Miracle-dz/UniFAR-FTUs huggingface dataset:
IMAGE PROCESSING AND IMAGE REGISTRATION ON SPIRAL ARCHITECTURE WITH saLib

The spiral architecture (SA) represents an alternative model of image representation which uses hexagonal rather than square picture elements. This data structure is not only closely related to biological vision systems but also offers many advantages compared to the normal rectangular representation. In this paper we present saLib, a toolbox and visualisation tool for image processing purposes on the spiral architecture under Matlab. saLib provides basic functionality such as storing, translating and rotating hexagon-based images, as well as methods to display them. Furthermore, a visualisation tool is provided which can be used for the convenient operation on images or single addresses and the presentation of the results. In addition we also show how SA operations can be used to perform efficient and effective image registration. saLib is available to fellow researchers for download.
HIV integration site distributions in resting and activated CD4+ T cells infected in culture

Objective:The goal of this study was to investigate whether the location of HIV integration differs in resting versus activated T cells, a feature that could contribute to the formation of latent viral reservoirs via effects on integration targeting. Design:Primary resting or activated CD4+ T cells were infected with purified X4-tropic HIV in the presence and absence of nucleoside triphosphates and genomic locations of integrated provirus determined. Methods:We sequenced and analyzed a total of 2661 HIV integration sites using linker-mediated PCR and 454 sequencing. Integration site data sets were then compared to each other and to computationally generated random distributions. Results:HIV integration was favored in active transcription units in both cell types, but integration sites from activated cells were found more often in genomic regions that were dense in genes, dense in CpG islands, and enriched in G/C bases. Integration sites from activated cells were also more strongly correlated with histone methylation patterns associated with active genes. Conclusion:These data indicate that integration site distributions show modest but significant differences between resting and activated CD4+ T cells, and that integration in resting cells occurs more often in regions that may be suboptimal for proviral gene expression.
Clinical score and arterial oxygen saturation in children with wheezing associated respiratory illness (WARI).

OBJECTIVES To determine the correlation between clinical score (based on respiratory rate, chest wall retractions, air entry, wheezing, consciousness and audible wheezing) and arterial oxygen saturation (SaO2: measured by pulse oximetry) as well as the most appropriate total score for predicting hypoxemia (SaO2 < or = 95%) in children diagnosed to have wheezing associated respiratory illness (WARI). SUBJECTS 70 children (1 month-5 years old) hospitalized in the Department of Pediatrics, Chulalongkorn Hospital with the diagnosis of WARI from January 1, 1996 to December 31, 1996 were studied. Half of them were diagnosed to have acute lower respiratory tract infection (LRI) with wheezing while the remainder had reactive airway disease (RAD). DESIGN Cross sectional, analytical study. METHODS In each group of patients, the clinical score and SaO2 were assessed by the same pediatrician throughout the study. The correlation between the clinical signs and SaO2 as well as the cut off point of total score for predicting hypoxemia were analyzed. The sensitivity, specificity and accuracy of that total score in predicting hypoxemia were also calculated. RESULT In both groups of patients (acute LRI with wheezing and RAD group), the clinical signs correlated with SaO2 were wheezing (rs = -0.67 and -0.47 respectively) and chest wall retractions (rs = -0.57 and -0.59 respectively). Total score was also correlated with SaO2 (rs = -0.68 and -0.5 respectively). The cut off point of total score in predicting hypoxemia was 4 providing 80 per cent sensitivity in both groups with accuracy 74.3 per cent and 80 per cent respectively. CONCLUSION This clinical score may be used to assess the severity of hypoxemia in WARI patients. Wheezing, chest wall retractions and total score correlated well with SaO2. The total score > 4 was most appropriate in predicting hypoxemia in both children with RAD and wheezing associated with LRI.
Collecting data for socially intelligent surveillance and monitoring approaches: The case of conflict in competitive conversations

