Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytotoxic CD8+ T cell ablation enhances the capacity of regulatory T cells to delay viral elimination in Theiler's murine encephalomyelitis

Theiler's murine encephalomyelitis (TME) of susceptible mouse strains is a commonly used infectious animal model for multiple sclerosis. The study aim was to test the hypothesis whether cytotoxic T cell responses account for the limited impact of regulatory T cells on antiviral immunity in TME virus‐induced demyelinating disease (TMEV‐IDD) resistant C57BL/6 mice. TME virus‐infected C57BL/6 mice were treated with (i) interleukin‐2/‐anti‐interleukin‐2‐antibody‐complexes to expand regulatory T cells (“Treg‐expansion”), (ii) anti‐CD8‐antibodies to deplete cytotoxic T cells (“CD8‐depletion”) or (iii) with a combination of Treg‐expansion and CD8‐depletion (“combined treatment”) prior to infection. Results showed that “combined treatment”, but neither sole “Treg‐expansion” nor “CD8‐depletion,” leads to sustained hippocampal infection and virus spread to the spinal cord in C57BL/6 mice. Prolonged infection reduces myelin basic protein expression in the spinal cord together with increased accumulation of β‐amyloid precursor protein in axons, characteristic of myelin loss and axonal damage, respectively. Chronic spinal cord infection upon “combined treatment” was also associated with increased T and B cell recruitment, accumulation of CD107b+ microglia/macrophages and enhanced mRNA expression of interleukin (IL)‐1α, IL‐10 and tumor necrosis factor α. In conclusion, data revealed that the suppressive capacity of Treg on viral elimination is efficiently boosted by CD8‐depletion, which renders C57BL/6 mice susceptible to develop chronic neuroinfection and TMEV‐IDD.
The compliance budget: managing security behaviour in organisations

A significant number of security breaches result from employees' failure to comply with security policies. Many organizations have tried to change or influence security behaviour, but found it a major challenge. Drawing on previous research on usable security and economics of security, we propose a new approach to managing employee security behaviour. We conducted interviews with 17 employees from two major commercial organizations, asking why they do or don't comply with security policies. Our results show that key factors in the compliance decision are the actual and anticipated cost and benefits of compliance to the individual employee, and perceived cost and benefits to the organization. We present a new paradigm -- the Compliance Budget - as a means of understanding how individuals perceive the costs and benefits of compliance with organisational security goals, and identify a range of approaches that security managers can use to influence employee's perceptions (which, in turn, influence security behaviour). The Compliance Budget should be understood and managed in the same way as any financial budget, as compliance directly affects, and can place a cap on, effectiveness of organisational security measures.
Formal refinement of informal GUI design artefacts

Before we build any piece of software we would, surely, need to be certain that what we intend to build is what is required by the users of that software. In addition, we would want to be sure that the proposed software will behave as expected, do the right thing under all circumstances and also be usable. These functional and usability requirements are often considered separately. The functional requirements may be considered by way of formal specifications or models which are then subjected to verification and validation to ensure that the required properties hold. Similarly, the usability and user requirements may be captured using task analysis methods and checked by design methods such as GOMS, scenario development and usability testing of incremental prototypes. This paper looks at one way of bringing these two processes together by including the graphical user interface (GUI) design process and design concerns in the formal process of specification and refinement. In particular it considers what it means for a prototype of a GUI to be considered as a formal refinement of a specification. In this paper we show how we can consider the visual display, or presentation, of the GUI as the refinement, rather than the code which produces that presentation, and how this allows us to apply standard and well-known refinement techniques to informal design artefacts
Increase in Cx45 Gap Junction Channels in Cerebral Smooth Muscle Cells from SHR

Abstract—We recently reported the novel finding of expression and function of connexin45 (Cx45) in cerebrovascular smooth muscle cells. We examined the hypothesis that Cx45 is altered in hypertension. Immunoblots for Cx45 showed a significant increase in Cx45 in cerebral arteries from adult spontaneously hypertensive rats (SHR) compared with adult Wistar-Kyoto (WKY) rats, with no difference in aorta or femoral artery. Patch-clamp of cerebral smooth muscle cells pairs from SHR versus WKY showed a significantly steeper voltage dependence of deactivation and partial block of junctional currents by quinine and by a peptide that interferes with docking of Cx45, consistent with dominance of functional Cx45 channels in SHR. We examined potential roles of blood pressure versus angiotensin in elevated Cx45 in SHR by measuring Cx45 protein in 4 groups: (1) long-term administration in Wistar rats of the nitric oxide synthase inhibitor L-NAME; (2) long-term administration in SHR of the ACE inhibitor captopril; (3) long-term administration in Wistar rats of angiotensin; and (4) exposure of basilar artery segments in organ culture to angiotensin. Blood pressure was significantly elevated in groups 1 and 3 and was normal in group 2. In groups 1, 2, and 4, there was no significant change in Cx45 protein. In group 3, there was a modest but insignificant increase in Cx45 protein but no change in voltage dependence of deactivation of junctional currents. Overall, our data show increased Cx45 in SHR that is unlikely to be due to either elevated blood pressure or to angiotensin. Relative dominance of Cx45 over Cx43 in cerebral vessels may predispose SHR to ischemic stroke.
Dynamic control of underactuated manipulators with free-swinging passive joints in Cartesian space

