Miracle-dz/UniFAR-FTUs huggingface dataset:
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia

Three closely related thermally dimorphic pathogens are causal agents of major fungal diseases affecting humans in the Americas: blastomycosis, histoplasmosis and paracoccidioidomycosis. Here we report the genome sequence and analysis of four strains of the etiological agent of blastomycosis, Blastomyces, and two species of the related genus Emmonsia, typically pathogens of small mammals. Compared to related species, Blastomyces genomes are highly expanded, with long, often sharply demarcated tracts of low GC-content sequence. These GC-poor isochore-like regions are enriched for gypsy elements, are variable in total size between isolates, and are least expanded in the avirulent B. dermatitidis strain ER-3 as compared with the virulent B. gilchristii strain SLH14081. The lack of similar regions in related species suggests these isochore-like regions originated recently in the ancestor of the Blastomyces lineage. While gene content is highly conserved between Blastomyces and related fungi, we identified changes in copy number of genes potentially involved in host interaction, including proteases and characterized antigens. In addition, we studied gene expression changes of B. dermatitidis during the interaction of the infectious yeast form with macrophages and in a mouse model. Both experiments highlight a strong antioxidant defense response in Blastomyces, and upregulation of dioxygenases in vivo suggests that dioxide produced by antioxidants may be further utilized for amino acid metabolism. We identify a number of functional categories upregulated exclusively in vivo, such as secreted proteins, zinc acquisition proteins, and cysteine and tryptophan metabolism, which may include critical virulence factors missed before in in vitro studies. Across the dimorphic fungi, loss of certain zinc acquisition genes and differences in amino acid metabolism suggest unique adaptations of Blastomyces to its host environment. These results reveal the dynamics of genome evolution and of factors contributing to virulence in Blastomyces.
Encoding Spatial Context in Local Image Descriptors

This work has two underlying themes. The main theme of this work is exploiting the relative orientations of local image descriptors as a means of increasing the discriminativeness of descriptors while retaining in-plane rotation invariance. We use the shallow image classification pipeline as the pertinent application setting to develop and examine the effect of this contextual information. We then port it to Convolutional Neural Networks. The secondary theme concerns understanding the mechanisms of capture and encoding of contextual information in both, shallow and deep, classification pipelines. Understanding the nature of feature hierarchies in both pipelines opens up the possibility of applying methods developed for one pipeline onto the other. We take a close look at Dense SIFT and deduce that implicit relative orientation information is the key to its efficacy. We then propose methods to explicitly capture this relative orientation context information from local descriptor neighbourhoods, while retaining in-plane rotation invariance. Towards this we propose a 2D Histogram approach for context and appearance capture. We additionally propose a directional pooling mechanism for context extracted from feature neighbourhoods that strives to reject clutter. We also discuss the capture of weak spatial co-occurrence relationship between descriptors as a means to further improve discriminativeness, while exploring various ways of encoding this information. We then propose modifications to Convolutional Networks to make a special allowance for feature orientation information. This coaxes the network to decouple feature appearance and rotational invariance learning, resulting in a reduction in the number of learnable parameters. Substituting relative orientation information in the proposed Convolutional Layers in place of absolute orientation information leads to the additional benefit of inherently in-rotation invariant representations.
Phase Advancement and Nucleus-Specific Timing of Thalamocortical Activity during Slow Cortical Oscillation

The exact timing of cortical afferent activity is instrumental for the correct coding and retrieval of internal and external stimuli. Thalamocortical inputs represent the most significant subcortical pathway to the cortex, but the precise timing and temporal variability of thalamocortical activity is not known. To examine this question, we studied the phase of thalamic action potentials relative to cortical oscillations and established correlations among phase, the nuclear location of the thalamocortical neurons, and the frequency of cortical activity. The phase of thalamic action potentials depended on the exact frequency of the slow cortical oscillation both on long (minutes) and short (single wave) time scales. Faster waves were accompanied by phase advancement in both cases. Thalamocortical neurons located in different nuclei fired at significantly different phases of the slow waves but were active at a similar phase of spindle oscillations. Different thalamic nuclei displayed distinct burst patterns. Bursts with a higher number of action potentials displayed progressive phase advancement in a nucleus-specific manner. Thalamic neurons located along nuclear borders were characterized by mixed burst and phase properties. Our data demonstrate that the temporal relationship between cortical and thalamic activity is not fixed but displays dynamic changes during oscillatory activity. The timing depends on the precise location and exact activity of thalamocortical cells and the ongoing cortical network pattern. This variability of thalamic output and its coupling to cortical activity can enable thalamocortical neurons to actively participate in the coding and retrieval of cortical signals.
An Automatic Surface Information Extraction System Using Hierarchical IR and Stochstic IE

