Miracle-dz/UniFAR-FTUs huggingface dataset:
Formal refinement patterns for goal-driven requirements elaboration

Requirements engineering is concerned with the identification of high-level goals to be achieved by the system envisioned, the refinement of such goals, the operationalization of goals into services and constraints, and the assignment of responsibilities for the resulting requirements to agents such as humans, devices and programs. Goal refinement and operationalization is a complex process which is not well supported by current requirements engineering technology. Ideally some form of formal support should be provided, but formal methods are difficult and costly to apply at this stage.This paper presents an approach to goal refinement and operationalization which is aimed at providing constructive formal support while hiding the underlying mathematics. The principle is to reuse generic refinement patterns from a library structured according to strengthening/weakening relationships among patterns. The patterns are once for all proved correct and complete. They can be used for guiding the refinement process or for pointing out missing elements in a refinement. The cost inherent to the use of a formal method is thus reduced significantly. Tactics are proposed to the requirements engineer for grounding pattern selection on semantic criteria.The approach is discussed in the context of the multi-paradigm language used in the KAOS method; this language has an external semantic net layer for capturing goals, constraints, agents, objects and actions together with their links, and an inner formal assertion layer that includes a real-time temporal logic for the specification of goals and constraints. Some frequent refinement patterns are high-lighted and illustrated through a variety of examples.The general principle is somewhat similar in spirit to the increasingly popular idea of design patterns, although it is grounded on a formal framework here.
The design and implementation of an object-oriented toolkit for 3D graphics and visualization

The Visualization Toolkit (vtk) is a freely available C++ class library for 3D graphics and visualization. We describe core characteristics of the toolkit. This includes a description of object oriented models for graphics and visualization; methods for synchronizing system execution; a summary of data representation schemes; the role of C++; issues in portability across PC and Unix systems; and how we automatically wrap the C++ class library with interpreted languages such as Java and Tcl. We also demonstrate the capabilities of the system for scalar, vector, tensor, and other visualization techniques.
Information Presentation in Spoken Dialogue Systems

To tackle the problem of presenting a large number of options in spoken dialogue systems, we identify compelling options based on a model of user preferences, and present tradeoffs between alternative options explicitly. Multiple attractive options are structured such that the user can gradually refine her request to find the optimal tradeoff. We show that our approach presents complex tradeoffs understandably, increases overall user satisfaction, and significantly improves the user’s overview of the available options. Moreover, our results suggest that presenting users with a brief summary of the irrelevant options increases users’ confidence in having heard about all relevant options.
The Jpred 3 secondary structure prediction server

Jpred (http://www.compbio.dundee.ac.uk/jpred) is a secondary structure prediction server powered by the Jnet algorithm. Jpred performs over 1000 predictions per week for users in more than 50 countries. The recently updated Jnet algorithm provides a three-state (α-helix, β-strand and coil) prediction of secondary structure at an accuracy of 81.5%. Given either a single protein sequence or a multiple sequence alignment, Jpred derives alignment profiles from which predictions of secondary structure and solvent accessibility are made. The predictions are presented as coloured HTML, plain text, PostScript, PDF and via the Jalview alignment editor to allow flexibility in viewing and applying the data. The new Jpred 3 server includes significant usability improvements that include clearer feedback of the progress or failure of submitted requests. Functional improvements include batch submission of sequences, summary results via email and updates to the search databases. A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions.
A Proximal Alternating Direction Method for Semi-Definite Rank Minimization

