Miracle-dz/UniFAR-FTUs huggingface dataset:
A harmonic bandwidth extension based on Gaussian mixture model

For conventional bandwidth extension, the spectral patching methods, such as spectral folding, spectral translation and non-linear processing, are employed to reconstruct high frequency signal, yet it leads to the spectral shifting between reconstructed and original signal, and does not retain the original harmonic relations. In this paper, a blind harmonic bandwidth extension method from wideband to super-wideband was proposed by estimating the energy of high frequency spectral envelope with Gaussian mixture model (GMM). Both the objective and subjective test results show that proposed algorithm performs better than conventional blind bandwidth extension algorithms.
Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae)

Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.
DiMP: Architectural Support for Direct Message Passing on Shared Memory Multi-cores

Thanks to programming approaches like actor-based models, message passing is regaining popularity outside large-scale scientific computing for building scalable distributed applications in many-core processors. Unfortunately, the mismatch between message passing models and today's shared-memory hardware provided by commercial vendors results in suboptimal performance and loss of efficiency. This paper presents a set of architectural extensions to reduce the overheads incurred by message passing workloads running on shared memory multi-core architectures. It describes the instruction set extensions and the hardware implementation. In order to facilitate programmability, the proposed extensions are used by a message passing library, allowing programs to take advantage of them transparently. As a proof-of-concept, we use a modified MPICH library and MPI programs to evaluate the proposal. Experimental results show that, on average, our proposal spends 60% less cycles performing data transfers in MPI functions, and reduces the L1 data cache misses in said functions to a fourth.
Draft Genome Sequence of a Humic Substance-Degrading Paenibacillus sp. Isolated from the Subarctic Grasslands at Low Temperature

ABSTRACT The Paenibacillus sp. strain PAMC 26794 was isolated from the tundra grasslands in Alaska for its high ability to degrade humic acids. We sequenced the PAMC 26794 genome to discover the degradative genes for natural humic substances and we propose the degradation pathway(s) of an abundant bacterial group (genus Paenibacillus) that inhabits cold environments.
Weighted Extreme Learning Machine for Digital Watermarking in DWT Domain

In this paper, a digital watermarking scheme has been implemented using Weighted Extreme Learning Machine (WELM) on images and results are compared with other existing methods. The neighbourhood relationship among the pixel in image can be used as an reference positions, WELM is used as a regressor. Digital watermarking problem can be treated as regression problem can be trained at the embedding procedure and watermark or logo or sequence can be embedded. The watermark as an information can be embedded into blue channel of input images used for watermarking taking into account of human vision system (HSV). As WELM algorithm is very fast, cost sensitive and has good learning and generalization ability, the watermark can be correctly extracted despite of the watermarked image subject to several malicious attacks. Experimental results show that the WELM based watermarking scheme outperformed other existing methods against different attacks including salt & peppers (0:04), scaling 50%, cropping 15%, rotation 150 etc. As implemented digital watermarking scheme is robust and imperceptible determined based on calculated metrics PSNR, BER.
Temporo-Parietal Brain Network Impairment Is Related To EEG ALPHA3/ ALPHA2 Frequency Power Ratio in Prodormal Alzheimer's Disease

Background: Reliable biomarkers are the new frontier for an early diagnosis of Alzheimer's disease and to monitor therapeutic options Objective: Volume reduction in temporo-parietal network is associated to mild cognitive impairment (MCI) due to Alzheimer disease (AD). The increase of EEG alpha3/alpha2 ratio has been associated with AD-converter MCI subjects. We investigated the association of alpha3/alpha2 ratio with patterns of cortical thickness in MCI. Methods: 74 adult subjects with MCI underwent clinical and neuropsychological evaluation, electroencephalogram (EEG) recording and high resolution 3D magnetic resonance imaging (MRI). Alpha3/alpha2 power ratio as well as cortical thickness was computed for each subject. Three MCI groups were detected according to increasing tertile values of alpha3/alpha2 and difference of cortical thikness among the groups estimated. Pearson’s r was used to assess the topography of the correlation between cortical thinning and memory impairment. Results: High a3/2 group had total cortical grey matter (CGM) volume reduction of 471 mm2 than Low a3/a2 group (p<.001). High a3/2 group showed a similar but less marked pattern (160 mm2) of cortical thinning when compared to Middle a3/a2 group (p<.001). Moreover, high a3/2 group had wider cortical thinning than other groups, mapped to the Supramarginal and Precuneus bilaterally. No significant cortical thickness difference was found between Middle and Low a3/a2 groups. Conclusion: High EEG alpha3/alpha2 ratio was associated with impairment of temporo-parietal cortical brain in MCI subjects. The combination of EEG alpha3/alpha2 power ratio and cortical thickness measure could be useful for identifying individuals at risk for progression to AD dementia and may be of value in clinical context
Acquisition of Pneumococci Specific Effector and Regulatory Cd4+ T Cells Localising within Human Upper Respiratory-Tract Mucosal Lymphoid Tissue

