Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Rankings for Seed Selection in Complex Networks: Balancing Costs and Coverage

Information spreading processes within the complex networks are usually initiated by a selection of highly influential nodes in accordance with the used seeding strategy. The majority of earlier studies assumed the usage of selected seeds at the beginning of the process. Our previous research revealed the advantage of using a sequence of seeds instead of a single stage approach. The current study extends sequential seeding and further improves results with the use of dynamic rankings, which are created by recalculation of network measures used for additional seed selection during the process instead of static ranking computed only once at the beginning. For calculation of network centrality measures such as degree, only non-infected nodes are taken into account. Results showed increased coverage represented by a percentage of activated nodes dependent on intervals between recalculations as well as the trade-off between outcome and computational costs. For over 90% of simulation cases, dynamic rankings with a high frequency of recalculations delivered better coverage than approaches based on static rankings.
Multi-criteria Energy Minimization with Boundedness, Edge-density and Rarity, for Object Saliency in Natural Images

Recent methods of bottom-up salient object detection have attempted to either: (i) obtain a probability map with a `contrast rarity' based functional, formed using low level cues; or (ii) Minimize an objective function, to detect the object. Most of these methods fail for complex, natural scenes, such as the PASCAL-VOC challenge dataset which contains images with diverse appearances, illumination conditions, multiple distracting objects and varying scene environments. We thus formulate a novel multi-criteria objective function which captures many dependencies and the scene structure for correct spatial propagation of low-level priors to perform salient object segmentation, in such cases. Our proposed formulation is based on CRF modeling where the minimization is performed using graph cut and the optimal parameters of the objective function are learned using a max-margin framework from the training set, without the use of class labels. Hence the method proposed is unsupervised, and works efficiently when compared to the very recent state-of-the art methods of saliency map detection and object proposals. Results, compared using F-measure and intersection-over-union scores, show that the proposed method exhibits superior performance in case of the complex PASCAL-VOC 2012 object segmentation dataset as well as the traditional MSRA-B saliency dataset.
Brain-derived neurotrophic factor controls dopamine D3 receptor expression: Implications for neurodevelopmental psychiatric disorders

Brain-derived neurotrophic factor (BDNF) belongs to a family of proteins related to nerve growth factor, which are responsible for neuron proliferation, survival and differentiation. A more diverse role for BDNF as a neuronal extracellular transmitter has, nevertheless, been proposed. The dopamine D3 receptor has been implicated in neuropsychiatric disorders including schizophrenia, drug addiction, depression and Parkinson’s disease. Its expression during development and in adulthood is highly dependent on dopaminergic innervation. Here we show that BDNF synthesized by dopamine neurons is responsible for the appearance of the D3 receptor during development and maintains D3 receptor expression in adults. Moreover, BDNF triggers D3 receptor overexpression and behavioral sensitization to levodopa in denervated animals. These results suggest that BDNF, by controlling the expression of specific genes such as the D3 receptor gene, may be an important factor in neurodevelopmental psychiatric diseases.
A Usability-Pattern-Based Requirements-Analysis Method to Bridge the Gap between User Tasks and Application Features

In software development, it is important to mediate various concerns coming from user experience (UX) designers and application developers. In Agile User-Centered Design (Agile-UCD), there is a special role called specialist who is dedicated to implement application features as well as to monitor user experiences. However, the specialist normally has difficulty in linking user tasks to be accessed via a user interface (UI) into application feature entities. In addition, the specialist may also have some unsettled usability risks that might result in the failure of meeting certain usability criteria and passing acceptance tests. To alleviate these difficulties of the specialists in Agile-UCD, we propose a usability-pattern-based requirement-analysis method. This method uses standardized and common representations of requirements specification to bridge the gap between user tasks and related application features of a UI. It also provides a guideline to allow the specialist to reduce usability risks in an early stage by reflecting usability factors of UI design patterns to an application design. A case study has been conducted to show how users can effectively specify user tasks and application features on UI workflows. It also shows how easy and practical it is to understand the common representations as well as to apply to usability patterns.
SPATA: A seeding and patching algorithm for de novo transcriptome assembly

RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.
A flexible replication framework for scalable and reliable .net services

We present a flexible framework for the development of reliable and scalable distributed services based on the Microsoft . NET framework. Scalability is obtained by load balancing among dynamically managed service replicas. Fault tolerance is achieved by redundancy among replicas and an active replication strategy to ensure replica consistency. The framework architecture features full replication transparency for client applications. True object-oriented programming is supported in the sense that remote references to replicated services may be passed transparently as serialised arguments in remote invocations. We compare our framework to other replication architectures and illustrate the performance with run-time measurements.
Dynamics of PHA-induced immune response and plasma carotenoids in birds: should we have a closer look?