A feedback linearizing decoupling dynamic control scheme of nonholonomic underactuated manipulators with free-swinging passive joints is proposed in Cartesian space where the task is planned. The presented control scheme does not require any braking process of passive joints. The presented dynamic control scheme has so-called "dynamic singularities" in the controller. Therefore, the singularities must be avoided an the path planning so as to guarantee the availability of the control scheme. Singularity-free desired paths in Cartesian space avoiding the dynamic singularities are obtained through a computer simulation. Simulation results for a three-link planar manipulator with one passive joint are presented to show the feasibility of the proposed control scheme with the singularity-free desired trajectory.
International Colloquium on Graph and Model Transformation On the occasion of the 65 th birthday of Hartmut Ehrig ( GraMoT 2010 ) Expressiveness of graph conditions with variables

Graph conditions are very important for graph transformation systems and graph programs in a large variety of application areas. Nevertheless, non-local graph properties like “there exists a path”, “the graph is connected”, and “the graph is cycle-free” are not expressible by finite graph conditions. In this paper, we generalize the notion of finite graph conditions, expressively equivalent to first-order formulas on graphs, to finite HR graph conditions, i.e., finite graph conditions with variables where the variables are place-holders for graphs generated by a hyperedge replacement system. We show that graphs with variables and replacement morphisms form a weak adhesive HLR category. We investigate the expressive power of HR graph conditions and show that finite HR graph conditions are more expressive than monadic second-order graph formulas.
Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities

Background Horizontal gene transfer (HGT) plays a major role in speciation and evolution of bacteria and archaea by controlling gene distribution within an environment. However, information that links HGT to a natural community using relevant population-genetics parameters and spatial considerations is scarce. The Great Salt Lake (Utah, USA) provides an excellent model for studying HGT in the context of biogeography because it is a contiguous system with dispersal limitations due to a strong selective salinity gradient. We hypothesize that in spite of the barrier to phylogenetic dispersal, functional characteristics—in the form of HGT—expand beyond phylogenetic limitations due to selective pressure. Methodology and Results To assay the functional genes and microorganisms throughout the GSL, we used a 16S rRNA oligonucleotide microarray (Phylochip) and a functional gene array (GeoChip) to measure biogeographic patterns of nine microbial communities. We found a significant difference in biogeography based on microarray analyses when comparing Sørensen similarity values for presence/absence of function and phylogeny (Student's t-test; p = 0.005). Conclusion and Significance Biogeographic patterns exhibit behavior associated with horizontal gene transfer in that informational genes (16S rRNA) have a lower similarity than functional genes, and functional similarity is positively correlated with lake-wide selective pressure. Specifically, high concentrations of chromium throughout GSL correspond to an average similarity of chromium resistance genes that is 22% higher than taxonomic similarity. This suggests active HGT may be measured at the population level in microbial communities and these biogeographic patterns may serve as a model to study bacteria adaptation and speciation.
Dodgson ’ s Rule Approximations and Absurdity

With the Dodgson rule, cloning the electorate can change the winner, which Young (1977) considers an “absurdity”. Removing this absurdity results in a new rule (Fishburn, 1977) for which we can compute the winner in polynomial time (Rothe et al., 2003), unlike the traditional Dodgson rule. We call this rule DC and introduce two new related rules (DR and D&). Dodgson did not explicitly propose the “Dodgson rule” (Tideman, 1987); we argue that DC and DR are better realizations of the principle behind the Dodgson rule than the traditional Dodgson rule. These rules, especially D&, are also effective approximations to the traditional Dodgson’s rule. We show that, unlike the rules we have considered previously, the DC, DR and D& scores differ from the Dodgson score by no more than a fixed amount given a fixed number of alternatives, and thus these new rules converge to Dodgson under any reasonable assumption on voter behaviour, including the Impartial Anonymous Culture assumption.
Retrospective analysis of the association between Demodex infestation and rosacea.

