Miracle-dz/UniFAR-FTUs huggingface dataset:
Geochemistry of sandstones and shales from the Ecca Group, Karoo Supergroup, in the Eastern Cape Province of South Africa: Implications for provenance, weathering and tectonic setting

Abstract Geochemical compositions of twenty-four sandstone and shale samples from the Ecca Group were analysed to decipher their provenance, paleoweathering conditions and tectonic setting. The shales have high Fe2O3, K2O, TiO2, Ce, Cu, Ga, La, Nb, Nd, Rb, Sc, Sr, Th and Y content more than the sandstones, whereas, sandstones are higher in SiO2, Hf and Zr than the shales. The positive correlations of Al2O3 with other elements as well as the abundance of Ba, Ce, Th, Rb, Zn and Zr suggest that these elements are primarily controlled by the dominant clay minerals. Tectonic discrimination diagrams revealed that the sandstones and shales are mostly of quartzose sedimentary provenance, suggesting that they were derived from a cratonic interior or recycled orogen. The binary plots of TiO2 versus Ni, TiO2 against Zr and La/Th versus Hf as well as the ternary diagrams of V-Ni-Th*10 indicate that the shales and sandstones were derived from felsic igneous rocks. A-CN-K (Al2O3-CaO-K2O) ternary diagram and indices of weathering (CIA, CIW and PIS) suggest that the granitic source rocks underwent moderate to high degree of chemical weathering. The CIA values range between 24.41% and 83.76%, indicating low to high weathering conditions. The CIW values for the studied sandstones and shales range from 25.90 to 96.25%, suggesting moderate to high intensive chemical weathering. ICV values for the sandstones and shales vary from 0.71 to 3.6 (averaging 1.20) and 0.41 to 1.05 (averaging 0.82), respectively. The k2O/Na2O ratios for the studied samples vary from 0.71 to 8.29, which reveal moderate to high maturity. The plot of CIA against ICV shows that most of the shales are geochemically mature and were derived from both weak and intensively weathered source rocks. The tectonic setting discrimination diagrams support passive-active continental margin setting of the provenance.
Toward Completeness in Concept Extraction and Classification

Many algorithms extract terms from text together with some kind of taxonomic classification (is-a) link. However, the general approaches used today, and specifically the methods of evaluating results, exhibit serious shortcomings. Harvesting without focusing on a specific conceptual area may deliver large numbers of terms, but they are scattered over an immense concept space, making Recall judgments impossible. Regarding Precision, simply judging the correctness of terms and their individual classification links may provide high scores, but this doesn't help with the eventual assembly of terms into a single coherent taxonomy. Furthermore, since there is no correct and complete gold standard to measure against, most work invents some ad hoc evaluation measure. We present an algorithm that is more precise and complete than previous ones for identifying from web text just those concepts 'below' a given seed term. Comparing the results to WordNet, we find that the algorithm misses terms, but also that it learns many new terms not in WordNet, and that it classifies them in ways acceptable to humans but different from WordNet.
Accurate estimation of joint motion trajectories for rehabilitation using Kinect

Kinect as an effective tool for clinical assessment and rehabilitation, suffers from drawbacks of lower accuracy of measuring human body kinematic data when compared to clinical gold standard motion capture devices. The accuracy of time-varying 3D locations of a fixed number of body joints obtained from Kinect skeletal tracking utility is affected by the presence of noise and precision limits of the Kinect depth sensor. In this paper, a framework for improving accuracy of Kinect skeletal tracking is proposed, that uses a set of parametric models to represent and track the human body. Each of the models represents the 3D geometric properties of a body segment connecting two adjacent joints. The temporal trajectories of the joints are recovered via particle filter-based motion tracking of each model. The proposed method was evaluated on Active Range of Motion exercises by 7 healthy subjects. The joint motion trajectories obtained using the proposed framework exhibit a greater motion smoothness (by 36%) along with reduced coefficient of variation of radius (by 34%), and lower value of root-mean-squared-error (by 53%), when compared to Kinect joint trajectories. This indicates an improvement in accuracy of joint motion trajectories using Kinect device, rendering it more suitable for clinical assessment and rehabilitation.
Experiments in the use of τ-simulations for the components-verification of real-time systems

We present a verification framework exploiting τ-simulations as a way to preserve local linear properties checked on the components of real-time systems. Therefore, we consider a component-based modeling of real-time systems. Their properties are expressed in a timed logic, MITL (Metric Interval Temporal Logic). For component-based models, traditional verification techniques are generally applied to the complete composed model, even if some properties only concern some components of the system, if not only one. We show that it is possible to check such local linear properties (safety as well as liveness) on the components they concern, and then to ensure their preservation using τ-simulation relations. We show the interest of the method by applying it on two real-time systems examples and by comparing the results with traditional verification techniques.
Conditional Site-Specific Integration into Human Chromosome 19 by Using a Ligand-Dependent Chimeric Adeno-Associated Virus/Rep Protein