Semi-definite rank minimization problems model a wide range of applications in both signal processing and machine learning fields. This class of problem is NP-hard in general. In this paper, we propose a proximal Alternating Direction Method (ADM) for the well-known semi-definite rank regularized minimization problem. Specifically, we first reformulate this NP-hard problem as an equivalent biconvex MPEC (Mathematical Program with Equilibrium Constraints), and then solve it using proximal ADM, which involves solving a sequence of structured convex semi-definite subproblems to find a desirable solution to the original rank regularized optimization problem. Moreover, based on the Kurdyka-Lojasiewicz inequality, we prove that the proposed method always converges to a KKT stationary point under mild conditions. We apply the proposed method to the widely studied and popular sensor network localization problem. Our extensive experiments demonstrate that the proposed algorithm outperforms state-of-the-art low-rank semi-definite minimization algorithms in terms of solution quality.
Increased frequencies of CD8+ T lymphocytes recognizing wild‐type p53‐derived epitopes in peripheral blood correlate with presence of epitope loss tumor variants in patients with hepatocellular carcinoma

Wild‐type (WT) sequence p53 peptides are attractive candidates for broadly applicable cancer vaccines. The aim of this study was to evaluate the potential of a WT p53‐based immunotherapeutic approach for patients with hepatocellular carcinoma (HCC). Circulating CD8+ T cells specific for WT p53149–157 and WT p53264–272 HLA‐A*0201 restricted epitopes were directly identified in the peripheral blood by the use of peptide/HLA‐A2.1 tetramers in 24 HCC patients. Cytotoxic T lymphocyte (CTL) activity after WT p53 peptide‐specific stimulation was assessed by analysis of granzyme B and interferon‐gamma mRNA transcription, using a quantitative real‐time polymerase chain reaction assay. Tumor immunophenotyping was performed to evaluate the p53 status, the expression of major histocompatibility complex (MHC) and costimulatory molecules in freshly isolated tumor cells. HCC patients exhibited significantly higher frequencies of WT p53‐specific memory CD8+ T cells and stronger WT p53‐specific CTL activity, when compared with healthy controls. Increased frequencies of p53‐specific CD8+ T cells and their activity correlated with selective HLA‐A2 allele loss and reduced costimulatory molecule expression of tumor cells. Moreover, augmented numbers of p53‐specific T cells coincided with high MHC class II expression in tumor cells but were inversely related to the T status of the tumor node metastasis staging system. Our results indicate the existence of natural immunosurveillance and tumor immune evasion, involving a T cell response against WT p53 tumor antigen in patients with HCC. These findings may have important implications for the future development of cancer vaccines. © 2006 Wiley‐Liss, Inc.
Feasibility of measuring event Related Desynchronization with electroencephalography during walking

Brain Computer Interfaces could be useful in rehabilitation of movement, perhaps also for gait. Until recently, research on movement related brain signals has not included measuring electroencephalography (EEG) during walking, because of the potential artifacts. We investigated if it is possible to measure the event Related Desynchronization (ERD) and event related spectral perturbations (ERSP) during walking. Six subjects walked on a treadmill with a slow speed, while EEG, electromyography (EMG) of the neck muscles and step cycle were measured. A Canonical Correlation Analysis (CCA) was used to remove EMG artifacts from the EEG signals. It was shown that this method correctly deleted EMG components. A strong ERD in the mu band and a somewhat less strong ERD in the beta band were found during walking compared to a baseline period. Furthermore, lateralized ERSPs were found, depending on the phase in the step cycle. It is concluded that this is a promising method to use in BCI research on walking. These results therefore pave the way for using brain signals related to walking in a BCI context.
Precise enforcement of progress-sensitive security

Program progress (or termination) is a covert channel that may leak sensitive information. To control information leakage on this channel, semantic definitions of security should be progress sensitive and enforcement mechanisms should restrict the channel's capacity. However, most state-of-the-art language-based information-flow mechanisms are progress insensitive---allowing arbitrary information leakage through this channel---and current progress-sensitive enforcement techniques are overly restrictive. We propose a type system and instrumented semantics that together enforce progress-sensitive security more precisely than existing approaches. Our system is permissive in that it is able to accept programs in which the termination behavior depends only on low-security (e.g., public or trusted) information. Our system is parameterized on a termination oracle, and controls the progress channel precisely, modulo the ability of the oracle to determine the termination behavior of a program based on low-security information. We have instantiated the oracle for a simple imperative language with a logical abstract interpretation that uses an SMT solver to synthesize linear rank functions. In addition, we extend the system to permit controlled leakage through the progress channel, with the leakage bound by an explicit budget. We empirically analyze progress channels in existing Jif code. Our evaluation suggests that security-critical programs appear to satisfy progress-sensitive security.
Arabidopsis Kinetochore Fiber-Associated MAP65-4 Cross-Links Microtubules and Promotes Microtubule Bundle Elongation[W][OA]