OBJECTIVES To explore the association between Demodex infestation and rosacea and the pathogenesis of demodicosis rosacea by means of a meta-analysis. DATA SOURCES Electronic searches of the ISI Web of Knowledge (Science Citation Index, ISTP [Index to Scientific & Technical Proceedings], Journal Citation Reports, BP [BIOSIS Preview], INSPEC [Ination Service in Physics, Electronics Technology, and Computer and Control], and DII [Derwent Innovation Index]), MEDLINE, and CNKI (China National Knowledge Infrastructure) databases (January 1, 1950, to December 31, 2009). We also performed hand searches of reference lists and conference proceedings. STUDY SELECTION Predefined selection criteria were applied to all published case-control studies that analyzed the association between Demodex infestation and rosacea. DATA EXTRACTION Two of us independently extracted data from the included studies. For disputed articles, a third party mediated whether to include the study. DATA SYNTHESIS Forty-eight English- and Chinese-language articles, which covered 10 different countries and 28 527 participants, were eligible. The pooled odds ratio in random-effects models is 7.57 (95% confidence interval, 5.39-10.62). Stability is good according to sensitivity analysis. The fail-safe number is 18 456 in the quantitative analysis of publication bias. CONCLUSIONS A significant association exists between Demodex infestation and the development of rosacea. Demodex infestation is a vital risk factor for rosacea according to the time-to-event relationship, and the degree of infestation played a more important role than did the mite infestation rate in the development of rosacea.
A Group-Based Personalized Model for Image Privacy Classification and Labeling

We address machine prediction of an individual’s label (private or public) for a given image. This problem is difﬁcult due to user subjectivity and in-adequate labeled examples to train individual, personalized models. It is also time and space consuming to train a classiﬁer for each user. We pro-pose a Group-Based Personalized Model for image privacy classiﬁcation in online social media sites, which learns a set of archetypical privacy models (groups), and associates a given user with one of these groups. Our system can be used to provide accurate “early warnings” with respect to a user’s privacy awareness level.
Learning Macro-Actions for Arbitrary Planners and Domains

Many complex domains and even larger problems in simple domains remain challenging in spite of the recent progress in planning. Besides developing and improving planning technologies, re-engineering a domain by utilising acquired knowledge opens up a potential avenue for further research. Moreover, macro-actions, when added to the domain as additional actions, provide a promising means by which to convey such knowledge. A macro-action, or macro in short, is a group of actions selected for application as a single choice. Most existing work on macros exploits properties explicitly specific to the planners or the domains. However, such properties are not likely to be common with arbitrary planners or domains. Therefore, a macro learning method that does not exploit any structural knowledge about planners or domains explicitly is of immense interest. This paper presents an offline macro learning method that works with arbitrarily chosen planners and domains. Given a planner, a domain, and a number of example problems, the learning method generates macros from plans of some of the given problems under the guidance of a genetic algorithm. It represents macros like regular actions, evaluates them individually by solving the remaining given problems, and suggests individual macros that are to be added to the domain permanently. Genetic algorithms are automatic learning methods that can capture inherent features of a system using no explicit knowledge about it. Our method thus does not strive to discover or utilise any structural properties specific to a planner or a domain.
Nested Mini-Batch K-Means

A new algorithm is proposed which accelerates the mini-batch k-means algorithm of Sculley (2010) by using the distance bounding approach of Elkan (2003). We argue that, when incorporating distance bounds into a mini-batch algorithm, already used data should preferentially be reused. To this end we propose using nested mini-batches, whereby data in a mini-batch at iteration t is automatically reused at iteration t+1. Using nested mini-batches presents two difficulties. The first is that unbalanced use of data can bias estimates, which we resolve by ensuring that each data sample contributes exactly once to centroids. The second is in choosing mini-batch sizes, which we address by balancing premature fine-tuning of centroids with redundancy induced slow-down. Experiments show that the resulting nmbatch algorithm is very effective, often arriving within 1% of the empirical minimum 100 times earlier than the standard mini-batch algorithm.
Patient-Derived Xenografts of Non Small Cell Lung Cancer: Resurgence of an Old Model for Investigation of Modern Concepts of Tailored Therapy and Cancer Stem Cells

Current chemotherapy regimens have unsatisfactory results in most advanced solid tumors. It is therefore imperative to devise novel therapeutic strategies and to optimize selection of patients, identifying early those who could benefit from available treatments. Mouse models are the most valuable tool for preclinical evaluation of novel therapeutic strategies in cancer and, among them, patient-derived xenografts models (PDX) have made a recent comeback in popularity. These models, obtained by direct implants of tissue fragments in immunocompromised mice, have great potential in drug development studies because they faithfully reproduce the patient's original tumor for both immunohistochemical markers and genetic alterations as well as in terms of response to common therapeutics They also maintain the original tumor heterogeneity, allowing studies of specific cellular subpopulations, including their modulation after drug treatment. Moreover PDXs maintain at least some aspects of the human microenvironment for weeks with the complete substitution with murine stroma occurring only after 2-3 passages in mouse and represent therefore a promising model for studies of tumor-microenvironment interaction. This review summarizes our present knowledge on mouse preclinical cancer models, with a particular attention on patient-derived xenografts of non small cell lung cancer and their relevance for preclinical and biological studies.
RBF shape histograms and their application to 3D face processing

