Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Scalability Study of the Smart-M 3 CuteSIB Implementation

According to the M3 architecture (multidevice, multivendor, multidomain), a smart space is created by deploying a Semantic Information Broker (SIB) in a given Internet of Things (IoT) environment. The deployed SIB enables information sharing for all digital devices participating in the IoT environment. In this study, we consider CuteSIB—a new SIB implementation for the Smart-M3 platform, where the class of SIB host devices covers such Qt-based equipment as common computers (e.g., laptops and personal computers), embedded computers (e.g., single-board computers and wireless routers), and personal mobile computers (e.g., smartphones and tablets). Our study focuses on performance evaluation of the CuteSIB operation with a multitude of devices that simultaneously participate in data sharing, information processing, and service delivery. Our simulation experiments applies a scalability model for a smart space application with the three functional groups of participating devices: sensors, reasoners, and mobile clients. In the experiments, the number of devices is varied in each group as well as the parameters of interaction behavior with SIB. The evaluation shows the scalability level that CuteSIB can achieve being deployed on a host device of moderate capacity in an IoT environment.
Lower limb skeletal muscle mass: development of dual-energy X-ray absorptiometry prediction model.

Although magnetic resonance imaging (MRI) can accurately measure lower limb skeletal muscle (SM) mass, this method is complex and costly. A potential practical alternative is to estimate lower limb SM with dual-energy X-ray absorptiometry (DXA). The aim of the present study was to develop and validate DXA-SM prediction equations. Identical landmarks (i.e., inferior border of the ischial tuberosity) were selected for separating lower limb from trunk. Lower limb SM was measured by MRI, and lower limb fat-free soft tissue was measured by DXA. A total of 207 adults (104 men and 103 women) were evaluated [age 43 +/- 16 (SD) yr, body mass index (BMI) 24.6 +/- 3.7 kg/m(2)]. Strong correlations were observed between lower limb SM and lower limb fat-free soft tissue (R(2) = 0.89, P < 0.001); age and BMI were small but significant SM predictor variables. In the cross-validation sample, the differences between MRI-measured and DXA-predicted SM mass were small (-0.006 +/- 1.07 and -0.016 +/- 1.05 kg) for two different proposed prediction equations, one with fat-free soft tissue and the other with added age and BMI as predictor variables. DXA-measured lower limb fat-free soft tissue, along with other easily acquired measures, can be used to reliably predict lower limb skeletal muscle mass.
Vascular Protection by Angiotensin Receptor Antagonism Involves Differential VEGF Expression in Both Hemispheres after Experimental Stroke

We identified that the angiotensin receptor antagonist, candesartan, has profound neurovascular protective properties when administered after ischemic stroke and was associated with a proangiogenic state at least partly explained by vascular endothelial growth factor A (VEGFA). However, the spatial distribution of vascular endothelial growth factor (VEGF) isoforms and their receptors remained unknown. Protein analysis identified a significant increase in vascular endothelial grow factor B (VEGFB) in the cerebrospinal fluid (CSF) and the ischemic hemispheres (with increased VEGF receptor 1 activation) of treated animals (p<0.05) which was co-occurring with an increase in protein kinase B (Akt) phosphorylation (p<0.05). An increase in VEGFA protein in the contralesional hemisphere corresponded to a significant increase in vascular density at seven days (p<0.01) after stroke onset. Vascular restoration by candesartan after stroke maybe related to differential regional upregulation of VEGFB and VEGFA, promoting a “prosurvival state” in the ischemic hemisphere and angiogenesis in the contralesional side, respectively. These vascular changes in both hemispheres after effective treatment are likely to contribute to enhanced recovery after stroke.
Differences in near‐mesopause summer winds, temperatures, and water vapor at northern and southern latitudes as possible causal factors for inter‐hemispheric PMSE differences

We report the results of a recent study to examine possible causal factors that could explain the observed differences in PMSE intensity in the northern and southern hemispheres. A variety of satellite data, models and ground‐based radar observations in the two hemispheres during local summer have been examined in this attempt. We will show results of inter‐hemispheric comparisons of temperatures, winds, and water vapor. The primary conclusions that can be drawn from these studies are that, while water vapor differences in the two hemispheres are difficult to interpret at near‐mesopause altitudes, the inter‐hemispheric temperature comparisons show clearly that the southern hemispheric mesopause is indeed a few degrees warmer. Moreover, southern summer mesospheric mean winds are considerably weaker than they are in the north. These results provide support for earlier speculations that were made to explain the observed inter‐hemispheric difference in PMSE occurrence.
A Maximum Likelihood Approach towards Aggregating Partial Orders

