Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data

This paper concerns a new method for identifying aberrant signal transduction pathways (STPs) in cancer using case/control gene expression-level datasets, and applying that method and an existing method to an ovarian carcinoma dataset. Both methods identify STPs that are plausibly linked to all cancers based on current knowledge. Thus, the paper is most appropriate for the cancer informatics community. Our hypothesis is that STPs that are altered in tumorous tissue can be identified by applying a new Bayesian network (BN)-based method (causal analysis of STP aberration (CASA)) and an existing method (signaling pathway impact analysis (SPIA)) to the cancer genome atlas (TCGA) gene expression-level datasets. To test this hypothesis, we analyzed 20 cancer-related STPs and 6 randomly chosen STPs using the 591 cases in the TCGA ovarian carcinoma dataset, and the 102 controls in all 5 TCGA cancer datasets. We identified all the genes related to each of the 26 pathways, and developed separate gene expression datasets for each pathway. The results of the two methods were highly correlated. Furthermore, many of the STPs that ranked highest according to both methods are plausibly linked to all cancers based on current knowledge. Finally, CASA ranked the cancer-related STPs over the randomly selected STPs at a significance level below 0.05 (P = 0.047), but SPIA did not (P = 0.083).
A Comparison of the Appraisal Systems and Appraisal-Compensation Interlinks Used by Estonian Public and Private Universities

The performance appraisal and compensation aspects in the public and private universities have growing importance. Even publicly funded universities have to seek for additional resources from private market and thus monitor and develop their performance accordingly. The purpose of this study is to compare performance appraisal as well as compensation policies and systems in Estonian public and private universities in order to determine the possible differences. The results indicate no major differences between two investigated sub-samples. Yet, private universities seem to value student feedback and other market-driven appraisal aspects slightly more than public universities, who value more development interviews.
Ontology-Based Deep Web Data Interface Schemas Integration Method

Ontology-Based Deep Web Interface Schema Integration (OBDIS) uses two levels structure to establish matching relationships and eliminate semantic heterogeneity among concepts and terms of Database schemas on the Web, coupled with the assistance from domain ontology and form ontologies, in which the former is used to describe the domain knowledge and provide the sharing vocabulary base, and the latter is used to describe the semantic information of local data sources. The semantic and structure heterogeneity problem arising during the integration process of Deep Web data interface integration can be properly solved through creating the mappings between form ontologies and domain ontology, and the mappings between form ontology and local data sources. This paper not only focuses on the system implementation and main functions of OBDIS, but also promotes the efficiency and precision of the integration.
Non-uniform image compression using biologically motivated saliency map model

We propose a new non-uniform image compression using a biologically motivated selective attention model for effective storage and transmission of natural images. One of the important issues in non-uniform image compression is to decide on a meaningful region according to a purpose. The proposed saliency map model can generate a scan path that contains plausible interesting objects in a natural scene. The proposed non-uniform image compression method uses the saliency map results, which differently compress the selected interesting areas and the uninteresting areas by a lossless coding algorithm and lossy compression, respectively. Experimental results show that the proposed non-uniform compression method gives better peak signal to noise ratio (PSNR) but slightly decreases the compression ratio.
Justice or Just between Us? Empirical Evidence of the Trade-off between Procedural and Interactional Justice in Workplace Dispute Resolution

In this article, the authors examine the relationship between an employer's implementation of a typical dispute resolution system (DRS) and organizational justice, perceived compliance with the law, and organizational commitment. They draw on unique data from a single, geographically expansive, U.S. firm with more than 100,000 employees in more than 1,000 locations. Holding all time-constant, location-level variables in place, they find that the introduction of a DRS is associated with elevated perceptions of interactional justice but diminished perceptions of procedural justice. They also find no discernible effect on organizational commitment, but a significant boost to perceived legal compliance by the company. The authors draw on these findings to offer a “differential-effects” model for conceptualizing the relationship among organizational justice, perceived legal compliance, and the implementation of dispute resolution mechanisms.
UNFOLDING | CLUSTERS : A MUSIC AND VISUAL MEDIA MODEL OF ALS PATHOPHYSIOLOGY

Unfolding | Clusters is a music and visual media installation modeled from published scientific data related to the pathophysiology of amyotrophic lateral sclerosis (ALS). The work aims to create an engaging multimodal experience useful for raising awareness in the greater public about the disease and its scientific process. This paper describes the motivation behind the adoption of a musification approach and the musical criteria applied to the data mapping process. Details regarding the mapping structure are illustrated in relation to the different phases of the progress of the disease. The results are then discussed, noting that adopting a musification approach not only helped in obtaining a more engaging audience experience but also in providing expressive solutions that would be useful for modeling other complex biomedical data and processes.
WebSurface: an interface for co-located collaborative information gathering