This study shows that Arabidopsis MAP65-4 associates with the forming spindle and kinetochore fibers during mitosis. In vitro, MAP65-4 induces microtubule (MT) bundling and modulates the MT dynamic instability parameters of individual MTs within a bundle, mainly by decreasing the frequency of catastrophes and increasing the frequency of rescue events, which results in the progressive lengthening of MT bundles. The acentrosomal plant mitotic spindle is uniquely structured in that it lacks opposing centrosomes at its poles and is equipped with a connective preprophase band that regulates the spatial framework for spindle orientation and mobility. These features are supported by specialized microtubule-associated proteins and motors. Here, we show that Arabidopsis thaliana MAP65-4, a non-motor microtubule associated protein (MAP) that belongs to the evolutionarily conserved MAP65 family, specifically associates with the forming mitotic spindle during prophase and with the kinetochore fibers from prometaphase to the end of anaphase. In vitro, MAP65-4 induces microtubule (MT) bundling through the formation of cross-bridges between adjacent MTs both in polar and antipolar orientations. The association of MAP65-4 with an MT bundle is concomitant with its elongation. Furthermore, MAP65-4 modulates the MT dynamic instability parameters of individual MTs within a bundle, mainly by decreasing the frequency of catastrophes and increasing the frequency of rescue events, and thereby supports the progressive lengthening of MT bundles over time. These properties are in line with its role of initiating kinetochore fibers during prospindle formation.
Changes in the Flexion Relaxation Response Following an Exercise Intervention

Study Design. Pre and post 12-week training study using surface electromyography to measure the flexion relaxation response. Objective. To evaluate whether the active or passive phases of the flexion relaxation measurement changes following an exercise intervention in patients with low back pain. Summary of Background Data. Impaired neuromuscular activation is an area of specific interest in patients with chronic nonspecific low back pain (LBP). The flexion relaxation phenomenon is commonly measured in LBP patients; however, there is insufficient evidence about the changes in this measure following an intervention. Methods. Fifteen subjects with chronic LBP (7 females, 8 males) performed a 12-week training intervention. The main outcome measures were the Oswestry disability index, visual analog scale, and flexion relaxation response analyzed by the raw electromyograph (EMG) signal, the relative EMG signal, and the flexion relaxation ratio. Results. Disability and pain scores improved significantly after the 12-week intervention. There were no changes in the active components of the flexion relaxation measurement but an approximate 67% decrease in the amount of activity measured during the relaxation phase at full trunk flexion. Conclusion. The data suggest that afferent feedback changes may be explaining why there is improved electrical relaxation following an exercise intervention.
A Scalable Architecture for Multi Agent Vision Based Robot Scavenging

This paper outlines the technical details and presents early results from our multi agent robot scavenging system, as demonstrated at the 2006 AAAI Robot Exhibition and Scavenger Hunt Competition. Our system is designed to be easily scalable in the number of agents, which are currently limited to Evolution ER1 laptop robots capable of monocular vision. Each individual robot possesses the ability to localize itself, recognize a set of objects, and communicate with peer robots to coordinate exploration.
Phosphodiesterase 2A is a major negative regulator of iNOS expression in lipopolysaccharide‐treated mouse alveolar macrophages

