Miracle-dz/UniFAR-FTUs huggingface dataset:
GRAPHITE : Polyhedral Analyses and Optimizations for GCC

We present a plan to add loop nest optimizations in GCC based on polyhedral representations of loop nests. We advocate a static analysis approach based on a hierarchy of interchangeable abstractions with solvers that range from the exact solvers such as OMEGA, to faster but less precise solvers based on more coarse abstractions. The intermediate representationGRAPHITE (GIMPLE Represented as Polyhedra with Interchangeable Envelopes), built on GIMPLE and the natural loops, hosts the high level loop transformations. We base this presentation on the WRaP-IT project developed in theAlchemy group at INRIA Futurs and Paris-Sud University, on the PIPS compiler developed at École des mines de Paris, and on a joint work with several members of the static analysis and polyhedral compilation community in France. The main goal of this project is to bring more high level loop optimizations toGCC: loop fusion, tiling, strip mining, etc. Thanks to the WRaP-IT experience, we know that the polyhedral analyzes and transformations are affordable in a production compiler. A second goal of this project is to experiment with compile time reduction versus attainable precision when replacing operations on polyhedra with faster operations on more abstract domains. However, the use of a too coarse representation for computing might also result in an over approximated solution that cannot be used in subsequent computations. There exists a trade off between speed of the computation and the attainable precision that has not yet been analyzed for real world programs.
Frequent subgraph mining based on the automorphism mapping

Frequent subgraph mining is an important research subject of graph mining. At present, there are many effective frequent subgraph mining algorithms, such as gSpan and FFSM. But these algorithms spend a lot of time solving the subgraph isomorphism or graph isomorphism problem, which affects the efficiency of the algorithm itself. According to the problem, we propose a novel frequent subgraph mining algorithm: FSMA, based on the automorphism mapping. The algorithm generate candidate subgraph through extending edges, and the extension location is determined by the automorphism mapping of subgraph. FSMA does not need to test the subgraph isomorphism or graph isomorphism throughout the process of mining frequent subgraph, so it achieves the time complexity of 0(n-2")(n is the number of frequent edges in graph dataset).
A Practical Stride Prefetching Implementation in Global Optimizer

Software data prefetching is a key technique for hiding memory latencies on modern high performance processors. Stride memory references are prime candidates for software prefetches on architectures with, and without, support for hardware prefetching. Compilers typically implement software prefetching in the context of loop nest optimizer (LNO), which focuses on affine references in well formed loops but miss out on opportunities in C++ STL style codes. In this paper, we describe a new inductive data prefetching algorithm implemented in the global optimizer. It bases the prefetching decisions on demand driven speculative recognition of inductive expressions, which equals to strongly connected component detection in data flow graph, thus eliminating the need to invoke the loop nest optimizer. This technique allows accurate computation of stride values and exploits phase ordering. We present an efficient implementation after SSAPRE optimization, which further includes sophisticated prefetch scheduling and loop transformations to reduce unnecessary prefetches, such as loop unrolling and splitting to further reduce unnecessary prefetches. Our experiments using SPEC2006 on IA-64 show that we have competitive performance to the LNO based algorithms.
Distribution and cellular localization of actin depolymerizing factor

Actin depolymerizing factor (ADF) is a low molecular mass (19 kD) protein that forms a tightly bound dimeric complex with actin. We have raised a rabbit antiserum to chick brain ADF and used it to analyze the distribution and cellular localization of ADF. We find that ADF is a major constituent of all chick embryonic and most adult tissues examined, accounting for 0.1-0.4% of the total protein. Some tissues have as much as 0.6 mol ADF per mole actin. Adult heart and skeletal muscle are unusual in having very low levels of ADF: less than 0.02% of the soluble protein. During the development of skeletal muscle, ADF levels are maximal up to approximately 11 d in ovo and then decline to reach their adult levels by 14 d posthatching. Brain tissue and cultured cell lines from several other vertebrates, including mammals, all possess proteins of identical size to ADF that are recognized by the ADF antiserum. No proteins are specifically recognized by the ADF antiserum in extracts from Acanthamoeba castellanii or from nerve tissue of several invertebrates. Indirect immunofluorescence shows that ADF is present throughout the cytosol of most cells and at the leading edge of ruffled membranes and in the neuronal growth cone. Its abundance and widespread distribution together with its ability to sequester actin molecules, even those in an already polymerized state, suggest that ADF is a major factor in the regulation of actin filaments in many vertebrate cells.
Local Selection Across a Latitudinal Gradient Shapes Nucleotide Diversity in Balsam Poplar, Populus balsamifera L

