Miracle-dz/UniFAR-FTUs huggingface dataset:
Eurographics Symposium on Geometry Processing 2015 Stable Topological Signatures for Points on 3d Shapes

Figure 1: Our signatures characterize a point x by the birth (leftmost) and death (second left) of the topological features (here, non-trivial loops) in the neighborhood of x in a provably stable way. We show how to compactly encode these events in a vector without losing the stability properties. This is useful in a variety of contexts, including shape segmentation and labeling (as shown on the right) using linear classifiers such as SVM. Abstract Comparing points on 3D shapes is among the fundamental operations in shape analysis. To facilitate this task, a great number of local point signatures or descriptors have been proposed in the past decades. However, the vast majority of these descriptors concentrate on the local geometry of the shape around the point, and thus are insensitive to its connectivity structure. By contrast, several global signatures have been proposed that successfully capture the overall topology of the shape and thus characterize the shape as a whole. In this paper, we propose the first point descriptor that captures the topology structure of the shape as 'seen' from a single point, in a multiscale and provably stable way. We also demonstrate how a large class of topological signatures, including ours, can be mapped to vectors, opening the door to many classical analysis and learning methods. We illustrate the performance of this approach on the problems of supervised shape labeling and shape matching. We show that our signatures provide complementary information to existing ones and allow to achieve better performance with less training data in both applications.
TOWARDS OPTIMAL PERFORMANCE IN DISTRIBUTED MEMORY SYSTEMS WITH BUFFER CONSTRAINTS USING DIVISIBLE LOAD ANALYSIS

This chapter investigates scheduling a divisible task in distributed memory systems with finite-size buffer constraints. Two types of network topologies are considered: a single-level tree network and a m-dimensional hypercube network. First, this chapter presents the closed-form solutions for the case with infinite-size buffers. Based on these solutions, an iterative strategy, referred to as Incremental Balancing Strategy (IBS), is proposed towards optimal performance. Algorithm IBS adopts a strategy to feed the divisible load in a step-by-step incremental balancing fashion by taking advantage of the available closed-form solutions of the optimal scheduling for the case without buffer size constraints. Based on the rigorous mathematical analysis, a number of interesting and useful properties exhibited by the algorithm is proved. Numerical examples are presented to ease the understanding.
Efficient kernels for sentence pair classification

In this paper, we propose a novel class of graphs, the tripartite directed acyclic graphs (tDAGs), to model first-order rule feature spaces for sentence pair classification. We introduce a novel algorithm for computing the similarity in first-order rewrite rule feature spaces. Our algorithm is extremely efficient and, as it computes the similarity of instances that can be represented in explicit feature spaces, it is a valid kernel function.
Molecular Crosstalking among Noncoding RNAs: A New Network Layer of Genome Regulation in Cancer

Over the past few years, noncoding RNAs (ncRNAs) have been extensively studied because of the significant biological roles that they play in regulation of cellular mechanisms. ncRNAs are associated to higher eukaryotes complexity; accordingly, their dysfunction results in pathological phenotypes, including cancer. To date, most research efforts have been mainly focused on how ncRNAs could modulate the expression of protein-coding genes in pathological phenotypes. However, recent evidence has shown the existence of an unexpected interplay among ncRNAs that strongly influences cancer development and progression. ncRNAs can interact with and regulate each other through various molecular mechanisms generating a complex network including different species of RNAs (e.g., mRNAs, miRNAs, lncRNAs, and circRNAs). Such a hidden network of RNA-RNA competitive interactions pervades and modulates the physiological functioning of canonical protein-coding pathways involved in proliferation, differentiation, and metastasis in cancer. Moreover, the pivotal role of ncRNAs as keystones of network structural integrity makes them very attractive and promising targets for innovative RNA-based therapeutics. In this review we will discuss: (1) the current knowledge on complex crosstalk among ncRNAs, with a special focus on cancer; and (2) the main issues and criticisms concerning ncRNAs targeting in therapeutics.
Optimal and Power Aware BIST for Delay Testing of System-On-Chip