The upper respiratory tract mucosa is the location for commensal Streptococcus (S.) pneumoniae colonization and therefore represents a major site of contact between host and bacteria. The CD4+ T cell response to pneumococcus is increasingly recognised as an important mediator of immunity that protects against invasive disease, with data suggesting a critical role for Th17 cells in mucosal clearance. By assessing CD4 T cell proliferative responses we demonstrate age-related sequestration of Th1 and Th17 CD4+ T cells reactive to pneumococcal protein antigens within mucosal lymphoid tissue. CD25hi T cell depletion and utilisation of pneumococcal specific MHCII tetramers revealed the presence of antigen specific Tregs that utilised CTLA-4 and PDL-1 surface molecules to suppress these responses. The balance between mucosal effector and regulatory CD4+ T cell immunity is likely to be critical to pneumococcal commensalism and the prevention of unwanted pathology associated with carriage. However, if dysregulated, such responses may render the host more susceptible to invasive pneumococcal infection and adversely affect the successful implementation of both polysaccharide-conjugate and novel protein-based pneumococcal vaccines.
A Survey on Incremental Model Transformation Approaches

Steadily evolving models are the heart and soul of ModelDriven Engineering. Consequently, dependent model transformations have to be re-executed to reflect changes in related models, accordingly. In case of frequent, but only marginal changes, the re-execution of complete transformations induces an unnecessary high overhead. To overcome this drawback, incremental model transformation approaches have been proposed in recent years. Since these approaches differ substantially in language coverage, execution, and the imposed overhead, an evaluation and comparison is essential to investigate their strengths and limitations. The contribution of this paper is a dedicated evaluation framework for incremental model transformation approaches and its application to compare a representative subset of recent approaches. Finally, we report on lessons learned to highlight past achievements and future challenges.
Running Reward Conditioned Place Preference Task

[Abstract] The conditioned place preference (CPP) test is a standard pre-clinical behavioral tool used to study the motivational effects of drugs and non-drug treatments in experimental animals. The basic characteristic of this task involves the association of a particular environment and contextual cues with a reward stimulus, followed by the association of a different environment with the absence of the reward stimulus (Prus and Rosecrans, 2009). Besides the motor component, voluntary wheel running exercise also has a rewarding component, and has been suggested as a strong natural reinforcer. Consistent with this notion, rodents will readily begin to run when a wheel is introduced (Eikelboom and Mills, 1988; Looy and Eikelboom, 1989), will work by lever pressing to gain access to a running wheel (Pierce et al., 1986), and spend more time in a place previously associated with the aftereffects of running (Lett et al., 2000; Lett et al., 2001). More recently, we underscored an important role for the adipocyte-derived hormone leptin in midbrain dopamine neurons in the modulation of running reward (Fernandes et al., 2015). Here, we describe a CPP protocol to measure the rewarding aftereffects of wheel running exercise in mice.
Robot emotions generated and modulated by visual features of the environment

Emotions are generated and modulated by many factors in the ever-changing surrounding environment. A new and challenging task is to emulate emotional responses on a robot that are caused by visual stimuli, such that the robot's responses mirror that of the human user. This paper presents the initial stage of an affective system that has been trained on-line using reinforcement learning to generate and modulate emotions. The inputs of the system comprise a subset of emotionally relevant visual features extracted from the environment: colours, fractal dimension, and facial pareidolia. These inputs are mapped onto an output that expresses the associated emotion in terms of language. Pilot experiments demonstrate how a humanoid robot tries to learn through interaction with a human companion to express emotions associated with different environmental scenes in a (near) human-like manner.
Eyeglass-based hands-free videophone

