Miracle-dz/UniFAR-FTUs huggingface dataset:
An Analysis of Genetic Changes during the Divergence of Drosophila Species

Background It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species. Principal Findings In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear. Conclusions Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.
Object Interoperability for Geospatial Applications: a Case Study *

In this paper, we analyze a geospatial application for visualizing U.S. election results in order to show the problems that need to be solved in the mapping between different XML representations and their conceptual models. We propose a framework that provides a number of core classes that allow applications to treat XML documents as graphs and to evaluate XPath expressions against such document graphs. We also propose a mechanism that allows information to be exchanged between document types. Our goal is to ultimately attain an overall framework for interop-eration where maintenance problems are minimized. To achieve this, we anticipate the need for introducing metadata in the semantic layer that will guide the translation process between document types.
Nutrition in the pathogenesis of alcoholic liver disease.

The data and experimental results reviewed here allow the construction of the following hypothesis: alcohol-induced liver disease results from a combination of two phenomena. The first is the induction of the maximum activity of CYP 2E1 by several dietary factors, i.e. (1) low carbohydrate-high fat diet; and (2) the dietary fats composed of PUFA (Yang et al., 1992). The second is the production of lipid peroxidation induced by CYP 2E1 oxidation of ethanol maintained at high blood alcohol levels (> 200 mg %) with the availability of PUFA as substrate (Ekstrom and Ingelman-Sundberg, 1988; Koop, 1992). Thus, lipid peroxidation may be the final common pathway which supports the induction of ALD. Further, it may provide the common denominator which links ALD pathogenesis to non-alcoholic steato-hepatitis (NASH) (French et al., 1989b), where CYP 2E1 is induced by high fat diet and/or diabetes (Dong et al., 1988).
Reactive liquid phase sintering of solution-derived YBa_2Cu_3O_7−x superconducting thin films: Part I. Ambient and precursor effects on BaO–CuO liquid phase formation

Processing atmosphere and precursor effects on liquid phase formation were investigated in the BaO–CuO thin film system. Liquid phase was observed at a significantly lower temperature (∼620 °C) under N_2 atmosphere with carboxylate solution precursors. In the processing of the YBCO oxide superconductors, formation of the liquid phase facilitated the decomposition of BaCO_3 and crystallization of the YBCO grains. Larger grains and greater (00 l ) preferred orientation were also observed in the YBCO films prepared with the presence of the liquid phase.
Plasma–Parathyroid Hormone Is Associated With Subclinical and Clinical Atherosclerotic Disease in 2 Community-Based Cohorts

Objective—Cardiovascular risk factors have different impact on different arterial territories. Diseases with elevated circulating parathyroid hormone (PTH) such as primary hyperparathyroidism and chronic renal failure have been shown to be associated with an increased risk of cardiovascular disease, predominantly heart or cerebrovascular diseases. However, data on the associations between circulating PTH and peripheral atherosclerosis are limited. Approach and Results—Two prospective, community-based studies were used. In 306 men and women, who were 70 years old, from the Prospective investigation of the vasculature in Uppsala seniors (PIVUS) study, cross-sectional relations between PTH and atherosclerotic burden assessed by whole-body magnetic resonance angiography were investigated. In 998 men, who were 71 years old, from the Uppsala longitudinal study of adult men (ULSAM) study, the association between PTH concentration and risk of subsequent nonfatal atherosclerotic disease (excluding coronary or cerebrovascular disease) was investigated. Adjusting for established vascular risk factors, PTH was associated with burden of atherosclerosis (increase in total atherosclerotic score per SD PTH increase: 0.04, 0.003–0.08; P=0.03) in the PIVUS study. During follow-up in the ULSAM study (median 16.7 years), 89 men were diagnosed with nonfatal atherosclerotic disease. In Cox-regression analyses adjusting for established vascular risk factors and mineral metabolism, higher PTH was associated with an increased risk of nonfatal atherosclerotic disease (hazard ratio for 1 SD increase of PTH: 1.55, 1.33–1.88; P<0.0001). Results were similar when including fatal atherosclerotic disease in the outcome. Conclusions—In 2 independent community-based cohorts, PTH was associated to the degree of atherosclerosis and risk of clinically overt atherosclerotic disease, respectively. Our data confirm and extend previous studies supporting a role for PTH in the development of atherosclerotic disease.
Neural networks for fast arbitration and switching noise reduction in large crossbars

