Miracle-dz/UniFAR-FTUs huggingface dataset:
Multipurpose Genetic Algorithm Based in Pareto Optimality to Design Logical Topologies in Reconfigurable WDM Networks

We propose a novel multipurpose genetic algorithm based in Pareto optimality to design logical topologies for wavelength-routed optical networks with the aim of minimizing both the global average end-to-end delay and the average end-to-end delay of the most delayed traffic flow. The algorithm determines which nodes should be connected by means of lightpaths, solves the routing and wavelength assignment problem, and routes the traffic in the logical topology. When compared with another multipurpose genetic algorithm based in random selections of two fitness functions (one for each parameter to be optimized), the novel algorithm leads to reductions of up to 5% in both parameters
The Upper Bound Conjecture for Arrangements of Halfspaces

For an arbitrary arrangement of n open hemispheres of S d , it is conjectured that the number of vertices contained in at most k of the hemispheres attains its maximum for each k < (n ? d)=2 in case the hemispheres determine the dual of a spherical cyclic polytope. This would imply a sharp upper bound on the analogous numbers for arrangements of half-spaces in E d. The latter is proved here for d 4.
Detection and preliminary evaluation of circulating tumor cells in the peripheral blood of patients with eight types of cancer using a telomerase-specific adenovirus

We developed a detection method for circulating tumor cells (CTCs) using the telomerase-specific adenovirus OBP-401. This recombinant virus has a telomerase promoter at the 5′-end of the viral genome and GFP at the 3′-end. To date, CTC enumeration using OBP-401 has shown prognostic impact for gastric and small cell lung cancer patients. In the present study, peripheral blood samples from patients with eight types of cancer, including some cancers previously untested with OBP-401 (i.e., esophagus, pancreas, and prostate cancers) were subjected to this method in order to evaluate its versatility. It was recently discovered that some white blood cells (WBCs) false-positively react with OBP-401. Although anti-CD45 antibodies can absorb these adverse cells from peripheral blood, the simplicity of the OBP-401 method would be diminished by the introduction of antibody treatment. Therefore, we evaluated another approach to minimize the false positivity of WBCs. Seven anti-CD antibodies were employed to stain the species of WBCs that false-positively reacted with OBP-401. We revealed that the false-positively reacted WBCs were monocytes in the peripheral blood of both healthy subjects and cancer patients. Based on a size distribution analysis of the GFP-positive monocytes, the size criterion for CTCs using OBP-401 was defined to be a cellular diameter >8.4 μm. In total, 43% of 86 cancer patients examined in the present study were CTC-positive using this definition. CTCs were enumerated from peripheral blood samples collected from patients with each of the eight types of cancer; the detectability of CTCs for esophagus, pancreas and prostate cancers by the OBP-401 method was confirmed for the first time in the present study. However, no clear correlation between CTC positivity and the clinical characteristics of patients with any type of cancer was observed because of the small number of patients with each type of cancer. An additional clinical study will be conducted to confirm the clinical meaning of CTCs enumerated by OBP-401.
A Finite Element Model of Electrode Placement During Stimulus Evoked Electromyographic Monitoring of Iliosacral Screw Insertion

Pelvic ring fractures that occur as a result of substantial orthopedic trauma are frequently repaired using iliosacral screws to stabilize the fracture. Stimulus evoked electromyography, using pulsed current stimuli provided through the drill bit cathode, has been advocated to prevent nerve root injury during iliosacral screw insertion. Our objective was to examine the effects of anode location, drill bit position, and anatomical structure on the nerve monitoring technique. A three-dimensional finite element model was constructed from computed tomography data to evaluate the effectiveness of five anode locations at four stations of drill bit insertion. Results indicate that the anode location should be at the midline or on the side contralateral to drill bit insertion. Locating the anode at other positions, such that the nerve root is outside of the primary electromagnetic field, leads to an attenuated electromyographic response that will ultimately lead to the failure of the monitoring technique.
IncH-Type Plasmid Harboring blaCTX-M-15, blaDHA-1, and qnrB4 Genes Recovered from Animal Isolates