We propose an eyeglass-based videophone that enables the wearer to make a video call without holding a phone (that is to say hands-free) in the mobile environment. The glasses have 4 (or 6) fish-eye cameras to widely capture the face of the wearer and the images are fused to yield 1 frontal face image. The face image is also combined with the background image captured by a rear-mounted camera; the result is a self-portrait image without holding any camera device at arm's length. Simulations confirm that 4 fish-eye cameras with 250-degree field of view (or 6 cameras with 180-degree field of view) can cover 83% of the frontal face. We fabricate a 6 camera prototype, and confirm the possibility of generating the self-portrait image. This system suits not only hands-free videophones but also other applications like visual life logging and augmented reality use.
Glotaran: A Java-Based Graphical User Interface for the R Package TIMP

In this work the software application called Glotaran is introduced as a Java-based graphical user interface to the R package TIMP, a problem solving environment for fitting superposition models to multi-dimensional data. TIMP uses a command-line user interface for the interaction with data, the specification of models and viewing of analysis results. Instead, Glotaran provides a graphical user interface which features interactive and dynamic data inspection, easier -- assisted by the user interface -- model specification and interactive viewing of results. The interactivity component is especially helpful when working with large, multi-dimensional datasets as often result from time-resolved spectroscopy measurements, allowing the user to easily pre-select and manipulate data before analysis and to quickly zoom in to regions of interest in the analysis results. Glotaran has been developed on top of the NetBeans rich client platform and communicates with R through the Java-to-R interface Rserve. The background and the functionality of the application are described here. In addition, the design, development and implementation process of Glotaran is documented in a generic way.
A Vocal-Based Analytical Method for Goose Behaviour Recognition

Since human-wildlife conflicts are increasing, the development of cost-effective methods for reducing damage or conflict levels is important in wildlife management. A wide range of devices to detect and deter animals causing conflict are used for this purpose, although their effectiveness is often highly variable, due to habituation to disruptive or disturbing stimuli. Automated recognition of behaviours could form a critical component of a system capable of altering the disruptive stimuli to avoid this. In this paper we present a novel method to automatically recognise goose behaviour based on vocalisations from flocks of free-living barnacle geese (Branta leucopsis). The geese were observed and recorded in a natural environment, using a shielded shotgun microphone. The classification used Support Vector Machines (SVMs), which had been trained with labeled data. Greenwood Function Cepstral Coefficients (GFCC) were used as features for the pattern recognition algorithm, as they can be adjusted to the hearing capabilities of different species. Three behaviours are classified based in this approach, and the method achieves a good recognition of foraging behaviour (86–97% sensitivity, 89–98% precision) and a reasonable recognition of flushing (79–86%, 66–80%) and landing behaviour(73–91%, 79–92%). The Support Vector Machine has proven to be a robust classifier for this kind of classification, as generality and non-linear capabilities are important. We conclude that vocalisations can be used to automatically detect behaviour of conflict wildlife species, and as such, may be used as an integrated part of a wildlife management system.
Xylem cavitation resistance can be estimated based on time‐dependent rate of acoustic emissions

Summary Acoustic emission (AE) analysis allows nondestructive monitoring of embolism formation in plant xylem, but signal interpretation and agreement of acoustically measured hydraulic vulnerability with reference hydraulic techniques remain under debate. We compared the hydraulic vulnerability of 16 species and three crop tree cultivars using hydraulic flow measurements and acoustic emission monitoring, proposing the use of time‐dependent AE rates as a novel parameter for AE analysis. There was a linear correlation between the water potential (Ψ) at 50% loss of hydraulic conductivity (P50) and the Ψ at maximum AE activity (Pmaxrate), where species with lower P50 also had lower Pmaxrate (P < 0.001, R 2 = 0.76). Using AE rates instead of cumulative counts for AE analysis allows more efficient estimation of P50, while excluding problematic AE at late stages of dehydration.
Automatic generation of emotions for social networking websites using text mining