A neural-network-based controller for the real-time arbitration of routing paths in large crossbar switches constructed from one-sided crosspoint chips is presented. This controller is suitable for a synchronous environment where a number of connection requests are simultaneously presented to the switch. The controller aims to maximize the effective bandwidth of the switch and to minimize the simultaneous-switching noise in the individual chips. The controller uses multiple winner-take-all networks coupled with some competitive-cooperative mechanisms to achieve the joint optimization. The effects of various network parameters are studied through simulation, and cases leading to nonoptimal solutions are analyzed. A hierarchical neural network controller for a packet-switched environment where connections are established and broken asynchronously is introduced. This controller provides almost the same level of performance as the first, but with significantly reduced computation for each connection request. >
Research on Multi-dimensional Association Rules Mining in Distributed Environments Based on Advanced SQL Query

This paper proposes the MDMA (Multi-dimensional Distributed Mining Association rules) algorithm based on advanced SQL query. The algorithm works on star-style structure networks. It uses CUBE operator in new standard SQL and combines with SQL powerful query function. So there is no need for the proposed algorithm to conduct a great deal of iterations to generate frequent itemsets in the process of mining association rules. Therefore, no matter what the number of the site in the distributed environments and the scale of the local database in the local site is, the algorithm always needs only two times of scanning the database and only three times of network communications to generate all the global frequent itemsets. Consequently, this algorithm has the merits of light network traffic, low time cost, better scalability and more simplicity.
Neuroimaging of Language: Why Hasn't a Clearer Picture Emerged?

Two broad questions have driven dozens of studies on the neural basis of language published in the last several decades: (i) Are distinct cortical regions engaged in different aspects of language? (ii) Are regions engaged in language processing specific to the domain of language? Neuroimaging has not yet provided clear answers to either question. In this paper, we discuss one factor that is a likely contributor to the unclear state of affairs in the neurocognition of language, and that, in our opinion, has not received sufficient attention in the recent literature. In particular, fMRI studies of language have relied, almost exclusively, on group analyses, in which data from multiple individuals are co-registered to and analyzed in a common space. We argue that this approach can obscure functional specificity because of the anatomical variability across individual brains, and we advocate the use of an alternative approach – the functional localization approach – that circumvents this problem.
HybridEarth: Social mixed reality at planet scale

Using Google Street View navigable imagery and adding users' avatars to it, we have implemented a virtual world copy of the real world. Thanks to a geolocation technique with a precision in centimeters, users wearing augmented reality devices are inserted at their actual location in the mirror virtual world and can see all its virtual elements, including avatars. As HybridEarth can potentially host millions of avatars-much more than today's virtual worlds - we have built it on top of Kiwano, a distributed infrastructure for scaling virtual worlds, designed and implemented by our team. HybridEarth is accessible from http://hybridearth.net where users can enter the world either by installing an application on their Android device or by walking their avatar in the virtual world. Running inside any recent web browser, the virtual world covers the planet wherever Google Street View is available and can be extended by adding new imagery with the provided smartphone application.
Three-Dimensional Electromagnetic Analysis of Attenuator-Coated Helix Support Rods of a Traveling-Wave Tube

Attenuator-coated helix support rods in a helical slow-wave structure (SWS) were modeled by considering them to be made up of lossy dielectric material having equivalent bulk conductivity varied along the length following the loss of the coating. The same conductivity values were used in 3-D modeling of the helical SWS having the helix supported by three such support rods inside a metal envelope, and the attenuation constant of the structure was found. The approach was used for characterizing the attenuation constants in the sever regions of two typical SWSs, one operating in the X-Ku-band and the other in K-Ka-band. The method is general and would be useful for analyzing sever loss in any type of helical SWS having different geometries as well.
The Ras Target AF-6 Interacts with ZO-1 and Serves as a Peripheral Component of Tight Junctions in Epithelial Cells

The dynamic rearrangement of cell–cell junctions such as tight junctions and adherens junctions is a critical step in various cellular processes, including establishment of epithelial cell polarity and developmental patterning. Tight junctions are mediated by molecules such as occludin and its associated ZO-1 and ZO-2, and adherens junctions are mediated by adhesion molecules such as cadherin and its associated catenins. The transformation of epithelial cells by activated Ras results in the perturbation of cell–cell contacts. We previously identified the ALL-1 fusion partner from chromosome 6 (AF-6) as a Ras target. AF-6 has the PDZ domain, which is thought to localize AF-6 at the specialized sites of plasma membranes such as cell–cell contact sites. We investigated roles of Ras and AF-6 in the regulation of cell–cell contacts and found that AF-6 accumulated at the cell–cell contact sites of polarized MDCKII epithelial cells and had a distribution similar to that of ZO-1 but somewhat different from those of catenins. Immunoelectron microscopy revealed a close association between AF-6 and ZO-1 at the tight junctions of MDCKII cells. Native and recombinant AF-6 interacted with ZO-1 in vitro. ZO-1 interacted with the Ras-binding domain of AF-6, and this interaction was inhibited by activated Ras. AF-6 accumulated with ZO-1 at the cell–cell contact sites in cells lacking tight junctions such as Rat1 fibroblasts and PC12 rat pheochromocytoma cells. The overexpression of activated Ras in Rat1 cells resulted in the perturbation of cell–cell contacts, followed by a decrease of the accumulation of AF-6 and ZO-1 at the cell surface. These results indicate that AF-6 serves as one of the peripheral components of tight junctions in epithelial cells and cell–cell adhesions in nonepithelial cells, and that AF-6 may participate in the regulation of cell–cell contacts, including tight junctions, via direct interaction with ZO-1 downstream of Ras.
Collaborative geospatial feature search

