Miracle-dz/UniFAR-FTUs huggingface dataset:
A new algorithm for finding the Shannon cover of shifts of finite type

A shift of finite type (SFT) is a shift space whose constraints can be represented by a finite list of forbidden words. The deterministic labeled graph with the fewest vertices presenting an irreducible SFT (called the Shannon cover) is obtained, in general, via a two-step procedure: The first step is to generate an initial deterministic presentation, and the second one is to apply a vertex-minimization algorithm to identify classes of equivalent vertices. We propose in this paper an algorithm to generate the Shannon cover of a SFT that firstly identify classes of follower set equivalent words derived from the collection of all first offenders. This identification is not based on the allowable sequences obtained from an initial presentation, as is usually done. Having defined the equivalence classes (or the vertices of the minimal presentation) we apply a procedure to connect the vertices and label the edges that yields the essential component of the follower set graph of the SFT.
Virtual Forum Theater – a CSCL environment for scenario generation and rehearsal for change

Virtual Forum Theater is a web-based participatory and collaborative digital drama designed to enhance expressive fluency, argumentation skills, and critical awareness. The theoretical framework is based on Pedagogy of the Oppressed (Freire, 1972), constructivism (Piaget, 1977), constructionism (Papert, 1980), Computer Supported Collaborative Learning (CSCL) (Koschmann, 1996) as well as Theater of the Oppressed (Boal, 1974) and Brecht’s theory on theater (1964). By situating Forum Theatre (FT) online I intend to provide an environment that removes the limitations of time and space from FT, and enables collaboration with a wider variety of “spect-actors”, generating more scenarios, and simulating more pathways of resolution. VFT is a safe environment in which to play out different responses to conflict like roleplaying and trials of solutions to conflict-inherent and oppressive environments. VFT proposes a new solution to an existing conflict, and interacting with peers on the WWW in order to pose and resolve characters’ motivations and actions and thus help validate or invalidate the solution.
View Synthesis for Advanced 3D Video Systems

Interest in 3D video applications and systems is growing rapidly and technology is maturating. It is expected that multiview autostereoscopic displays will play an important role in home user environments, since they support multiuser 3D sensation and motion parallax impression. The tremendous data rate cannot be handled efficiently by representation and coding formats such as MVC or MPEG-C Part 3. Multiview video plus depth (MVD) is a new format that efficiently supports such advanced 3DV systems, but this requires high-quality intermediate view synthesis. For this, a new approach is presented that separates unreliable image regions along depth discontinuities from reliable image regions, which are treated separately and fused to the final interpolated view. In contrast to previous layered approaches, our algorithm uses two boundary layers and one reliable layer, performs image-based 3D warping only, and was generically implemented, that is, does not necessarily rely on 3D graphics support. Furthermore, different hole-filling and filtering methods are added to provide high-quality intermediate views. As a result, high-quality intermediate views for an existing 9-view auto-stereoscopic display as well as other stereo- and multiscopic displays are presented, which prove the suitability of our approach for advanced 3DV systems.
Biological and Physical Effects of Brine Discharge from the Carlsbad Desalination Plant and Implications for Future Desalination Plant Constructions

Seawater reverse osmosis (SWRO) desalination is increasingly used as a technology for addressing shortages of freshwater supply and desalination plants are in operation or being planned world-wide and specifically in California, USA. However, the effects of continuous discharge of high-salinity brine into coastal environments are ill-constrained and in California are an issue of public debate. We collected in situ measurements of water chemistry and biological indicators in coastal waters (up to ~2 km from shore) before and after the newly constructed Carlsbad Desalination Plant (Carlsbad, CA, USA) began operations. A bottom water salinity anomaly indicates that the spatial footprint of the brine discharge plume extended about 600 m offshore with salinity up to 2.7 units above ambient (33.2). This exceeds the maximum salinity permitted for this location based on the California Ocean Plan (2015 Amendment to Water Quality Control Plan). However, no significant changes in the assessed biological indicators (benthic macrofauna, BOPA-index, brittle-star survival and growth) were observed at the discharge site. A model of mean ocean wave potential was used as an indicator of coastal mixing at Carlsbad Beach and at other locations in southern and central CA where desalination facilities are proposed. Our results indicated that to minimize environmental impacts discharge should target waters where a long history of anthropogenic activity has already compromised the natural setting. To ensure adequate mixing of the discharge brine desalination plants should be constructed at high-energy sites with sandy substrates, and discharge through diffusor systems.
Can surgical simulation be used to train detection and classification of neural networks?

