Miracle-dz/UniFAR-FTUs huggingface dataset:
Alias and Union Types for Delegation

We adapt the aliasing constraints approach for designing a flexible typing of evolving objects. Types are singleton types (addresses of objects, as a matter of fact) or finite "unions" of these. Their relevance is mainly due to the sort of safety property they guarantee. In particular we provide a type system for an imperative object based calculus with delegation and conditional expressions and which supports method and delegate overriding, addition, and removing.
Interventional magnetic resonance imaging-guided subthalamic nucleus deep brain stimulation for Parkinson's disease: Patient selection

Background: Interventional magnetic resonance imaging (iMRI) guided deep brain stimulation (DBS) for Parkinson's disease (PD) has been shown to be effective. The costs of a dedicated intraoperative MRI may be prohibitive. The procedure can also be performed in a diagnostic scanner, however this presents challenges for utilization of time when the scanner is used both as a diagnostic and an interventional unit. This report outlines our novel methodology for patient selection for implantation in a diagnostic MR scanner, as an attempt to streamline the use of resources. A retrospective review of our outcomes is also presented. Methods: DBS candidacy evaluation included a PD questionnaire-39. Anxiety, age, difficulties in communication and body habitus were factors that were assessed in selecting patients for this technique. Eleven patients underwent iMRI-guided DBS implantation in the subthalamic nucleus. All patients were implanted bilaterally. Unified PD rating scale (UPDRS) part III and L-dopa dose were compared pre- and post-stimulation. A cohort of 11 DBS patients not selected for iMRI-guided DBS were also reported for comparison. Results: For the iMRI-guided patients, mean “Off” UPDRS III score was 47.6 (standard deviation [SD] 8.26). Postoperative “On” medication, “On” stimulation UPDRS III was 13.6 (SD 5.23). Mean preoperative L-dopa dose was 1060 mg (SD 474.3) and mean postoperative L-dopa dose was 320 (SD 298.3). Conclusion: iMRI-guided DBS is a newly emerging technique for surgical treatment of patients with PD. We present a novel scoring system for patient selection assessing anxiety, age, ability to communicate, and body habitus to identify patients who will be benefited most from this technique.
TRAFFIC GROOMING, ROUTING AND WAVELENGTH ASSIGNMENT IN OPTICAL WDM MESH NETWORKS

In this paper, we consider the traffic grooming routing, and wavelength assignment (GRWA) problem for optical mesh networks. In most previous studies on optical mesh networks, traffic demands are usually assumed to be wavelength demands, in which case no traffic grooming is needed. In practice, optical networks are typically required to carry a large number of lower rate (sub-wavelength) traffic demands. Hence, the issue of traffic grooming becomes very important since it can significantly impact the overall network cost. In our study, we consider traffic grooming in combination with traffic routing and wavelength assignment. Our objective is to minimize the total number of transponders required in the network. We first formulate the GRWA problem as an integer linear programming (ILP) problem. Unfortunately, for large networks it is computationally infeasible to solve the ILP problem. Therefore, we propose a decomposition method that divides the GRWA problem into two smaller problems: the traffic grooming and routing problem and the wavelength assignment problem, which can then be solved much more efficiently. In general, the decom-position method only produces an approximate solution for the GRWA problem. However, we also provide some sufficient condition under which the decomposition method gives an optimal solution. Finally, some numerical results are provided to demonstrate the efficiency of our method.
Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

The WDR5 subunit of the MLL complex enforces active chromatin and can bind RNA; the relationship between these two activities is unclear. Here we identify a RNA binding pocket on WDR5, and discover a WDR5 mutant (F266A) that selectively abrogates RNA binding without affecting MLL complex assembly or catalytic activity. Complementation in ESCs shows that WDR5 F266A mutant is unable to accumulate on chromatin, and is defective in gene activation, maintenance of histone H3 lysine 4 trimethylation, and ESC self renewal. We identify a family of ESC messenger and lncRNAs that interact with wild type WDR5 but not F266A mutant, including several lncRNAs known to be important for ESC gene expression. These results suggest that specific RNAs are integral inputs into the WDR5-MLL complex for maintenance of the active chromatin state and embryonic stem cell fates. DOI: http://dx.doi. org/10.7554/eLife.02046. 001
Neural Network Macromodel for High-Level Power Estimation of CMOS Circuits