The rapid growth of the World Wide Web has increased the online communication. The use of social networking sites is one of the important approaches for communication. In order to improve the textual methods of communication such as tweets, blogs and chat; it is needed to analyze the emotion of user by studying the input text. Much of the current work in this area of emotion recognition from text has typically focused on recognizing the polarity of sentiment (positive/negative). This paper presents a novel approach for emotion estimation from the text entered by user on social networking sites. The work proposed in this paper uses affective words and sentence context analysis methods for emotion recognition. Also for helping the users to effectively express their emotion, we have developed visual image generation approach that generates images according to emotion in text. The results of evaluations show that the proposed system obtains better results for emotion prediction than the existing methods.
Construction of a Membrane Protein Database and an Evaluation of Several Prediction Methods of Trans

How reliable and useful are predictions of transmembrane segments(TMSs) of membrane proteins from the amino acid sequences? It remains still under debate. Kyte and Doolittle proposed a simple scheme for the prediction of TMSs [1]. It is based on the hydropathy plot and is widely accepted as a basic and standard method. Since then, a large number of more sophisticated predictive algorithms have been proposed, which are improved varieties of the Kyte-Doolittle's approach. Although these methods have been considered to give rather good results, their abilities are still not enough to predict the number and positions of TMSs precisely; they often give totally di erent predictive results with proteins having many TMSs, in particular [2, 3]. One reason for this situation can be attributable to the low quality of the information on TMSs described in general amino acid sequence databases. The information included within the SWISS-PROT database, for example, is mostly not based on any experimental evidence but on predicted models; there is often no explicit description about whether the data comes from experiments or calculations in databases. Higher quality of information on TMSs from experimental evidence only is essential to evaluate existing prediction methods more precisely and to develop an algorithm overcoming their problems. We have collected 128 references reporting the membrane topology of proteins, and are continuing our e orts to triple this number. From them, we selected 54 topology models based on experimental evidence, at least partially. Combining these data with the sequence information from the SWISS-PROT database, we have constructed a membrane protein database in the form of relational database. Current version includes 54 proteins which are classi ed into 3 õÆ ød ]MâQ Q m 036 ]M=£3e 3 ? E û» Çõ 9$õ Öj Ç`÷Qõ m 444 Çõ=gâdecýR? 38 prokaryote (29) eukaryote (25) non-helical (3) Figure 1: Content of Membrane Protein Database. Number of data in parentheses groups (eukaryotic proteins, prokaryotic proteins, and the proteins with non-helical segments) as shown in Figure 1. Using this database we evaluated the predictability of the algorithms of following authors: Eisenberg [4]; Klein, Kanehisa and DeLisi(KKD method) [5]; von Heijne(TopPred method) [6]; and Persson and Argos [7]. The KKD method and the TopPred method predicted the exact number of TMSs for 59% and 67% of proteins in our database, respectively. These values could be increased to 63% and 74% by optimizing respective parameter values. The KKD method tends to predict fewer number of TMSs than the correct number, while the TopPred method shows the opposite tendency. We are now testing our previous idea to use di erent cut-o parameters for one TMS proteins and multiple TMS proteins in the KKD method and are also trying to develop a new predictive algorithm, by taking more precise position-dependent information on TMS into account.
Licensed under Creative Commons Attribution Cc by a Memory Efficient -fully Parallel Qc-ldpc Encoder

Low-Density Parity Check codes are a special class of linear block codes widely used in communication and disk storage systems, due to their Shannon limit approaching performance and their favourable structure. A special class of LDPC codes, called QC-LDPC codes, allows for efficient hardware implementations of encoding and decoding algorithms by exploiting the structure of the Parity Check Matrix (PCM), which is composed of circulant permutation matrices. These codes have encoding advantage over other types of LDPC codes. In this paper an efficient QC-LDPC encoder and decoder are developed. Belief propagation algorithm is used for decoding . Overall system is developed in Matlab and performances are compared for different rates. This work also introduces a memory efficient high throughput VHDL implementation for the encoder. Due to their error correction strength, QC-LDPC codes have been recently adopted in several industrial standards such as wireless local area networks (Wi-Fi, IEEE802.11 n, ac, and ad) and Digital Video Broadcasting-Satellite-Second Generation (DVB-S2).
Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.