The ever-increasing stream of Web and mobile applications addressing geospatial data creation has been producing a large number of user-contributed geospatial datasets. This work proposes a means to query such data using a collaborative Web-based approach. We employ crowdsourcing to the fullest in that used-generated point-cloud data will be mined by the crowd not only by providing feature names, but also by contributing computing resources. We employ browser-based collaborative search for deriving the extents of geospatial objects (Points of Interest) from point-cloud data such as Flickr image locations and tags. The data is aggregated by means of a hierarchical grid in connection with an exploratory and a refinement search phase. A performance study establishes the effectiveness of our approach with respect to the amount of data that needs to be retrieved from the sources and the quality of the derived spatial features.
Influence of dietary condensed tannin on microbial crude protein supply in sheep

Excessive intakes of condensed tannin (CT) are associated with a reduction in N retention in ruminants. It is commonly presumed that part of this reduction is explained by an inhibitory effect of CT on the production of microbial crude protein (MCP). Recent data from our group questions this presumption. Neutralisation of CT in Leucaena foliage, by supplementing sheep fed Leucaena with the tannin-neutralising agent polyethylene glycol (PEG), induced no change in MCP production. Similarly, MCP production remained unchanged when sheep fed lucerne hay were supplemented with increasing amounts of Quebracho CT. Some decline was observed when MCP production was compared in sheep fed Leucaena genotypes differing in CT content. The less than expected effects of CT at the level of the rumen lend support to the hypothesis that CT exert their major effects post-ruminally.
Determinants of bone mineral density in older men

Osteoporosis is a significant health problem and contributor to disability and premature mortality among older men. Incidence rates for hip fracture have stabilized in women, but continue to increase in men. A major risk factor for hip fracture is bone mineral density level. The determinants of bone mineral density (BMD) are well defined in women, but not in men. The primary goal of the current research was to increase our understanding of the determinants of BMD of the proximal femur in a large community‐based sample of older male volunteers. Eligibility requirements included age of 50 years or older, ambulatory, and not having undergone a bilateral hip replacement. Five hundred twenty‐three men, mean age 66.6 years, met all eligibility requirements and participated in the Study of Osteoporotic Risk in Men or STORM. Information on demographics, medical history, anthropometry, leisure‐time and occupational physical activity, muscular strength, cigarette smoking, alcohol consumption, dietary calcium intake, and medication use (thiazide diuretics and glucocorticoids) were obtained by questionnaire, interview, and examination. BMD of the proximal femur (femoral neck, greater trochanter, and Ward's triangle) was measured by dual‐energy X‐ray absorptiometry using the Hologic QDR‐1000 and QDR‐2000. The cross‐sectional determinants of BMD included age, blond hair color, current body weight, thiazide diuretic use, historical physical activity, and quadriceps strength. Several variables commonly thought to be determinants of BMD were not related to BMD in this population of older men, including current cigarette smoking, alcohol consumption, current leisure‐time physical activity, dietary calcium intake, vitamin D use, and caffeine intake. However, failure to find associations among BMD and some of the potential determinants may be due to lack of statistical power. Identification of the determinants of BMD could lead to the development of interventions aimed at maximizing BMD in men and could potentially decrease the risk of hip fractures.
Difference between Highlight and Object Colors Enhances Glossiness

The effect of highlight and object colors on perception of glossiness was examined. Ten participants rated glossiness of object images. The color coordinates of objects and highlights were varied while luminance of each pixel was unchanged. Four colors were used for objects and highlights. Objects were perceived as glossier when the highlight color was different from the object color than when they were the same. Objects with some unnatural combinations of highlight and object colors were perceived to be as glossy as those with natural color combinations. The results suggested that differences between highlight and object colors enhance perceived glossiness and that perceived glossiness does not depend on naturalness of color combination for highlights and objects.
Non-invasive low cost method for linear and angular accelerations measurement in biped locomotion mechanisms

