Miracle-dz/UniFAR-FTUs huggingface dataset:
VR1‐positive primary afferents contact NK1‐positive spinoparabrachial neurons

Neurons in rat superficial dorsal horn that express neurokinin receptor 1 (NK1), a receptor for substance P, play a critical role in the development of hyperalgesia. Thermal hyperalgesia is dramatically reduced after ablation of these neurons, but, paradoxically, not in mice that lack the NK1 receptor (Mantyh et al. [1997] Science 278:275–279). Because primary afferents that express vanilloid receptor 1 (VR1), a receptor for noxious heat, are essential for thermal nociception and hyperalgesia, we reasoned that VR1‐positive fibers may terminate onto NK1‐expressing dorsal horn neurons. We therefore combined immunofluorescent staining for VR1 and NK1 to show that NK1‐positive neurons in lamina I are contacted by VR1‐positive fibers. That these contacts represent synapses was verified by staining for the presynaptic marker synaptophysin and by electron microscopy. By combining retrograde tracing with immunocytochemistry, we also found that most NK1‐positive cells contacted by VR1‐positive fibers project to the lateral parabrachial nucleus. Because quantitative evaluation suggests a preferential targeting of NK1‐positive lamina I neurons by fibers containing VR1, these results demonstrate a significant monosynaptic innervation of spinoparabrachial neurons by VR1‐positive afferents. J. Comp. Neurol. 460:255–265, 2003. © 2003 Wiley‐Liss, Inc.
Energy Efficiency via the N-way Model

With core counts as well as heterogeneity on the rise, the sequential components of applications are becoming the major bottleneck in performance scaling as predicted by Amdahl's law. We are therefore faced with the simultaneous problems of occupying an increasing number of cores and improving sequential performance. In this work, we specifically focus on improving the energy efficiency of sequential algorithms through the n-way programming model. In previous work, we introduced the n-way programming model which seeks to exploit the algorithmic diversity present in certain computations in order to speedup or improve the quality-of-result. The core idea behind n-way parallelism is to launch a number of instances of a key computational step and benefit from either the algorithmic diversity present in the algorithm or the diversity in algorithms available to express the computation. In this paper, we propose to combine metrics measuring the algorithmic progress of a computation with metrics measuring the energy expenditure to compute an efficiency metric. This metric can then be used to quickly pick which instance of a n-way computation is the most energy efficient and cull the inefficient ones. The evaluation of our idea on sorting benchmarks shows that our technique is promising.
The SGI Origin: A ccnuma Highly Scalable Server

The SGI Origin 2000 is a cache-coherent non-uniform memory access (ccNUMA) multiprocessor designed and manufactured by Silicon Graphics, Inc. The Origin system was designed from the ground up as a multiprocessor capable of scaling to both small and large processor counts without any bandwidth, latency, or cost cliffs. The Origin system consists of up to 512 nodes interconnected by a scalable Craylink network. Each node consists of one or two R10000 processors, up to 4 GB of coherent memory, and a connection to a portion of the XIO IO subsystem. This paper discusses the motivation for building the Origin 2000 and then describes its architecture and implementation. In addition, performance results are presented for the NAS Parallel Benchmarks V2.2 and the SPLASH2 applications. Finally, the Origin system is compared to other contemporary commercial ccNUMA systems.
Measles virus transmembrane fusion protein synthesized de novo or presented in immunostimulating complexes is endogenously processed for HLA class I- and class II-restricted cytotoxic T cell recognition

The routes used by antigen-presenting cells (APC) to convert the transmembrane fusion glycoprotein (F) of measles virus (MV) to HLA class I and class II presentable peptides have been examined, using cloned cytotoxic T lymphocytes in functional assays. Presentation by Epstein-Barr virus-transformed B lymphoblastoid cell lines was achieved using live virus, ultraviolet light-inactivated virus, and purified MV- F delivered either as such or incorporated in immunostimulating complexes (MV-F-ISCOM). Only live virus and MV-F-ISCOM allow presentation by class I molecules, while all antigen preparations permit class II-restricted presentation. We observe presentation of MV- F from live virus and as MV-F-ISCOM by class II molecules in a fashion that is not perturbed by chloroquine. Our studies visualize novel presentation pathways of type I transmembrane proteins.
Lucky 13 - microtubule depolymerisation by kinesin-13 motors