Molecular studies of adaptive evolution often focus on detecting selective sweeps driven by positive selection on a species-wide scale; however, much adaptation is local, particularly of ecologically important traits. Here, we look for evidence of range-wide and local adaptation at candidate genes for adaptive phenology in balsam poplar, Populus balsamifera, a widespread forest tree whose range extends across environmental gradients of photoperiod and growing season length. We examined nucleotide diversity of 27 poplar homologs of the flowering-time network—a group of genes that control plant developmental phenology through interactions with environmental cues such as photoperiod and temperature. Only one gene, ZTL2, showed evidence of reduced diversity and an excess of fixed replacement sites, consistent with a species-wide selective sweep. Two other genes, LFY and FRI, harbored high levels of nucleotide diversity and exhibited elevated differentiation between northern and southern accessions, suggesting local adaptation along a latitudinal gradient. Interestingly, FRI has also been identified as a target of local selection between northern and southern accessions of Arabidopsis thaliana, indicating that this gene may be commonly involved in ecological adaptation in distantly related species. Our findings suggest an important role for local selection shaping molecular diversity and reveal limitations of inferring molecular adaptation from analyses designed only to detect species-wide selective sweeps.
Surface Plasmon Resonance-Based Fiber and Planar Waveguide Sensors

Bulk surface Plasmons resonance devices have been researched for several decades. These devices have found a special niche as high-sensitivity refractive index sensor in biomedical applications. Recent advances in guided wave devices are rapidly changing the capabilities of such sensors, not only increasing convenience of use but also opening opportunities due to their versatility. This paper reviews many of these devices and presents some of their salient features.
Neural Integration of Information Specifying Human Structure from Form, Motion, and Depth

Recent computational models of biological motion perception operate on ambiguous two-dimensional representations of the body (e.g., snapshots, posture templates) and contain no explicit means for disambiguating the three-dimensional orientation of a perceived human figure. Are there neural mechanisms in the visual system that represent a moving human figure's orientation in three dimensions? To isolate and characterize the neural mechanisms mediating perception of biological motion, we used an adaptation paradigm together with bistable point-light (PL) animations whose perceived direction of heading fluctuates over time. After exposure to a PL walker with a particular stereoscopically defined heading direction, observers experienced a consistent aftereffect: a bistable PL walker, which could be perceived in the adapted orientation or reversed in depth, was perceived predominantly reversed in depth. A phase-scrambled adaptor produced no aftereffect, yet when adapting and test walkers differed in size or appeared on opposite sides of fixation aftereffects did occur. Thus, this heading direction aftereffect cannot be explained by local, disparity-specific motion adaptation, and the properties of scale and position invariance imply higher-level origins of neural adaptation. Nor is disparity essential for producing adaptation: when suspended on top of a stereoscopically defined, rotating globe, a context-disambiguated “globetrotter” was sufficient to bias the bistable walker's direction, as were full-body adaptors. In sum, these results imply that the neural signals supporting biomotion perception integrate information on the form, motion, and three-dimensional depth orientation of the moving human figure. Models of biomotion perception should incorporate mechanisms to disambiguate depth ambiguities in two-dimensional body representations.
Secreted Frizzled-related proteins enhance the diffusion of Wnt ligands and expand their signalling range

