Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Protein-Protein Docking Algorithm Using Pre-Identified Binding Site Patches

Interaction of proteins is essential for many biological processes in a cell. In recent years protein interaction networks have been drawing much attention, because of the availability of a large scale of experimental data of protein-protein interactions. The tertiary structure of a protein complex provides an essential information of its function, thus toward this end, several protein docking algorithms have been proposed [1]. Examples include algorithms based on the Fast Fourier Transform (FFT) [2] and the geometric hashing technique [3]. Recent algorithms can make good predictions for a pairwise rigid body docking, but their excessive computational time is almost prohibitive for a large scale use, e.g. in a genome-scale. Here, we describe our system for a fast protein docking prediction. First, query proteins are voxelized, which facilitates the comparison of local surface shapes of proteins. Possible binding sites are identifying as cavity and protrusion regions in protein surface using the novel voxel visibility method. The docking algorithm is based on the geometric hashing.
Working notes of the KI'95 Workshop : KRDB-95 - Reasoning about structured objects : knowledge representation meets databases ; Bielefeld, Germany, Sept. 11-12, 1995

Two different aspects of data management are addressed by description logics (DL) and databases (DB): the semantic organization of data and powerful reasoning services (by DL) and their efficient management and access (by DB). It is recently emerging that experiences from both DL and DB should profitably cross-fertilize each other, and a great interest is rising about this topic. In the present paper our technique, that allows uniform access by means of a DL-based query language to information distributed over knowledge bases and databases, is briefty reviewed. Our extended paradigm integrates the separately existing retrieving functions of description logics management systems (DLMS) and of database management systems (DBMS) in order to allow, via a query language grounded on a DL-based schema knowledge, uniformly formulating and ans wering queries, so that uniform retrieval from mixed knowledge/data bases is possible. In particular, some new developments extending those presented in [Bresciani, 1994] are introduced. By means of them the mapping between DL concepts and DB views is not more limited to primitive concepts, but also to some non-primitively defined ones.
Entity Disambiguation using Link based Relations extracted from Wikipedia

We present an approach for the disambiguation of textual mentions of ambiguous names: disambiguation means here the identification of the true entity denoted by a name phrase appearing in a query context through its assignment to the corresponding Wikipedia article. If this article does not exist, we assign this query to a default entity. Ambiguity of names is a major problem in information retrieval and causes uncertainty in the assignment of name phrases to existing knowledge base entries. We propose a kernel classifier to approach this problem and compare two Wikipedia structures to construct a rich feature space. The first approach relies on Wikipedia categories, the second on relations constructed from Wikipedia’s hyper link structure. We evaluate both approaches on the German version of Wikipedia and show that both outperform a baseline approach using simple cosine similarity.
A novel potential field method for obstacle avoidance and path planning of mobile robot

This paper presents a novel artificial potential field method for obstacle avoidance and path planning of mobile robots. By analyzing the shortcoming of the artificial potential field methods for robot path planning, we propose an obstacle avoidance method based on gravity chain. Suppose that there is a rubber band which connects with the beginning and the ending in the obstacle potential field space. As the rubber band will be the role of potential field power, we can build a model to simulate the shape of the rubber band. Then this method will generate a steer angle tangent to the rubber band instead of the angle of artificial potential field. By putting effective obstacle avoidance information into potential field through gravity chain, we solve the problems that the artificial potential field method often converges to local minima, as well as it hardly reach the ending and oscillatory movement. The Simulation results show that the method proposed is correct and effective.
Improving Community Relations: How Police Strategies to Improve Accountability for Social Equity Affect Citizen Perceptions

Social equity research increasingly focuses on how accountability for social equity is achieved, or how public administrators improve the access, outcomes, processes, and quality of public services. This is particularly important to examine in police departments, which are more frequently using strategies such as community policing programs (CPPs), social equity performance measurement (SEPM), and ethics training to yield better community relations. This article explores how these strategies affect citizen perceptions through testing three propositions related to CPPs, SEPM, and ethics training. Findings are reported from interviews with 72 citizens, local-level elected leaders, and police officers from 12 purposively selected locales in the United States. Findings reveal that when CPPs foster more citizen involvement as decision-makers, SEPM is used to shape practice, and more ethics training is required, citizen perceptions of how socially equitable departments are increase. Further, as political leaders and departments more actively incorporate community groups, perceptions of social equity are more positive. These findings are discussed in terms of what they reveal about accountability for social equity.
Discourse Markers and (Dis)Fluency: Forms and Functions Across Languages and Registers

