Miracle-dz/UniFAR-FTUs huggingface dataset:
Circular genome visualization and exploration using CGView

UNLABELLED CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes. It converts XML or tab-delimited input into a graphical map (PNG, JPG or Scalable Vector Graphics format), complete with sequence features, labels, legends and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any Web browser, allowing rapid genome browsing and facilitating data sharing. AVAILABILITY CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology. ualberta.ca/cgview/ CONTACT david.wishart@ualberta.ca.
Holistic Management of the GPGPU Memory Hierarchy to Manage Warp-level Latency Tolerance

In a modern GPU architecture, all threads within a warp execute the same instruction in lockstep. For a memory instruction, this can lead to memory divergence: the memory requests for some threads are serviced early, while the remaining requests incur long latencies. This divergence stalls the warp, as it cannot execute the next instruction until all requests from the current instruction complete. In this work, we make three new observations. First, GPGPU warps exhibit heterogeneous memory divergence behavior at the shared cache: some warps have most of their requests hit in the cache, while other warps see most of their request miss. Second, a warp retains the same divergence behavior for long periods of execution. Third, requests going to the shared cache can incur queuing delays as large as hundreds of cycles, exacerbating the effects of memory divergence. We propose a set of techniques, collectively called Memory Divergence Correction (MeDiC), that reduce the negative performance impact of memory divergence and cache queuing. MeDiC delivers an average speedup of 21.8%, and 20.1% higher energy efficiency, over a state-of-the-art GPU cache management mechanism across 15 different GPGPU applications.
3D MODELLING OF CHUA'S CIRCUIT BOUNDARY SURFACE

In this paper is presented the 3D model of Chua's circuit boundary surfaces. This represents the boundary between the two attractors - chaos and a stable limit cycle. In the first part is described short history of Chua’s circuit and sequential circuits boundary surface modelling and visualization. Second part describes 3D modeling of boundary surface. Three dimensional model of boundary surface is created by appropriate combination lot of 2D cross-sections in surface u1=const using triangulation. The modelling and visualization of boundary surface represents modelling and visualization of large graphical data set and is timeconsuming process.
Speaker-independent raw waveform model for glottal excitation

Recent speech technology research has seen a growing interest in using WaveNets as statistical vocoders, i.e., generating speech waveforms from acoustic features. These models have been shown to improve the generated speech quality over classical vocoders in many tasks, such as text-to-speech synthesis and voice conversion. Furthermore, conditioning WaveNets with acoustic features allows sharing the waveform generator model across multiple speakers without additional speaker codes. However, multi-speaker WaveNet models require large amounts of training data and computation to cover the entire acoustic space. This paper proposes leveraging the source-filter model of speech production to more effectively train a speaker-independent waveform generator with limited resources. We present a multi-speaker 'GlotNet' vocoder, which utilizes a WaveNet to generate glottal excitation waveforms, which are then used to excite the corresponding vocal tract filter to produce speech. Listening tests show that the proposed model performs favourably to a direct WaveNet vocoder trained with the same model architecture and data.
Relationships of loading history and structural and material characteristics of bone: Development of the mule deer calcaneus

If a bone's morphologic organization exhibits the accumulated effects of its strain history, then the relative contributions of a given strain stimulus to a bone's development may be inferred from a bone's hierarchical organization. The artiodactyl calcaneus is a short cantilever, loaded habitually in bending, with prevalent compression in the cranial (Cr) cortex, tension in the caudal (Cd) cortex, and shear in the medial and lateral cortices (i.e., neutral axis). Artiodactyl calcanei demonstrate unusually heterogeneous structural and material organization between these cortices. This study examines potential relationships between developmental morphologic variations and the functional strain distribution of the deer calcaneus. One calcaneus was obtained from each of 36 (fetus to adult) wild deer. Predominant collagen fiber orientation (CFO), microstructural characteristics, mineral content (% ash), and geometric parameters were determined from transversely cut segments. Radiographs were examined for arched trabeculae, which may reflect tension/compression stress trajectories. Results showed that cross‐sectional shape changes with age from quasi‐circular to quasi‐elliptical, with the long axis in the cranial–caudal direction of habitual bending. Cranial (“compression”) cortical thickness increased at a greater rate than the Cd (“tension”) cortex. Fetal bones exhibited arched trabeculae. Percent ash was not uniform (Cr > Cd), and this disparity increased with age (absolute differences: 2.5% fetuses, 4.3% adults). Subadult bones showed progressively more secondary osteons and osteocyte lacunae in the Cr cortex, but the Cd cortex tended to have more active remodeling in the subadult and adult bones. Nonuniform Cr:Cd CFO patterns first consistently appear in the subadults, and are correlated with secondary bone formation and habitual strain mode. Medial and lateral cortices in these groups exhibited elongated secondary osteons. These variations may represent “strain‐mode‐specific” (i.e., tension, compression, shear) adaptations. The heterogeneous organization may also be influenced by variations in longitudinal strain magnitude (highest in the Cr cortex) and principal strain direction—oblique in medial‐lateral cortices (where shear strains also predominate). Other factors such as local reductions in longitudinal strain may influence the increased remodeling activity of the Cd cortex. Some structural variations, such as arched trabeculae, that are established early in ontogeny may be strongly influenced by genetic‐ or epigenetic‐derived processes. Material variations, such as secondary osteon population densities and CFO, which appear later, may be products of extragenetic factors, including microdamage. J. Morphol. 259:281–307, 2004. Published 2004 Wiley‐Liss, Inc.
Post-traumatic stress disorder and the outcome of dialectical behaviour therapy for borderline personality disorder.