Test engineering for fault tolerant VLSI systems is encumbered with optimization requisites for hardware overhead, test power and test time. The high level quality of these complex high-speed VLSI circuits can be assured only through delay testing, which involves checking for accurate temporal behavior. In the present paper, a data-path based built-in test pattern generator (TPG) that generates iterative pseudo-exhaustive two-patterns (IPET) for parallel delay testing of modules with different input cone capacities is implemented. Further, in the present study a CMOS implementation of low power architecture (LPA) for scan based built-in self test (BIST) for delay testing and combinational testing is carried out. This reduces test power dissipation in the circuit under test (CUT). Experimental results and comparisons with pre-existing methods prove the reduction in hardware overhead and test-time.
Dynamic Taint Tracking in Managed Runtimes

This paper provides a taxonomy of runtime taint tracking approaches for managed code, such as code written in Java, C#, PHP, Perl, or Ruby. It covers main applications of data tainting such as preventing web application vulnerabilities including crosssite scripting and SQL injection attacks, along with disallowing privacy-sensitive data leaks. In addition to giving an overview of related literature from the last decade, this paper provides guidance and describes the trade-offs of different instrumentation approaches. Lastly, we provide a list of open problems whose solutions would aid practical adaption of runtime tainting
Opportunistic Communication and Human Mobility

Many mobility models currently used for evaluating wireless communication systems have weak resemblance to reality and there is a lack of understanding on which characteristics of human mobility affect system performance. In particular, most current mobility models assume a free flow of nodes and do not consider how mobility is affected by interactions with other persons and with the physical environment. They also assume a closed system, not considering the effect of node arrival and departure. The structure of space in which the mobility occurs is either not considered at all, or only in a limited way. In this work, we address human pedestrian mobility for evaluation of wireless communication to determine which of the aforementioned aspects need to be captured and to what level of detail. We focus on opportunistic communication in the form of ad-hoc and delay-tolerant networks. For the evaluation, we use mobility models from the field of transportation and urban planning that are used for designing and dimensioning public spaces for comfort and safety of pedestrians in rush hour and emergency evacuation. The models capture micro-mobility of pedestrians better than most mobility models used in mobile networking since the application domain requires realistic representation of node interactions with the physical environment and with other nodes. Our results show that the free flow assumption used in most models does not have a significant performance impact. We also conclude that performance is not very sensitive to accurate estimation of the probability distributions of mobility parameters such as speed and arrival process. Our results, however, suggest that it is important to capture the scenario and space in which mobility occurs since these may affect performance significantly.
Complement factor C3 deposition and serum resistance in isogenic capsule and lipooligosaccharide sialic acid mutants of serogroup B Neisseria meningitidis

Serogroup B meningococci express sialic acids on their surfaces as a modification of the lipooligosaccharide (LOS) and as capsular material consisting of alpha2,8-linked sialic acid homopolymers. The aim of this study was to elucidate the impact of each sialic acid component on the deposition of complement factor C3 and serum resistance. For this purpose, we used isogenic mutants deficient in capsule expression (a polysialyltransferase mutant) or sialylation of the LOS (a galE mutant) or both (a mutant with a deletion of the cps gene locus). Bactericidal assays using 40% normal human serum (NHS) demonstrated that both the capsule and LOS sialic acid are indispensable for serum resistance. By immunoblotting with monoclonal antibody MAb755 that is specific for the C3 alpha-chain, we were able to demonstrate that C3 from 40% NHS was covalently linked to the surface structures of meningococci as C3b and iC3b, irrespective of the surface sialic acid compounds. However, C3b linkage was more pronounced and occurred on a larger number of target molecules in galE mutants with nonsialylated LOS than in meningococci with wild-type LOS, irrespective of the capsule phenotype. C3b deposition was caused by both the classical pathway (CP) and the alternative pathway of complement activation. Use of 10% NHS revealed that at low serum concentrations, C3 deposition occurred via the CP and was detected primarily on nonsialylated-LOS galE mutants, irrespective of the capsular phenotype. Accordingly, immunoglobulin M (IgM) binding to meningococci from heat-inactivated NHS was demonstrated only in both encapsulated and unencapsulated galE mutants. In contrast, inhibition of IgA binding required both encapsulation and LOS sialylation. We conclude that serum resistance in wild-type serogroup B meningococci can only be partly explained by an alteration of the C3b linkage pattern, which seems to depend primarily on the presence of wild-type LOS, since a serum-resistant phenotype also requires capsule expression.
A Sub-mW IoT-Endnode for Always-On Visual Monitoring and Smart Triggering

