Miracle-dz/UniFAR-FTUs huggingface dataset:
Building an Online Computing Service over Volunteer Grid Resources

Volunteer computing grids have traditionally been used for massively parallel workloads, such as processing data from large scientific experiments. We argue that the domain of volunteer grids can be extended well beyond this specific niche, by enhancing them with built-in mechanisms for integration with with standard clusters, grids and clouds, to compensate for unexpected fluctuations in resource availability and quality of service. The resulting capabilities for on-demand dynamic expansion of the resource pool, together with sophisticated scheduling mechanisms will turn volunteer grids into a powerful execution platform for on-line interactive computing services. We will show our experience with the GridBoT system, which implements these ideas. GridBoT is part of a production high performance online service for genetic linkage analysis, called Super link-online. The system enables anyone with the Internet access to submit genetic data, and easily and quickly analyze it as if using a supercomputer. The analyses are automatically parallelized and executed via GridBoT on over 45,000 non-dedicated machines from the Superlink@Technion volunteer grid, as well as on 9 other grids and clouds, including the Aamazon EC2. Since 2009 the system has served more than 300 geneticists from leading research institutions worldwide, and executed over 6500 different real analysis runs, with about 10 million tasks consumed over 420 CPU years.
Towards Purpose-Driven Virtual Machines

Virtual machines (VMs) are often generic though they are meant to serve a specific purpose. The redundancy of generic VMs may incur costs in security (due to bigger attack surface and a larger trusted com- puting base) and performance (due to extra VM image size as well as overheads in CPU and memory). We are working on techniques to build minimal, application-specific and secure virtual machines from declar- ative descriptions. An application running in a VM has dependencies on other applications, libraries, kernel features and (virtual) hardware. We model such a dependency as a graph. The VM is treated as an op- timized system built specifically to satisfy this dependency out of a set of interdependent components such as packages and kernels from OS distributions. Such distributions and installations based on them are inherently complex networks that could benefit from a formal, rigorous treatment in order to perform security and performance optimization. In this paper, we describe our motivation and vision for this project, outline our approach, briefly report on current status, discuss challenges and research problems that we intend to work on in the future.
Framework for Outsourcing : Based on Theoretical Review and Empirical Findings from Danish Heavy Industry

This paper examines the process of outsourcing manufacturing to cost-efficient and innovative suppliers in support of internal core competencies. A framework that links the phases of the entire outsourcing process to strategic planning is presented. The framework includes a logical sequence of key activities with built-in performance measures and expected output for each of the phases. In addition, it indicates the critical workflow interfaces between the production system and relevant support functions to determine the cross-functional interdependencies. Collectively, the framework aims to facilitate start-up, operations and maintenance of the buyersupplier relationship. The research methodology is rooted in an in-depth theory study and a longitudinal case study of the Danish company Aalborg Industries, which operates in the heavy industry. Thereby, the research pursues both academic and industrial application.
Circulating cytokines and cytokine receptors in infliximab treatment failure due to TNF-independent Crohn disease

receptors in Abstract: The inﬂammatory response at inﬂiximab (IFX) treatment failure due to tumor necrosisfactor (TNF)- a -independent Crohn disease activity is unknown. This is an exploratory, hypothesis-generating study based on samples collected in a clinical trial among patients failing conventional IFX dosages and treated with an intensiﬁed IFX regimen for 12 weeks. Patients with clinical response at week 12, as deﬁned by a reduction of Crohn disease activity index by (cid:2) 70, were considered to suffer from nonimmune pharmacokinetic (PK) treatment failure (n ¼ 18), and non- responders had a presumed pharmacodynamic (PD) failure due to non-TNF-driven disease (n ¼ 8). Patients failing IFX due to functional anti- IFX antibodies (n ¼ 2) were excluded. The study population also comprised a group of 12 patients in long-term remission on IFX. A functional cell-based reporter gene assay was applied to measure IFX and anti-IFX antibodies. Circulating cytokines and cytokine receptors were assessed by enzyme-linked immunosorbent assay: granulocyte-macrophage colony-stimulating factor, interferon- g , interleukin (IL)- 1 a , IL-1 b , IL-1Ra, IL-6, IL-10, IL-12p70, soluble TNF receptor (sTNF-R) 1, sTNF-R2, IL-17A, and monocyte chemotactic protein 1. The IFX levels were similar between patients with IFX failure caused by nonimmune PK or PD at treatment failure (median 1.4 vs 2.4 m g/mL; P ¼ 0.52), during treatment intensiﬁcation (8.1 vs 5.6; P ¼ 0.85), and after 12 weeks (8.8 vs 7.7; P ¼ 0.93), congruent with nonresponders failing IFX due to predominantly TNF- a -independent signaling pathways in their disease. Cytokine and cytokine receptor levels were comparable between patients with nonimmune PK failure and PD failure at time of manifestation of IFX failure, but with higher IL-6 and sTNF-R2 levels among IFX treatment failures as compared with patients in remission (IL-6 median 3.6 vs < 3.1pg/mL; P ¼ 0.03; sTNF-R2 3207 vs 2547pg/mL; P ¼ 0.01). IL-6 and sTNF-R2 were lower after12weeksinnonimmunePKfailuresthaninPDfailures( < 3.1vs4.0; P ¼ 0.02; 3209 vs 4740; P ¼ 0.04, respectively), and were measured at levelscomparablewith patientsinremission.Further,trendsofdecreased IL-6 and sTNF-R2 levels among nonimmune PK failures during IFX intensiﬁcation ( P < 0.05 and P ¼ 0.12) were observed. These observations indicate that IL-6 and sTNF-R2 are of potential relevance in driving the inﬂammatory response in IFX refractory Crohn disease caused by TNF- a -independent disease activity. ( 95(16):e3417) dosing in weeks, ra = receptor antagonist, RGA = reporter gene assay, SES-CD = Simple Endoscopic Score for Crohn disease, sTNF-R = soluble TNF receptor, TNF = tumor necrosis factor.
Creating a multi-purpose first person shooter bot with reinforcement learning