Computer-assisted interventions (CAI) aim to increase the effectiveness, precision and repeatability of procedures to improve surgical outcomes. The presence and motion of surgical tools is a key information input for CAI surgical phase recognition algorithms. Vision-based tool detection and recognition approaches are an attractive solution and can be designed to take advantage of the powerful deep learning paradigm that is rapidly advancing image recognition and classification. The challenge for such algorithms is the availability and quality of labelled data used for training. In this Letter, surgical simulation is used to train tool detection and segmentation based on deep convolutional neural networks and generative adversarial networks. The authors experiment with two network architectures for image segmentation in tool classes commonly encountered during cataract surgery. A commercially-available simulator is used to create a simulated cataract dataset for training models prior to performing transfer learning on real surgical data. To the best of authors’ knowledge, this is the first attempt to train deep learning models for surgical instrument detection on simulated data while demonstrating promising results to generalise on real data. Results indicate that simulated data does have some potential for training advanced classification methods for CAI systems.
Robotically Assisted Microsurgery: Development of Basic Skills Course

Robotically assisted microsurgery or telemicrosurgery is a new technique using robotic telemanipulators. This allows for the addition of optical magnification (which defines conventional microsurgery) to robotic instrument arms to allow the microsurgeon to perform complex microsurgical procedures. There are several possible applications for this platform in various microsurgical disciplines. Since 2009, basic skills training courses have been organized by the Robotic Assisted Microsurgical and Endoscopic Society. These basic courses are performed on training models in five levels of increasing complexity. This paper reviews the current state of the art in robotically asisted microsurgical training.
Modulation of Env Content in Virions of Simian Immunodeficiency Virus: Correlation with Cell Surface Expression and Virion Infectivity

ABSTRACT Specific mutations were created in the cytoplasmic domain of the gp41 transmembrane protein of simian immunodeficiency virus strain 239 (SIV239). The resultant strains included a mutant in which Env residue 767 was changed to a stop codon, a double mutant in which positions 738 and 739 were changed to stop codons, another mutant in which a prominent endocytosis motif was changed from YRPV to GRPV by the substitution of tyrosine 721, and a final combination mutant bearing Q738stop, Q739stop, and Y721G mutations. The effects of these mutations on cell surface expression, on Env incorporation into virions, and on viral infectivity were examined. The molar ratio of Gag to gp120 of 54:1 that we report here for SIV239 virions agrees very well with the ratio of 60:1 reported previously by Chertova et al. (E. Chertova, J. W. Bess, Jr., B. J. Crise, R. C. Sowder II, T. M. Schaden, J. M. Hilburn, J. A. Hoxie, R. E. Benveniste, J. D. Lifson, L. E. Henderson, and L. O. Arthur, J. Virol. 76:5315-5325, 2002), although they were determined by very different methodologies. Assuming 1,200 to 2,500 Gag molecules per virion, this corresponds to 7 to 16 Env trimers per SIV239 virion particle. Although all of the mutations increased Env levels in virions, E767stop had the most dramatic effect, increasing the Env content per virion 25- to 50-fold. Increased levels of Env content in virions correlated strictly with higher levels of Env expression on the cell surface. The increased Env content with the E767stop mutation also correlated with an increased infectivity, but the degree of change was not proportional: the 25- to 50-fold increase in Env content only increased infectivity 2- to 3-fold. All of the mutants replicated efficiently in the CEMx174 and Rh221-89 cell lines. Although some of these findings have been reported previously, our findings show that the effects of the cytoplasmic domain of gp41 on the Env content in virions can be dramatic, that the Env content in virions correlates strictly with the levels of cell surface expression, and that the Env content in virions can determine infectivity; furthermore, our results define a particular change with the most dramatic effects.
Fast Sparse Matrix-Vector Multiplication on GPUs: Implications for Graph Mining

Scaling up the sparse matrix-vector multiplication kernel on modern Graphics Processing Units (GPU) has been at the heart of numerous studies in both academia and industry. In this article we present a novel non-parametric, self-tunable, approach to data representation for computing this kernel, particularly targeting sparse matrices representing power-law graphs. Using real web graph data, we show how our representation scheme, coupled with a novel tiling algorithm, can yield significant benefits over the current state of the art GPU efforts on a number of core data mining algorithms such as PageRank, HITS and Random Walk with Restart.
Under Consideration for Publication in J. Functional Programming Parameterised Notions of Computation