BACKGROUND Individuals with borderline personality disorder (BPD) and comorbid post-traumatic stress disorder (PTSD) have a worse prognosis than individuals with BPD alone. A common view is that the emotional instability and impulsivity of BPD should be treated before attempting to address trauma. However, PTSD symptoms may interfere with patients' ability to benefit from such 'stabilizing' treatments. METHODS The effect of BPD-PTSD comorbidity on self-harm and BPD symptom outcomes was evaluated in 89 patients receiving dialectical behaviour therapy, using multilevel modelling. RESULTS Patients with comorbid BPD-PTSD showed a trend towards elevated BPD symptoms throughout the treatment year (β = 2.12, 95% CI = -0.21-4.44, p = 0.07). There was a three-way interaction between PTSD comorbidity, treatment completion and time, whereby PTSD comorbidity was associated with less reduction in self-harm frequency over time, but only in those completing the full 12 months of treatment (incident risk ratio = 1.16, 95% CI = 1.04-1.30, p < 0.01). CONCLUSION Patients with comorbid PTSD had a poorer outcome from dialectical behaviour therapy than those with BPD alone, possibly because of the negative impact of unaddressed trauma. The results provide further grounds for recently developed treatments targeting BPD traits and PTSD symptoms simultaneously.
Epidermal Growth Factor Receptor Phosphorylation Sites Ser991 and Tyr998 Are Implicated in the Regulation of Receptor Endocytosis and Phosphorylations at Ser1039 and Thr1041*

Aberrant expression, activation, and down-regulation of the epidermal growth factor receptor (EGFR) have causal roles in many human cancers, and post-translational modifications including phosphorylation and ubiquitination and protein-protein interactions directly modulate EGFR function. Quantitative mass spectrometric analyses including selected reaction monitoring (also known as multiple reaction monitoring) were applied to the EGFR and associated proteins. In response to epidermal growth factor (EGF) stimulation of cells, phosphorylations at EGFR Ser991 and Tyr998 accumulated more slowly than at receptor sites involved in RAS-ERK signaling. Phosphorylation-deficient mutant receptors S991A and Y998F activated ERK in response to EGF but were impaired for receptor endocytosis. Consistent with these results, the mutant receptors retained a network of interactions with known signaling proteins including EGF-stimulated binding to the adaptor GRB2. Compared with wild type EGFR the Y998F variant had diminished EGF-stimulated interaction with the ubiquitin E3 ligase CBL, and the S991A variant had decreased associated ubiquitin. The endocytosis-defective mutant receptors were found to have elevated phosphorylation at positions Ser1039 and Thr1041. These residues reside in a serine/threonine-rich region of the receptor previously implicated in p38 mitogen-activated protein kinase-dependent stress/cytokine-induced EGFR internalization and recycling (Zwang, Y., and Yarden, Y. (2006) p38 MAP kinase mediates stress-induced internalization of EGFR: implications for cancer chemotherapy. EMBO J. 25, 4195–4206). EGF-induced phosphorylations at Ser1039 and Thr1041 were blocked by treatment of cells with SB-202190, a selective inhibitor of p38. These results suggest that coordinated phosphorylation of EGFR involving sites Tyr998, Ser991, Ser1039, and Thr1041 governs the trafficking of EGF receptors. This reinforces the notion that EGFR function is manifest through spatially and temporally controlled protein-protein interactions and phosphorylations.
A novel method for reduction of error rates in K-means clustering algorithm