The kinesin-13 class of motors catalyses microtubule depolymerisation by bending tubulins at microtubule ends. Depolymerisation activity is intrinsic to the kinesin-13 motor core but the activity of the core alone is very low compared with that of constructs that also contain a conserved neck sequence. The full-length dimeric motor is an efficient depolymeriser and also diffuses along the microtubule lattice, which helps it to find microtubule ends. Current evidence supports the idea of a generic mechanism for kinesin-13-catalysed depolymerisation. However, the activity of kinesin-13 motors is precisely localised and regulated in vivo to enable a wide range of cellular roles. The proteins are involved in global control of microtubule dynamics. They also localise to mitotic and meiotic spindles, where they contribute to formation and maintenance of spindle bipolarity, chromosomal congression, attachment correction and chromatid separation. In interphase cells, intricate and subtle mechanisms appear to allow kinesin-13 motors to act on specific populations of microtubules. Such carefully controlled localisation and regulation makes these kinesins efficient, multi-tasking molecular motors.
Voting procedures with incomplete preferences

We extend the application of a voting procedure (usually defined on complete preference relations over candidates) when the voters’ preferences consist of partial orders. We define possible (resp. necessary) winners for a given partial preference profile R with respect to a given voting procedure as the candidates being the winners in some (resp. all) of the complete extensions of R. We show that, although the computation of possible and necessary winners may be hard in general case, it is polynomial for the family of positional scoring procedures. We show that the possible and necessary Condorcet winners for a partial preference profile can be computed in polynomial time as well. Lastly, we point out connections to vote manipulation and elicitation.
Adaptive sparse representation of depth maps targeting view synthesis quality

Completely embedded in the 3D era, depth maps coding becomes a must in order to favor 3D admission to different fields of application, ranging from video games to medical imaging. This paper presents a novel depth coding approach that decomposes a decimated version of the original depth image on a sparse set of coefficients and mixed discrete cosine and B-splines atoms. The upstream decimation step reduces encoding bitrate without significant loss of virtual views quality. Depth decomposition is performed through minimization of an adaptive Rate/Distortion cost function, where we manipulate its weight parameter according to depth discontinuities. We then refine the choice of distortion metric in order to quantify the effect of depth maps coding on rendered views quality. Experiments show the relevance of the proposed method, able to obtain considerable tradeoffs between bitrate and synthesized views distortion.
Routing Metrics Used for Path Calculation in Low-Power and Lossy Networks

Low power and Lossy Networks (LLNs) have unique characteristics compared with traditional wired and ad-hoc networks that require the specification of new routing metrics and constraints. By contrast with typical Interior Gateway Protocol (IGP) routing metrics using hop counts or link metrics, this document specifies a set of link and node routing metrics and constraints suitable to LLNs.
Distributed stochastic subgrandient-based design for support vector machines

This paper develops a distributed stochastic subgrandient-based support vector machine algorithm when training data to train support vector machines are distributed in the network. In this situation, all the data are decentralized stored and unavailable to all agents and each agent has to make its own update based on its computation and communication with neighbors. With mild connectivity conditions, we show the convergence of the proposed algorithm even though the network topology is time-varying. Convergent rate is also given for the proposed algorithm. Moreover, we provide numerical simulations on a real classification training set to illustrate the effectiveness of the fully distributed algorithm.
Static flow-sensitive & context-sensitive information-flow analysis for software product lines: position paper

A software product line encodes a potentially large variety of software products as variants of some common code base, e.g., through the use of #ifdef statements or other forms of conditional compilation. Traditional information-flow analyses cannot cope with such constructs. Hence, to check for possibly insecure information flow in a product line, one currently has to analyze each resulting product separately, of which there may be thousands, making this task intractable. We report about ongoing work that will instead enable users to check the security of information flows in entire software product lines in one single pass, without having to generate individual products from the product line. Executing the analysis on the product line promises to be orders of magnitude more faster than analyzing products individually. We discuss the design of our information-flow analysis and our ongoing implementation using the IFDS/IDE framework by Reps, Horwitz and Sagiv.
Efficient unified Montgomery inversion with multibit shifting

Computation of multiplicative inverses in finite fields GF(p) and GF(2/sup n/) is the most time-consuming operation in elliptic curve cryptography, especially when affine co-ordinates are used. Since the existing algorithms based on the extended Euclidean algorithm do not permit a fast software implementation, projective co-ordinates, which eliminate almost all of the inversion operations from the curve arithmetic, are preferred. In the paper, the authors demonstrate that affine co-ordinate implementation provides a comparable speed to that of projective co-ordinates with careful hardware realisation of existing algorithms for calculating inverses in both fields without utilising special moduli or irreducible polynomials. They present two inversion algorithms for binary extension and prime fields, which are slightly modified versions of the Montgomery inversion algorithm. The similarity of the two algorithms allows the design of a single unified hardware architecture that performs the computation of inversion in both fields. They also propose a hardware structure where the field elements are represented using a multi-word format. This feature allows a scalable architecture able to operate in a broad range of precision, which has certain advantages in cryptographic applications. In addition, they include statistical comparison of four inversion algorithms in order to help choose the best one amongst them for implementation onto hardware.
Laser-Assisted Subepithelial Keratectomy versus Laser In Situ Keratomileusis in Myopia: A Systematic Review and Meta-Analysis