ABSTRACT The whole sequence of plasmid pENVA carrying the extended-spectrum β-lactamase gene blaCTX-M-15 was determined. It was identified from a series of clonally related Klebsiella pneumoniae sequence type 274 strains recovered from companion animals. This plasmid was 253,984 bp in size and harbored, in addition to blaCTX-M-15, a large array of genes encoding resistance to many antibiotic molecules, including β-lactams (blaTEM-1, blaDHA-1), aminoglycosides (aacA2, aadA1), tetracycline (tetA), quinolones (qnrB4), trimethoprim (dfrA15), and sulfonamides (two copies of sul1). In addition, genes encoding resistance to mercury, tellurium, nickel, and quaternary compounds were identified. It also carried genes encoding DNA damage protection and mutagenesis repair and a locus for a CRISPR system, which corresponds to an immune system involved in protection against bacteriophages and plasmids. Comparative analysis of the plasmid scaffold showed that it possessed a structure similar to that of only a single plasmid, which was pNDM-MAR encoding the carbapenemase NDM-1 and identified from human K. pneumoniae isolates. Both plasmids possessed two replicons, namely, those of IncFIB-like and IncHIB-like plasmids, which were significantly different from those previously characterized. The blaCTX-M-15 gene, together with the other antibiotic resistance genes, was part of a large module likely acquired through a transposition process. We characterized here a new plasmid type carrying the blaCTX-M-15 gene identified in a K. pneumoniae isolate of animal origin. The extent to which this plasmid type may spread efficiently and possibly further enhance the dissemination of blaCTX-M-15 among animal and human isolates remains to be determined.
Causal Diagrams 2 November 2009 1 of 16 CAUSAL DIAGRAMS

From their inception, causal systems models (more commonly known as structural-equations models) have been accompanied by graphical representations or path diagrams that provide compact summaries of qualitative assumptions made by the models. These diagrams can be reinterpreted as probability models, enabling use of graph theory in probabilistic inference, and allowing easy deduction of independence conditions implied by the assumptions. They can also be used as a formal tool for causal inference, such as predicting the effects of external interventions. Given that the diagram is correct, one can see whether the causal effects of interest (target effects, or causal estimands) can be estimated from available data, or what additional observations are needed to validly estimate those effects. One can also see how to represent the effects as familiar standardized effect measures. The present article gives an overview of: (1) components of causal graph theory; (2) probability interpretations of graphical models; and (3) methodologic implications of the causal and probability structures encoded in the graph, such as sources of bias and the data needed for their control.
A new method of fitting conic to scattered data

Using the implicit conic to fit the given data points is an important problem in the fields of geometric modeling and numerical calculation. If the implicit conic is constructed by minimizing the algebraic distance, the selection of the coordinate system and the setting of the constraint are the two key issues that will affect the approximation accuracy heavily. This paper discusses the problems that how to select the coordinate system and the constraint to make the constructed implicit conic approach the given data points better. Many experiments also show that the coordinate system and the constraint determined by the new method improve the conic approximation accuracy greatly.
Individualizing and Combining Treatments in Autism Spectrum Disorder

Although several early intervention programs can be efficacious in improving outcomes of children with autism, treatment response is variable, leading most families to enroll their child in several interventions simultaneously. Because knowledge on the effects of combining different therapies is limited, it is critically important to develop and test predictions on how the “active ingredients” of different interventions interact with child characteristics and with one another when combined. An obstacle to this research agenda is the “pre-paradigmatic” stage of the autism early intervention field, in which many practices are organized around seemingly irreconcilable vocabularies. I argue that a formalization of the explanatory structures informing different treatments—based on the four parameters of logical coherence, falsifiability, parsimony, and consilience—can provide a conceptual lingua franca for the formulation of testable hypotheses on treatment individualization and combination, thus facilitating a more coherent and rational approach to research in this area.
3D reconstruction based on Kinect