Spoken language is characterized by the occurrence of linguistic devices such as discourse markers (e.g. so, well, you know, I mean ) and other so-called “disfluent” phenomena, which reflect the temporal nature of the cognitive mechanisms underlying speech production and comprehension. The purpose of this book is to distinguish between strategic vs. symptomatic uses of these markers on the basis of their combination, function and distribution across several registers in English and French. Through deep quantitative and qualitative analyses of manually annotated features in the new DisFrEn corpus, this usage-based study provides (i) an exhaustive portrait of discourse markers in English and French and (ii) a scale of (dis)fluency against which different configurations of discourse markers can be diagnosed as rather fluent or disfluent. By bringing together discourse markers and (dis)fluency under one coherent framework, this book is a unique contribution to corpus-based pragmatics, discourse analysis and crosslinguistic fluency research.
Key Exchange Protocol over Insecure Channel

— Key management represents a major and the most sensitive part of cryptographic systems. It includes key generation, key distribution, key storage, and key deletion. It is also considered the hardest part of cryptography. Designing secure cryptographic algorithms is hard, and keeping the keys secret is much harder. Cryptanalysts usually attack both symmetric and public key cryptosystems through their key management. We introduce a protocol to exchange cipher keys over insecure communication channel. This protocol is based on public key cryptosystem, especially elliptic curve cryptosystem. Meanwhile, it tests the cipher keys and selects only the good keys and rejects the weak one.
‘Buff boys’ with brooms: shifting representations of masculinity in Canadian men’s curling

ABSTRACT This paper explores a shift in masculine sporting identities associated with the sport of curling in Canada. We argue that as curling has become increasingly professionalized, there has been a corresponding shift to representations of male curlers that valourize youth, strength and aggression, in contrast to a previous emphasis on maturity and sportsmanship. After a review of the history and context of curling’s popularity as a sport in Canada, we recount these representational shifts, drawing on official documents of curling associations and media coverage of the sport. At the same time, we suggest that extending conventional forms of sporting masculinity to curling sits uneasily beside new initiatives to encourage lifelong participation in sport. We draw on critical masculinity studies and sport studies to argue that age needs to be taken into account when mapping the diversity of masculinities. We further argue that sport is an important context for understanding complex intersections of age and gender, especially as physical activity is increasingly posited as essential to ‘successful aging. ’ We suggest that curling provides an instructive and under-studied example of how these issues conjoin in constructing aging male embodiment, and suggest some directions for further study.
Research on the WeChat Information Transmission Topology Based on Social Network Analysis

With the rapid development of mobile internet technology, Social Media has become an important way for us to communicate with others. Meanwhile, Social Media is regarded as the most popular information exchange and knowl- edge-sharing platformS by more and more people, making its network structure and information transmission topology at- tracted a wide attention. WeChat is one of the most commonly used Social Media in China, which was developed by Tencent in 2011. Due to the number of WeChat customer is very huge, traditional analytical methods become not applica- ble. In this paper, we try to use Social Network Analysis (SNA), which being capable of handling huge data, to reveal the relationship networks of WeChat. On this basis, we choose a WeChat user randomly, and listed part of groups that he par- ticipated in. Through analyzing its network architectures and data indicators, we found out three main information trans- mission topology of WeChat.
Modelling protein–protein interaction networks via a stickiness index

What type of connectivity structure are we seeing in protein–protein interaction networks? A number of random graph models have been mooted. After fitting model parameters to real data, the models can be judged by their success in reproducing key network properties. Here, we propose a very simple random graph model that inserts a connection according to the degree, or ‘stickiness’, of the two proteins involved. This model can be regarded as a testable distillation of more sophisticated versions that attempt to account for the presence of interaction surfaces or binding domains. By computing a range of network similarity measures, including relative graphlet frequency distance, we find that our model outperforms other random graph classes. In particular, we show that given the underlying degree information, fitting a stickiness model produces better results than simply choosing a degree-matching graph uniformly at random. Therefore, the results lend support to the basic modelling methodology.
Verbal Aggression in Romantic Relationships: The Influence of Family History, Destructive Beliefs About Conflict, and Conflict Goals