Reinforcement learning is well suited to first person shooter bot artificial intelligence as it has the potential to create diverse behaviors without the need to implicitly code them. This paper compares three different reinforcement learning approaches to create a bot with a universal behavior set. Results show that using a hierarchical or rule based approach, combined with reinforcement learning, is a promising solution to creating first person shooter bots that offer a rich and diverse behavior set.
An effective subsequence-to-subsequence time series matching approach

The success of time series data mining applications, such as query by content, clustering, and classification, is greatly determined by the performance of the algorithm used for the determination of similarity between two time series. The previous research on time series matching has mainly focused on whole sequence matching and sequence-to-subsequence matching. Relatively, very little work has been done on subsequence-to-subsequence matching, where two time series are considered similar if they contain similar subsequences or patterns in the same time order. This paper presents an effective approach capable of handling whole sequence, sequence-to-subsequence and subsequence-to-subsequence matching. The proposed approach derives its strength from the novel two stage segmentation algorithm, which facilitates aligning the two time series by retaining perceptually important points in both time series as break points.
RSSI localisation with sensors placed on the user

We examine the indoor single-room localisation problem while using multiple fixed transmitters (anchors) and multiple mobile receivers placed on the user (mobiles). Anchors transmit a periodic beacon that the mobiles receive and of which they measure the received power level value (RSSI). Using this information only, which requires no specialised hardware, the mobiles estimate the position and orientation of the user. Many methods have been proposed to tackle this problem. In this paper we describe a purely theoretical procedure that aims to evaluate the maximum attainable performance of any real methods using RSSI for localisation purpose. Our analysis we present is based on a fine grid of RSSI values in a room, which are computed via ray-tracing, and a maximum-likelihood approach to localisation. Here we illustrate the performance gains of using multiple mobiles versus using a single one and and the attainable performance of user orientation estimation.
Standing out: how new firms in emerging markets build reputation

While strategy and organizational researchers increasingly recognize that observers' perceptions and beliefs about firms have a substantive effect on firms' access to resources and performance, the processes through which these perceptions form are not well understood. To address this question, we examined how three new firms - Amazon.com, barnesandnoble.com and CDNow - that entered the emerging e-commerce domain in the mid-1990s built their initial reputations in the media. Given the limited theory and empirical evidence about the process of reputation accumulation by new firms in emerging markets, we used the case study method to develop inductively a model that relates the visible external actions of the three firms to the patterns of media coverage they accumulated. Patterns of media coverage are likely to both reflect and affect the process of reputation accumulation, as the media constitute an influential audience of critics, who first form their own perceptions and opinions, thereby reflecting the process of reputation accumulation, and then disseminate these perceptions and opinions to the public, thereby influencing the perceptions and opinions of other stakeholder audiences. Our analysis indicates that the pattern of market actions of new firms influences the pattern of media coverage they receive in terms of levels (visibility), content (strategic character), tenor (favorability) and distinction (esteem). The observed inter-firm differences in these characteristics of received coverage suggest that reputation may be better understood as a composite construct and that firms' reputational assets may vary in their composition. Our study offers an inductively developed process model that relates the market actions of new firms to the accumulation of the different components of their initial reputations in the media.
Modal Nonassociative Lambek Calculus