SUMMARY Allocation trade-offs of limited resources are thought to ensure the honesty of sexual signals and are often studied using controlled immune challenges. One such trade-off between immunity and ornaments is that involving carotenoids. Phytohemagglutinin (PHA)-induced immune response is a widely used immune challenge, yet more details on the underlying physiological mechanisms and potential costs are needed. We investigated the temporal dynamics of PHA-induced immune response and associated changes in blood carotenoids, body mass and a carotenoid-based coloured signal. We found variation in individual response patterns to PHA after peak swelling was reached, with birds showing either a rapid or a slow subsequent decrease in swelling, suggesting variation in the duration of the immune response and/or inflammation. Body mass did not affect immune response. Plasma carotenoids followed a transient decrease closely matching the dynamics of the swelling. The peak of the immune response was negatively related to initial plasma carotenoid levels and positively correlated to the relative decrease in plasma carotenoids. Individual variation in duration of the swelling could be partly explained by plasma carotenoids; high initial carotenoid levels were associated with a slower decrease of the swelling. These contradictory effects of carotenoids suggest a complex role in the immune response. Bill colour was positively correlated to initial plasma carotenoid concentration but it did not predict or change as a consequence of immune response to PHA. Bill colour thus reflects medium- or long-term quality rather than immediate quality. Taking into account the dynamics of the immune response and that of associated physiological parameters would thus yield new insights into our interpretation of variation in PHA response.
Utilizing Semantic Policies for Secure BGP Route Dissemination

Policies in BGP are expressed as routing configurations that determine how route information is shared among neighbors to control traffic flows across networks. This process is limited in its expressibility, time consuming and error prone which can lead to configurations where policies are violated or there are unintended consequences that are difficult to detect and resolve. In this paper, we propose an alternate mechanism for policy based networking that relies on using additional semantic information associated with routes expressed in an OWL ontology. Policies are expressed using SWRL to provide fine-grained control where the routers can reason over their routes and determine how they need to be exchanged. In this paper, we focus on security related BGP policies and show how our framework can be used in implementing them. Additional contextual information such as affiliations and route restrictions are incorporated and polices specified which can be reasoned over to infer the correct configurations that need to be applied which is easy to deploy, manage and verify for consistency.
A micromachined electrostatically suspended gyroscope with digital force feedback

This paper presents the design and system modeling of a micromachined electrostatically suspended gyroscope incorporated in a ZA force-feedback system. Unlike a typical micromachined gyro, the gyroscope reported here employs a levitated proof mass. The micromachined disk-shaped proof mass, which has no mechanical support, is suspended and spun electrostatically to function similar to a mechanical flywheel gyro. The precession of the disk caused by angular motion is sensed capacitively. The disk is rebalanced to its nominal position by a ZA control system. Such a system provides a direct digital output, which is a measure of the external rate of rotation. Analytical and finite element models are used to study the behavior of the sensor. The geometry of the sense and control electrodes is optimized to obtain maximum pick-off signal. System level simulations are performed to study the device performance of such a gyro
NOLTA 2006 PROCEEDINGS

This paper is concerned with the number of operating points in two-transistor circuits. Recently, a new method was proposed for analyzing twotransistor circuit and an Ebers-Moll BJT circuit possessing five operating points was shown numerically. In this paper, applying the technique of numerical validation, we verify the numerical results rigorously and prove that the circuit have more than three operating points rigorously.
Immunohistologic and functional characterization of a vascular addressin involved in lymphocyte homing into peripheral lymph nodes