Co-located collaborative Web browsing is a relatively common task and yet is poorly supported by conventional tools. Prior research in this area has focused on adapting conventional browsing interfaces to add collaboration support. We propose an alternative approach, drawing on ideas from tabletop interfaces. We present WebSurface, a novel tabletop interface for collaborative Web browsing. WebSurface explores two design challenges of this approach: providing sufficient resolution for legible text; and navigating through information. We report our early experiences with an exploratory user study, in which pairs of collaborators gathered information using WebSurface. The findings suggest that a tabletop approach for collaborative Web browsing can help address limitations of conventional tools, and presents beneficial affordances for information layout.
Selective and transparent acceleration of OpenFlow switches

We present the design and implementation of a transparent and selective offload architecture, accelerating a mature software OpenFlow implementation (Open vSwitch) using a programmable network processor. Our design combines the flexibility offered by software OpenFlow implementations with the performance of specialised switch hardware. It is targeted at accelerating the emerging class of edge/gateway switches which are becoming increasingly important in some SDN designs. Our prototype implementation offers at least a 8-10x performance improvement over software only Open vSwitch for benchmarks where the majority of the packets can be handled by the network processor.
Detection Thresholds and Bias Correction in Polarized Intensity

Abstract Detection thresholds in polarized intensity and polarization bias correction are investigated for surveys where the polarization information is obtained from rotation measure (RM) synthesis. Considering unresolved sources with a single RM, a detection threshold of 8 σQU applied to the Faraday spectrum will retrieve the RM with a false detection rate less than 10−4, but polarized intensity is more strongly biased than Ricean statistics suggest. For a detection threshold of 5 σQU, the false detection rate increases to ∼4%, depending also on λ2 coverage and the extent of the Faraday spectrum. Non-Gaussian noise in Stokes Q and U due to imperfect imaging and calibration can be represented by a distribution that is the sum of a Gaussian and an exponential. The non-Gaussian wings of the noise distribution increase the false detection rate in polarized intensity by orders of magnitude. Monte Carlo simulations assuming non-Gaussian noise in Q and U give false detection rates at 8 σQU similar to Ricean false detection rates at 4.9 σQU.
Synthesis and Characterization of Corona-resistant Polyimide/AluminaHybrid Films

A new class of polyimide hybrid films with various amounts of alumina has been synthesized by the sol-gel reaction and characterized. The hybrid films were obtained by the hydrolysis and polycondensation of heteropropyl-alumina in polyamic acid (PAA) solution of N,N'-dimethylacetamide (DMAc), followed by heating to 350degC. The chemical structure, surface morphology of the composites films were characterized by atomic forced microscope (AFM) and Fourier transform infrared spectroscope (FTIR). The thermal stability of the composites films was tested on Perkin-Elmer TGA7. With nano scale inorganic oxides adding, thermal stability of hybrid film was increased. The PI hybrid films showed improved electrical aging performance as compared with pure PI film
Marc-applying multiagent systems to service robot control

The development of mobile robots, capable of interacting with other agents in real-world environments, provides researchers in both Science and Engineering with a large body of theoretical and implementation problems that need to be overcome. One of these is the question of how to construct a complete robot control architecture, which allows the robot to perform different tasks, while processing numerous sources of information from the outside world. This topic of robot control architectures has been widely studied for a number of years. This thesis proposes the adoption of the Multi-Agent System (MAS) metaphor as the main modelling and design abstraction in the construction of software systems for service robot control. Based on this proposal, a MAS Architecture for Robot Control (MARC) was developed. This architecture directly aims to bridge the limitations of robustness, openness, and scalability currently seen in many service robot applications. MARC was realised via an implemented framework, which provides for the creation of robot control agents in a complete agent community. With an agent infrastructure in place, a scenario aimed at demonstrating the usefulness of MARC was conceived, and coded for with the creation of appropriate agents. Although the capabilities of the robot used were limited, it was sufficient to demonstrate how the MARC architecture gave the robot an amount of intrinsic social and task performance intelligence.
When the struggle against dejection becomes a part of everyday life: a qualitative study of coping strategies in older abused people