We study Nonassociative Lambek Calculus (NL) enriched with modal operations ♦ and ↓, satisfying the adjoint law:♦A⇒ B iff A⇒ ↓ B and the following S4-modal structural postulates: (T) A⇒ ♦A, (4)♦♦A⇒ ♦A. (K) ♦(A •B)⇒ ♦A • ♦B. This system, denoted by NLS4 here, was studied by e.g. Moortgat [13] and Plummer [14] in connection with Type-Logical Grammar. An algebraic model of NLS4, called a S4-modal residuated groupoid (S4-rg), is a residuated groupoid with a unary operator ♦ and its residual ↓, satisfying the S4-axioms: T a ≤ ♦a, 4 ♦♦a ≤ ♦a and K ♦(a · b) ≤ ♦a · ♦b. Farulewski [5] proves Finite Embeddability Property (FEP) of the class of all residuated groupoids, solving an open problem from Blok and van Alten [4]. Buszkowski and Farulewski [2] and Buszkowski [3] show many other results of this kind, not assuming integrality. The present paper extends such results and prove the FEP of S4-rgs and S4-rgs with operations of a distributive lattice but without axiom K (S4-dlrgs). In [10], we prove that the polynomial time decidability of the consequence relation of NLS4 and the context-freeness of the corresponding grammars, which extends earlier results of Buszkowski [1] for NL, Buszkowski and Farulewski [2] for DFNL and Plummer [14] for a weaker version of NLS4 without assumptions. The key argument of the proofs in [10] and in present paper are the extended subformula property for Gentzen style axiomatization and the interpolation lemma (interpolation of formula-trees by formulae, taken from [1]) Besides by omitting the extra axiom K, we can obtain a more elegant form of the interpolation lemma, which yields a simpler description of the set of possible intepolants. Further, we directly prove the extended subformula property for NLS4 with assumptions, using a cut elimination theorem for these systems. (This theorem also holds for many other substuctural logics, e.g Lambek calculus, Full Lambek Calculus.) Our interest in modal postulates and non-logical assumptions can be partly motivated by linguistics application. Non-logical assumptions are useful in linguist, especially when we need some sequents, which can not be derivable in
Choice in the Age of Opinion How Opinion Voicing Reconfigures the Psychological Meaning of Choosing

The aim of this thesis is to study how opinion voicing can affect choice at a basic psychological level. Seven experiments lend empirical support to the premise that opinion voicing reconfigures the psychological meaning of choice through two different ways. First, it was argued that the availability of opinion voicing opportunities can undermine choice self-expressiveness and hence reduce post-choice rationalization. Second, it was suggested that the subjective construal of opinionation can reduce preference-choice consistency. As a whole, the overarching idea informing all studies is that opinion voicing reconfigures the psychological function of choice, as studied through well-established effects associated with the relation between preferences and choices through an experimental social psychological perspective. Unlike prior research that has largely focused on the interpersonal influence of expressed opinions on others’ choices, this research proposes an intrapersonal approach. Insofar as opinion and choice are parts of the self-concept, one’s opinions can interact with one’s own choices. In view of groundbreaking technological developments and societal changes that render opinion voicing at once all the more accessible and all the more valued, this research highlights how the proliferation of opportunities to express ourselves through opinions might change the way we relate to our choices, and how different construals of opinion voicing might also affect the extent to which we are driven by our preferences when choosing.
Incidence of Genome Structure, DNA Asymmetry, and Cell Physiology on T-DNA Integration in Chromosomes of the Phytopathogenic Fungus Leptosphaeria maculans

The ever-increasing generation of sequence data is accompanied by unsatisfactory functional annotation, and complex genomes, such as those of plants and filamentous fungi, show a large number of genes with no predicted or known function. For functional annotation of unknown or hypothetical genes, the production of collections of mutants using Agrobacterium tumefaciens–mediated transformation (ATMT) associated with genotyping and phenotyping has gained wide acceptance. ATMT is also widely used to identify pathogenicity determinants in pathogenic fungi. A systematic analysis of T-DNA borders was performed in an ATMT-mutagenized collection of the phytopathogenic fungus Leptosphaeria maculans to evaluate the features of T-DNA integration in its particular transposable element-rich compartmentalized genome. A total of 318 T-DNA tags were recovered and analyzed for biases in chromosome and genic compartments, existence of CG/AT skews at the insertion site, and occurrence of microhomologies between the T-DNA left border (LB) and the target sequence. Functional annotation of targeted genes was done using the Gene Ontology annotation. The T-DNA integration mainly targeted gene-rich, transcriptionally active regions, and it favored biological processes consistent with the physiological status of a germinating spore. T-DNA integration was strongly biased toward regulatory regions, and mainly promoters. Consistent with the T-DNA intranuclear-targeting model, the density of T-DNA insertion correlated with CG skew near the transcription initiation site. The existence of microhomologies between promoter sequences and the T-DNA LB flanking sequence was also consistent with T-DNA integration to host DNA mediated by homologous recombination based on the microhomology-mediated end-joining pathway.
New Functionalities in "SINDBAD" Software for Realistic X-Ray Simulation Devoted to Complex Parts Inspection