One of the most recent trends in surveillance research is the application of socially aware approaches, i.e. approaches that integrate human sciences findings in order to better understand, model and predict the behaviour of people under observation. One of the key requirements for the development of such approaches is the collection of corpora that provide sufficient and reliable information about social phenomena of interest. However, the computing community still pays relatively little attention to the application of methodologies suitable for observational data collection, possibly inspired by human sciences experimental work. This paper tries to fill, at least partially, such a gap by providing an introduction to data collection techniques applied in nonverbal behaviour research. The collection of a corpus aimed at the study of conflict in conversations is used as a case study and example.
AIsHockey—A Platform for Studying Synthetic Players

We introduce a computer game platform, AIsHockey, which is based on the real-world game of ice hockey. The platform allows us to implement and study autonomous, realtime synthetic players (i.e., computer-controlled actors in a game). By applying the Model-View-Controller architectural pattern we define the role of a synthetic player and recognize its responsibilities and interfaces in the software. We describe the AIsHockey system and discuss our experiences and observations in educational and research perspectives.
Computation of a single-scattering matrix for nonspherical particles randomly or horizontally oriented in space.

The computation of the scattering properties of cirrus cloud ice crystals by the ray-tracing approach is described. A light beam is represented by its Stokes quadrivector I, which describes intensity as well as polarization, and the scattering properties of particles (molecules, droplets, or ice crystals) are introduced by means of a 4 x 4 transformation matrix M known as the Mueller matrix, or M matrix. Obtaining such a matrix for each kind of particle gives access to a complete description of the scattering medium. Most computations of the M matrices of cirrus ice crystals have introduced several simplifying hypotheses, by using basic shapes, by assuming a random orientation of the particles, or both. The present study focuses on the calculation of the complete M matrix for a specific shape of particles (i.e., hexagonally based crystals) either with optional oscillation about the horizontal plane or with random orientation. The validity of the computation code is checked against specific well-known cases for randomly oriented particles. For horizontally oscillating particles the computation of this matrix is a new result. Sensitivity of the M matrix to the following variables is studied: refractive index, amplitude of oscillation, particle shape and size, and angle of incidence.
Trailing mobile sinks: A proactive data reporting protocol for Wireless Sensor Networks

In Wireless Sensor Networks (WSN), data gathering using mobile sinks typically incurs constant propagation of sink location indication messages to guide the direction of data reporting. Such behavior is undesirable, especially when the sensor network scale increases, as frequent message flooding will cause serious congestion in network communication and significantly impair the sensor network lifetime. In this paper, we propose a proactive data reporting protocol, SinkTrail, which achieves energy efficient data forwarding to multiple mobile sinks, and effectively reduces the number of sink location broadcasting messages. SinkTrail is unique in two aspects: (1) it allows sufficient flexibility in the movement of mobile sinks to dynamically adapt to unknown terrestrial changes; and (2) without assistance of GPS or predefined landmarks, SinkTrail establishes a logical coordinate system for predicting and tracking mobile sinks' locations, thereby significantly saves energy consumed during the data reporting process. We systematically analyze the impact of several design factors in SinkTrail and explore potential design improvements. The simulation results demonstrate that SinkTrail outperforms the Frequent Flooding Method (FFM) in finding shorter routing path and consumes less energy during data gathering process.
Simulation of photonic crystal diode lasers with plane-wave admittance method

The paper presents simulations of photonic band gap structures with the novel fully-vectorial three-dimensional calculation method-the plane wave admittance method. The band structure of a photonic crystal slab is computed and the influence of photonic crystal on the fundamental mode of vertical-cavity surface-emitting laser is analyzed. In both cases the plane-wave admittance method proves to be an efficient computational tool.
Open Wireless Positioning System: A Wi-Fi-Based Indoor Positioning System