Moggi's Computational Monads and Power et al 's equivalent notion of Freyd category have captured a large range of computational effects present in programming languages. Examples include non-termination, non-determinism, exceptions, continuations, side-effects and input/output. We present generalisations of both computational monads and Freyd categories , which we call parameterised monads and parameterised Freyd categories, that also capture computational effects with parameters. Examples of such are composable continuations , side-effects where the type of the state varies and input/output where the range of inputs and outputs varies. By also considering structured parameterisation, we extend the range of effects to cover separated side-effects and multiple independent streams of I/O. We also present two typed λ-calculi that soundly and completely model our categorical definitions — with and without symmetric monoidal parameterisation — and act as prototypical languages with parameterised effects.
MULTIBIN : A BINAURAL AUDITION TOOL

MultiBin is a new tool for binaural audition of multiple sound sources in a user definable environment. Although designed to be flexible in its application, its primary function is to provide dynamic multi-channel binaural simulation. It is built upon two new Csound binaural reverberation opcodes. An early reflection opcode, based on an image source method and a Head-Related Transfer Function interpolation algorithm previously introduced by the authors provides dynamic source and listener location. This is complemented by a later reverberation opcode which provides a diffuse reverb based on a parametric Feedback Delay Network model which considers interaural coherence.
Tumour dormancy and clinical implications in breast cancer

The aim of adjuvant therapy in breast cancer is to reduce the risk of recurrence. Some patients develop metastases many years after apparently successful treatment of their primary cancer. Tumour dormancy may explain the long time between initial diagnosis and treatment of cancer, and occurrence of relapse. The regulation of the switch from clinical dormancy to cancer regrowth in locoregional and distant sites is poorly understood. In this review, we report some data supporting the existence of various factors that may explain cancer dormancy including genetic and epigenetic changes, angiogenic switch, microenvironment, and immunosurveillance. A better definition and understanding of these factors should allow the identification of patients at high risk of relapse and to develop new therapeutic strategies in order to improve prognosis.
Prime-Boost Strategies in Mucosal Immunization Affect Local IgA Production and the Type of Th Response

Combinations of different delivery routes for priming and boosting represent vaccination strategies that can modulate magnitude, quality, and localization of the immune response. A murine model was used to study T cell clonal expansion following intranasal (IN) or subcutaneous (SC) priming, and secondary immune responses after boosting by either homologous or heterologous routes. T cell primary activation was studied by using the adoptive transfer model of ovalbumin-specific transgenic CD4+ T cells. Both IN and SC immunization efficiently elicited, in the respective draining lymph nodes, primary clonal expansion of antigen-specific CD4+ T cells that disseminated toward distal lymph nodes (mesenteric and iliac) and the spleen. After boosting, a significant serum IgG response was induced in all groups independent of the combination of immunization routes used, while significant levels of local IgA were detected only in mice boosted by the IN route. Mucosal priming drove a stronger Th1 polarization than the systemic route, as shown by serum IgG subclass analysis. IFN-gamma production was observed in splenocytes of all groups, while prime-boost vaccine combinations that included the mucosal route, yielded higher levels of IL-17. Memory lymphocytes were identified in both spleen and draining lymph nodes in all immunized mice, with the highest number of IL-2 producing cells detected in mice primed and boosted by the nasal route. This work shows the critical role of immunization routes in modulating quality and localization of immune responses in prime-boost vaccine strategies.
Person analysis in stereoscopic movies