In NDT studies, the availability of a radiographic devices simulation is of primary interest to design the most suitable system and to predict the future device performance. Numerical simulation of radiographs and CT scans makes inspections more reliable and efficient by providing realistic quantitative answers to non-trivial non-destructive evaluations of complex components. In this context, the X-ray radiographic simulation software, Sindbad, has been developed in our laboratory. This software can model any radiographic set-up, including the X-ray source, the beam interaction (direct and scattered) inside the object represented by its CAD model, and the imaging process in the detector (different types). For each step of the virtual experimental bench, Sindbad combine different modelling modules, accessed via Graphical User Interfaces, to provide realistic synthetic images. In this paper, we present the new functionalities which have been recently integrated in Sindbad to improve the simulation of radiographs of complex parts including defects, under specific and typical configurations. First of all, the interface of the new version of BRL-CAD allows the operator to insert easily flaws of various shapes, sizes, and materials within the CAD representation of the part. Moreover, as Sindbad raytracing functions called for the computing of the direct image have been adapted for small details projection, Sindbad can now efficiently compute realistic radiographs of small defects included in complex parts. Some geometric improvements have also been recently integrated: the modelling of panoramic sources, curved detectors and the possibility to place the detector inside the object. Concerning scattered modelling, the Monte Carlo code has been accelerated in cases of low stopping power detectors, like films. Finally, the new version of Sindbad contains a new model of detector: the cascaded system model which is especially useful for flat panel detectors.
Social Interaction as Constituting Element of Routines: Incorporating Social Network Analysis into IS research

The resource-based view (RBV) considers organizational routines as fundamental for IT value creation as they determine the efficiency with which firms transform inputs to outputs. Yet, our understanding of how routines affect firm performance is still incomplete, especially concerning the contribution and complementarities between IT and non-IT-resources. As routines involve humans and consist of more than just technical aspects, we propose to use methods of Social Network Analysis (SNA) to formalize the social aspects of routines. We extend central findings of the RBV by considering the impact of the social embeddedness of a firm’s employees using Granovetter’s strength of ties argument. By considering RBV and SNA perspectives, we develop a model regarding the role of routines for alignment explaining how and why routines are able to generate positive outcomes of IT. The model provides good support for the effects cited in the literature and is illustrated by a case.
Using Matrix Exponentials to Explore Spatial Structure in Regression Relationships

Spatial regression relationships typically specify the structure of spatial relationships among observations using a fixed n by n weight matrix, where n denotes the number of observations. For computational convenience, this weight matrix is usually assumed to represent fixed sample information, making inferences conditional on the particular spatial structure embodied in the weight matrix used in the model. In an economic context, where the spatial structure can arise from externalities or spillovers, the magnitude and extent of influence from one observation or spatial location on other observations at nearby locations may be a subject of interest and inference. To address the dual goals of improving inference and understanding spatial structure, we set forth a flexible specification for the spatial weights that allows hyperparameters to control the number of neighboring entities as well as decay of influence over space. This specification is combined with the matrix exponential spatial specification (MESS) introduced in Pace and LeSage (2000) leading to a Bayesian model that allows posterior inferences regarding the magnitude and extent of spatial influence. We illustrate the method in an application that examines the role of geographical proximity in the economic growth of 219 urban zip-code areas in northeast Ohio. Inferences regarding the magnitude and extent of spatial influence in this setting may be of interest because theories of economic growth have increasingly stressed technological spillovers as a source of growth (see Romer, 1994; Grossman and Helpman, 1994).
Parallel tempering is efficient for learning restricted Boltzmann machines

A new interest towards restricted Boltzmann machines (RBMs) has risen due to their usefulness in greedy learning of deep neural networks. While contrastive divergence learning has been considered an efficient way to learn an RBM, it has a drawback due to a biased approximation in the learning gradient. We propose to use an advanced Monte Carlo method called parallel tempering instead, and show experimentally that it works efficiently.