Secreted Frizzled-related proteins (sFRPs) are thought to negatively modulate Wnt signalling. Although Wnt proteins are thought to diffuse extracellularly and act as morphogens, little is known about the diffusibility of either Wnts or sFRPs. Here we show that Frzb and Crescent (Cres), which are members of the sFRP family, have the ability to regulate the diffusibility and signalling areas of the Wnt ligands Wnt8 and Wnt11. We found, using the Xenopus embryo, that Wnts do not diffuse effectively, whereas Frzb and Cres spread very widely. Interestingly, Frzb and Cres substantially promoted the diffusion of Wnt8 and Wnt11 through extracellular interactions. Importantly, we show that Wnt8 conveyed by sFRPs can activate canonical Wnt signalling despite the function of sFRPs as Wnt inhibitors, suggesting a novel regulatory system for Wnts by sFRPs.
Smart table surface: A novel approach to pervasive dining monitoring

We present a novel sensor system for the support of nutrition monitoring. The system is based on smart table cloth equipped with a fine grained pressure textile matrix and a weight sensitive tablet. Unlike many other nutrition monitoring approaches, our system is unobtrusive, non privacy invasive and easily deployable in every day life. It allows the spotting and recognition of food intake related actions, such as cutting, scooping, stirring, etc., the identification of the plate/container on which the action is executed, and the tracking of the weight change in the containers. In other words, we can determine how many pieces are cut on the main dish plate, how many are taken from the side dish, how many sips are taken from the drink, how fast the food is being consumed and how much weight is taken overall. In addition, the distinction between different eating actions, such as cutting, scooping, poking, provides clues to the type of food taken and the way the meal is consumed. We have evaluated our system on 40 meals (5 subjects) in a real life living environment: for seven eating related actions (cutting, scooping, stirring, etc.), resulting in above 90% average recognition rate for person dependent cases, and spotting each action out of continuous data streams (average F1 score 87%).
Direct Estimation of Genetic Principal Components

Estimating the genetic and environmental variances for multivariate and function-valued phenotypes poses problems for estimation and interpretation. Even when the phenotype of interest has a large number of dimensions, most variation is typically associated with a small number of principal components (eigen-vectors or eigenfunctions). We propose an approach that directly estimates these leading principal components; these then give estimates for the covariance matrices (or functions). Direct estimation of the principal components reduces the number of parameters to be estimated, uses the data efficiently, and provides the basis for new estimation algorithms. We develop these concepts for both multivariate and function-valued phenotypes and illustrate their application in the restricted maximum-likelihood framework.
A comparison of AUC estimators in small-sample studies

Reliable estimation of the classification performance of learned predictive models is difficult, when working in the small sample setting. When dealing with biological data it is often the case that separate test data cannot be afforded. Cross-validation is in this case a typical strategy for estimating the performance. Recent results, further supported by experimental evidence presented in this article, show that many standard approaches to cross-validation suffer from extensive bias or variance when the area under ROC curve (AUC) is used as performance measure. We advocate the use of leave-pair-out cross-validation (LPOCV) for performance estimation, as it avoids many of these problems. A method previously proposed by us can be used to efficiently calculate this estimate for regularized least-squares (RLS) based learners.
Empirical Research on Expropriation Behavior of Controlling Shareholder Based on Legal Perspective

With the changes of the themes in the study of listed companies, the research on the controlling shareholders' expropriation to minority shareholders has generally become the core problem in the exploration of modern corporate governance. Foreign research shows that the construction of the legal system has an important role in the constraints to the controlling shareholders expropriation. By empirical analysis on the Chinese listed companies which conducted equity transfer in A-share markets of Shanghai and Shenzhen during 2000-2005, this article draws the conclusion that the perfection of legislation can effectively restrict controlling shareholders' expropriation. The stronger the application of law enforcement, the higher the controlling shareholders' violating standard to the investors' interests. The reason may be that although the whole legislation environment was improving during 2000-2005, yet the legislation shortage in some specific areas resulted in the increase of law enforcement cost, and eventually got little effect with improving law enforcement. This shows that China should continuously perfect its legislation in various specific areas in the improvement of overall legal environment.
Competitive Algorithms for Mobile Centers ∗