This article aimed to achieve two complimentary goals. First, this study examined verbal aggression in romantic relationships as a function of exposure to family verbal aggression in childhood and beliefs about the destructive nature of conflict. Second, this study considered the influence of conflict goals on the use of verbal aggression in romantic relationships. As predicted, history of family verbal aggression was negatively associated with destructive beliefs about conflict, and destructive beliefs about conflict partially mediated the association between history of family verbal aggression and verbal aggression in current romantic relationships. In addition, destructive beliefs about conflict were negatively associated with verbal aggression in current romantic relationships at high levels of importance of revenge-motivated goals; destructive beliefs about conflict were not significantly associated with verbal aggression in current romantic relationships at moderate or low levels of revenge-motivated goals.
A Study of Driver Behavior Under Potential Threats in Vehicle Traffic

Although, in recent years, significant developments have been made in road safety, traffic statistics indicate that we still need significant improvements in the field. Since traffic accidents usually reflect human factors, in this paper, we focus on clarifying the understanding of driver behaviors under hazardous scenarios. Brake pedal signals or driver speech, or both, are utilized to detect incidents from a real-world driving database of 373 drivers. Results are then analyzed to address the individuality in driver behaviors, the multimodality of driver reactions, and the detection of potentially dangerous locations. All of the existing 25 potentially hazardous scenes in the database are hand labeled and categorized. Based on the joint histograms of behavioral signals and their time derivatives, a detection feature is proposed and satisfactorily applied to the indication of anomalies in driving behavior. Seventeen scenes, where a reaction utilizing the brake pedal was observed, are detected with a true positive (TP) rate of 100% and a false positive (FP) rate of 4.1%. We demonstrate the relevance of considering behavior individuality. During 11 scenes, the drivers verbally reacted. Scenes that included high-energy words are adequately detected by the speech-based method, which achieved a TP rate of 54% for an FP rate of 6.4%. The integration of different behavior modalities satisfactorily boosts the detection of the most subjectively hazardous situations, which suggests the importance of considering multimodal reactions. Finally, a strong relationship is presented between locations where potentially hazardous situations occurred and areas of frequent strong braking.
Primary student-teachers' perceptions of the role of digital literacy in their lives

In considering the potential for new student-teachers to draw from personal experience to arrive at transformative uses of technology in classrooms, this study investigates the nature of student-teachers’ ‘digital insidership’. It explores seven primary studentteachers’ perceptions of the role of digital literacy in their lives both within and beyond primary classrooms. Adopting a methodology influenced by phenomenology, it draws primarily from interviews, exploring participants’ experience of digital texts as social practice whilst adopting a reflexive approach to interpretation. The study draws on Gee’s concepts of ‘Big D’ Discourses and ‘borderland discourses’ to focus on how student-teachers’ perceptions of their digital practices interacted with different identity positions as they moved between personal and professional discourses. Exploring the varied feelings and levels of empowerment associated with digital practices, the study argues that these student-teachers’ sense of their own digital insidership was uneven and highly contingent on context. It describes both the new kinds of possibilities associated with their digital practices and the tensions they experienced when entering environments patterned by unfamiliar discourses. Highlighting what is termed ‘borderland activity’, it explores how personal and professional practices merged or contrasted as student-teachers found different ways of crossing, avoiding or spanning the borderlands between discourses. In particular, student-teachers’ stories of the accommodation of technology-use within teaching identities suggested that, whilst they may see technology-use as an important part of enacting a teacher identity, opportunities for transformation were limited as technology seemed chiefly to be accommodated, albeit in different ways, within discourses of standardisation and teacher control. Whilst some student-teachers may therefore see new opportunities for using technologies in innovative ways, they may receive most affirmation when using them in ways that are aligned to existing discourses. The study concludes by suggesting a series of strategies through which policy makers, researchers and initial teacher educators may investigate further student-teachers’ experiences of digital practices and,through promoting critical reflection on the discourses which frame technology use,encourage student-teachers to engage with technology in innovative and possibly transformative ways.
Dynamic Weaving for Building Reconfigurable Software Systems

Aspect-oriented technology is a programming paradigm that provides the user with the ability to modularize the representation of crosscutting concerns in order to maximize reusability and ensure flexibility of the software system. In this position paper we present the dynamic Weaver Framework (DWF), which is an aspect-oriented framework that supports the dynamic attachment and detachment of aspects to components at run-time, as well as the capability to add and remove aspects and pointcuts during runtime. This capability is the prime factor that enables us to support reconfigurability of the software system. The need to adapt to environmental changes and cope gracefully with the challenges that may have an impact on performance degradation, safety and liveness properties of the running system requires recongfigurability of both the functional and aspectual properties of the system software.
A Watermarking-Based Medical Image Integrity Control System and an Image Moment Signature for Tampering Characterization