A novel power macromodeling technique was developed for high-level power estimation of complementary metal-oxide-semiconductor (CMOS) circuits based on backpropagation neural network (BPNN). The dependence of power dissipation on a circuit's primary input/output statistics was captured to construct the power macromodel by extracting certain features from the input/output streams. In contrast to previous modeling techniques, it does not require empirically construct specialized analytical equations, and achieves better accuracy by taking into account the statistics of not only the primary inputs, but also the primary outputs. It could yield power estimates within seconds, because it does not perform any simulation during estimation. In experiments with the ISCAS-85 circuits, the average absolute relative error of the macromodel was below 5.0% for most of the circuits. The root-mean-square (RMS) error is about 1 - 2%. In addition to power dissipation, statistics of a circuit's primary outputs could be simultaneously obtained as a by-product, which is very useful for power estimation of core-based systems-on-chip (SoCs) with pre-designed blocks
Comparison between power gating and DVFS from the viewpoint of energy efficiency

To increase the energy efficiency of modern LSIs, supply voltage control techniques (power gating and dynamic voltage frequency scaling) have been widely used and the energy efficiency of fine grain temporal controls in both cases have been discussed. In this paper, we applied dead time constraint, compared the energy efficiencies and formulated the boundary condition that power gating is more energy efficient than DVFS. The formulation is applied to discuss the future trend of energy efficiency using ITRS roadmap and it was found that DVFS would be still effective with high-performance technology, however, it will not be effective with low-operating-power technology.
Formation Control of Multi Agent System in Cyclic Pursuit with Varying Inter-Agent Distance

—This paper is concerned with formation control of multi-agent system under cyclic pursuit strategy. The object is to control inter-agent distance between the agents hetero-geneously. We propose a control algorithm based on bearing angle information of the pursuing agent. The algorithm consist of heading control only. The control law is simple and easy to implement in real world application. The effectiveness of the proposed control law are demonstrated through various simulations
Aspects , Models and Model Transformations

Besides the obvious importance of PIMs and PSMs in MDA, model transformations are undoubtedly the key technology in the realization of the MDA vision [1]. Among other usages, model transformations are the ones responsible for refining PIMs into PSMs (or abstracting away from PSMs to PIMs) and mapping PSMs to concrete middlewarebased implementations, providing thus an elegant approach to adapt PIMs to the peculiarities of the new middleware infrastructures that do not cease to appear.
Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity

The budding yeast, Saccharomyces cerevisiae, is a leading system in genetics, genomics and molecular biology and is becoming a powerful tool to illuminate ecological and evolutionary principles. However, little is known of the ecology and population structure of this species in nature. Here, we present a field survey of this yeast at an unprecedented scale and have performed population genetics analysis of Chinese wild isolates with different ecological and geographical origins. We also included a set of worldwide isolates that represent the maximum genetic variation of S. cerevisiae documented so far. We clearly show that S. cerevisiae is a ubiquitous species in nature, occurring in highly diversified substrates from human‐associated environments as well as habitats remote from human activity. Chinese isolates of S. cerevisiae exhibited strong population structure with nearly double the combined genetic variation of isolates from the rest of the world. We identified eight new distinct wild lineages (CHN I–VIII) from a set of 99 characterized Chinese isolates. Isolates from primeval forests occur in ancient and significantly diverged basal lineages, while those from human‐associated environments generally cluster in less differentiated domestic or mosaic groups. Basal lineages from primeval forests are usually inbred, exhibit lineage‐specific karyotypes and are partially reproductively isolated. Our results suggest that greatly diverged populations of wild S. cerevisiae exist independently of and predate domesticated isolates. We find that China harbours a reservoir of natural genetic variation of S. cerevisiae and perhaps gives an indication of the origin of the species.
Differential Distributions of Synechococcus Subgroups Across the California Current System

Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria) obtained previously from isolates and the environment (e.g., North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, CA, USA) were used to develop quantitative PCR (qPCR) assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS), a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups) had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1, and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate, and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below). E_O1, A_C1, and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California current water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system.
Social Skills at Work: Deficits and Predictors of Improvement in Schizophrenia

While the impact of social learning programs upon social deficits in schizophrenia has been widely studied, less is understood about which patients have the poorest social skills, and among those which patients have deficits most refractory to rehabilitation. To explore these questions, this study compared the symptom levels and performance on neuropsychological testing of 91 subjects with impaired and unimpaired social skills enrolled in a vocational rehabilitation program. After 10 weeks of rehabilitation and a supportive group treatment, social skills among a subsample of 41 subjects with initially impaired social skills were reassessed. Results indicate that subjects with initially impaired social skills had significantly higher levels of negative symptoms. However, multiple regression analysis revealed that cognitive impairments at intake, rather than level of negative symptoms, predicted improvement among subjects with initially impoverished social skills (R2 = .35). Results suggest that level of cognitive impairment is associated with the persistence of social skills deficits in schizophrenia. —J Nerv Ment Dis 183:688–692, 1995
Exclusion of RPGRIP1 ins44 from primary causal association with early-onset cone-rod dystrophy in dogs.