This paper investigated K-means Algorithm, a well known clustering algorithm. K-means clustering algorithms have some shortfalls and defects, and one defect is reviewed in this study. One of the disadvantages of kmeans clustering algorithms is that they can produce clusters that do not always include all the correct components. It is due to the presence of the error rate during the clustering process. The purpose of this research was to decrease error rates in the k-means clustering algorithm and to reduce iteration of running this algorithm. A novel method is proposed to calculate the distance between cluster members and cluster center. To evaluate the algorithm proposed in this study, seven well-known data sets consisting of Balance, Blood, Breast, Glass, Iris, Pima and Wine data sets were used. This investigation revealed that the performance of K-means algorithms was increased and resulted in valid clusters and that it reduced error rates, run time and iteration.
MX-LSTM: Mixing Tracklets and Vislets to Jointly Forecast Trajectories and Head Poses

Recent approaches on trajectory forecasting use tracklets to predict the future positions of pedestrians exploiting Long Short Term Memory (LSTM) architectures. This paper shows that adding vislets, that is, short sequences of head pose estimations, allows to increase significantly the trajectory forecasting performance. We then propose to use vislets in a novel framework called MX-LSTM, capturing the interplay between tracklets and vislets thanks to a joint unconstrained optimization of full covariance matrices during the LSTM backpropagation. At the same time, MX-LSTM predicts the future head poses, increasing the standard capabilities of the long-term trajectory forecasting approaches. With standard head pose estimators and an attentional-based social pooling, MX-LSTM scores the new trajectory forecasting state-of-the-art in all the considered datasets (Zara01, Zara02, UCY, and TownCentre) with a dramatic margin when the pedestrians slow down, a case where most of the forecasting approaches struggle to provide an accurate solution.
Link and Code: Fast Indexing with Graphs and Compact Regression Codes

Similarity search approaches based on graph walks have recently attained outstanding speed-accuracy trade-offs, taking aside the memory requirements. In this paper, we revisit these approaches by considering, additionally, the memory constraint required to index billions of images on a single server. This leads us to propose a method based both on graph traversal and compact representations. We encode the indexed vectors using quantization and exploit the graph structure to refine the similarity estimation. In essence, our method takes the best of these two worlds: the search strategy is based on nested graphs, thereby providing high precision with a relatively small set of comparisons. At the same time it offers a significant memory compression. As a result, our approach outperforms the state of the art on operating points considering 64-128 bytes per vector, as demonstrated by our results on two billion-scale public benchmarks.
Enhanced detection in CT colonography using adaptive diffusion filtering

Computer-aided detection (CAD) is a computerized procedure in medical science that supports the medical team's interpretations and decisions. CAD often uses information from a medical imaging modality such as Computed Tomography to detect suspicious lesions. Algorithms to detect these lesions are based on geometric models which can describe the local structures and thus provide potential region candidates. Geometrical descriptive models are very dependent on the data quality which may affect the false positive rates in CAD. In this paper we propose an efficient adaptive diffusion technique that adaptively controls the diffusion flux of the local structures in the data using robust statistics. The proposed method acts isotropically in the homogeneous regions and anisotropically in the vicinity of jump discontinuities. This method structurally enhances the data and makes the geometrical descriptive models robust. For the iterative solver, we use an efficient gradient descent flow solver based on a PDE formulation of the problem. The whole proposed strategy, which makes use of adaptive diffusion filter coupled with gradient descent flows has been developed and evaluated on clinical data in the application to colonic polyp detection in Computed Tomography Colonography.
Performance Analysis of Correlated Massive MIMO Systems With Spatially Distributed Users

In this paper, we analyze the performance of an uplink large-scale multiple-input-multiple-output system with a single base station (BS) serving spatially distributed multiantenna user devices (UDs) within a fixed coverage area. Stochastic geometry is used to characterize the spatially distributed users while large dimensional random matrix theory is used to achieve deterministic approximations of the sum rate of the system. In particular, the users in the vicinity of the BS are considered to follow a Poisson point process within the fixed coverage area. The sum rate of this system is analyzed with respect to different number of antennas at the BS as well as the intensity of the users within the coverage area of the cell. Closed-form approximations for the deterministic rate at low and high signal-to-noise ratio regimes are derived that have very low computational complexity. The deterministic rate for a general $k$th ordered user is also derived. It is shown that the deterministic approximations offer a reliable estimate of the ergodic sum rate obtained by Monte Carlo simulations. We also briefly touch on the growing issue of power consumption in wireless systems by analyzing the energy efficiency of the system using a power consumption model, taking into consideration the circuit power consumption, which is a function of the number of antennas of the BS and UDs.
Ares: Triggering Payload of Evasive Android Malware