In many of the possible applications as well as the theoretical models of computational social choice, the agents' preferences are represented as partial orders. In this paper, we extend the maximum likelihood approach for defining "optimal" voting rules to this setting. We consider distributions in which the pairwise comparisons/incomparabilities between alternatives are drawn i.i. d. We call such models pairwise-independent models and show that they correspond to a class of voting rules that we call pairwise scoring rules. This generalizes rules such as Kemeny and Borda. Moreover, we show that Borda is the only pairwise scoring rule that satisfies neutrality, when the outcome space is the set of all alternatives. We then study which voting rules defined for linear orders can be extended to partial orders via our MLE model. We show that any weakly neutral outcome scoring rule (including any ranking/candidate scoring rule) based on the weighted majority graph can be represented as the MLE of a weakly neutral pairwise-independent model. Therefore, all such rules admit natural extensions to profiles of partial orders. Finally, we propose a specific MLE model πk for generating a set of k winning alternatives, and study the computational complexity of winner determination for the MLE of πk.
Gctf: Real-time CTF determination and correction

Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, I present a GPU-accelerated computer program, Gctf, for accurate and robust, real-time CTF determination. Similar to alternative programs, the main target of Gctf is to maximize the cross-correlation of a simulated CTF with the power spectra of observed micrographs after background reduction. However, novel approaches in Gctf improve both speed and accuracy. In addition to GPU acceleration, a fast ‘1-dimensional search plus 2-dimensional refinement (1S2R)’ procedure significantly speeds up Gctf. Based on the global CTF determination, the local defocus for each particle and for single frames of movies is accurately refined, which improves CTF parameters of all particles for subsequent image processing. Novel diagnosis method using equiphase averaging(EFA) and self-consistency verification procedures have also been implemented in the program for practical use, especially for aims of near-atomic reconstruction. Gctf is an independent program and the outputs can be easily imported into other cryoEM software such as Relion and Frealign. The results from several representative datasets are shown and discussed in this paper.
Domain Adaptive Information Extraction From Text

An information extraction system is designed to operate over a specific domain, and cannot be applied to new domains without being adapted if it is to perform well. We will investigate the problem of adapting information extraction systems to new domains by first defining the task of information extraction and giving an example of an information extraction system. We will then outline the modules comprising a typical system designed to solve the task and comment on their impact on domain adaptation. Previous work on adapting systems to new domains will be reviewed, along with work by the author. We will conclude with open problems and future areas of research in this field.
Experiences with NIMI

NIMI (National Internet Measurement Infrastructure) is a software system for building network measurement infrastructures. Its design emphasizes: (i) large-scale infrastructures composed from diversely-administered hosts, rather than infrastructures controlled by a single entity, and (ii) facilitating diverse types of measurements by diverse parties, some of whom are allowed richer access to certain portions of the infrastructure than others. We discuss our experiences with developing and operating the infrastructure to date: problems we have encountered, both foreseen and unanticipated, mistakes we made, and how we have adapted the design to address these. We also explore two key issues for developing a large-scale, extensible infrastructure: the problem of securely updating software on the measurement platforms, and the problem of constraining the resources consumed by different measurements. We argue that both of these can be unified in terms of controlling the behavior of the measurement software. But we also argue that, due to the varying burdens and benefits of the different mechanisms for providing this control, NIMI will need to provide "gradations" of security for different sites to choose from as best fits their requirements and resources.
On the nature of regional seismic phases—III. The influence of crustal heterogeneity on the wavefield for subduction earthquakes: the 1985 Michoacan and 1995 Copala, Guerrero, Mexico earthquakes