This paper presents a fully programmable Internet of Things visual sensing node that targets sub-mW power consumption in always-on monitoring scenarios. The system features a spatial-contrast <inline-formula> <tex-math notation="LaTeX">${128\times 64}$ </tex-math></inline-formula> binary pixel imager with focal-plane processing. The sensor, when working at its lowest power mode (<inline-formula> <tex-math notation="LaTeX">${10 ~\mu }\text{W}$ </tex-math></inline-formula> at 10 frames/s), provides as output the number of changed pixels. Based on this information, a dedicated camera interface, implemented on a low-power field-programmable gate array, wakes up an ultralow-power parallel processing unit to extract context-aware visual information. We evaluate the smart sensor on three always-on visual triggering application scenarios. Triggering accuracy comparable to RGB image sensors is achieved at nominal lighting conditions, while consuming an average power between 193 and <inline-formula> <tex-math notation="LaTeX">${277 ~\mu }\text{W}$ </tex-math></inline-formula>, depending on context activity. The digital subsystem is extremely flexible, thanks to a fully programmable digital signal processing engine, but still achieves <inline-formula> <tex-math notation="LaTeX">$19 {\times }$ </tex-math></inline-formula> lower power consumption compared to MCU-based cameras with significantly lower on-board computing capabilities.
Interference with cyclophosphamide-induced skin allograft tolerance by cyclosporin A.

In a murine strain combination identical in H-2 Ag but disparate in minor histocompatibility (H) Ag consisting of C3H/He (C3H; H-2k, Mls-1b) mice as recipients and AKR/J (AKR; H-2k, Mls-1a) mice as donors, a permanent skin allograft tolerance can be achieved by the cyclophosphamide (CP)-induced tolerance system that consists of i.v. injection of donor spleen cells (day -2) and i.p. injection of CP 2 days later (day 0). Such permanent take of allografts in CP-induced tolerant mice was interfered with by intramuscular injection of cyclosporin A (CsA) from day -5 to day -1 and their grafts were rejected by 21 days after grafting. Mls-1a-reactive CD4+V beta 6+ T cells in the periphery, as the indicator to follow the kinetics of donor-reactive T cells, increased on day 0 and day 3 in the C3H mice treated with AKR spleen cells alone, whereas they disappeared rapidly from day 0 to day 3 in CP-induced tolerant mice. When CsA capable of interfering with IL-2 production and T cell proliferation was administered before CP treatment in CP-induced tolerance system, the number of CD4+V beta 6+ T cells in periphery did not increase on day 0 and 3, but increased on day 7 in contrast to the decreased number of those in CP-induced tolerant mice. On day 7, MLR against donor cells was decreased in CP-induced tolerant mice, but maintained in CsA-interfered tolerant mice. These result may indicate that the destruction of donor-Ag-stimulated, proliferating T cells by CP is interfered with by CsA, probably because CsA inhibits the proliferation of donor-reactive T cells at the time of CP treatment. Furthermore, these results also implicate that the protocol for immunosuppression with CsA and antimetabolites has to be designed carefully in clinical transplantation.
Medaka Fish Parkinson's Disease Model

