self-Organizing Cellular Radio Access Network with Deep Learning

Network operators require a high level of performance and reliability for the cellular radio access network (RAN) to deliver high quality of service for mobile users. However, these network do experience some rare and hard-to-predict anomaly events, for example, hardware failures and high radio interference, which can significantly degrade performance and end-user experience. In this work, we propose SORA, a self-organizing cellular radio access network system enhanced with deep learning. SORA involves four core components: self-KPIs monitoring, self-anomaly prediction, self-root cause analysis, and self-healing. In particular, we design and implement the anomaly prediction and root cause analysis components with deep learning methods and evaluate the system performance with 6 months of real-world data from a top-tier US cellular network operator. We demonstrate that the proposed methods can achieve 86.9% accuracy in predicting anomalies and 99.5% accuracy for root cause analysis of network faults.
Coordination within International Manufacturing Networks: A Comparative Study of Three Industrial Practices

The globalisation of manufacturing activities has led to the emergence of internationally dispersed manufacturing plants. Coordination of such networks is a complex task and entails several management challenges. The purpose of this paper is to increase the understanding regarding the coordination issues and how they could be managed in IMN environment. Using a multiple case study approach, data from three multi-plant manufacturing businesses were collected and analysed. The results include discussions on coordination aspects such as autonomy and mechanisms to conduct coordination. Furthermore, a model for assigning autonomy level to the plant in an IMN is suggested as well as mechanisms to conduct the coordination work.
A multiscale approach to environment and its influence on the colour distribution of galaxies

We present a multiscale approach for measurements of galaxy density, applied to a volume-limited sample constructed from the Sloan Digital Sky Survey Data Release 5 (SDSS DR5). We populate a rich parameter space by obtaining independent measurements of density on different scales for each galaxy. This parametrization purely relies on observations and avoids the implicit assumptions involved, e.g. in the construction of group catalogues. As the first application of this method, we study how the bimodality in galaxy colour distribution (specifically u - r) depends on multiscale density. The u - r galaxy colour distribution is described as the sum of two Gaussians (a red and a blue one) with five parameters: the fraction of red galaxies (f red ) and the position and width of the red and blue peaks (μ red , μ blue , σ red and Q blue )· Galaxies mostly react to their smallest scale ( 2 Mpc scales at fixed density on smaller scales, and μ red anticorrelates with density on > 1 Mpc scales. We examine these trends qualitatively in the context of the halo model, utilizing the properties of haloes within which the galaxies are embedded, derived by Yang et al. and applied to a group catalogue. This yields an excellent description of the trends with multiscale density, including the anticorrelations on large scales, which map the region of accretion on to massive haloes. Thus we conclude that galaxies become red only once they have been accreted on to haloes of a certain mass. The mean colour of red galaxies μ red depends positively only on <0.5 Mpc scale density, which can most easily be explained if correlations of μ red with environment are driven by metallicity via the enrichment history of a galaxy within its subhalo, during its epoch of star formation.
st century climate change scenario for the Mediterranean using a coupled Atmosphere-Ocean Regional Climate Model

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. 21st century climate change scenario for the Mediterranean using a coupled Atmosphere-Ocean Regional Climate Model Samuel Somot, Florence Sevault, Michel Déqué, Michel Crépon
Group on Human-ComputerInteraction 12-13-2018 Designing Caring and Informative Decision Aids

The focus in decision aid research and practice has largely been on the utilitarian aspects of their design. We propose that these aids should also be designed as effective social partners, especially when their use involves the exchange of sensitive information. In this paper, we investigate the effects of designing caring and informative decision aids on users’ evaluations of these aids. Our results show that the use of explanations and expressive speech acts can enhance users’ beliefs that the aid is informative and cares about the user. These strengthened beliefs subsequently enhance perceptions of its competence and benevolence, and improve the interaction atmosphere, subsequently increasing satisfaction with the decision aid.
Series A Fourth Normal Form for Possibilistic Data