ABSTRACT It is of great interest for gene therapy to develop vectors that drive the insertion of a therapeutic gene into a chosen specific site on the cellular genome. Adeno-associated virus (AAV) is unique among mammalian viruses in that it integrates into a distinct region of human chromosome 19 (integration site AAVS1). The inverted terminal repeats (ITRs) flanking the AAV genome and the AAV-encoded nonstructural proteins Rep78 and/or Rep68 are the only viral elements necessary and sufficient for site-specific integration. However, it is also known that unrestrained Rep activity may cause nonspecific genomic rearrangements at AAVS1 and/or have detrimental effects on cell physiology. In this paper we describe the generation of a ligand-dependent form of Rep, obtained by fusing a C-terminally deleted Rep68 with a truncated form of the hormone binding domain of the human progesterone receptor, which does not bind progesterone but binds only its synthetic antagonist RU486. The activity of this chimeric protein, named Rep1-491/P, is highly dependent on RU486 in various assays: in particular, it triggers site-specific integration at AAVS1 of an ITR-flanked cassette in a ligand-dependent manner, as efficiently as wild-type Rep68 but without generating unwanted genomic rearrangement at AAVS1.
HSV-1 ICP27 represses NF-κB activity by regulating Daxx sumoylation

Herpes simplex virus type 1 ICP27 is a multifunctional protein responsible for viral replication, late gene expression, and reactivation from latency. ICP27 interacts with various cellular proteins, including Daxx. However, the role of interaction between ICP27 and Daxx is largely unknown. Since Daxx is known to repress NF-κB activity, there is a possibility that ICP27 may influence the inhibitory effect of Daxx on NF-κB activity. In this study, we tested whether ICP27 affects the NF-κB activity through its interaction with Daxx. Interestingly, ICP27 enhanced the Daxx-mediated repression of NF-κB activity. In addition, we found that sumoylation of Daxx regulates its interaction with p65. ICP27 binds to Daxx, inhibits Daxx sumoylation, and enhances p65 deacetylation induced by Daxx. Consequently, ICP27 represses the NF-κB activity, by elevating the inhibitory effect of Daxx on NF-κB activity through desumoylation of Daxx.
Bone marrow mesenchymal stem cells

Following the identification of bone marrow multipotent cells that could adhere to plastic and differentiate along numerous mesenchymal lineages in vitro, a considerable effort has been invested in characterizing and expanding these cells, which are now called “mesenchymal stem cells” (MSCs), in vitro. Over the years, numerous lines of evidence have been provided in support of their plasticity, their extraordinary immunomodulatory properties, their potential use for tissue engineering purposes, as well as their ability to be recruited to sites of injury, where they might contribute a “natural in vivo system for tissue repair. ” Moreover, some studies have attempted the characterization of their cell‐surface specific antigens and of their anatomical location in vivo. Lastly, it has been shown that similar cells could be also isolated from organs other than the bone marrow. Despite this impressive body of investigations, numerous questions related to the developmental origin of these cells, their proposed pluripotency, and their role in bone modeling and remodeling and tissue repair in vivo are still largely unanswered. In addition, both a systematic phenotypic in vivo characterization of the MSC population and the development of a reproducible and faithful in vivo assay that would test the ability of MSCs to self‐renew, proliferate, and differentiate in vivo are just beginning. This brief review summarizes the current knowledge in the field of study of MSCs and the outstanding questions. J. Cell. Biochem. 109: 277–282, 2010. © 2009 Wiley‐Liss, Inc.
[A relationship between dehydroepiandrosterone sulphate and insulin resistance in obese men and women].

UNLABELLED The aim of our study was to investigate if there is any significant relationship between adrenal steroid hormone dehydroepiandrosterone-sulphate (DHEAS) and insulin resistance, as there are some previous signs in the literature suggesting such relationship but the results are not conclusive. METHODS In our study participated 50 obese women and 20 obese men both with BMI over 27 kg/m2. Insulin resistance was calculated using HOMA insulin resistance index (HOMA-IR) that is based on fasting glycaemia and basal insulin levels. RESULTS The negative correlation between DHEAS and HOMA-IR was found in the whole group of obese women but close behind statistical significance (r = -0.27, p = 0.055). But the group of obese women does not seem to be homogenous in correlation between DHEAS and insulin resistance. The significant negative correlation between DHEAS and insulin resistance was found in the subgroup (n = 21) of obese type 2 diabetic women (r = -0.55, p = 0.01) but no correlation was found in the subgroup (n = 29) of obese non-diabetic women (r = -0.06, p = 0.77). The relationship between DHEAS and glycaemia homeostasis was also confirmed by significant negative correlation between DHEAS and glycated haemoglobin (HbA1c) both in the subgroup of type 2 diabetic women (r = -0.51, p = 0.03) and in the subgroup of non-diabetic women (r = -0.70, p = 0.001). There was not found any significant correlation between DHEAS and insulin resistance neither in the whole group (n = 20) of obese men (r = 0.04, p = 0.87) nor in the subgroup (n = 11) of obese type 2 diabetic men (r = 0.55, p = 0.08) or in the subgroup (n = 9) of obese non-diabetic men (r = -0.42, p = 0.26). CONCLUSIONS Significant negative correlation between DHEAS and HOMA-IR was found in the group of obese type 2 diabetic women but not in obese non-diabetic women suggesting that low DHEAS level might be connected to the development of insulin resistance and type 2 diabetes mellitus in obese women.
Crystal Structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe

Sm-like (Lsm) proteins are ubiquitous and function in many aspects of RNA metabolism, including pre-mRNA splicing, nuclear RNA processing, mRNA decay and miRNA biogenesis. Here three crystal structures including Lsm3, Lsm4 and Lsm5/6/7 sub-complex from S. pombe are reported. These structures show that all the five individual Lsm subunits share a conserved Sm fold, and Lsm3, Lsm4, and Lsm5/6/7 form a heptamer, a trimer and a hexamer within the crystal lattice, respectively. Analytical ultracentrifugation indicates that Lsm3 and Lsm5/6/7 sub-complex exist in solution as a heptamer and a hexamer, respectively while Lsm4 undergoes a dynamic equilibrium between monomer and trimer in solution. RNA binding assays show that Lsm2/3 and Lsm5/6/7 bind to oligo(U) whereas no RNA binding is observed for Lsm3 and Lsm4. Analysis of the inter-subunit interactions in Lsm5/6/7 reveals the organization order among Lsm5, Lsm6 and Lsm7.
Surface current measurements by HF radar in freshwater lakes

HF radar has become an increasingly important tool for mapping surface currents in the coastal ocean. However, the limited range, due to much higher propagation loss and smaller wave heights (relative to the saltwater ocean), has discouraged HF radar use over fresh water, Nevertheless, the potential usefulness of HF radar in measuring circulation patterns in freshwater lakes has stimulated pilot experiments to explore HF radar capabilities over fresh water. The Episodic Events Great Lakes Experiment (EEGLE), which studied the impact of intermittent strong wind events on the resuspension of pollutants from lake-bottom sediments, provided an excellent venue for a pilot experiment. A Multifrequency Coastal HF Radar (MCR) was deployed for 10 days at two sites on the shore of Lake Michigan near St. Joseph, MI. Similarly, a single-frequency CODAR SeaSonde instrument was deployed on the California shore of Lake Tahoe. These two experiments showed that when sufficiently strong surface winds (2 about 7 m/s) exist for an hour or more, a single HE radar can be effective in measuring the radial component of surface currents out to ranges of 10-15 km. We also show the effectiveness of using HF radar in concert with acoustic Doppler current profilers (ADCPs) for measuring a radial component of the current profile to depths as shallow as 50 cm and thus potentially extending the vertical coverage of an ADCP array.
User Action Prediction for Computational Advertisement Using Local Graph Algorithms

User behavior modeling is essential in computational advertisement, which builds users’ profiles by tracking their online behaviors and then delivers the relevant ads according to each user’s interests and needs. Accurate models will lead to higher targeting accuracy and thus improved advertising performance. Intuitively, similar users tend to have similar behaviors towards the displayed ads. However, to the best of our knowledge, there is not much previous work that explicitly investigates such similarities and incorporates them into ad response targeting and prediction, largely due to the prohibitive scale of the problem. To bridge this gap, in this paper, we use bipartite graphs to represent historical user behaviors, which consist of both user nodes and advertiser campaign nodes, as well as edges reflecting user-campaign interactions in the past. Based on this representation, we study random-walk-based local algorithms for user behavior modeling and action prediction, whose computational complexity depends only on the size of the output cluster, rather than the entire graph. Our goal is to improve action prediction by leveraging historical user-user, campaign-campaign, and user-campaign interactions. In particular, we propose the bipartite graphs AdvUserGraph accompanied with the ADNI algorithm. ADNI extends the NIBBLE algorithm to AdvUserGraph, and it is able to find the local cluster consisting of interested users towards a specific advertiser campaign. We also propose two extensions of ADNI with improved efficiencies. The performance of the proposed algorithms is demonstrated on both synthetic data and a world leading Demand Side Platform (DSP), showing that they are able to discriminate extremely rare events in terms of their action propensity.
Physics faculty and educational researchers: Divergent expectations as barriers to the diffusion of innovations