Summary The most prominent feature of the regional seismic wavefield from about 150 to over 1000 km is usually the Lg phase. This arrival represents trapped S-wave propagation within the crust as a superposition of multiple reflections, and its amplitude is quite sensitive to the lateral variation in the crust along a propagation path. In an environment where the events occur in a subduction zone, such as the western coast of Mexico, quite complex influences on the character of the regional wavefield arise from the presence of the subduction zone. The great 1985 Michoacan earthquake (MW=8.1), which occurred in the Mexican subduction zone, was one of the most destructive earthquakes in modern history and its notable character was that at Mexico City, located over 350 km from the epicentre, there was strong ground shaking almost comparable to that in the epicentral region that lasted for several minutes. Considerable effort has been expended to explain the origin of the unusual observed waves that caused the severe damage in the capital city during the destructive earthquake. The nature of the propagation process in this region can be understood in part by using the detailed strong-motion records from the 1995 Copala, Guerrero (MW=7.4) earthquake near the coast to the south of Mexico City, which also had an enhanced amplitude in the Valley of Mexico. Numerical modelling of both P and S seismic waves in 2-D and 3-D heterogeneous crustal models for western Mexico using the pseudospectral method provides direct insight into the nature of the propagation processes through the use of sequences of snapshots of the wavefield and synthetic seismograms at the surface. A comparison of different models allows the influences of different aspects of the structure to be isolated. 2-D and 3-D modelling of the 1985 Michoacan and 1995 Copala earthquakes clearly demonstrates that the origin of the long duration of strong ground shaking comes from the Sn and Lg wave trains. These S-wave arrivals are produced efficiently from shallow subduction earthquakes and are strongly enhanced during their propagation within the laterally heterogeneous waveguide produced by the subduction of the Cocos Plate beneath the Mexican mainland. The amplitude and duration of the Lg coda is also strongly reinforced by transmission through the Mexican Volcanic Belt from the amplification of S waves in the low-velocity surficial layer associated withS-to-P conversions in the volcanic zone. The further amplification of the large and long Lg wave train impinging on the shallow structure in the basin of Mexico City, with very soft soil underlain by nearly rigid bedrock with a strong impedance contrast, gives rise to the destructive strong ground shaking from the Mexican subduction earthquakes.
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations

We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein–DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein–DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.
TAC AdX'14: Autonomous Agents for Realtime Ad Exchange

Ad exchange, as a new advertising trading form, has been widely applied nowadays. It is an automatic marketplace requiring autonomous ad networks to bid for ad slots on web pages in realtime. The Trading Agent Competition Ad Exchange (TAC AdX) is a new challenging competition for agents who focus on the autonomous ad trading marketplace and the competing strategies on behalf of ad networks. Specifically, agents are required to compete for adverting contracts and to fulfill them in the ad exchange. In this paper, we present our agent, namely ANL, who won the first TAC AdX, with a total profit 1.592 times that of the runner up. We further propose a more adaptive and active agent, called AdvANL, which performs even better than ANL in our simulated competition environment.
Pattern of Mutation Rates in the Germline of Drosophila melanogaster Males from a Large-Scale Mutation Screening Experiment

The sperm or eggs of sexual organisms go through a series of cell divisions from the fertilized egg; mutations can occur at each division. Mutations in the lineage of cells leading to the sperm or eggs are of particular importance because many such mutations may be shared by somatic tissues and also may be inherited, thus having a lasting consequence. For decades, little has been known about the pattern of the mutation rates along the germline development. Recently it was shown from a small portion of data that resulted from a large-scale mutation screening experiment that the rates of recessive lethal or nearly lethal mutations differ dramatically during the germline development of Drosophila melanogaster males. In this paper the full data set from the experiment and its analysis are reported by taking advantage of a recent methodologic advance. By analyzing the mutation patterns with different levels of recessive lethality, earlier published conclusions based on partial data are found to remain valid. Furthermore, it is found that for most nearly lethal mutations, the mutation rate at the first cell division is even greater than previous thought compared with those at other divisions. There is also some evidence that the mutation rate at the second division decreases rapidly but is still appreciably greater than those for the rest of the cleavage stage. The mutation rate at spermatogenesis is greater than late cleavage and stem-cell stages, but there is no evidence that rates are different among the five cell divisions of the spermatogenesis. We also found that a modestly biased sampling, leading to slightly more primordial germ cells after the eighth division than those reported in the literature, provides the best fit to the data. These findings provide conceptual and numerical basis for exploring the consequences of differential mutation rates during individual development.
Filling-in stochastic texture

Overview We present a dynamic patch (DP) method for filling-in a hole of a stochastic/dynamic texture image using a Graph Cut (GC) [2], the advection equation (AE), and optical flow (OF) database. The GC method is iteratively applied with spatio-temporally changing the patch texture over time. This synthesizes naturally changing texture inside and boundary of the filling hole. Previously, an exemplar-based [3,4] and diffusion equation [1] based method have been reported. Issue: Most of them failed to non-periodically fill in dynamic texture/stochastic pattern [6] such as ocean and cloud when a gap becomes wide. Only copying of neighboring similiarity from a source image to a hole limits this because of no dynamic change in an inner patch, i.e., essentially static. An incomplete seamless boundary is synthesized by the previous methods [4]. A trial to transform an inner patch by such as rotation did not solve this issue. One possibility to solve this is to change the topology of a patch like a flow-guidance [3]. We extended this idea.
The South Atlantic: Present and Past Circulation