The teleost fish has been widely used in creating neurodegenerative models. Here we describe the teleost medaka fish Parkinson's disease (PD) models we developed using toxin treatment and genetic engineering. 1-Methyl-4-phenyl-1,2,3,4-tetrahydropyridine (MPTP), 6-hydroxydopamine (6-OHDA), proteasome inhibitors, lysosome inhibitors and tunicamycin treatment in our model fish replicated some salient features of PD: selective dopamine cell loss and reduced spontaneous movement with the last three toxins producing inclusion bodies ubiquitously in the brain. Despite the ubiquitous distribution of the inclusion bodies, the middle diencephalic dopaminergic neurons were particularly vulnerable to these toxins, supporting the idea that this dopamine cluster is similar to the human substantia nigra. PTEN-induced putative kinase 1 (PINK1) homozygous mutants also showed reduced spontaneous swimming movements. These data indicate that medaka fish can serve as a new model animal of PD. In this review we summarize our previous data and discuss future prospects.
Systems biology Metatool 5.0: fast and ﬂexible elementary modes analysis

Summary: Elementary modes analysis is a powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence, the program Metatool, which is one of the first programs dedicated to this purpose, hasbeenreimplementedinordertomakeuseofthesenewapproaches. The performance of Metatool has been significantly increased and the new version 5.0 can now be run inside the GNU octave or Matlab environments to allow more flexible usage and integration with other tools. Metatool consists of script files (m-files) for GNU octave as well as Matlab and shared libraries. The scripts are licensed under the GNU Public License and the use of the shared libraries is free for academic users and testing purposes. Commercial use of Metatool requires a special contract.
Security and privacy architectures for biomedical cloud computing

Biomedical research often relies on having access to vast amounts of sensitive information. Patient data in electronic form are held in medical databases and bio-repositories and have to be queried, data mined and operated on by doctors and researchers. Lately, all this information has been migrating to the cloud making access easier for all interested parties. While this helps with dissemination and access, it may have unintended consequences in terms of security and privacy. In this work we propose an architecture that combines distributed access control mechanisms with privacy preserving cryptographic protocols to enable secure sharing and computations on clouds holding sensitive biomedical data. The data shared are tagged with security policies that define who has access to it and how they should be used. Access rights may be delegated to other parties making collaborations easier. Finally, data can be operated on cryptographically to extract specific information without compromising the entire data set.
Endosomal Trafficking Defects Can Induce Calcium-Dependent Azole Tolerance in Candida albicans

ABSTRACT The azole antifungals arrest fungal growth through inhibition of ergosterol biosynthesis. We recently reported that a Candida albicans vps21Δ/Δ mutant, deficient in membrane trafficking through the late endosome/prevacuolar compartment (PVC), continues to grow in the presence of the azoles despite the depletion of cellular ergosterol. Here, we report that the vps21Δ/Δ mutant exhibits less plasma membrane damage upon azole treatment than the wild type, as measured by the release of a cytoplasmic luciferase reporter into the culture supernatant. Our results also reveal that the vps21Δ/Δ mutant has abnormal levels of intracellular Ca2+ and, in the presence of fluconazole, enhanced expression of a calcineurin-responsive RTA2-GFP reporter. Furthermore, the azole tolerance phenotype of the vps21Δ/Δ mutant is dependent upon both extracellular calcium levels and calcineurin activity. These findings underscore the importance of endosomal trafficking in determining the cellular consequences of azole treatment and indicate that this may occur through modulation of calcium- and calcineurin-dependent responses.
A particulate viral protein vaccine reduces viral load and delays progression to disease in immunized ponies challenged with equine infectious anemia virus.