We present novel, pose invariant 3D shape descriptors and we test the performance of these descriptors, when applied to the problems of nose identification and localisation in 3D face data. We generate an implicit radial basis function (RBF) model of the facial surface and construction of our novel features is based on sampling this RBF model over a set of concentric spheres to give a spherically-sampled RBF (SSR) histogram. In addition to providing a feature identification mechanism, SSR histograms can be processed, with very little computational overhead, to estimate the volumetric intersection of the object (face) and a bounding sphere, centred on any object surface point. A minimisation of this volume, at an appropriate scale, can be used to both define and localise the facial nose tip to an arbitrary resolution. We test our descriptors on a subset of the particularly challenging University of York 3D face database. This data set consists of 1736 3D faces, with facial expression variations, pose variations, data spikes and missing parts. Noses vertices are identified at a rate of 99.6% on unseen subjects and our approach significantly outperforms three variants of spin images.
The Use of Plants for the Removal of Toxic Metals from Contaminated Soil

Phytoremediation is an emerging technology that employs the use of higher plants for the cleanup of contaminated environments. Fundamental and applied research have unequivocally demonstrated that selected plant species possess the genetic potential to remove, degrade, metabolize, or immobilize a wide range of contaminants. Despite this tremendous potential, phytoremediation is yet to become a commercial technology. Progress in the field is precluded by limited knowledge of basic plant remedial mechanisms. In addition, the effect of agronomic practices on these mechanisms is poorly understood. Another limitation lies within the very biological nature of this novel approach. For example, potential for phytoremediation depends upon the interaction among soil, contaminants, microbes, and plants. This complex interaction, affected by a variety of factors, such as climatic conditions, soil properties, and site hydrogeology, argues against generalization, and in favor of site-specific phytoremediating practices. Thus, an understanding of the basic plant mechanisms, and the effect of agronomic practices on plant/soil/contaminant interaction would allow practitioners to optimize phytoremediation by customizing the process to site specific conditions. Remediation of metal contaminated soil faces a particular challenge. Unlike organic contaminants, metals cannot be degraded. Commonly, decontamination of metal-contaminated soils requires the removal of toxic metals. Recently, phytoextraction, the use of plants to extract toxic metals from contaminated soils, has emerged as a cost-effective, environment-friendly cleanup alternative. In this paper, we review the processes and mechanisms that allow plants to remove metals from contaminated soils and discuss the effects of agronomic practices on these processes.
Time-aware topic recommendation based on micro-blogs

Topic recommendation can help users deal with the information overload issue in micro-blogging communities. This paper proposes to use the implicit information network formed by the multiple relationships among users, topics and micro-blogs, and the temporal information of micro-blogs to find semantically and temporally relevant topics of each topic, and to profile users' time-drifting topic interests. The Content based, Nearest Neighborhood based and Matrix Factorization models are used to make personalized recommendations. The effectiveness of the proposed approaches is demonstrated in the experiments conducted on a real world dataset that collected from Twitter.com.
Adaptive duplexer implemented using feedforward technique with a BST phase shifter

As the complexity of modern modulation schemes increases, the noise levels inserted in the receive band by the transmitter are also increased. In this paper a technique to enhance the isolation of a duplexer is introduced, which reduces the noise levels in the receive band of the system. Feedforward techniques are used to create an adaptive null in the receive band, which can be targeted at any channel across the band. This null has been shown to give an improved isolation of 20 dB for the duplexer over a 2 MHz bandwidth. This feedforward system is implemented using a BST phase shifter to enable tenability of the enhancement null.
A body-machine interface for training selective pelvis movements in stroke survivors: A pilot study

The body-machine interfaces (BMIs) map the subjects' movements into the low dimensional control space of external devices to reach assistive and/or rehabilitative goals. This work is a first proof of concept of this kind of BMI as tool for rehabilitation after stroke. We designed an exercise to improve the control of selective movements of the pelvis in stroke survivors, increasing the ability to decouple the motion in the sagittal and frontal planes and decreasing compensatory adjustments at the shoulder girdle. A Kinect sensor recorded the movements of the subjects. Subjects played different games by controlling the vertical and horizontal motion of a cursor on a screen with respectively the lateral tilt and the ante/retroversion of their pelvis. We monitored also the degrees of freedom not directly involved in cursor control, thus subjects could complete the task only with a correct posture. Our preliminary results highlight significant improvement not only in cursor control, but also in the Trunk Impairment Scale (TIS) and in the Five Times Sit to Stand Test (5xSST).