Wireless network positioning is the main pillar of the continuity of rich and mobile multimedia applications. Good position accuracy is particularly difficult to obtain in urban or leafy areas and indoors or in mixed (both indoor and outdoor) environments. A system proposing such positioning must localize any mobile terminal accurately within hostile environments and ideally be low-cost and easy to deploy. We propose an indoor positioning system, based on the IEEE 802.11 wireless network. This system, named OWLPS (Open WireLess Positioning System), implements several of the major mobile position computation algorithms and techniques: fin- gerprinting location, topology-based and viterbi-like algorithm, propagation models. These algorithms result from community work and our personal researches. Index Terms—Wireless LAN, Radio position measurement, Indoor radio communication
Economics for the future

Many of us decided to study economics because we were interested in issues such aseconomic growth, unemployment, poverty, discrimination and social exclusion. Andfor much of the history of the discipline, economists grappled with explaining suchphenomena and, hopefully, helped to improve the development of economic policy.But now the discipline is increasingly dominated by other concerns, such asmathematical rigour and econometric modelling. The New York Times columnist,Michael Weinstein, recalled how his passion to learn economics, which was driven bya desire to understand the causes of poverty and the impact of technical change, wasimmediately quelled when on his ﬁrst day as a graduate student at the MassachusettsInstitute of Technology the professor announced that ‘all of economics is a subset ofthe theory of separating hyperplans’ (Weinstein, 2000). The subject has become soobscure that even orthodox economists are bemoaning its intellectual poverty.AccordingtoMiltonFriedman,‘economicshasbecomeincreasinglyanarcanebranchof mathematics rather than dealing with real economic problems’ (Friedman, 1999,p.137). And Robert Solow has observed: ‘Today if you ask a mainstream economista question about almost any aspect of economic life, the response will be: suppose wemodel that situation and see what happens.modern mainstream economics consistsof little else but examples of this process’ (quoted in Lawson, 2005). So many economists are now increasingly engaged in research and teaching that isdisconnected from the issues that inﬂuence people’s lives, as Long (2005) observed:‘academiceconomistsremainhiddenintheirivorytowers.Theyareneitherhouseholdnames nor a signiﬁcant presence in newspaper commentary pages. How strange fora country that produced the most famous economists of all time: Adam Smith, DavidRicardo and John Maynard Keynes’. But not all remain hidden in their ivory towers:there are a few who do inﬂuence the policy domain, but they come from the intel-lectually narrow sect of neoclassical economics. And there are those from the neo-classical sect who have managed to inﬁltrate popular culture by throwing away themaths, packaging their prose in airport-style books and entertaining their readerswithstories about why sumo wrestlers cheat and why drug pushers live with their mums(see Levitt and Dubner, 2005). As modern orthodox economics moves away from reality, there is both theopportunity and the need for heterodox economics to orientate economics towards
Velocity constancy in a virtual reality environment

The advantage of the virtual reality (VR) environment is that it is more like the real visual world. Hence we can test how cues (Landy et al 1995; Norman et al 1996) that are found to be important in reduced visual environments, often employed in psycho-physical studies, apply in more natural conditions. Velocity constancy is a (higher-level) perceptual ability whereby observers can perceptually equate the speeds of objects, located at different distances away from the observer (depths), that are moving at the same physical speed. Observers equate the speeds despite the fact that the objects are moving at different angular speeds on the retina. There are two main ways that this ability could be achieved: judging object speed against a reference frame (temporal frequency) or scaling retinal velocity by perceived distance between the objects (McKee and Smallman 1998). Evidence from psychophysical studies is most often interpreted as favouring the first possibility (Wallach 1939; McKee and Smallman 1998), thereby excluding depth cues, such as disparity and motion parallax, that give a relative object ^ object distance (Johnston et al 1994) from a role in scaling for velocity constancy. The ability to correctly judge the physical velocity of moving objects was shown by Brown (1931) to be invariant with the distance of the object from the observer. He called this velocity constancy. The image of a moving object has an angular velocity on the retina, so that objects moving at the same physical speed but at different distances will have different angular retinal velocities. All current models of human motion estimation are based on retinal speed exclusively Yet human observers can judge objects at different distances to be moving at the same physical speed, even though their retinal speed is different. How is this transformation from an angular to apparent physical speed accomplished?
Parvovirus DNA Replication