In this paper we investigate the problem of locating a mobile facility at (or near) the center of a set of clients that move independently, continuously, and with bounded velocity. It is shown that the Euclidean 1-center of the clients may move with arbitrarily high velocity relative to the maximum client velocity. This motivates the search for strategies for moving a facility so as to closely approximate the Euclidean 1-center while guaranteeing low (relative) velocity. We present lower bounds and efficient competitive algorithms for the exact and approximate maintenance of the Euclidean 1-center for a set of moving points in the plane. These results serve to accurately quantify the intrinsic velocity/ approximation quality tradeoff associated with the maintenance of the mobile Euclidean 1-center. Preliminary versions of some of the results in this paper first appeared in the 4th International ACM Workshop on Discrete Algorithms and Methods for Mobile Computing and Communications (DIAL M for Mobility). This work has been supported by NSERC and MITACS. The work by Michael Segal was supported in part by the Pacific Institute for Mathematical Studies. Department of Computer Science, University of Texas at Dallas, Box 830688, Richardson, TX 75083, USA. E-mail: besp@utdallas.edu School of Computing Science, Simon Fraser University, Burnaby, B.C. Canada, V5A 1S6. Email: binay@cs.sfu. ca. Department of Computer Science, University of British Columbia Vancouver, B.C. Canada V6T 1Z4. Email: kirk@cs.ubc. ca. Communication Systems Engineering Department, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel. Email: segal@cse.bgu. ac.il.
A proactive scheme for securing ID/locator split architecture

The ID/locator split-based approach has been widely recognized as a promising approach for the design of future networks. However, the existing ID/locator split architectures are still vulnerable to various attacks, such as impersonation attacks and man-in-the-middle attacks. They cannot be simply protected by the existing security mechanisms, which have the limitations especially on scalability. To solve these problems, we propose a proactive scheme for securing ID/locator split architecture, which embeds built-in security features to enable proactive protections of the architecture. Through this scheme, hosts register their information to the network securely, obtain trustworthy information of destination hosts, authenticate each other, and securely update their locators without requiring an involvement of a trusted third party (TTP). Compared to other existing security mechanisms, the proposed scheme does not require additional authentication mechanism and it can provide the thorough protections of the whole architecture.
Top-k Consistency of Learning to Rank Methods

This paper is concerned with the consistency analysis on lis twise ranking methods. Among various ranking methods, the listwise methods ha ve competitive performances on benchmark datasets and are regarded as one of th e state-of-the-art approaches. Most listwise ranking methods manage to optimi ze ranking on the whole list (permutation) of objects, however, in practical applications such as information retrieval, correct ranking at the top k positions is much more important. This paper aims to analyze whether existing listwise rankin g methods are statistically consistent in the topk setting. For this purpose, we define a topk ranking framework, where the true loss (and thus the risks) are define d o the basis of topk subgroup of permutations. This framework can include the pe rmutation-level ranking framework proposed in previous work as a special cas e. Based on the new framework, we derive sufficient conditions for a listwis e ranking method to be consistent with the topk true loss, and show an effective way of modifying the surrogate loss functions in existing methods to satisfy the se conditions. Experimental results show that after the modification, the methods can work significantly better than their original versions, indicating the correc tn ss of our theoretical analysis.
Compact generation of the category of D-modules on the stack of G-bundles on a curve

The goal of the paper is to show that the (derived) category of D-modules on the stack Bun_G(X) is compactly generated. Here X is a smooth complete curve, and G is a reductive group. The problem is that Bun_G(X) is not quasi-compact, so the above compact generation is not automatic. The proof is based on the following observation: Bun_G(X) can be written as a union of quasi-compact open substacks, which are "co-truncative", i.e., the j_! extension functor is defined on the entire category of D-modules.
Seizure-Related Gene 6 (Sez-6) in Amacrine Cells of the Rodent Retina and the Consequence of Gene Deletion