Central Themes of South Atlantic Circulation. - On the Circulation of the South Atlantic Ocean. - Transient-Tracer Information on Ventilation and Transport of South Atlantic Waters. - The Circulation and its Variability of the South Atlantic Ocean: First Results from the TOPEX/POSEIDON Mission. - The Zonal WOCE Sections in the South Atlantic. - South Atlantic Heat Transport at 11 S. - Comment on the South Atlantic's Role in the Global Circulation 121 -. - The Exchange of Water between the South Indian and South Atlantic Oceans. - The Benguela: Large Scale Features and Processes and System Variability. - The Southern Boundary of the South Atlantic. - Antarctic Intermediate Water in the South Atlantic. - Lagrangian Measurements in the Malvinas Current. - Circulation in the Deep Brazil Basin. - The Deep Water Regime in the Equatorial. - Chlorofluoromethanes in the Deep Equatorial Atlantic Revisited. - Modelling the Ocean Circulation in the South Atlantic: A Strategy for Dealing with Open Boundaries. - Mass and Heat Transports in the South Atlantic Derived from Historical Hydrographic Data. - Long-term Observation of Particle Fluxes in the Eastern Atlantic: Seasonality, Changes of Flux with Depth and Comparison with the Sediment Record. - Silica Signals in the South Atlantic. - On the Bathymetry of the Hunter Channel. - Expeditions into the Past: Paleoceanographic Studies in the South Atlantic. - Inverse Modelling of the Glacial Atlantic CirculationSystem: Investigation of Data Requirements. - Chemical Hydrography of the South Atlantic During the Last Glacial Maximum: Cd vs. ? 13C. - High Latitude Deep Water Sources During the Last Glacial Maximum and the Intensity of the Global Oceanic Circulation. - Late Quaternary Surface Circulation in the South Atlantic: The Stable Isotope Record and implications for Heat Transport and Productivity. - Climate Feedback and Pleistocene Variations in the Atlantic South Equatorial Current. - Late Quaternary Surface Temperatures and Productivity in the East-Equatorial South Atlantic: Response to Changes in Trade/Monsoon Wind Forcing and Surface Water Advection. - Late Quaternary Movements of the Angola- Benguela Front, SE Atlantic, and Implications for Advection in the Equatorial Ocean. - Late Quaternary Deep Circulation in the Western Equatorial Atlantic. - Late Quaternary Deep Water Circulation in the South Atlantic: Reconstruction from Carbonate Dissolution and Benthic Stable Isotopes. - Clay Mineral Fluctuations in Late Quaternary Sediments of the Southeastern South Atlantic: Implications for Past Changes of Deep Water Advection.
Convergence of Cells from the Progenitor Fraction of Adult Olfactory Bulb Tissue to Remyelinating Glia in Demyelinating Spinal Cord Lesions

Background Progenitor cells isolated from adult brain tissue are important tools for experimental studies of remyelination. Cells harvested from neurogenic regions in the adult brain such as the subependymal zone have demonstrated remyelination potential. Multipotent cells from the progenitor fraction have been isolated from the adult olfactory bulb (OB) but their potential to remyelinate has not been studied. Methodology/Principal Findings We used the buoyant density gradient centrifugation method to isolate the progenitor fraction and harvest self-renewing multipotent neural cells grown in monolayers from the adult green-fluorescent protein (GFP) transgenic rat OB. OB tissue was mechanically and chemically dissociated and the resultant cell suspension fractionated on a Percoll gradient. The progenitor fraction was isolated and these cells were plated in growth media with serum for 24 hrs. Cells were then propagated in N2 supplemented serum-free media containing b-FGF. Cells at passage 4 (P4) were introduced into a demyelinated spinal cord lesion. The GFP+ cells survived and integrated into the lesion, and extensive remyelination was observed in plastic sections. Immunohistochemistry revealed GFP+ cells in the spinal cord to be glial fibrillary acidic protein (GFAP), neuronal nuclei (NeuN), and neurofilament negative. The GFP+ cells were found among primarily P0+ myelin profiles, although some myelin basic protein (MBP) profiles were present. Immuno-electron microscopy for GFP revealed GFP+ cell bodies adjacent to and surrounding peripheral-type myelin rings. Conclusions/Significance We report that neural cells from the progenitor fraction of the adult rat OB grown in monolayers can be expanded for several passages in culture and that upon transplantation into a demyelinated spinal cord lesion provide extensive remyelination without ectopic neuronal differentiation.