PURPOSE Canine cone-rod dystrophy 1 (cord1) has been previously mapped to CFA15, and a homozygous 44-bp insertion in exon 2 (Ins44) of canine RPGRIP1 (cRPGRIP1(Ins/Ins)) has been associated with the disease. However, from the recent identification of a significant discordance in genotype-phenotype association, we have reexamined the role of cRPGRIP1 in cord1. METHODS Retinal structure and function was assessed by clinical retinal examination, noninvasive imaging, electroretinography, and histopathology/immunohistochemistry. cRPGRIP1 splicing was analyzed by RT-PCR. Retinal gene expression was determined by quantitative RT-PCR (qRT-PCR). Five markers spanning the entire cRPGRIP1 were identified and used for haplotyping. RESULTS Electroretinography demonstrated that cone responses were absent or present in cRPGRIP1(Ins/Ins) individuals. Moreover, performance in vision testing and optical coherence tomography (OCT) were comparable in cRPGRIP1(Ins/Ins) dogs, regardless of the cone ERG status. While histologic changes in retinal structure were minimal, immunohistochemistry demonstrated a lack of cone opsin labeling in cRPGRIP1(Ins/Ins) dogs. cDNA analysis revealed that Ins44 disrupts a putative exonic splicing enhancer that allows for skipping of exon 2, while retaining the functional RPGR-interacting domain (RID) of the protein. New cRPGRIP1 sequence changes were identified, including a 3-bp deletion affecting the 3' acceptor splice site of alternative exon 19c. The extended haplotype spanning cRPGRIP1 was identical in cRPGRIP1(Ins/Ins) dogs with and without retinal degeneration. Gene expression analysis showed that expression levels were not associated with Ins44 genotype. CONCLUSIONS The results indicated that cRPGRIP1 Ins44 is an unlikely primary cause of cord1, and that the causal gene and mutation are likely located elsewhere in the critical disease interval.
A Comparison Study on Key Exchange-Authentication protocol

A key exchange protocol enables two parties to share a common key for encrypting a large amount of data. Authentication is an essential requirement prior to the key exchange process in order to prevent man-in-the-middle attack. It is important to understand the capabilities and performance of the existing key exchange protocols before employing the protocols in our applications. In this paper, we compare Secure Socket Layer, Secure Shell, and Identity-based key exchange protocols by quantifying the performance, complexity, and level of security of each protocol. Detailed experiments and observations are conducted to examine the protocols in terms of disk usage, computation time, and data transmission time. The analysis shows that the identity-based key exchange maintains similar security level as the other protocols, while conveying better performance. General Terms Security, protocol, cryptography.
Opening Embedded Systems for Open Innovation

Openness for open innovation is becoming increasingly important in the field of embedded systems (ES). ES are traditionally designed for a particular purpose, however most ES firms are beginning to open up their systems. This allows third parties to enhance them with additional software, or hardware components. It is not enough to just provide access to a system though, it also requires that it be modularized accordingly. A specific challenge when modularizing for open innovation, is the consideration of ES characteristics such as safety, security and or real-time requirements. In this multiple case study, our goal is to explore how ES producers can technically open their systems for open innovation. To address this question, this paper first systematizes the different forms of openness in ES. Secondly, it uses modularity theory to analyze the implications of the specific requirements of ES on the encountered forms of openness. It turns out that, different types of openness require differing levels of effort, with regard to modularization. Overall, the study shows that, in order to guarantee the proper functioning of their systems, ES firms tend to partition their systems in accordance to the specific requirements of ES.
Chapter 20 Generating , Refining and Using Sentiment Lexicons

In this chapter, which is based on [7–9], we report on work on the generation, refinement and use of sentiment lexicons that was carried out within the DuOMAn project. The project was focused on the development of language technology to support online media analysis. In the area of media analysis, one of the key tasks is collecting detailed information about opinions and attitudes toward specific topics from various sources, both offline (traditional newspapers, archives) and online (news sites, blogs, forums). Specifically, media analysis concerns the following system task: given a topic and list of documents (discussing the topic), find all instances of attitudes toward the topic (e.g., positive/negative sentiments, or, if the topic is an organisation or person, support/criticism of this entity). For every such instance, one should identify the source of the sentiment, the polarity and, possibly, subtopics that this attitude relates to (e.g., specific targets of criticism or support). Subsequently, a (human) media analyst must be able to aggregate the extracted information by source, polarity or subtopics, allowing him to build support/criticism networks etc. [1]. Recent advances in language technology, especially in sentiment analysis, promise to (partially) automate this task. Sentiment analysis is often considered in the context of the following two tasks:
String stability of interconnected systems