This paper realizes a 3D reconstruction system with Kinect, which can rebuild high-level, geometrically accurate 3D models in real-time with texture feature. Now the data formats, such as . obj, . stl, . ply etc are supported in the system, which can be directly applied in Maya, CAD and other 3D animation modeling software. The implementation of the system in our paper only requires a low-cost Kinect, therefore, it is more convenient and simpler by comparison with other traditional 3D reconstruction methods. Using the system, we just need to handhold the Kinect to scan the target object in different viewpoints or rotate the target object in front of the Kinect to reconstruct a 3D model timely with a GPU accelerated support machine. The results are validated by the experiments with the proposed system.
Exploiting Wikipedia in query understanding systems

In recent years, the free online encyclopaedia Wikipedia has become a standard resource to exploit to build knowledge base for various Natural Language Processing applications. In this paper, we exploit that resource to design a new query classification system. We explain and justify the steps we take to extract information from Wikipedia into a structured database, in order to demonstrate the validity of our design. We then show, both with mathematical reasoning and with experimental results, how to exploit the information in the database for the purpose of query classification.
Neural Network Spectral Robustness under Perturbations of the Underlying Graph

Recent studies have been using graph-theoretical approaches to model complex networks (such as social, infrastructural, or biological networks) and how their hardwired circuitry relates to their dynamic evolution in time. Understanding how configuration reflects on the coupled behavior in a system of dynamic nodes can be of great importance, for example, in the context of how the brain connectome is affecting brain function. However, the effect of connectivity patterns on network dynamics is far from being fully understood. We study the connections between edge configuration and dynamics in a simple oriented network composed of two interconnected cliques (representative of brain feedback regulatory circuitry). In this article our main goal is to study the spectra of the graph adjacency and Laplacian matrices, with a focus on three aspects in particular: (1) the sensitivity and robustness of the spectrum in response to varying the intra- and intermodular edge density, (2) the effects on the spectrum of perturbing the edge configuration while keeping the densities fixed, and (3) the effects of increasing the network size. We study some tractable aspects analytically, then simulate more general results numerically, thus aiming to motivate and explain our further work on the effect of these patterns on the network temporal dynamics and phase transitions. We discuss the implications of such results to modeling brain connectomics. We suggest potential applications to understanding synaptic restructuring in learning networks and the effects of network configuration on function of regulatory neural circuits.
Affordances for self-tracking wearable devices

Wearable devices for self-tracking are gradually spreading on the market, allowing people to monitor their own behaviors almost everywhere at every time. However, their integration in people's daily life poses a variety of challenges. In this landscape the concept of affordance becomes crucial: it can reframe the design of wearable devices by focusing it on their "smart materiality".
A dynamic minimal model of the listener for feedback-based dialogue coordination

Although the notion of grounding in dialogue is widely acknowledged, the exact nature of the representations of common ground and its specific role in language processing are topics of ongoing debate. Proposals range from rich, explicit representations of common ground in the minds of speakers (Clark,1996) to implicit representations, or even none at all (Pickering and Garrod, 2004). We argue that a minimal model of mentalising that tracks the interlocutor's state in terms of general states of perception, understanding, acceptance and agreement, and is continuously updated based on communicative listener feedback, is a viable and practical concept for the purpose of building conversational agents. We present such a model based on a dynamic Bayesian network that takes listener feedback and dialogue context into account, and whose temporal dynamics are modelled with respect to discourse structure. The potential benefit of this approach is discussed with two applications: generation of feedback elicitation cues, and anticipatory adaptation.
Dynamic priority scheduling of periodic tasks with extended precedences

The software architecture of a critical embedded control system generally consists of a set of multi-periodic communicating tasks. In order to be able to describe such a system, we define the notion of semaphore precedence constraint, which supports multi-rate communications that follow regular repetitive patterns. We propose a feasibility test for EDF and we study three implementations, for periodic task sets related by such extended precedences on monoprocessor architectures.
The trading profits of SOES bandits 1