This systematic review was to compare the clinical outcomes between laser-assisted subepithelial keratectomy (LASEK) and laser in situ keratomileusis (LASIK) for myopia. Primary parameters included mean manifest refraction spherical equivalent (MRSE), MRSE within ±0.50 diopters, uncorrected visual acuity (UCVA) ≥20/20, and loss of ≥1 line of best-corrected visual acuity (BCVA). Secondary parameters included flap complications and corneal haze. Twelve clinical controlled trials were identified and used for comparing LASEK (780 eyes) to LASIK (915 eyes). There were no significant differences in visual and refractive outcomes between the two surgeries for low to moderate myopia. The incidence of loss of ≥1 line of BCVA was significantly higher in moderate to high myopia treated by LASEK than LASIK in the mid-term and long-term followup. The efficacy (MRSE and UCVA) of LASEK appeared to be a significant worsening trend in the long-term followup. Corneal haze was more severe in moderate to high myopia treated by LASEK than LASIK in the mid-term and long-term followup. The flap-related complications still occurred in LASIK, but the incidence was not significantly higher than that in LASEK. LASEK and LASIK were safe and effective for low to moderate myopia. The advantage of LASEK was the absence of flap-related complications, and such procedure complication may occur in LASIK and affect the visual results. The increased incidence of stromal haze and regression in LASEK significantly affected the visual and refractive results for high myopia.
Content classification of development emails

Emails related to the development of a software system contain information about design choices and issues encountered during the development process. Exploiting the knowledge embedded in emails with automatic tools is challenging, due to the unstructured, noisy, and mixed language nature of this communication medium. Natural language text is often not well-formed and is interleaved with languages with other syntaxes, such as code or stack traces. We present an approach to classify email content at line level. Our technique classifies email lines in five categories (i.e., text, junk, code, patch, and stack trace) to allow one to subsequently apply ad hoc analysis techniques for each category. We evaluated our approach on a statistically significant set of emails gathered from mailing lists of four unrelated open source systems.
An Empirical Model for Saturation and Capacity in Classifier Spaces

When assessing reported classification results based on selection of members from a database (e.g. a face database), one would like to know what an achievable classification rate is, given the noise level, dimensionality of the feature set and number of classes in the database. As best we can tell, no general results exist for this question, although many classification rates appear in different papers. This paper presents an empirical formula for MAP classification that links the number of discriminable classes to the error rate, dimensionality of the feature data and the feature noise level
Genethics: The Clash Between the New Genetics and Human Values

Modern genetics allows us to interfere directly with the fundamental material of life. We can redesign structures to suit our own needs in just a few days. At the same time, we subvert mechanisms that nature was able to achieve only after millions of years. Even when considerable care is taken, the consequences are not always predictable. The current literature reflects these concerns, with prominent theorists agonizing over the implications of our guerrilla warfare against genes. Genethics is an attempt to agonize less and resolve more. The first five chapters are meant to introduce the uninitiated reader to the world of modern genetics; these can easily be skipped if you have a biology background. Although well written, they are unfortunately too intimidating for all but the most dedicated novice. The chapter on recombinant DNA, for example, includes detailed steps on creating gene libraries and sequencing techniques. As the remainder of the book does not depend on understanding all of the intricate science, little is lost by jumping ahead. Each of the next nine chapters focuses on a particular case study. These case studies result in a total of ten "genethic principles," or moral guidelines, for the reader to consider. The authors begin by discussing the controversy over the XYY genotype and its unclear association with criminal behavior. Genetic screening in the workplace is analyzed from the perspective of employers (who may prematurely misuse these tests in a discriminatory fashion) and from the perspective of workers (who may become "6economic untouchables" if their increased risk of disease is known). Gene therapy is also covered, along with the "moral difference" between altering somatic and germ cells. Although the authors believe somatic cell therapy may be valuable in the future, they speak strongly against germ cell therapy with well-reasoned arguments. The chapter on biological warfare is particularly notable for its lack of wild speculation. While many researchers try desperately to maintain the "purity" of science by ignoring the military applications of their work, these authors deal directly with the secrecy and potential for deliberate destruction of life. Their practical conclusions should be of universal interest. Environmental damage to DNA and the exchange of genetic material between distantly related species are the next topics. The "curious case of the crown gall bacterium" is discussed as the possible exception to the rule prohibiting genetic transfer between procaryotic and eucaryotic organisms. The importance of genetic diversity is then shown by a serious look at the Iowa cornfield. The world population now depends on only six main types of corn, each so inbred that only a few points of genetic variability exist. The vulnerability of this corn makes it easily exploited by an ingenious predator such as the Southern leaf blight fungus. As a result, the whole monoculture crop of a country could be devastated. The final chapter on sequencing the human genome is an excellent discussion of its
BMP signaling is required for septation of the outflow tract of the mammalian heart