Relational database design addresses applications for data that is certain. Modern applications require the handling of uncertain data. Indeed, one dimension of big data is veracity. Ideally, the design of databases helps users quantify their trust in the data. For that purpose, we need to establish a design framework that handles responsibly any knowledge of an organization about the uncertainty in their data. Naturally, such knowledge helps us find database designs that process data more efficiently. In this paper, we apply possibility theory to introduce the class of possibilistic multivalued dependencies that are a significant source of data redundancy. Redundant data may occur with different degrees, derived from the different degrees of uncertainty in the data. We propose a family of fourth normal forms for uncertain data. We justify our proposal showing that its members characterize schemata that are free from any redundant data occurrences in any of their instances at the targeted level of uncertainty in the data. We show how to automatically transform any schema into one that satisfies our proposal, without loss of any information. Our results are founded on axiomatic and algorithmic solutions to the implication problem of possibilistic functional and multivalued dependencies which we also establish.
PrototypAR: Prototyping and Simulating Complex Systems with Paper Craft and Augmented Reality

We introduce PrototypAR, an Augmented Reality (AR) system that allows children to rapidly build complex systems using paper crafts and to test their designs in a digital environment. PrototypAR combines lo-fidelity prototyping to facilitate iterative design, real-time AR feedback to scaffold learning, and a virtual simulation environment to support personalized experiments. Informed by three participatory design sessions, we developed three PrototypAR applications: build-a-bike, build-a-camera, and build-an-aquarium---each highlights different aspects of our system. To evaluate PrototypAR, we conducted four single-session qualitative evaluations with 21 children working in teams. Our findings show how children build and explore complex systems models, how they use AR scaffolds, and the challenges they face when conducting experiments with their own prototypes.
Rapid Vulnerability Mitigation with Security Workarounds

The existence of pre-patch windows allows adversaries to exploit vulnerabilities before they are patched. Prior work has proposed to harden programs with security workarounds to enable users to mitigate vulnerabilities before a patch is available. However, it requires access to the source code of the programs. This paper introduces RVM, an approach to automatically hardening binary code with security workarounds. RVM statically analyzes binary code of programs to identify error-handling code in the programs, in order to synthesize security workarounds. We designed and implemented a prototype of RVM for Windows and Linux binaries. We evaluate the coverage and performance of RVM on binaries of popular Windows and Linux applications containing real-world vulnerabilities.
Estimation of near-surface geotechnical parameters using seismic measurements at phase ǀǀ site, Ahmadu Bello University Zaria, North-western Nigeria

Determination of the dynamic geotechnical properties and seismic wave velocities serves as essential inputs for a foundation design cognizant of seismic site response and rock strength. This study evaluates competent zones for construction at Ahmadu Bello University Zaria, Phase II site. Four shallow seismic refraction profiles were carried out using the ABEM Terraloc Pro seismograph. Compressional (P) and shear (S) waves were acquired and the time-term technique, which is a combination of linear least squares and delay time analysis to invert the first arrivals for a velocity section and then to tomography section was adopted. These sections were correlated with a borehole report and a good matching was observed. The result shows that the area consists of three subsurface layers; an overburden with average thickness of about 10.5 m and P- and S-wave velocities (velocities) of about 550 m/s and 345 m/s respectively, the weathered basement with an average thickness of 12.5 m and velocities of 950 m/s and 550 m/s respectively, while the fresh basement was found at a depth of about 24 m with velocities of 1250 m/s and 680 m/s respectively. The Concentration Index, Material Index, Poisson’s Ratio, and Stress Ratio were calculated to be in the range of 4.869 to 6.128, -0.032 to 0.312, 0.172 to 0.258, and 0.267 to 0.346 respectively in the study area. The seismic velocity values, engineering consolidation, and strength parameters showed that the subsurface soil/rock at the eastern parts of the study area is characterized by less competent soil/rock quality while the western parts are characterized by more competent soil/rock quality. Hence, the western and north-western parts are more preferable for the foundation of structures to be erected.
Sustainability in multi-aged stands: an analysis of long-term plenter systems