SOES bandits are individual investors who use Nasdaq’s Small Order Execution System (SOES) for day trading. Their average profit per trade is small, but they trade dozens or hundreds of times per week. Bandits usually establish a position before most market-makers have updated their quotes, and lay off the position at favorable prices through Instinet or SelectNet. It is noteworthy that they trade profitably with marketmakers despite having less information. Bandits keep the profits and bear the losses from their trades. Thus they have greater incentives to trade well than the employees of market-making firms. ( 1998 Elsevier Science S.A. All rights reserved. JEL classification: G14; D82; D83
Complex software systems : Formalization and Applications

A mathematical denotation is proposed for the notion of complex software systems whose behavior is specified by rigorous formalisms. Complex systems are described in a recursive way as an interconnection of subsystems by means of architectural connectors. In order to consider the largest family of specification formalisms and architec tural connectors, this denotation is essentially formalis m, specification and connector independent. For this, we build our denotation on Goguen’s institution theory. In this abstract framework, we characterize complexity by the notion of property emergence. This work is a revised and extended version of Aiguier, Le Gall and Mabrouki (3rd International Conference on Software Engineering Advanced (ICSEA), IEEE Computer Society Press, 2008).
Personality Traits and Subjective Health Complaints in Female TMD Patients and Healthy Controls

Background: Personality traits and general health complaints may influence the course of and treatment of chronic pain. However, only few studies compare more than one or two personality characteristics in chronic pain patients and healthy controls. This study compares the comprehensive non-pathological personality structure of female patients with temporomandibular disorders (TMD) and pain-free controls. Moreover, this study controls for the influence of Neu- roticism, self-presentation bias, and acute pain sensitivity on the subjective report of general health complaints. Methods: Twenty-five TMD patients were compared to 25 matched controls on personality traits (NEO Personality Inven- tory-Revised; NEO-PI-R), self-presentation bias (Social Desirability Scale; SDS), psychological distress (Symptom Checklist 90-Revised; SCL-90-R), and general somatic complaints. Experimental pain sensitivity was assessed by electro- cutaneous and pressure pain stimulation. Results: Compared to the controls, Extraversion and Openness were lower in the TMD group, and the TMD patients ex- hibited higher levels of psychological and musculoskeletal complaints also when Neuroticism, self-presentation bias, and acute pain sensitivity were held constant. Conclusions: Low levels of Extraversion and Openness may dispose TMD patients to isolation and negative thought pat- terns. The elevated levels of psychological distress and general musculoskeletal pain in the TMD group add to previous reports of TMD as a complex condition also involving structures and processes outside of the orofacial region.
Multi-touch pinch gestures: performance and ergonomics

Multi-touch gestures are prevalent interaction techniques for many different types of devices and applications. One of the most common gestures is the pinch gesture, which involves the expansion or contraction of a finger spread. There are multiple uses for this gesture--zooming and scaling being the most common--but little is known about the factors affecting performance and ergonomics of the gesture motion itself. In this note, we present the results from a study where we manipulated angle, direction, distance, and position of two-finger pinch gestures. The study provides insight into how variables interact with each other to affect performance and how certain combinations of pinch gesture characteristics can result in uncomfortable or difficult pinch gestures. Our results can help designers select faster pinch gestures and avoid difficult pinch tasks.
Functional Annotation of Genes in Saccharomyces cerevisiae based on Joint Betweenness

The major objective of this paper is to introduce a novel method for the functional annotation of genes. Our method is based on a graph theoretical measure we call joint betweenness, which is an extension of the well known betweenness centrality measure, involving pairs of genes. We apply our method to the transcriptional regulatory network of yeast to, first, provide a large scale proof of concept of our method and, second, make predictions about the biological function of previously unknown genes.
Caspase Regulation in Non–Small Cell Lung Cancer and its Potential for Therapeutic Exploitation