Parvoviruses are unique among all known viruses in having singlestranded DNA genomes which are linear. Virions are non-enveloped, containing a single copy of the small (4-6 kb) viral chromosome encapsidated in a rugged icosahedral protein capsid 18-26 nm in diameter. Although lacking associated enzymes or nucleosomal proteins, the particles have been shown, in some cases, to contain polyamines such as spermidine, spermine, and putrescine (Berns et al. 1995). The family Parvoviridae contains a broad spectrum of physically similar viruses that replicate in the nuclei of both invertebrate and vertebrate hosts. Viruses infecting mammalian cells form the subfamily Parvovirinae and include a number of helper-independent viruses, represented in this review by minute virus of mice (MVM), and the adeno-associated (AAV) viruses, represented here by AAV2, which, in general, only replicate in cells coinfected with a helper adenovirus or herpes virus. Further background information on the structure and biology of the parvoviruses can be obtained from reviews published elsewhere (Cotmore and Tattersall 1987; Berns 1990, 1995; Tjissen 1990; Muzyczka 1992). Space constraints allow only a representative selection of the most directly pertinent references to be cited herein. Whereas AAV encapsidates, in separate virions, DNA strands of either sense, MVM selectively encapsidates (to 99%) strands that are minus sense with respect to transcription. Both viruses encode all of their known proteins from a single-sense DNA strand, and each encodes two separate gene complexes. Transcripts from one half of the genome, designated by convention the right-hand side, program synthesis of an overlapping set of capsid polypeptides, whereas the left half gives rise to a series of nonstructural proteins essential for viral DNA replication. These latter are designated the Rep proteins in AAV and the NS (nonstructural) proteins in MVM. Genome usage in all parvoviruses is remarkably efficient, so that some protein sequences are encoded in overlapping reading frames, and others contain regulatory elements for tran-
Segregation of Platelet Aggregatory and Procoagulant Microdomains in Thrombus Formation: Regulation by Transient Integrin Activation

Objective—Platelets play a dual role in thrombosis by forming aggregates and stimulating coagulation. We investigated the commitment of platelets to these separate functions during collagen-induced thrombus formation in vitro and in vivo. Methods and Results—High-resolution 2-photon fluorescence microscopy revealed that in thrombus formation under flow, fibrin(ogen)-binding platelets assembled into separate aggregates, whereas distinct patches of nonaggregated platelets exposed phosphatidylserine. The latter platelet population had inactivated αIIbβ3 integrins and displayed increased binding of coagulation factors. Coated platelets, expressing serotonin binding sites, were not identified as a separate population. Thrombin generation and coagulation favored the transformation to phosphatidylserine-exposing platelets with inactivated integrins and reduced adhesion. Prolonged tyrosine phosphorylation in vitro resulted in secondary downregulation of active αIIbβ3. Conclusions—These results lead to a new spatial model of thrombus formation, in which aggregated platelets ensure thrombus stability, whereas distinct patches of nonaggregated platelets effectuate procoagulant activity and generate thrombin and fibrin. Herein, the hemostatic activity of a developing thrombus is determined by the balance in formation of proaggregatory and procoagulant platelets. This balance is influenced by antiplatelet and anticoagulant medication.
PlexinA4 is necessary as a downstream target of Islet2 to mediate Slit signaling for promotion of sensory axon branching