Summary Long-term research plots in multi-aged stands managed with the plenter system were assessed to evaluate sustainability of the plenter system in Central Europe. Plots primarily consisted of Norway spruce ( Picea abies (L.) Karst. , silver fi r ( Abies alba Mill.) or European beech ( Fagus sylvatica L.) and were measured for seven to 16 measurement intervals over 60 – 91 years. Sustainability was assessed with four types of criteria: stand density, tree species diversity, basal area increment, and stand structure. Comparable even-aged stands were also analysed to compare and evaluate the performance of the measures of sustainability. Measures of species diversity, increment and stand structural diversity generally experienced increasing trends over time in these even-aged stands. Basal area generally increased and trees ha -1 decreased in multi-aged stands following similar patterns as in even-aged stands. These results suggest that the plenter system is still evolving and is not the model of sustainability often assumed. Many of the measures used have potential as indicators of sustainability in multi-aged stands.
Abnormal N 400 word repetition effects in fragile X-associated tremor / ataxia syndrome

1 Department of Neurology, University of California Davis, Davis, CA 95618, USA 2 Center for Mind and Brain, Davis, CA 95618, USA 3 English Department, National Taiwan Normal University, Taipei, Taiwan (106) 4 NeuroTherapeutics Research Institute, University of California Davis, Davis, CA 95616, USA 5 M.I. N.D. Institute, University of California Davis, Sacramento, CA 95817, USA 6 Department of Psychiatry and Behavioural Sciences, University of California Davis, Sacramento, CA 95817, USA 7 Department of Psychology, University of Iowa, Iowa City, IA 52242, USA 8 Department of Neurobiology, Physiology & Behavior, University of California Davis, Davis, CA 95616, USA 9 Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA 95616, USA 10 Department of Pediatrics, University of California at Davis School of Medicine, Sacramento, CA 95817, USA
A Comparative Study on Dry Sliding Wear Characteristics of Al 2 O 3 and Bone Powder Filled Hybrid Composites

The aim of the research was to develop E-glass/jute fiber reinforced epoxy composites with an addition of Al2O3 and bone powder by using hand layup technique and to compare tribological properties of these composites under similar test conditions. The wear experiments were designed according to Taguchi’s (L27) orthogonal array with three control variables such as sliding velocity, filler content and normal load. The results indicated that the normal load for Al2O3 and filler content for bone powder emerged as the significant factors affecting specific wear rate of hybrid composites. An addition of 10 wt% of bone powder or Al2O3 into E-glass/jute fiber reinforced epoxy composites increased the wear resistance considerably, and natural waste bone powder can be used instead of ceramic filler Al2O3 in hybrid composites. After the analysis of control factors, an optimal factor setting has been suggested for specific wear rate and coefficient of friction. Further, the scanning electron microscopy (SEM) images for worn surfaces of hybrid composites were studied. Finally, a confirmation test was carried out to validate the results.
Identity Politic Contestation in the Public Sphere: A Steep Road of Democracy in Indonesia

This article aims to analyse and describe efforts to exploit public sphere by political elites in Indonesia through the use of mass media by spreading identity political propaganda, and efforts to find the agendasetting of the mass media, especially behind the rampant loading of news about identity politics. The results show, first, that identity politics is considered as a powerful weapon by political elites to bring down the popularity and electability of their political rivals or efforts to gain political support from the public. The issue of ethnicity and religion are two things that are always included in the political agenda of the identity of the elite in Indonesia, especially the condition of Indonesian society where the atmosphere of primordialism and sectarianism is still strong enough so that it is very easy to win public sympathy, ignite anger and sentiment of the masses by propagating ethnic issues and religion. However, the results of the DKI Jakarta governor election in 2018 and the presidential election in 2019 which were enlivened by the use of identity politics did not influence the increase in voter support. Identity politics only strengthens a small number of swing voters who have not yet determined their political choices, whereas most voters have political preferences about their respective candidates. Second, the political elite has succeeded in making the issue of identity politics into the public sphere which is supposed to be free of ethnic, religious and racial nuances. The media which should be a gatekeeper does not perform this function properly because there is no process of filtering information including the use of social media in spreading the propaganda of identity politics which further exacerbates the conflict.
Religion and the European Union

We review a recent literature on cultural differences across euro member states. We point out that this literature fails to address cultural differences between Protestants and Catholics, which are likely a major underlying reason for cross-country differences. We argue that confessional culture explains why Catholic countries tend to have weaker institutions but are more open to economic and political integration. EU policies after the economic crisis looked clumsy and failed to address all concerns, but were viable, caused only a manageable amount of serious backlash and tied in well with Europe’s cultural diversity, also providing scope for learning and adaption.
An In Vitro Study of Anticariogenic Compounds Incorporated Into Bis-GMA/TEGDMA Copolymer