Bone morphogenetic proteins (BMPs) constitute a family of ∼20 growth factors involved in a tremendous variety of embryonic inductive processes. BMPs elicit dose-dependent effects on patterning during gastrulation and gradients of BMP activity are thought to be established through regulation of the relative concentrations of BMP receptors, ligands and antagonists. We tested whether later developmental events also are sensitive to reduced levels of BMP signaling. We engineered a knockout mouse that expresses a BMP type II receptor that lacks half of the ligand-binding domain. This altered receptor is expressed at levels comparable with the wild-type allele, but has reduced signaling capability. Unlike Bmpr2-null mice, mice homozygous for this hypomorphic receptor undergo normal gastrulation, providing genetic evidence of the dose-dependent effects of BMPs during mammalian development. Mutants, however, die at midgestation with cardiovascular and skeletal defects, demonstrating that the development of these tissues requires wild-type levels of BMP signaling. The most striking defects occur in the outflow tract of the heart, with absence of septation of the conotruncus below the valve level and interrupted aortic arch, a phenotype known in humans as persistent truncus arteriosus (type A4). In addition, semilunar valves do not form in mutants, while the atrioventricular valves appear unaffected. Abnormal septation of the heart and valve anomalies are the most frequent forms of congenital cardiac defects in humans; however, most mouse models display broad defects throughout cardiac tissues. The more restricted spectrum of cardiac anomalies in Bmpr2ΔE2 mutants makes this strain a key murine model to understand the embryonic defects of persistent truncus arteriosus and impaired semilunar valve formation in humans.
The CUIDADO Project

The CUIDADO Project (Content-based Unified Interfaces and Descriptors for Audio/music Databases available Online) aims at developing a new chain of applications through the use of audio/music content descriptors, in the spirit of the MPEG-7 standard. The project includes the design of appropriate description structures, the development of extractors for deriving high-level information from audio signals, and the design and implementation of two applications: the Sound Palette and the Music Browser. These applications include new features, which systematically exploit high-level descriptors and provide users with content-based access to large catalogues of audio/music material. The Sound Palette focuses on audio samples and targets professional users, whereas the Music Browser addresses a broader user target through the management of Popular music titles. After a presentation of the project objectives and methodology, we describe the original features of the two applications based on the systematic use of descriptors and the technical architecture framework on which they rely.
Animation planning for virtual characters cooperation

This paper presents an approach to automatically compute animations for virtual (human-like and robot) characters cooperating to move bulky objects in cluttered environments. The main challenge is to deal with 3D collision avoidance while preserving the believability of the agent's behaviors. To accomplish the coordinated task, a geometric and kinematic decoupling of the system is proposed. This decomposition enables us to plan a collision-free path for a reduced system, then to animate locomotion and grasping behaviors independently, and finally to automatically tune the animation to avoid residual collisions. These three steps are applied consecutively to synthesize an animation. The different techniques used, such as probabilistic path planning, locomotion controllers, inverse kinematics and path planning for closed kinematic chains are explained, and the way to integrate them into a single scheme is described.
Multi-pitch estimation by a joint 2-d representation of pitch and pitch dynamics

Multi-pitch estimation of co-channel speech is especially challenging when the underlying pitch tracks are close in pitch value (e.g., when pitch tracks cross). Building on our previous work in [1], we demonstrate the utility of a two-dimensional (2-D) analysis method of speech for this problem by exploiting its joint representation of pitch and pitch-derivative information from distinct speakers. Specifically, we propose a novel multi-pitch estimation method consisting of 1) a datadriven classifier for pitch candidate selection, 2) local pitch and pitch-derivative estimation by k-means clustering, and 3) a Kalman filtering mechanism for pitch tracking and assignment. We evaluate our method on a database of allvoiced speech mixtures and illustrate its capability to estimate pitch tracks in cases where pitch tracks are separate and when they are close in pitch value (e.g., at crossings). Index Terms: Grating Compression Transform, multi-pitch estimation, pitch dynamics, pitch crossings, all-voiced speech
Tree Exploration for Bayesian RL Exploration

Research in reinforcement learning has produced algorithms for optimal decision making under uncertainty that fall within two main types. The first employs a Bayesian framework, where optimality improves with increased computational time. This is because the resulting planning task takes the form of a dynamic programming problem on a be-lief tree with an infinite number of states. The second type employs relatively simple algorithm which are shown to suffer small regret within a distribution-free framework. This paper presents a lower bound and a high probability up-per bound on the optimal value function for the nodes in the Bayesian belief tree, which are analogous to similar bounds in POMDPs. The bounds are then used to create more efficient strategies for exploring the tree. The resulting algorithms are compared with the distribution-free algorithm UCB1, as well as a simpler baseline algorithm on multi-armed bandit problems.