PDE2A is a dual‐function PDE that is stimulated by cGMP to hydrolyze cAMP preferentially. In a two‐hit model of ALI, we found previously that PDE2A decreased lung cAMP, up‐regulated lung iNOS, and exacerbated ALI. Recent data suggest that macrophage iNOS expression contributes to ALI but later, promotes lung‐injury resolution. However, macrophage iNOS is increased by cAMP, suggesting that PDE2A could negatively regulate macrophage iNOS expression. To test this, we examined the effects of manipulating PDE2A expression and function on LPS‐induced iNOS expression in a mouse AM cell line (MH‐S) and primary mouse AMs. In MH‐S cells, LPS (100 ng/ml) increased PDE2A expression by 15% at 15 min and 50% at 6 h before decreasing at 24 h and 48 h. iNOS expression appeared at 6 h and remained increased 48 h post‐LPS. Compared with control Ad, Ad.PDE2A‐shRNA enhanced LPS‐induced iNOS expression further by fourfold, an effect mimicked by the PDE2A inhibitor BAY 60–7550. Adenoviral PDE2A overexpression or treatment with ANP decreased LPS‐induced iNOS expression. ANP‐induced inhibition of iNOS was lost by knocking down PDE2A and was not mimicked by 8‐pCPT‐cGMP, a cGMP analog that does not stimulate PDE2A activity. Finally, we found that in primary AMs from LPS‐treated mice, PDE2A knockdown also increased iNOS expression, consistent with the MH‐S cell data. We conclude that increased AM PDE2A is an important negative regulator of macrophage iNOS expression.
Spatial Distribution and Transcriptional Activity of an Uncultured Clade of Planktonic Diazotrophic γ-Proteobacteria in the Arabian Sea

ABSTRACT The spatial distribution of an uncultured clade of marine diazotrophic γ-proteobacteria in the Arabian Sea was investigated by the development of a specific primer pair to amplify an internal fragment of nifH by PCR. These organisms were most readily detected in highly oligotrophic surface waters but could also be found in deeper waters below the nutricline. nifH transcripts originating from this clade were detected in oligotrophic surface waters and, in addition, in the deeper and the more productive near-coastal waters. The nifH sequences most closely related to the unidentified marine bacterial group are from environmental clones amplified from the Atlantic and Pacific Oceans. These findings suggest that these γ-proteobacteria are widespread and likely to be an important component of the heterotrophic diazotrophic microbial community of the tropical and subtropical oceans.
A Jacobi-Davidson Iteration Method for Linear Eigenvalue Problems

In this paper we propose a new method for the iterative computation of a few of the extremal eigenvalues of a symmetric matrix and their associated eigenvectors. The method is based on an old and almost unknown method of Jacobi. Jacobi's approach, combined with Davidson's method, leads to a new method that has improved convergence properties and that may be used for general matrices. We also propose a variant of the new method that may be useful for the computation of nonextremal eigenvalues as well.
Extinction and the U.S. Endangered Species Act

The U.S. Endangered Species Act is one of the strongest laws of any nation for preventing species extinction, but quantifying the Act’s effectiveness has proven difficult. To provide one measure of effectiveness, we identified listed species that have gone extinct and used previously developed methods to update an estimate of the number of species extinctions prevented by the Act. To date, only four species have been confirmed extinct with another 22 possibly extinct following protection. Another 71 listed species are extinct or possibly extinct, but were last seen before protections were enacted, meaning the Act’s protections never had the opportunity to save these species. In contrast, a total of 39 species have been fully recovered, including 23 in the last 10 years. We estimate the Endangered Species Act has prevented the extinction of roughly 291 species since passage in 1973, and has to date saved more than 99% of species under its protection.
Linking Heterogeneous Data in the Semantic Web Using Scalable and Domain-Independent Candidate Selection