Composite resins continue to evolve and are increas ingly favoured by the people. However, drawbacks such as decreased longevity, secondary ca ries and costs make choosing composites a dilemma. This study evaluated drug release, inhibit ory growth against Streptococcus mutans and drug stability of epigallocatechin-gallate (EGCg) i ncorporated into dental copolymer compared to resins containing chlorhexidine (CHX). Resin dis cs (5mm × 3mm) were prepared from 70 mol% Bis-GMA and 30 mol% TEGDMA comonomers containi ng: placebo, CHX and EGCg. Two corresponding concentrations in weight% of each drug for 0.5 and 1.0 × MIC were incorporated into paste resins and tested at time p oints: 24 hours, 7 days, 30 days, 60 days and 90 days. There is a significant difference in the 90 d ays drug delivery and bacterial inhibition among different drugs and drug ratios, which showed stabi li y after 90 days. The results indicate that drug-based composites may reduce bacterial growth, which may improve its longevity.
Temporary agency workers’ well-being and human resource management sustainability: A qualitative case study

This qualitative case study explores the seemingly paradoxical relationship between the proliferation of companies’ involvement in temporary agency work and their pursuit of HRM sustainability. The case is an extreme one; the case company is comprised of half permanent and half temporary agency work staff. Due to unclear strategy towards managing a mixed workforce, the company has been suffering high turnover rate and low organisational efficiency. Contributing to the quantitative research methods dominated well-being studies in temporary work context, and to the insufficient academic research on temporary agency work featured by a triangular structure, we draw upon longitudinal qualitative empirical data. Which has given voices to employees, a business unit and the HR department, and is considered valuable to demonstrate the complex reality of employee groups and the implications to different actors. Through building a sensitising framework that incorporates sustainable HRM and workplace well-being resources models, our study suggests nuances to tailor the existing framework into a temporary agency work specific context for future generalisation studies. The findings suggest that to achieve organisational efficiency and ultimately corporate sustainability, the case company needs to address all employees’ well-being in strategy and HR practices.
Hypersensitivity to mGluR 5 and ERK 1 / 2 Leads to Excessive Protein Synthesis in the Hippocampus of a Mouse Model of Fragile X Syndrome

Fragile X syndrome (FXS) is caused by loss of the FMR1 gene product FMRP, a repressor of mRNA translation. According to the mGluR theory of FXS, excessive protein synthesis downstream of metabotropic glutamate receptor 5 (mGluR5) activation causes the synaptic pathophysiology that underlies multiple aspects of fragile X syndrome (FXS). Here, we utilize an in vitro assay of protein synthesis in the hippocampus of male Fmr1 KO mice to explore the molecular mechanisms involved in this core biochemical phenotype under conditions where aberrant synaptic physiology has been observed. We find that elevated basal protein synthesis in Fmr1 KO mice is selectively reduced to wild type (WT) levels by acute inhibition of mGluR5 or ERK1/2, but not by inhibition of mTOR. The mGluR5-ERK1/2 pathway is not constitutively overactive in the Fmr1 KO, however, suggesting that mRNA translation is hypersensitive to basal ERK1/2 activation in the absence of FMRP. We find that hypersensitivity to ERK1/2 pathway activation also contributes to audiogenic seizure susceptibility in the Fmr1 KO. These results suggest that the ERK1/2 pathway, and other neurotransmitter systems that stimulate protein synthesis via ERK1/2, represent additional therapeutic targets for FXS.
A Novel Modular Optimization Framework for Modelling Investment and Operation of Energy Systems at European Level

Project plan4res (www.plan4res.eu) involves the development of a modular framework for the modeling and analysis of energy system strategies at the European level. It will include models describing the investment and operation decisions for a wide variety of technologies related to electricity and non-electricity energy sectors across generation, consumption, transmission and distribution. The modularity of the framework allows for detailed modelling of major areas of energy systems that can help stakeholders from different backgrounds to focus on specific topics related to the energy landscape in Europe and to receive relevant outputs and insights tailored to their needs. The current paper presents a qualitative description of key concepts and methods of the novel modular optimization framework and provides insights into the corresponding energy landscape.