Metastatic non–small cell lung cancer (NSCLC, stages IIIB/IV) is one of the most common and rapidly lethal causes of cancer related mortality worldwide. Efficacy of chemotherapy, the mainstay of treatment, is limited due to resistance in the vast majority of patients. NSCLC cells exhibit intrinsic apoptosis resistance. Understanding the molecular basis of this phenotype is critical, if therapy is to move beyond the therapeutic plateau that has been reached with conventional chemotherapy. Caspases occupy a pivotal position in the final common pathway of apoptosis. Increasing evidence suggests that these proteases are constitutively inhibited in NSCLC. This review discusses current knowledge relating to caspase regulation in NSCLC and highlights novel strategies for reversing the apoptosis resistant phenotype, with potential to accelerate development of effective therapy.
HYS-32-Induced Microtubule Catastrophes in Rat Astrocytes Involves the PI3K-GSK3beta Signaling Pathway

HYS-32 is a novel derivative of combretastatin-A4 (CA-4) previously shown to induce microtubule coiling in rat primary astrocytes. In this study, we further investigated the signaling mechanism and EB1, a microtubule-associated end binding protein, involved in HYS-32-induced microtubule catastrophes. Confocal microscopy with double immunofluorescence staining revealed that EB1 accumulates at the growing microtubule plus ends, where they exhibit a bright comet-like staining pattern in control astrocytes. HYS-32 induced microtubule catastrophes in both a dose- and time-dependent manner and dramatically increased the distances between microtubule tips and the cell border. Treatment of HYS-32 (5 μM) eliminated EB1 localization at the microtubule plus ends and resulted in an extensive redistribution of EB1 to the microtubule lattice without affecting the β-tubulin or EB1 protein expression. Time-lapse experiments with immunoprecipitation further displayed that the association between EB-1 and β-tubulin was significantly decreased following a short-term treatment (2 h), but gradually increased in a prolonged treatment (6-24 h) with HYS-32. Further, HYS-32 treatment induced GSK3β phosphorylation at Y216 and S9, where the ratio of GSK3β-pY216 to GSK3β-pS9 was first elevated followed by a decrease over time. Co-treatment of astrocytes with HYS-32 and GSK3β inhibitor SB415286 attenuated the HYS-32-induced microtubule catastrophes and partially prevented EB1 dissociation from the plus end of microtubules. Furthermore, co-treatment with PI3K inhibitor LY294002 inhibited HYS-32-induced GSK3β-pS9 and partially restored EB1 distribution from the microtubule lattice to plus ends. Together these findings suggest that HYS-32 induces microtubule catastrophes by preventing EB1 from targeting to microtubule plus ends through the GSK3β signaling pathway.
Deep brain stimulation of the ventral striatum increases BDNF in the fear extinction circuit

Deep brain stimulation (DBS) of the ventral capsule/ventral striatum (VC/VS) reduces the symptoms of treatment-resistant obsessive compulsive disorder (OCD), and improves response to extinction-based therapies. We recently reported that DBS-like stimulation of a rat homologue of VC/VS, the dorsal-VS, reduced conditioned fear and enhanced extinction memory (Rodriguez-Romaguera et al., 2012). In contrast, DBS of the ventral-VS had the opposite effects. To examine possible mechanisms of these effects, we assessed the effects of VS DBS on the expression of the neural activity marker Fos and brain-derived neurotrophic factor (BDNF), a key mediator of extinction plasticity in prefrontal-amygdala circuits. Consistent with decreased fear expression, DBS of dorsal-VS increased Fos expression in prelimbic and infralimbic prefrontal cortices and in the lateral division of the central nucleus of amygdala, an area that inhibits amygdala output. Consistent with improved extinction memory, we found that DBS of dorsal-VS, but not ventral-VS, increased neuronal BDNF expression in prelimbic and infralimbic prefrontal cortices. These rodent findings are consistent with the idea that clinical DBS of VC/VS may augment fear extinction through an increase in BDNF expression.