The tissue localization or "homing" of circulating lymphocytes is directed in part by specialized vessels that define sites of lymphocyte exit from the blood. In peripheral lymph nodes, mucosal lymphoid tissues (Peyer's patches and appendix), and sites of chronic inflammation, for example, lymphocytes leave the blood by adhering to and migrating between those endothelial cells lining postcapillary high endothelial venules (HEV). Functional analyses of lymphocyte interactions with HEV have shown the lymphocytes can discriminate between HEV in different tissues, indicating that HEV express tissue- specific determinants or address signals for lymphocyte recognition. We recently described such a tissue-specific "vascular addressin" that is selectively expressed by endothelial cells supporting lymphocyte extravasation into mucosal tissues and that appears to be required for mucosa-specific lymphocyte homing (Streeter, P. R., E. L. Berg, B. N. Rouse, R. F. Bargatze, and E. C. Butcher. 1988. Nature (Lond.). 331:41- 46). Here we document the existence and tissue-specific distribution of a distinct HEV differentiation antigen. Defined by monoclonal antibody MECA-79, this antigen is expressed at high levels on the lumenal surface and in the cytoplasm of HEV in peripheral lymph nodes. By contrast, although MECA-79 stains many HEV in the mucosal Peyer's patches, expression in most cases is restricted to the perivascular or ablumenal aspect of these venules. In the small intestine lamina propria, a mucosa-associated site that supports the extravasation of lymphocytes, venules do not stain with MECA-79. Finally, we demonstrate that MECA-79 blocks binding of both normal lymphocytes and a peripheral lymph node-specific lymphoma to peripheral lymph node HEV in vitro and that it also inhibits normal lymphocyte homing to peripheral lymph nodes in vivo without significantly influencing lymphocyte interactions with Peyer's patch HEV in vitro or in vivo. Thus, MECA-79 defines a novel vascular addressin involved in directing lymphocyte homing to peripheral lymph nodes.
How Good is Almost Perfect?

Heuristic search using algorithms such as A* and IDA* is the prevalent method for obtaining optimal sequential solutions for classical planning tasks. Theoretical analyses of these classical search algorithms, such as the well-known results of Pohl, Gaschnig and Pearl, suggest that such heuristic search algorithms can obtain better than exponential scaling behaviour, provided that the heuristics are accurate enough. Here, we show that for a number of common planning benchmark domains, including ones that admit optimal solution in polynomial time, general search algorithms such as A* must necessarily explore an exponential number of search nodes even under the optimistic assumption of almost perfect heuristic estimators, whose heuristic error is bounded by a small additive constant. Our results shed some light on the comparatively bad performance of optimal heuristic search approaches in "simple" planning domains such as GRIPPER. They suggest that in many applications, further improvements in run-time require changes to other parts of the search algorithm than the heuristic estimator.
Evolutionary Theories and the Issue of Nuclear War: Implications for Mental Health

The process by which societal stressors are expressed in individual illness is not well understood. The need is ever present to adjust to such exigencies as uncertainty about the future, the alienating pressures of modern society, and destructive situations out of the control of the person affected. Such stressful adjustments seem to have face validity as a process that would debilitate human consciousness. When these stressful conditions are coupled with the notion that some preordained force is moving humans to be aggressive and exploitative and to create such conditions, the possibility of the healthy survival of the individual and society may be irreversibly weakened. The widespread acceptance of such a force, namely, genetic determinism, needs to be examined in light of the complex stresses of contemporary life. In the last one hundred and thirty years, formulations derived from the Darwinian theory of evolution have been the wellspring of theories relating a formidable human history marked by military events and interindividual hostility to evolutionary processes, emphasizing, in particular, the hereditary aspects. The outstanding contemporary examples of such theories of instinctive, inborn or innate behavior are ethology and sociobiology [1,2]. Both offer theories about social behavior that are based on genetic determinismi.e. , that genetic processes set the limits for development of all structures and functions and
Key Advances and Supporting Methodology

Polymorphism is a feature of many programming languages, including typed functional languages (e.g., SML, Haskell), and recent “generic” versions of Java. Relational parametricity, introduced by Reynolds in 1983, is a powerful principle for reasoning about polymorphic programs and types. Previously, relational parametricity has been mainly studied for the second-order lambda calculus, a simple, but theoretically important formalism for polymorphism, developed independently by Girard and Reynolds, and, more recently, for extensions of this language with recursion. Such investigations have provided an understanding of polymorphism in the context of pure functional programming languages. However, in the majority of computational scenarios, computations are not merely functions. The many non-functional aspects of computation (for example, nondeterminism, probabilistic choice, input/output, side effects, continuations, etc.) are often classified collectively as computational effects. The goal of this project was to develop foundations for applying the techniques of relational parametricity to programming languages that exhibit such non-functional effects. In particular, our aims were to study semantic models combining parametric polymorphism and effects, and to uncover the type theories and associated reasoning principles they support.
Dominator Tree Certification and Divergent Spanning Trees