Due to the decentralized nature of the Semantic Web, the same real-world entity may be described in various data sources with different ontologies and assigned syntactically distinct identifiers. In order to facilitate data utilization and consumption in the Semantic Web, without compromising the freedom of people to publish their data, one critical problem is to appropriately interlink such heterogeneous data. This interlinking process is sometimes referred to as Entity Matching, i.e., finding which identifiers refer to the same real-world entity. In this paper, we propose two candidate selection algorithms to improve the scalability of entity matching systems. First of all, we propose HistSim that utilizes the matching histories of the instances to prune instance pairs that are not sufficiently similar to the same pool of other instances. A sigmoid function based thresholding method is proposed to automatically adjust the threshold for such commonality on-the-fly. Furthermore, we propose DisNGram that selects candidate instance pairs by computing a character-level similarity metric on discriminating literal values that are chosen using domain-independent unsupervised learning. Instances are indexed on the chosen predicates' literal values to enable efficient look-up for similar instances. Finally, in order to be able to handle heterogeneous datasets with a large number of predicates, a mechanism for automatically determining predicate comparability is proposed. We evaluate our two candidate selection algorithms against six state-of-the-art systems on three Semantic Web datasets, and demonstrate that our proposed algorithms frequently outperform state-of-the-art systems on F1-score and runtime.
On model-based testing advanced GUIs

Graphical User Interface (GUI) design is currently shifting from designing GUIs composed of standard widgets to designing GUIs relying on more natural interactions and ad hoc widgets. This shift is meant to support the advent of GUIs providing users with more adapted and natural interactions, and the support of new input devices such as multi-touch screens. Standard widgets (e.g. buttons) are more and more replaced by ad hoc ones (e.g. the drawing area of graphical editors), and interactions are shifting from mono-event (e.g. button pressures) to multi-event interactions (e.g. multi-touch and gesture-based interactions). As a consequence, the current GUI model-based testing approaches, which target event-based systems, show their limits when applied to test such new advanced GUIs. The work introduced in this paper establishes three contributions: a precise analysis of the reasons of these current limits; a proposition to tackle the identified limits by leveraging the Malai GUI specification language and by proposing the concept of interaction-action-flow graph; feedback from two use cases, an industrial project and an open-source application, where the proposed approach has been applied.
Morton neuroma: MR imaging in prone, supine, and upright weight-bearing body positions.

PURPOSE To assess the effect of prone, supine, and upright weight-bearing body positions on visibility, position, shape, and size of Morton neuroma during magnetic resonance (MR) imaging. MATERIALS AND METHODS Eighteen patients with 20 Morton neuromas underwent MR imaging of the forefoot in prone (plantar flexion of the foot), supine (dorsiflexion of the foot), and upright weight-bearing positions. Visibility (3 = good, 2 = moderate, 1 = poor), position relative to the metatarsal bone, shape, and transverse diameter of Morton neuroma were assessed on transverse T1-weighted MR images. Associations between different body positions and variables of interest were calculated with Wilcoxon signed rank test, chi2 test, and paired Student t test. RESULTS In the prone position, visibility of all 20 Morton neuromas was rated with a score of 3; visibility in the supine and weight-bearing positions was inferior (mean score, 2.4). All 20 (100%) Morton neuromas changed their position relative to the metatarsal bone between prone and supine and between prone and weight-bearing positions. When compared with the prone position, there was a difference in the shape of all 20 Morton neuromas in the weight-bearing position (P <.001). Between prone (mean transverse diameter of Morton neuroma, 8 mm) and supine (mean transverse diameter of Morton neuroma, 6 mm) positions, the transverse diameter of Morton neuroma significantly decreased by 2 mm (P =.03); between prone and weight-bearing positions, the decrease of the mean transverse diameter was also significant (difference, 2 mm; P =.03). CONCLUSION Morton neuroma appears significantly different during MR imaging in prone, supine, or weight-bearing positions. The transverse diameter of Morton neuroma is significantly larger on images obtained in the prone position than it is on images obtained in the supine and upright weight-bearing positions. Visibility of Morton neuroma is best on MR images obtained in the prone position.