With the emergence of mobile application markets, there has been a dramatic increase in mobile malware. Mobile platform providers are constantly creating and refining their malware-detection techniques, including static analysis and behavioral monitoring. The goal of malware writers is to hide the malware payload from those analyzers. In parallel, security analysts want to quickly detect if any software is malware in order to prevent harm to users. This confrontation is pushing malware writers to develop new evasion techniques that prevent their malware from being detected or making analysis harder. This paper describes Ares, a system built on top of an existing behavioral analysis, based on static information-flow analysis, binary instrumentation, and multiexecution analysis, to detect and bypass many common evasive techniques used by mobile malware. Additionally, this paper presents our implementation of Ares, and shows that, when run against real-world software, Ares is able to reveal previously unknown malicious components. We also developed a test suite for evasion detection techniques: Evadroid, which we have made fully available to other researchers.
The Reduction of the Permeability of a Lateritic Soil through the Application of Microbially Induced Calcite Precipitation

Lateritic soils are frequently utilised in tropical areas of the developing world as an engineering material in the construction of rural earth roads, usually in the form of engineered natural surface (ENS) roads. The heavy, seasonal rainfalls common to the tropics results in ENS roads becoming quickly saturated with rainwater, and no longer accessible to motorised transportation. Microbially induced calcite precipitation (MICP) has been successfully used as a treatment process to decrease the permeability of clean, cohesionless sands by studies trying to impede the movement of groundwater, and any pollutants they may contain. In order to see if MICP treatment can also reduce the susceptibility of ENS road lateritic soils to rainwater saturation, this study has treated a Brazilian sample extracted from an ENS road in Espirito do Santo, Brazil, using the MICP bacterium Sporosarcina pasteurii contained within a urea-calcium chloride solution inoculum. Investigation, by means of a Rowe cell, of the post-treatment permeability, to untreated control samples, has shown an average decrease in the vertical coefficient of permeability of 83%, from 1.15 × 10-7 m/s for the untreated control samples, to 1.92 × 10-8 m/s in treated samples.
Automatic detection of colour charts in images

This paper presents an algorithm of automatic colour chart detection and colour patch value extraction.The algorithm can detect different types of colour charts in various images. The efficiency of algorithm is measured by successful detection of the X-Rite ColorChecker and compared with the performance of the X-Rite ColorChecker Camera Calibration software. The experimental study shows that proposed algorithm successfully found the colour chart in 77.3% of tested images while the X-Rite software in 53.8% of tested images. The experiments specify optimal image acquisition conditions for successful colour chart detection. Streszczenie. W artykule przedstawiono algorytm automatycznej detekcji wzornika barw i ekstrakcji wartości barw jego pol. Algorytm umozliwia wykrycie roznych typow wzornikow barw w roznych obrazach. Efektywnośc poprawnej detekcji badano wykorzystując wzornik ColorChecker firmy X-Rite i porownywano z efektywnością detekcji programu X-Rite ColorChecker Camera Calibration. Badania doświadczalne wykazaly, ze zaproponowany algorytm poprawnie wykrywal wzornik barw w 77,3% badanych przypadkow, podczas gdy oprogramowanie firmy X-Rite w 53,8% badanych obrazow. Eksperymenty pozwolily określic optymalne warunki akwizycji obrazu dla pomyślnej detekcji wzornika barw. (Automatyczna detekcja wzornika barw w obrazach)
Travelling Profile Solutions For Nonlinear Degenerate Parabolic Equation And Contour Enhancement In Image Processing

We propose in this work to find explicit exact solutions called travelling profile solutions to a nonlinear diffusion equation that occurs in image processing. Some of these explicit solutions are related with the phenomenon of contour enhancement in image processing. We present a generalization of the results obtained by Barenblatt to study the contour enhancement in image processing for exponent range of parameter enhancement.
Efficient Transfer Route for Mobile Crowd Sensing (ETR-MCS)

 — The smartphone became a necessity in the personal life, and this device invoked in Mobile Crowd Sensing MCS to cover the smart cities requirements. There are two challenge factors with MCS are energy consumption and data uploading cost. This paper presented a new framework to manage these two challenge factors, this framework called "Efficient Transfer Route for Mobile Crowd Sensing (ETR-MCS)", this framework began with clustering the participant users with two areas, master area, and slave area, the users in slave area have two responsibilities, first, collect the data from the environment, second, the users would build a transfer route called "three-way handshaking route" to transfer the data to the users in master area. The users in Master area will be responsible to upload the data to the server with low energy and zero data uploading cost, this gain got from choosing the best clustering areas, where the master area prefer to choose the users how are at home or in work, therefore; they will upload the data using Wi-Fi or piggyback with 3G communication with considering the priority to the message should be transferred or upload first. This framework also presented precise equations for "time of sense", "time to transfer data" for the user in slave area, also give equations for energy consumption by the participants in both areas. The evaluations to this framework shows outperform of our proposed framework with compare to the previous articles in Mobile Crowd Sensing.