Background Abuse of older people is a serious issue and is associated with an increased risk of morbidity and mortality, and professionals will encounter elderly victims of abuse in all areas of the health care system. An important health determinant is behavioral factors, including coping style, which will impact on how older people manage stress and maintain control in their lives, and thereby protect themselves from abuse. The aim of this study was to explore the coping strategies elderly people abused by their offspring used to manage everyday life. Methods A qualitative approach was used and 14 elderly victims of abuse were interviewed. The interviews were recorded, transcribed, and subjected to qualitative content analysis. Results Five main coping strategies were identified. The main strategy was linked to the role of parent. Another prominent strategy was attitude towards being victimized. Further strategies were associated with hope for a better relationship with offspring in the future, while others felt that they had done the best they could, or that their offspring were no longer their responsibility. The results are discussed in light of theoretical perspectives related to coping and resilience. Conclusion Abuse of older people by their offspring imposes severe stress on victims and challenges the values and beliefs about the caring nature of families. The findings of this study indicate that victims of abuse use a wide range of coping techniques to manage everyday life, and that some strategies help them to maintain their self-respect in their role as parents and find some sort of resilience.
Therapy-Related Myeloid Neoplasm in Non-Hodgkin Lymphoma Survivors

Relatively little data on secondary cancers is available regarding patients treated for non-Hodgkin lymphoma (NHL), compared with those treated for Hodgkin lymphoma. Evolving treatment regimens have improved survival outcomes for NHL patients. As a result of this improvement, secondary malignancies are becoming an important issue in NHL survivors. This review aims to report data on this topic previously published by our group, adding unpublished results from the Modena Cancer Registry (MCR). We recently performed four studies about secondary neoplasms in NHL survivors: two studies analysing the risk of secondary neoplasms in patients treated for indolent and aggressive NHL; a meta-analysis of 23 studies investigating the risk of secondary malignant neoplasm (SMN) after NHL treatment; and a still-unpublished study evaluating the incidence of therapy-related myeloid neoplasm (t-MN) in patients treated for NHL (from the MCR database). The first two studies analysed 563 patients with indolent NHL and 1280 patients with diffuse large B-cell lymphoma (DLBCL) enrolled in the Gruppo Italiano Studio Linfomi (GISL) trials. Results showed that the cumulative incidence of secondary tumours was 10.5% at 12 years for indolent NHL and 8.2% at 15 years for DLBCL. Results of the meta-analysis indicated that NHL patients experienced a 1.88-fold increased risk for SMN compared with the general population; the standardized incidence risk (SIR) for secondary acute myeloid leukaemia (AML) was 11.07. Based on data from the MCR from 2000 through 2008, we found that the SIR was 1.63 for developing a secondary malignancy after NHL, and 1.99 for developing secondary haematological malignancies. Regarding myelodysplastic syndrome and/or AML incidence, nine NHL patients developed t-MN with a higher risk than expected (SIR 8.8, 95% CI: 4.0–16.6). In conclusion, patients treated for NHL are at increased risk of developing SMN. Regarding t-MN, data from the meta-analysis and the MCR demonstrate an excessive risk of developing AML (SIR 11.07 and 5.7, respectively) compared with solid SMN after treatment for NHL. Thus long-term monitoring should be considered for NHL survivors.
Adaptive divergence in the bovine genome 1 2

21 Cattle diverged during the Pleistocene into two subspecies, one in temperate and one in 22 tropical environments. Here we have used next generation sequencing of the indicine 23 subspecies of cattle and compared it to the taurine subspecies. Although 23.8 million 24 single nucleotide polymorphisms (SNP) were found, the number of fixed amino acid 25 substitutions between the taurine and indicine subspecies was low and consistent with the 26 Haldane predictions for adaptive selection rather than with Neutral Theory. We noted 33 27 regions of enhanced divergence of nonsynonymous SNP between the subspecies, which 28 included an increased rate of deleterious variants. Signals of positive selection were found 29 for genes associated with immunity, including the Bovine Major Histocompatibility 30 Complex, which also showed an increased rate of deleterious amino acid variants. The 31 genes important in sensing the environment, especially the olfactory system, showed a 32 network wide signal of positive selection. 33 34 2 Introduction 38 39 Cattle are a rare example of adaptive divergence into temperate and tropical environments 40 in which the subspecies show hybrid vigour on being crossed. Genome wide analyses of 41 evolution in cattle have focussed on the expansion of gene families or on evidence of 42 selection signatures using population genetic evidence based on genotype or haplotype 43 frequencies, mainly in the taurine subspecies. The initial sequencing of cattle found gene 44 families that were expanded in cattle lineages, identifying genes associated with the 45 immune system in particular that were increased in number compared to other mammalian 46 species (Elsik et al. 2009). In addition, analyses of genotype or haplotype frequencies have 47 been used to identify signatures of selection and in some cases have linked these to the 48 known locations of quantitative trait loci (Barendse et al. Analyses of nonsynonymous and synonymous DNA variants 50 have been performed for a limited number of amplicons for genes expected to be involved 51 in animal production (MacEachern et al. 2009b). 52 53 The description of the genomic variation and structure of the indicus subspecies lags 54 behind that of the taurus subspecies of cattle. The taurine subspecies is of temperate origin 55 while the indicine subspecies is of tropical origin. Individuals of several of the breeds of 56 taurine cattle, 61 sequencing studies have documented variation, not only at the single nucleotide 62 polymorphism (SNP) level, but also structural variation …
Robots In The Theatre And The Media