In this paper, we present a medical image integrity verification system to detect and approximate local malevolent image alterations (e.g., removal or addition of lesions) as well as identifying the nature of a global processing an image may have undergone (e.g., lossy compression, filtering, etc.). The proposed integrity analysis process is based on nonsignificant region watermarking with signatures extracted from different pixel blocks of interest, which are compared with the recomputed ones at the verification stage. A set of three signatures is proposed. The first two devoted to detection and modification location are cryptographic hashes and checksums, while the last one is issued from the image moment theory. In this paper, we first show how geometric moments can be used to approximate any local modification by its nearest generalized 2-D Gaussian. We then demonstrate how ratios between original and recomputed geometric moments can be used as image features in a classifier-based strategy in order to determine the nature of a global image processing. Experimental results considering both local and global modifications in MRI and retina images illustrate the overall performances of our approach. With a pixel block signature of about 200 bit long, it is possible to detect, to roughly localize, and to get an idea about the image tamper.
Fast Spectral Clustering with Landmark-Based Subspace Iteration

Spectral clustering has received a great deal of attention due to its flexibility on various type of geometry and its high-quality clustering results. However, with the rapid increase of data size, spectral clustering quickly becomes unfeasible because of its cubical complexity. Various sampling methods with at best quadratic complexity in time and space have been purposed. However, they are not able to jump out of the box for their dependency on eigen-decomposition. In this paper, we propose a novel framework called Landmark-based Subspace Iteration Spectral Clustering (LSISC), which scales linearly on both time and space with data size. Specifically, we use the similarity between points and landmarks as the new feature of points, and exploit subspace iteration to perform spectral clustering in near-linear time, while no pair-wise information is dropped. We show that the running time of LSISC is not sensitive to the number of landmarks, which allows more landmarks to be chosen for better accuracy. Experimental results show that our approach gives better clustering results in much less time than other state-of-the-art spectral methods.
Title Assessment of the dysexecutive syndrome in schizophrenia

Background. Cognitive neuropsychological theories hypothesize a role for frontal lobe executive deficits in the aetiology of schizophrenic symptoms. The study examined the performance of a schizophrenic group on the Behavioural Assessment of the Dysexecutive Syndrome (BADS; Wilson et al. 1996), a test battery which assesses the ‘everyday’ difficulties associated with the dysexecutive syndrome. Performance of the schizophrenics was contrasted with that of brain injured and healthy volunteer groups. Methods. Matched groups of 31 schizophrenic patients, 35 patients with brain injuries and 26 healthy volunteers were administered the BADS. Patients were also given tests of general intelligence and memory. Patients and their relatives}carers also completed a questionnaire rating day-to-day failures of executive functioning. Results. Schizophrenic and brain-injured patients showed impairment on the BADS, compared to healthy controls. There were no significant differences between the two patient groups. Significant impairment was found in a subgroup of 16 schizophrenics who showed otherwise intact general intellectual functioning, suggesting the existence of a specific executive deficit. Among the schizophrenic patient group there was evidence of a dissociation between executive and memory impairments. A significant correlation existed between performance on the BADS and relatives ratings of executive problems for the brain injured group, but not for the schizophrenic group. Conclusions. The BADS is a useful tool for identifying executive deficits in people with a diagnosis of schizophrenia, especially thosewho are otherwise generally intellectually intact. This is particularly important in the context of rehabilitation and community transition programmes.
Creation of fundamental string in m(atrix) theory

The potential between two D4-branes at angles with partially unbroken supersymmetry is computed, and is used to discuss the creation of a fundamental string when two such D4-branes cross each other in M(atrix) theory. The effective Lagrangian is shown to be anomalous at 1-loop approximation, but it can be modified by bare Chern-Simons terms to preserve the invariance under the large gauge transformation. The resulting effective potential agrees with that obtained from the string calculations. The result shows that a fundamental string is created in order to cancel the repulsive force between two D4-branes at proper angles.
A Comparative Study between Level Set and Watershed Image Segmentation for Tracking Stem Cells in Time-Lapse Microscopy

This paper evaluates the performance of two methods, level set active contours and watershed region growing, applied to live cell image segmentation. These methods suffer from opposite problems. As the level set method tends to merge clustered cells, the watershed method often results in oversegmentation. These problems can be reduced by adding an image pre-processing step, consisting of multi-scale Laplacianof-Gaussian filtering, enabling an accurate cell detection even in low-contrast images. Applying this new method to a difficult data set, the result was 76% and 66% correctly tracked cells for the level set and watershed methods, respectively. Given a reasonable initial level set, the computation time is about the same for both methods.