How does one verify that the output of a complicated program is correct? One can formally prove that the program is correct, but this may be beyond the power of existing methods. Alternatively, one can check that the output produced for a particular input satisfies the desired input--output relation by running a checker on the input--output pair. Then one only needs to prove the correctness of the checker. For some problems, however, even such a checker may be too complicated to formally verify. There is a third alternative: augment the original program to produce not only an output but also a correctness certificate, with the property that a very simple program (whose correctness is easy to prove) can use the certificate to verify that the input--output pair satisfies the desired input--output relation. We consider the following important instance of this general question: How does one verify that the dominator tree of a flow graph is correct? Existing fast algorithms for finding dominators are complicated, and even verifying the correctness of a dominator tree in the absence of additional information seems complicated. We define a correctness certificate for a dominator tree, show how to use it to easily verify the correctness of the tree, and show how to augment fast dominator-finding algorithms so that they produce a correctness certificate. We also relate the dominator certificate problem to the problem of finding divergent spanning trees in a flow graph, and we develop algorithms to find such trees. All our algorithms run in linear time. Previous algorithms apply just to the special case of only trivial dominators, and they take at least quadratic time.
An empirical study into the robustness of split covariance addition (SCA) for human motion tracking

Accurate human body tracking is extremely important for many virtual and augmented reality systems. However, tracking human motion is extremely difficult. Some of the difficulties arise from the fact that accurate process models of human motion are difficult to derive. Approximate models can have substantial time-correlated process noise terms. We examine the effectiveness of using the split covariance addition (SCA) algorithm as part of a human head orientation estimation system. We perform a series of empirical experiments to compare the performance of several implementations of SCA with an extended Kalman filter (EKF). The results suggest that the benefits of SCA are mixed. It leads to filters, which are slightly more robust and have slightly more accurate angular velocity estimates than the EKF. However, the absolute orientation estimate is slightly worse than the EKF.
Coordination des transports et de l'occupation de l'espace pour réduire la dépendance automobile dans la région métropolitaine de Londres

Nous proposons d'evaluer la pertinence de la coordination des politiques de transport et d'occupation de l'espace pour reduire les nuisances de la mobilite quotidienne dans la region metropolitaine de Londres. Le diagnostic d'une dependance automobile est dresse. Les causes, les manifestations, les consequences et les remedes a la dependance automobile sont alors contextualises dans la complexite du fonctionnement et de la gestion de la region. Dans le contexte de developpement durable, les autorites londoniennes souhaitent reduire la dependance automobile. Malgre des resultats de recherche divergents sur les liens presumes entre transport, occupation de l'espace et pratiques de mobilite, la coordination des politiques de transport et d'occupation de l'espace est privilegiee. Cette posture revele la consecration d'un nouveau paradigme de l'amenagement urbain et regional que nous souhaitons deconstruire. Deconstruction du cheminement par lequel ce type de politique a ete consacre et par l'evaluation des relations entre transports, occupation de l'espace et deplacements domicile-travail dans la region metropolitaine de Londres. Si la reduction de la dependance est conditionnee par la coordination des politiques, notamment de celles qui encouragent les hautes densites et l'amelioration conjointe de la desserte des transports collectifs, elle induit egalement la necessaire pratique d'un « grand ecart » tant les objectifs divergent.
Regulation of the Jak2 Tyrosine Kinase by Its Pseudokinase Domain

ABSTRACT Activation of Jak tyrosine kinases through hematopoietic cytokine receptors occurs as a consequence of ligand-induced aggregation of receptor-associated Jaks and their subsequent autophosphorylation. Jak kinases consist of a C-terminal tyrosine kinase domain, a pseudokinase domain of unknown function, and Jak homology (JH) domains 3 to 7, implicated in receptor-Jak interaction. We analyzed the functional roles of the different protein domains in activation of Jak2. Deletion analysis of Jak2 showed that the pseudokinase domain but not JH domains 3 to 7 negatively regulated the catalytic activity of Jak2 as well as Jak2-mediated activation of Stat5. Phosphorylation of Stat5 by wild-type Jak2 was dependent on the SH2 domain of Stat5; however, this requirement was lost upon deletion of the pseudokinase domain of Jak2. Investigation of the mechanisms of the pseudokinase domain-mediated inhibition of Jak2 suggested that this regulation did not involve protein tyrosine phosphatases. Instead, analysis of interactions between the tyrosine kinase domain and Jak2 suggested that the pseudokinase domain interacted with the kinase domain. Furthermore, coexpression of the pseudokinase domain inhibited the activity of the single tyrosine kinase domain. Finally, deletion of the pseudokinase domain of Jak2 deregulated signal transduction through the gamma interferon receptor by significantly increasing ligand-independent activation of Stat transcription factors. These results indicate that the pseudokinase domain negatively regulates the activity of Jak2, probably through an interaction with the kinase domain, and this regulation is required to keep Jak2 inactive in the absence of ligand stimulation. Furthermore, the pseudokinase domain may have a role in regulation of Jak2-substrate interactions.