Immunization regimens that induce a broadly reactive cytolytic T lymphocyte (CTL) response specific for lentiviral antigens have emerged as the leading candidates in efficacy trials conducted in both animal modelshumans. To date, lentivirus vaccination strategies have overlooked one such immunization strategy, namely the use of particulate antigens. To evaluate the efficacy of targeting antigen into the phagocytic pathway to elicit a cell-mediated immune response to lentiviral antigens, we initiated the first study of a particulate-based vaccination protocol using a large animal model system. Gradient-purified equine infectious anemia virus (EIAV) was covalently coupled to glutaraldehyde-activated iron oxide beads. In vitro studies demonstrated the effectiveness of the inactivated whole virus particulate to prime antigen presenting cells for the activationexpansion of virus-specific CD8(+) CTL. The in vivo effectiveness of the particulate antigen was evaluated by experimental immunization of ponies. Ponies receiving the viral particulate vaccinechallenged with infectious EIAV had a delayed progression to diseasea reduced viral load compared with infected ponies that had not been vaccinated. Interestingly, in vitro virus-specific CTL activity was detected in only one of four immunized animals at the day of challenge. The beneficial effects of the particulate vaccine regimen were not clearly associated with any in vitro measurable parameters of the virus-specific cellular or humoral immune responses elicited by the vaccine at the day of challenge. However, within 3 weeks after virus challenge, anamnestic humoral responses characterized by a rapid emergence of neutralizing activity in the seruma predominance of conformationally dependent epitopes recognized by virus-specific antibodies were observed in the vaccinates. Taken together, further studies are clearly warranted in large animal model systems using a particulate-based vaccine regimen considering the beneficial effects of this regimen in our studythe protective effects of particulate antigen delivery in the murine model.
VisMeB: A Visual Metadata Browser

The video-paper describes a java prototype of a generic visual information retrieval system called VisMeB, developed to visualize metadata within various contexts. We reconsidered common visualization strategies and applied them to different domains. The system we describe offers visual assistance in exploring large amounts of datasets from different application domains like geographical metadata, movie databases and the Web. The video demonstrates a scenario using a movie database.
Recycling of Furin from the Plasma Membrane

The predominant intracellular localization of the eukaryotic subtilisin-like endoprotease furin is the trans-Golgi network (TGN), but a small fraction is also found on the cell surface. Furin on the cell surface is internalized and delivered to the TGN. The identification of three endocytosis motifs, a tyrosine (YKGL765) motif, a leucine-isoleucine (LI760) motif, and a phenylalanine (Phe790) signal, in the furin cytoplasmic domain suggested that endocytosis of furin occurs via an AP-2/clathrin-dependent pathway. Since little is known about proteins containing multiple sorting components in their cytoplasmic domain, the combination of diverse internalization signals in the furin tail raised the question of their individual role. Here we present data showing that the furin tail interacts with the medium (μ2) subunit of the AP-2 plasma membrane-specific adaptor complex in vitro and that this interaction primarily depends on recognition of the tyrosine-based sorting signal and to less extent on the leucine-isoleucine motif. We further provide evidence that the three endocytosis signals are of different functional importance for furin internalization and retrieval to the TGN in vivo, with the tyrosine-based motif being the major determinant, followed by the phenylalanine signal, whereas the leucine-isoleucine motif is only a minor component. Finally, we report that phosphorylation of the furin tail by casein kinase II is not only important for efficient interaction with μ2 and internalization from the plasma membrane but also determines fast retrieval of the protein from the plasma membrane to the TGN.
Research challenges for cross-cloud applications

Federated clouds can expose the Internet as a homogeneous compute fabric. There is an opportunity for developing cross-cloud applications that can be deployed pervasively over the Internet, dynamically adapting their internal topology to their needs. In this paper we explore the main challenges for fully realizing the potential of cross-cloud applications. First, we focus on the networking dimension of these applications. We evaluate what support is needed from the infrastructure, and what are the further implications of opening the networking side. On a second part, we examine the impact of a distributed deployment for applications, assessing the implications from a management perspective, and how it affects the delivery of quality of service and non-functional requirements.