A new non-invasive low cost method for accelerations measurement in biped locomotion mechanisms is presented. The aim is to measure all the joint accelerations of the locomotion system during the walking that is difficult because of the non-accessibility of several joint axes. Our measurement approach is non-direct using two triaxial accelerometers aligned on the main axis of each body, that ensures measurement of five accelerations per joint, two angular and three linear. By considering negligible the vertical rotation of a leg in the absolute frame during walking, the vertical rotational acceleration of the hip is measurable by two accelerometers aligned along the sagittal axis. For tibia and thigh, the accelerometers are aligned along vertical axes. The calculation of accelerations in articulation references is achieved by solving a system of Newton mechanics equations. The theoretical statements were validated experimentally on the robot for vertical flexion-extension movement.
Addition of a Novel, Protective Family History Category Allows Better Profiling of Cardiovascular Risk and Atherosclerotic Burden in the General Population. The Asklepios Study

Objectives Whereas the importance of family history (FH) is widely recognized in cardiovascular risk assessment, its full potential could be underutilized, when applied with its current simple guidelines-based definition (cFH): presence of premature cardiovascular disease (CVD) in a first-degree relative. We tested the added value of a new, extended family history definition (eFH), also taking into account later onset of disease, second-degree relatives and number of affected relatives, on profiling cardiovascular risk and atherosclerotic burden in the general population. Design longitudinal population study. Setting random, representative population sample from Erpe-Mere and Nieuwerkerken (Belgium, primary care). Subjects 2524 male/female volunteers, aged 35–55 years, free from overt CVD. Main outcome measures Subjects were extensively phenotyped including presence of atherosclerosis (ultrasound) and a newly developed FH questionnaire (4 generations). Results Compared to cFH, eFH was superior in predicting an adverse risk profile (glycemic state, elevated blood pressure, lipid abnormalities, presence of metabolic syndrome components) and presence of atherosclerosis (all age & sex-adjusted p<0.05). Unlike cFH, eFH remained a significant predictor of subclinical atherosclerosis after adjusting for confounders. Most relations with eFH were not graded but showed clear informational breakpoints, with absence of CVD (including late onset) in any first-degree relative being a negative predictor of atherosclerosis, and a particularly interesting phenotype for further study. Conclusions A novel, extended FH definition is superior to the conventional definition in profiling cardiovascular risk and atherosclerotic burden in the general population. There remain clear opportunities to refine and increase the performance and informational content of this simple, readily-available inexpensive tool.
Tile-Level Annotation of Satellite Images Using Multi-Level Max-Margin Discriminative Random Field

This paper proposes a multi-level max-margin discriminative analysis (M3DA) framework, which takes both coarse and fine semantics into consideration, for the annotation of high-resolution satellite images. In order to generate more discriminative topic-level features, the M3DA uses the maximum entropy discrimination latent Dirichlet Allocation (MedLDA) model. Moreover, for improving the spatial coherence of visual words neglected by M3DA, conditional random field (CRF) is employed to optimize the soft label field composed of multiple label posteriors. The framework of M3DA enables one to combine word-level features (generated by support vector machines) and topic-level features (generated by MedLDA) via the bag-of-words representation. The experimental results on high-resolution satellite images have demonstrated that, using the proposed method can not only obtain suitable semantic interpretation, but also improve the annotation performance by taking into account the multi-level semantics and the contextual information.
Characteristics and electrical properties of epoxy resin surface layers fluorinated at different temperatures

Epoxy resin sheets were surface fluorinated in a laboratory vessel using a F2/N2 mixture with 12.5% F2 by volume at the different temperatures of 25, 55, 75, and 95 °C for the same time of 30 min, to investigate the effect of fluorination temperature on surface electrical properties. ATR-IR analyses indicate that fluorination led to substantial changes in surface chemical composition and structure, depending on fluorination temperature, and SEM surface and cross section images show an evolution of surface morphology and an increase of thickness of the fluorinated layer with fluorination temperature. Conductivity measurements reveal that the surface fluorinated samples have higher surface conductivities than the unfluorinated sample, and surface conductivity significantly increases with fluorination temperature. Surface potential measurements, performed about 10 s after corona charging, indicate lower initial surface potentials for the surface fluorinated samples than the unfluorinated sample, and a decrease of the initial surface potential with surface conductivity. The initial surface potential was found to decrease dramatically above a critical surface conductivity (3.0×10-14 S), and almost to zero when surface conductivity increased to 10-12 S. Contact angle measurements and surface energy calculations show a much higher surface polarity of the surface fluorinated samples compared to the unfluorinated sample and a dramatic increase of the surface polarity with fluorination temperature. An increase in degree of chain scission is considered to be the main cause for the increases of surface conductivity and surface polarity with fluorination temperature.