Robots frequently feature in the movies and occasionally in the theatre. Their presence in the media is of major importance on how users interact with them. Due to the scarcity of robots in everyday life, most of the users’ expectations and interpretations about robots stem from the media. This paper provides a framework of robots in the media that will help robot interaction designers to assess preconceptions about robots.
High Quality Force Field Approximation in Linear Time and its Application to Skeletonization

Force fields of 3d objects are used for different purposes in computer graphics as skeletonization and collision detection. In this paper we present a novel method to approximate the force field of a discrete 3d object in linear time. Similar to the distance transformation we define a rule that describe how the forces associated with boundary points are propagated into the interior of the object. The result of this propagation depends on the order in which the points of the object are processed. Therefore we analyze how to obtain an order-invariant approximation formula. For a chosen iteration order (i, j, k) the set of boundary points that influence the force of a particular point p of the object can be described by a spatial region Rijk. The geometries of these regions are characterized both for the Cartesian and the body-centered cubic grid (bcc grid). We show that in the case of the bcc grid these regions can be combined in such a way that E3 is uniformly covered which basically means that each boundary point is contained in the same number of regions. Based on the covering an approximation formula for the force field is proposed that has linear complexity and gives good results for standard objects. We also show that such a uniform covering can not be built from the regions of influence of the Cartesian grid. With our method it becomes possible to use features of the force field for a fast and topology preserving skeletonization. We use a thinning strategy on the bcc grid to compute the skeleton and ensure that critical points of the force field are not removed. This leads to improved skeletons with respect to the properties of centeredness and rotational invariance.
The Open University ’ s repository of research publications and other research outputs Using discovered , polyphonic patterns to filter computer-generated music Conference Item

A metric for evaluating the creativity of a music-generating system is presented, the objective being to generate mazurka-style music that inherits salient patterns from an original excerpt by Frédéric Chopin. The metric acts as a filter within our overall system, causing rejection of generated passages that do not inherit salient patterns, until a generated passage survives. Over fifty iterations, the mean number of generations required until survival was 12.7, with standard deviation 13.2. In the interests of clarity and replicability, the system is described with reference to specific excerpts of music. Four concepts—Markov modelling for generation, pattern discovery, pattern quantification, and statistical testing—are presented quite distinctly, so that the reader might adopt (or ignore) each concept as they wish. 1 Aim and Motivation A stylistic composition (or pastiche) is a work similar in style to that of another composer or period. Examples exist in ‘classical’ music (Sergey Prokofiev’s Symphony No. 1 is in the style of Joseph Haydn) as well as in music for film and television, and in educational establishments, where stylistic composition is taught ‘as a means of furthering students’ historical and analytical understanding’ (Cochrane 2009). If a computational system produces successful stylistic compositions (‘successful’ in the sense of the ‘indistinguishability test’ of Pearce and Wiggins (2001) for instance), then it is capable of a task that, in the human sphere, is labelled creative. The creativity metric presented below is intended as preliminary to (not a replacement of) an ‘indistinguishability test’. This paper relates ongoing research on a computational system with the aim of modelling a musical style. The motivation for the system is as follows. Cope (2005, pp. 87-95) describes a data-driven model that can be used to generate passages of music in the style of Johann Sebastian Bach’s chorale harmonisations. His model can be cast as a first-order Markov chain and we have replicated this aspect of his model, with some modifications (see Sect. 2 for details). Our method is applied to a database consisting of Frédéric Chopin’s mazurkas. This choice 1 See Pearce et al. (2002) on how computational modelling of musical styles constitutes one motivation for automating the compositional process.
Local-SURF based 3D scene reconstruction for mobile robot

Traditional SURF based 3D reconstruction methods need to extract features on the whole image. Although this technique can provide rich and accurate environment information, however, it is too time consuming and not practical. To solve that problem, a local SURF based 3D reconstruction algorithm for mobile robot is proposed, which includes three main steps: first, the posture variations were captured from posture sensor and milemeter, and then the initial transition matrix was established; second, when finishing extracting features of the previous frame, searching areas were computed from the initial transition matrix and search radius; last, final transition matrix was computed according to the matching points. Experiments showed that the proposed algorithm did improve the speed of scene reconstruction while preserving precision, and moreover, our approach also can correct the posture variation of robot according to the matching results.