Physics Education Research (PER) practitioners have engaged in substantial curriculum development and dissemination work in recent years. Yet, it appears that this work has had minimal influence on the fundamental teaching practices of the typical physics faculty. To better understand this situation, interviews were conducted with five likely users of physics education research. All reported making changes in their instructional practices and all were influenced, to some extent, by educational research. Yet, none made full use of educational research and most had complaints about their interactions with educational researchers. In this paper we examine how these instructors used educational research in making instructional decisions and identify divergent expectations about how researchers and faculty can work together to improve student learning. Although different instructors emphasized different aspects of this discrepancy between expectations, we believe that they are all related to a single underlyin.
Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals

The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host–parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104–110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum ‘lookback’ times, with subsequent implications for the field of paleovirology.
Microstructural penetrometry of asteroid regolith analogues and Titan ’ s surface

Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online's data policy on reuse of materials please consult the policies page. Abstract: We investigate essential aspects of penetrometer design required to measure particle properties on asteroids using a combination of laboratory analogue regoliths and spaceflight data returned by the Huygens probe from Titan. Penetrometery in granular material is complicated due to multiple and interdependent mechanical processes that occur during penetration. A numerical impact model is developed that simulates the behaviour of a penetrometer and its force sensor in a granular medium. The model is based on the Huygens ACC-E instrument that successfully returned penetrometery data from the surface of Titan. Penetrometry measurements are made in analogue asteroid regoliths using a laboratory copy of ACC-E. The average particle size in the targets ranged from 0.1 to 0.9 of the penetrometer tip diameter. To describe the structure seen in the data a number of metrics are defined to characterise the peaks seen in the returned signal. The significance of the variation of the metrics (such as peak height or width) with particle mass and radius are analysed in terms of penetrometer properties such as impact velocity, elastic properties and data logging parameters. We find the penetrometer can be used to measure average particle radius and mass adequately for a mid-range of particle radii. Electronic noise effects mostly the results from very small and very large particles. For high mass particles there is evidence that particle-particle impacts, within the target are being felt by the tip that make any straight forward interpretations using peak frequency a challenge. Using our numerical model the Huygens penetrometry data from Titan is analysed. A particle diameter, of around half a centimetre, is found to be consistant with the penetrometry data returned by Huygens. Recommendations and lessons learned, regarding data interpretation techniques are made for asteroid penetrometry (or any other extraterrestrial surface) when using this instrument. Dear Icarus, We would like to submit a revised version of our paper called " Microstructural penetrometry of asteroid regolith analogue and of Titan's surface " to your journal. The comments from referee #1 have been addressed with the corrections made in the manuscript noted for reference. Referee 1. The friction term needs to be addressed in the paper and its affect on the author's …
Robust piecewise-planar 3D reconstruction and completion from large-scale unstructured point data

In this paper, we present a novel method, the first to date to our knowledge, which is capable of directly and automatically producing a concise and idealized 3D representation from unstructured point data of complex cluttered real-world scenes, with a high level of noise and a significant proportion of outliers, such as those obtained from passive stereo. Our algorithm can digest millions of input points into an optimized lightweight watertight polygonal mesh free of self-intersection, that preserves the structural components of the scene at a user-defined scale, and completes missing scene parts in a plausible manner. To achieve this, our algorithm incorporates priors on urban and architectural scenes, notably the prevalence of vertical structures and orthogonal intersections. A major contribution of our work is an adaptive decomposition of 3D space induced by planar primitives, namely a polyhedral cell complex. We experimentally validate our approach on several challenging noisy point clouds of urban and architectural scenes.
Designing a Multi-Agent Portfolio Management System

The voluminous and readily available information on the Internet has given rise to exploration of Intelligent Agent technology for accessing, filtering, evaluating and integrating information. In contrast to most current research that has investigated single-agent approaches, we are developing a collection of multiple agents that team up on demand, depending on the user, the task and the situation, to access, filter and integrate information in support of user tasks. We are investigating techniques for developing distributed adaptive collections of information agents that coordinate to retrieve, filter and fuse information relevant to the user, task and situation, as well as anticipate user’s information needs. Our approach is based on (I) case-based task and situation models, (2) flexible o~ganizational structuring, and (3) reusable agent architecture. We are currently implementing the system in the domain of financial portfolio management. While this paper focuses on the big picture, the final section will describe the current implementation and point to our work on detailed technical solutions.
Do tangible interfaces enhance learning?

Conceptual work on tangible interfaces has focused primarily on the production of descriptive frameworks. While this work has been successful in mapping out a space of technical possibilities and providing a terminology to ground discussion, it provides little guidance on the cognitive or social effects of using one type of interface or another. In this paper we look at the area of learning with tangible interfaces, suggesting that more empirically grounded research is needed to guide development. We provide an analytic framework of six perspectives, which describes latent trends and assumptions that might be used to motivate and guide this work, and makes links with existing research in cognitive science and education.