We address the problem of constructing an automated information extraction system from a corpus of text. We present in this paper a novel approach to textual information extraction (IE) combining information retrieval (IR) techniques and stochastic language modelling in a hierarchical system. This permits to largely reduce the amount of data treated with complex (slow) analysis systems, it allows for a successive refinement of the features extracted, and shows better performances than non-hierarchical models. At the lowest level of the hierarchy, documents and paragraphs are successively filtered with IR techniques. At the top level, a stochastic language model extracts the most relevant phrases, according to an extraction task. The approach and preliminary results are demonstrated on a subset of the MUC-6 Scenario Templates task.
Software test cases generation based on improved particle swarm optimization

The analysis of test case generation based on particle swarm algorithm introduced the group self-activity feedback (SAF) operator and Gauss mutation (G) changing inertia weight to improve the performance of particle swarm optimization (PSO). Using the improved algorithm in software test case, experiments show that the introduction of a single path fitness function structure and multi-path fitness calculation of parallel thinking are superior to the iteration time in single path test than standard PSO, and more efficient in multi-path test case generation.
Antibacterial Compounds from Propolis of Tetragonula laeviceps and Tetrigona melanoleuca (Hymenoptera: Apidae) from Thailand

This study investigated the chemical composition and antimicrobial activity of propolis collected from two stingless bee species Tetragonula laeviceps and Tetrigona melanoleuca (Hymenoptera: Apidae). Six xanthones, one triterpene and one lignane were isolated from Tetragonula laeviceps propolis. Triterpenes were the main constituents in T. melanoleuca propolis. The ethanol extract and isolated compounds from T. laeviceps propolis showed a higher antibacterial activity than those of T. melanoleuca propolis as the constituent α-mangostin exhibited the strongest activity. Xanthones were found in propolis for the first time; Garcinia mangostana (Mangosteen) was the most probable plant source. In addition, this is the first report on the chemical composition and bioactivity of propolis from T. melanoleuca.
Usage of multimodal maps for blind people: why and how

Multimodal interactive maps are a solution for providing the blind with access to geographic information. Current projects use a tactile map set down on a monotouch display with additional sound output. In our current project we investigated the usage of multitouch displays for this purpose. In this paper, we outline our requirements concerning the appropriate multitouch tactile device and we present a first prototype. We conclude with future working propositions.
Comparison between various notions of conserved charges in asymptotically AdS spacetimes

We derive Hamiltonian generators of asymptotic symmetries for general relativity with asymptotic AdS boundary conditions using the ‘covariant phase space’ method of Wald et al. We then compare our results with other definitions that have been proposed in the literature. We find that our definition agrees with that proposed by Ashtekar et al, with the spinor definition, and with the background-dependent definition of Henneaux and Teitelboim. Our definition disagrees with that obtained from the ‘counterterm subtraction method’, but the difference is found to consist only of a ‘constant offset’ that is determined entirely in terms of the boundary metric. We finally discuss and justify our boundary conditions by a linear perturbation analysis, and we comment on generalizations of our boundary conditions, as well as inclusion of matter fields.
Population-Based Study of Incidence and Outcome of Acute Aortic Dissection and Premorbid Risk Factor Control: 10-Year Results From the Oxford Vascular Study

Background— Acute aortic dissection is a preventable life-threatening condition. However, there have been no prospective population-based studies of incidence or outcome to inform an understanding of risk factors, strategies for prevention, or projections for future clinical service provision. Methods and Results— We prospectively determined incidence and outcomes of all acute aortic dissections in a population of 92 728 in Oxfordshire, United Kingdom, from 2002 to 2012. Among 155 patients with 174 acute aortic events, 54 patients had 59 thoracoabdominal aortic dissections (52 incident events: 6/100 000, 95% confidence interval, 4–7; 37 Stanford type A, 15 Stanford type B; 31 men, mean age=72.0 years). Among patients with type A incident events, 18 (48.6%) died before hospital assessment (61.1% women). The 30-day fatality rate was 47.4% for patients with type A dissections who survived to hospital admission and 13.3% for patients with type B dissections, although subsequent 5-year survival rates were high (85.7% for type A; 83.3% for type B). Even though 67.3% of patients were on antihypertensive drugs, 46.0% of all patients had at least 1 systolic BP ≥180 mm Hg in their primary care records over the preceding 5 years, and the proportion of blood pressures in the hypertensive range (>140/90 mm Hg) averaged 56.0%. Premorbid blood pressure was higher in patients with type A dissections that were immediately fatal than in those who survived to admission (mean/standard deviation pre-event systolic blood pressure=151.2/19.3 versus 137.9/17.9; P<0.001). Conclusions— Uncontrolled hypertension remains the most significant treatable risk factor for acute aortic dissection. Prospective population-based ascertainment showed that hospital-based registries will underestimate not only incidence and case fatality, but also the association with premorbid hypertension.
Alimentando relações e marcando diferenças: Comida brasileira entre imigrantes brasileiros na Grande Boston