Background Seizure-related gene 6 (Sez-6) is expressed in neurons of the mouse brain, retina and spinal cord. In the cortex, Sez-6 plays a role in specifying dendritic branching patterns and excitatory synapse numbers during development. Methodology/Principal Findings The distribution pattern of Sez-6 in the retina was studied using a polyclonal antibody that detects the multiple isoforms of Sez-6. Prominent immunostaining was detected in GABAergic, but not in AII glycinergic, amacrine cell subpopulations of the rat and mouse retina. Amacrine cell somata displayed a distinct staining pattern with the Sez-6 antibody: a discrete, often roughly triangular-shaped bright spot positioned between the nucleus and the apical dendrite superimposed over weaker general cytoplasmic staining. Displaced amacrines in the ganglion cell layer were also positive for Sez-6 and weaker staining was occasionally observed in neurons with the morphology of alpha ganglion cells. Two distinct Sez-6 positive strata were present in the inner plexiform layer in addition to generalized punctate staining. Certain inner nuclear layer cells, including bipolar cells, stained more weakly and diffusely than amacrine cells, although some bipolar cells exhibited a perinuclear “bright spot” similar to amacrine cells. In order to assess the role of Sez-6 in the retina, we analyzed the morphology of the Sez-6 knockout mouse retina with immunohistochemical markers and compared ganglion cell dendritic arbor patterning in Sez-6 null retinae with controls. The functional importance of Sez-6 was assessed by dark-adapted paired-flash electroretinography (ERG). Conclusions In summary, we have reported the detailed expression pattern of a novel retinal marker with broad cell specificity, useful for retinal characterization in rodent experimental models. Retinal morphology, ganglion cell dendritic branching and ERG waveforms appeared normal in the Sez-6 knockout mouse suggesting that, in spite of widespread expression of Sez-6, retinal function in the absence of Sez-6 is not affected.
Post Abortion Syndrome is a Clinical Reality: A Critical and Methodological Reflection on the Politics, Biology and Phenomenology of Unwanted Pregnancy and Abortion

Macleod (2009) criticizes Boulind and Edwards (2008) for using the concept of post-abortion syndrome (PAS) in their conceptualization of the case of Grace. This article responds to this by arguing the following points: 1) the appropriation of PAS into anti-abortion rhetoric is not sufficient reason to abandon it since this rhetoric distorts the facts, 2) methodological difficulties cited by Macleod in identifying the nature of the distress experienced by some women post-abortion are an artifact of the use of multivariate statistical methods which are not appropriate for answering these questions; 3) the well documented process of maternal foetal attachment, which has a neurobiological basis, shapes a pregnant women's experience of the foetus in the direction of experiencing it in personal terms; 4) the incorporation of this into the clinical concept of PAS carries no implications about foetal personhood; 5) there is considerable documentation of the loss of a foetus being experienced as a bereavement by some women and giving rise to a traumatic grief response; 6) there is a difference between a formal diagnosis in a diagnostic manual and a clinical syndrome which can guide case formulation. It is concluded that the presentation of the case of Grace, rather than offering evidence that supports a pro-life stance on abortion, is an example of the kind of emancipatory theory and practice that is advocated by Macleod.
The Bers-Greenberg Theorem and the Maskit Embedding for Teichmüller spaces

The Bers-Greenberg theorem tells that the Teichmüller space of a Riemann surface with branch points (orbifold) depends only on the genus and the number of special points, but not on the particular ramification values. On the other hand, the Maskit embedding provides a mapping from the Teichmüller space of an orbifold, into the product of one dimensional Teichmüller spaces. In this paper we prove that there is a set of isomorphisms between one dimensional Teichmüller spaces that, when restricted to the image of the Teichmüller space of an orbifold under the Maskit embedding, provides the Bers-Greenberg isomorphism.