People are at the center of many computer vision tasks, such as surveillance systems or self-driving cars. They are also at the center of most visual contents, potentially providing very large datasets for training models and algorithms. While stereoscopic data has been studied for long, it is only recently that feature-length stereoscopic ("3D") movies became widely available. In this thesis, we study how we can exploit the additional information provided by 3D movies for person analysis. We first explore how to extract a notion of depth from stereo movies in the form of disparity maps. We then evaluate how person detection and human pose estimation methods perform on such data. Leveraging the relative ease of the person detection task in 3D movies, we develop a method to automatically harvest examples of persons in 3D movies and train a person detector for standard color movies. We then focus on the task of segmenting multiple people in videos. We first propose a method to segment multiple people in 3D videos by combining cues derived from pose estimates with ones derived from disparity maps. We formulate the segmentation problem as a multi-label Conditional Random Field problem, and our method integrates an occlusion model to produce a layered, multi-instance segmentation. After showing the effectiveness of this approach as well as its limitations, we propose a second model which only relies on tracks of person detections and not on pose estimates. We formulate our problem as a convex optimization one, with the minimization of a quadratic cost under linear equality or inequality constraints. These constraints weakly encode the localization information provided by person detections. This method does not explicitly require pose estimates or disparity maps but can integrate these additional cues. Our method can also be used for segmenting instances of other object classes from videos. We evaluate all these aspects and demonstrate the superior performance of this new method.
A major gene for host response to porcine reproductive and respiratory syndrome is not unfavorably associated with overall performance under nonchallenging conditions in commercial pig lines1

ABSTRACT A QTL for host response to porcine reproductive and respiratory syndrome (PRRS) was identified in a previous study. The SNP WUR10000125 (WUR) is used as a tag SNP for this QTL. The favorable (B) allele at this SNP is in low frequency in commercial populations, possibly because this allele is unfavorably associated with an important trait under nonchallenging conditions and, therefore, may have been selected against. Therefore, objectives of this study were to estimate the effect of WUR on traits under selection in commercial lines under nonchallenging conditions and to estimate the effect of WUR genotype of parents on performance of crossbred progeny in a commercial-like environment. Data were collected on 4 purebred lines: a Landrace dam line (D1), a Large White dam line (D2), a synthetic sire line (S1), and a Pietrain sire line (S2). Traits analyzed included total number born, number stillborn, farrowing survival, lactation survival, litter mortality, daily feed intake (DFI), backfat, average test daily gain (TGR), average lifetime daily gain (LGR), and Topigs Norsvin selection index (TSI) value, indicative of overall economic value. Deregressed EBV were calculated for each trait (except TSI) and analyzed within line. In the S1 line, AB and BB pigs had significantly lower TGR (P = 0.002) and LGR (P = 0.001) than AA pigs but also lower DFI (P = 0.004). Conversely, AB and BB pigs had significantly higher DFI (P < 0.001) and AB pigs had significantly higher TGR (P = 0.03) than AA pigs in the S2 line. The effect of WUR on TSI was not significant for any line (P ≥ 0.15). Analyses of phenotypic records collected on crossbred progeny of S1 sires and D1 × D2 F1 females showed no significant effect of parent WUR genotype on DFI, backfat, TGR, or LGR (P ≥ 0.07). In conclusion, the effect of WUR was nonsignificant for most traits but the magnitude and direction of the effect differed by trait and by line. The favorable allele for host response to PRRS was associated with greater DFI and a tendency for greater TGR in the S2 line, but the opposite direction of effect was detected for the S1 line. Regardless of the effect on individual traits, no significant effect of WUR on TSI was detected for any line. Therefore, selecting for the B allele is expected to result in progeny with increased resistance to PRRS without compromising overall economic value under normal, nonchallenging conditions.
Plug-and-play control of interconnected systems with a changing number of subsystems

This paper proposes a new method for designing decentralised controllers of interconnected systems with a changing number of subsystems. When a new subsystem is added to an existing interconnected system, the control station of this subsystem should be designed by the design agent of this new subsystem based only on local information and some gathered model information over the network. As the dynamics of the overall system depends upon all existing subsystems, the main difficulty of this design problem is to ensure the stability of the overall interconnected system based on limited information and, furthermore, to evaluate the overall input-output performance locally. The main results of this paper are conditions that can be used to analyse the overall system by means of a limited amount of model information. As a consequence, the new subsystem can be “plugged in”, its design agent collects relevant model information over the network to check the conditions and the new control station “plays” together with the existing controllers. The method is illustrated by its application to a multizone furnace for crystal growth.
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile–profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.
Evaluation of ADC non-linearity correction based on INL(n) approximation

Accuracy of AD conversion can be improved using correction of ADC non-linearity. An application of the analytical inverse function of INL(n) curve (except other possibilities) can be used. The application of this method is dependent on the possibility to derive the inverse function to the function approximating the INL(n) curve. The first achieved result was published in [4]. The results of further simulations, which take into account also additive noise, jitter in sampling, non-zero sampled signal phase and hysteretic behavior of the ADC, are published in this paper.