Baseado em dados etnograficos, este artigo destaca mudancas e continuidades nas praticas alimentares cotidianas de imigrantes brasileiros na Grande Boston. A alimentacao e entendida como parte das estrategias que os sujeitos estabelecem para lidar as dificuldades e os desafios de um novo contexto sociocultural. Argumenta-se que, ao se alimentarem de “comida brasileira”, os imigrantes brasileiros estao “alimentando” relacoes, principalmente as familiares, que tem e mantem no Brasil. Neste sentido, a “comida brasileira” esta associada ao ambiente domestico e a comida caseira. O artigo tambem mostra que as mudancas importantes na alimentacao dos sujeitos da pesquisa sao narradas em relacao a rotina alimentar, devido ao horario de trabalho. Destaca ainda a comida como um marcador de identidades e diferencas, servindo como fonte de distincoes entre imigrantes brasileiros e norte-americanos, imigrantes de outras nacionalidades, ou ate mesmo entre brasileiros, em um complexo contexto intercultural.
Rank-two beamforming for single-group multicasting networks using OSTBC

This paper addresses the problem of transmit beamforming for single-group multicasting, where common information is transmitted to a group of users. Beamformers are designed to minimize the total transmitted power subject to quality-of-service (QoS) constraints for all users. In the conventional approach, a single weight vector is computed to jointly satisfy all requirements. However, in the case of a large number of users, the performance of the conventional beamforming methods usually degrades severely due to the limited degrees of freedom for designing spatially selective beamformers. Motivated by this, we propose a novel approach with increased flexibility in which the idea of single-group beamforming is combined with orthogonal space-time block coding (OSTBC). The proposed approach is particularly attractive in combination with the semi-definite relaxation (SDR) technique for which our approach is optimal in the case of rank-one and rank-two SDR solutions whereas the conventional approach is only optimal for rank-one solutions.
Pushing SDN to the end-host, network load balancing using OpenFlow

The concept of Software Defined Networking (SDN) has been successfully applied to efficiently configure and manage network infrastructure, e.g. in the context of data centres or WANs, and increasingly for ubiquitous communication. In this paper, we explore the idea of pushing SDN to the end-host. In particular, we consider the scenario of load balancing across multiple host network interfaces. We have explored and implemented different SDN-based load balancing approaches based on OpenFlow software switches, and have demonstrated the feasibility and potential of this approach.
Multiproduct Firms and Product Differentiation: A Survey

We start the survey by reviewing the implications of horizontal and vertical product differentiation on market structure under the assumption of single-product firms. Then, we analyse the main results of the multi-product firm models, both when variants are assumed differentiated in vertical attributes only and when variants are assumed differentiated in two dimensions (vertical and horizontal). Finally, we review the empirical literature about discrete-choice models of product differentiation.
Juvenile idiopathic arthritis: what is the utility of ultrasound?

Juvenile idiopathic arthritis (JIA) is a heterogeneous condition and an important cause of acquired disability in children. Evidence supports early treatment to prevent future complications. This relies on prompt diagnosis, achieved by a high index of clinical suspicion and supportive evidence, including the detection of joint and or tendon inflammation. Ultrasound is a readily accessible, well-tolerated, safe and accurate modality for assessing joints and the surrounding soft tissues. It can also be used to guide therapy into those joints and tendon sheaths resistant to systemic treatments. Ultrasound imaging is highly operator dependent, and the developing skeleton poses unique challenges in interpretation with sonographic findings that can mimic pathology and vice versa . Ultrasound technology has been rapidly improving and is more accessible than ever before. In this article, we review the normal appearances, highlight potential pitfalls and present the key pathological findings commonly seen in JIA.
A comparison of set-based and graph-based visualisations of overlapping classification hierarchies

The visualisation of hierarchical information sets has been a staple of Information Visualisation since the field came into being in the early 1990's. However, at present, support for visualising the correlations between multiple, overlapping sets of hierarchical information has been lacking. This is despite the realisation that for certain tasks this information is as important as the information that forms the individual hierarchies. In response to this, we have produced two early visualisation prototypes, one based on a graph visualisation, and the other on a set-based metaphor, that endeavour to display such information in a readily perceived form to potential users. The science of botanical taxonomy is used as an example of a field where such a visualisation would be useful, and also as a resource for example information sets that the prototypes can act upon. Technical and perceptual issues involved in the design and implementation of both prototypes are discussed. Following this, informal user testing on both prototypes is described, which utilised user observation techniques to elicit qualitative feedback from the taxonomists. These findings are then used to emphasise the shortcomings and advantages of each prototype, and from these probable issues for future prototyping and development are drawn.
Virtual Exhibition of Traditional Dances by Blending Colors of Multiple Images