Slit is a secreted protein known to repulse the growth cones of commissural neurons. By contrast, Slit also promotes elongation and branching of axons of sensory neurons. The reason why different neurons respond to Slit in different ways is largely unknown. Islet2 is a LIM/homeodomain-type transcription factor that specifically regulates elongation and branching of the peripheral axons of the primary sensory neurons in zebrafish embryos. We found that PlexinA4, a transmembrane protein known to be a co-receptor for class III semaphorins, acts downstream of Islet2 to promote branching of the peripheral axons of the primary sensory neurons. Intriguingly, repression of PlexinA4 function by injection of the antisense morpholino oligonucleotide specific to PlexinA4 or by overexpression of the dominant-negative variant of PlexinA4 counteracted the effects of overexpression of Slit2 to induce branching of the peripheral axons of the primary sensory neurons in zebrafish embryos, suggesting involvement of PlexinA4 in the Slit signaling cascades for promotion of axonal branching of the sensory neurons. Colocalized expression of Robo, a receptor for Slit2, and PlexinA4 is observed not only in the primary sensory neurons of zebrafish embryos but also in the dendrites of the pyramidal neurons of the cortex of the mammals, and may be important for promoting the branching of either axons or dendrites in response to Slit, as opposed to the growth cone collapse.
Resource-Aware Migratory Services in Wide-Area Shared Computing Environments

In this paper we present the design and evaluation of a system for deploying highly available and migratable services in shared infrastructures, such as the PlanetLab, where the available resource capacities at a node can fluctuate significantly. A migratable service can monitor its operating conditions and autonomously relocate itself to another node when the available resource capacities at the current node fall below certain acceptable limits. We utilize the autonomous mobile agent paradigm for building such migratable services. Such agents can monitor their operating conditions and follow various migration policies. We investigate here the mechanisms for service relocation, and client-side protocols to access migratory services. The ``blackout periods'', i.e. the time during which the clients are unable to access a migrating service, need to be minimized and kept within some tolerable limits for services required to be highly available. We first present the design of a migratable service implemented using a mobile agent, and evaluate its performance in terms of the blackout periods and the service agent's abilities to autonomously migrate in the network. We replicate service agents to reduce the blackout periods, and develop the coordination protocols for autonomous agent migration in a group of service agents. We also present here our work for monitoring PlanetLab nodes for their available resource capacities in order to assist a migratory service in selecting a target node for relocation.
Simplified high throughput protocol for northern hybridization.

H.Yang, J.McLeese, M.Weisbart, J.-LDionne, I.Lemaire and R.A. Aubin* Laboratory of Immunopharmacology, Department of Pharmacology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario, 1 Department of Biology, University of Regina, Regina, Saskatchewan and Health and Welfare Canada, Life Sciences Division, Biotechnology Section, Sir F.G. Banting Res. Centre, Tunney's Pasture, Ottawa, Ontario K1A OL2, Canada
Progressive and selective degeneration of motoneurons in a mouse model of SMA

Spinal muscular atrophy (SMA), an autosomal recessive disorder characterized by the degeneration of motoneurons of the spinal cord and brainstem, results from loss-of-function mutations in the survival motor neuron gene (smn). The goal of these experiments was to analyse axons and cell bodies of motoneurons in different regions of the CNS during disease progression in a mouse model of SMA carrying a deletion of the exon 7 directed to neurons. These experiments demonstrate a progressive loss of motor axons and of motoneurons in the CNS. This is the first study that describes a selective neurodegeneration in this line of mice and underlines the importance of exon 7 in some populations of motoneurons for survival in vivo.
Considerations of Fairness and Strategy: Experimental Data from Sequential Games

Laboratory data from bargaining experiments have started a debate about the prospects for various parts of game theory as descriptive theories of observable behavior, and about whether, to what extent, and how a successful descriptive theory must take into account peoples' perceptions of "fairness. " Plausible explanations of the observed bargaining phenomena advanced by different investigators lead to markedly different predictions about what should be observed in three different games. A sharp experimental test is thus possible on this class of games, and the present paper reports the results of such a test.