In this paper we introduce the notion of string stability of a countably infinite interconnection of a class of nonlinear systems. Intuitively, string stability implies uniform boundedness of all the states of the interconnected system for all time if the initial states of the interconnected system are uniformly bounded. It is well known that the I/O gain of all the subsystems less than unity guarantees that the interconnected system is I/O stable. We derive sufficient ("weak coupling") conditions which guarantee asymptotic string stability of a class of interconnected systems. Under the same "weak coupling" conditions, string stable interconnected systems remain string stable in the presence of small structural/singular perturbations. In the presence of parameter mismatch, these "weak coupling" conditions ensure that the states of all the subsystems are all uniformly bounded when gradient based parameter adaptation law is used and that they go to zero asymptotically.
Differential Regulation by Tumor Necrosis Factor-α of β1-, β2-, and β3-Adrenoreceptor Gene Expression in 3T3-F442A Adipocytes*

Modulation of β-adrenoreceptor expression by tumor necrosis factor-α (TNF-α) was investigated in murine 3T3-F442A adipocytes. TNF-α treatment of mature adipocytes decreased β3-adrenoreceptor mRNA content in a time- and concentration-dependent manner, with a 8.5-fold decrease observed after a 6-h exposure to 300 pm TNF-α. β1-Adrenoreceptor mRNA abundance was slightly decreased by TNF-α treatment, while β2-adrenoreceptor mRNA levels were potently induced (6-fold increase at 6 h). (−)-[125I]Iodocyanopindolol saturation and competition binding experiments indicated that TNF-α induced a 2-fold decrease in β3-adrenoreceptor number, a nonsignificant reduction in β1-subtype population, and a ∼4.5-fold increase in β2-adrenoreceptor density. This correlated with a lower EC50 value measured for epinephrine in stimulating adenylyl cyclase, whereas the EC50 value for norepinephrine increased. Nuclear run-on assays on isolated nuclei and mRNA stability measurements showed that TNF-α increased both β2-adrenoreceptor gene transcription and β2-adrenoreceptor mRNA half-life, while β1- and β3-adrenoreceptor gene expression was modulated only at the transcriptional level by the cytokine. These findings demonstrate a differential modulation by TNF-α of the three β-adrenoreceptor subtypes in adipocytes, which may contribute to metabolic disorders induced by the cytokine in the adipocyte.
Event-based runtime verification of java programs

We introduce the temporal logic HAWK and its supporting tool for runtime verification of Java programs. A monitor for a HAWK formula checks if a finite trace of program events satisfies the formula. HAWK is a programming-oriented extension of the rule-based EAGLE logic that has been shown capable of defining and implementing a range of finite trace monitoring logics, including future and past time temporal logic, metric (real-time) temporal logics, interval logics, forms of quantified temporal logics, extended regular expressions, state machines, and others. Monitoring is achieved on a state-by-state basis avoiding any need to store the input trace. HAWK extends EAGLE with constructs for capturing parameterized program events such as method calls and method returns. Parameters can be executing thread, the objects that methods are called upon, arguments to methods, and return values. HAWK allows one to refer to these in formulae. The tool synthesizes monitors from formulae and automates program instrumentation.
Subcutaneous Reaction of Rat Tissues to Nanosilver Coated Gutta-Percha

Introduction: Gutta-percha (GP), is a neutral and non-toxic material. The aim of this animal study was to compare the biocompatibility of nanosilver coated GP (NS-GP) with conventional GP in subcutaneous tissues in a rat model. Methods and Materials: Conventional GP and NS-GP were subcutaneously implanted in the backs of 20 male Wistar rats (n=10). A control animal was assigned for each trial period. Ten animals were sacrificed after 7 and 30 days and light microscopic evaluation of tissue reaction to NS-GP (n=20) and conventional GP (n=20) was accomplished. The Mann-Whitney U, Wilcoxon Signed Ranks, Fisher Exact, and McNemar tests were used for statistical analysis of the data. Results: After 7 days, inflammation was moderate and mild for NS-GP and conventional GP, respectively (P<0.001). After 30 days, no inflammation was discernible in conventional GP. However, mild inflammation was reported for NS-GP (P<0.001). Regarding inflammatory cell type, there was a significant difference between two experimental groups at both times (P<0.001). Conclusion: Inflammation decreased over time in both groups. Fibrous connective tissue, a representative of healing and control of inflammatory process, surrounded both test materials. NS-GP was biocompatible and might be a reasonable endodontic obturation material.