A color blending method for generating a high quality image sequence of human motion is presented. The 3D human shape is reconstructed by volume intersection and expressed as a set of voxels. As each voxel is observed as different colors from different cameras, voxel color needs to be assigned appropriately from several colors. We present a color blending method which calculates voxel color from a linear combination of the colors observed by multiple cameras. The weightings in the linear combination are calculated based on both viewpoint and surface normal. As surface normal is taken into account, the images with clear texture can be generated. Moreover, since viewpoint is also taken into account, high quality images free of unnatural warping can be generated. To examine the effectiveness of the algorithm, a traditional dance motion was captured and new images were generated from arbitrary viewpoints. Compared to conventional methods, quality at the boundaries was confirmed to be improved.
An Improved Game-Theoretic Algorithm for Competitive Spectrum Sharing

Cognitive Radio (CR) is a promising technology for dynamic spectrum access with the ability of observing the surrounding environment and adapting itself to the change of network environment. For the problem of spectrum sharing among a primary user and multiple secondary users based on Game Theory, an improved utility function of the second user is proposed. In this function, the influence of the shared spectrum on the spectrum demand is considered. The more spectrum the second user shared, the demand for spectrum is relatively less. The demand degree in the utility function is a function of spectrum sharing, so it is a variable which can more accurately describes the cognitive radio system features. The theoretical analysis and simulation results show the validity of the proposed algorithm and the existence of Nash equilibrium. With the improved utility function, the fairness is introduced to the process of spectrum sharing.
Bioluminescence Resonance Energy Transfer Assay to Characterize Gi‐Like G Protein Subtype‐Dependent Functional Selectivity

G protein–coupled receptors (GPCRs) comprise the single most targeted protein class in pharmacology. G protein signaling transduces extracellular stimuli such as neurotransmitters into cellular responses. Although preference for a specific GPCR among different G protein families (e.g., Gs‐, Gi‐, or Gq‐like proteins) is often well studied, preference for a specific G protein subtype (e.g., Gi1, Gi2, Gi3, Go1, and Go2) has received little attention. Due to tissue expression differences and potentially exploitable functional differences, G protein subtype‐dependent functional selectivity is an attractive framework to expand GPCR drug development. Herein we present a bioluminescence resonance energy transfer (BRET)‐based method to characterize functional selectivity among Gi‐like protein subtypes. © 2017 by John Wiley & Sons, Inc.
FEVES: Framework for Efficient Parallel Video Encoding on Heterogeneous Systems

Lead by high performance computing potential of modern heterogeneous desktop systems and predominance of video content in general applications, we propose herein an autonomous unified video encoding framework for hybrid multi-core CPU and multi-GPU platforms. To fully exploit the capabilities of these platforms, the proposed framework integrates simultaneous execution control, automatic data access management, and adaptive scheduling and load balancing strategies to deal with the overall complexity of the video encoding procedure. These strategies consider the collaborative inter-loop encoding as a unified optimization problem to efficiently exploit several levels of concurrency between computation and communication. To support a wide range of CPU and GPU architectures, a specific encoding library is developed with highly optimized algorithms for all inter-loop modules. The obtained experimental results show that the proposed framework allows achieving a real-time encoding of full high-definition sequences in the state-of-the-art CPU+GPU systems, by outperforming individual GPU and quad-core CPU executions for more than 2 and 5 times, respectively.
Network-coded cooperation algorithm for multiple source - multiple relay topologies in cellular networks

This paper analyzes the performance provided on the uplink connection by a cooperative cluster, composed of user terminals and relays, which employ a XOR-based network coding algorithm. The paper presents the construction of the graphs that describe the operation of the algorithm within the selected topology. It then provides a theoretical analysis of the performance ensured by this algorithm in terms of the outage probability. The Block Error Rate (BLER) performance of the user terminals involved in cooperation are also evaluated for two cooperation topologies characterized by different cooperation graphs.
A non-parametric approach to visual correspondence

We describe a method for computing visual correspondence based on the local ordering of intensities. Ordering information is robust to outliers and invariant to mono-tonic intensity distortions such as image gain. Our approach is based on non-parametric measures of association but also accounts for the spatial variation of disparities. We describe some of the mathematical properties of our algorithms, and demonstrate their utility on both synthetic and real imagery with ground truth. These methods are extremely eecient, and have been used for video-rate stereo and motion.