Miracle-dz/UniFAR-FTUs huggingface dataset:
Separation matrix optimization using associative memory model for blind source separation

A source signal is estimated using an associative memory model (AMM) and used for separation matrix optimization in linear blind source separation (BSS) to yield high quality and less distorted speech. Linear-filtering-based BSS, such as independent vector analysis (IVA), has been shown to be effective in sound source separation while avoiding non-linear signal distortion. This technique, however, requires several assumptions of sound sources being independent and generated from non-Gaussian distribution. We propose a method for estimating a linear separation matrix without any assumptions about the sources by repeating the following two steps: estimating non-distorted reference signals by using an AMM and optimizing the separation matrix to minimize an error between the estimated signal and reference signal. Experimental comparisons carried out in simultaneous speech separation suggest that the proposed method can reduce the residual distortion caused by IVA.
Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

Breed utilization, genetic improvement, and industry consolidation are predicted to have major impacts on the genetic composition of commercial chickens. Consequently, the question arises as to whether sufficient genetic diversity remains within industry stocks to address future needs. With the chicken genome sequence and more than 2.8 million single-nucleotide polymorphisms (SNPs), it is now possible to address biodiversity using a previously unattainable metric: missing alleles. To achieve this assessment, 2551 informative SNPs were genotyped on 2580 individuals, including 1440 commercial birds. The proportion of alleles lacking in commercial populations was assessed by (1) estimating the global SNP allele frequency distribution from a hypothetical ancestral population as a reference, then determining the portion of the distribution lost, and then (2) determining the relationship between allele loss and the inbreeding coefficient. The results indicate that 50% or more of the genetic diversity in ancestral breeds is absent in commercial pure lines. The missing genetic diversity resulted from the limited number of incorporated breeds. As such, hypothetically combining stocks within a company could recover only preexisting within-breed variability, but not more rare ancestral alleles. We establish that SNP weights act as sentinels of biodiversity and provide an objective assessment of the strains that are most valuable for preserving genetic diversity. This is the first experimental analysis investigating the extant genetic diversity of virtually an entire agricultural commodity. The methods presented are the first to characterize biodiversity in terms of allelic diversity and to objectively link rate of allele loss with the inbreeding coefficient.
A complex microsatellite at chromosome 7q33 as a new prognostic marker of colorectal cancer

Disease-specific markers are critical for early diagnosis, targeted therapy and prognostic prediction of diseases. Current study reports a complex microsatellite as a new prognostic marker of sporadic colorectal cancer. This microsatellite located at Chromosome 7q33 is composed of three tetranucleotide tandem repeats, (TTCC)2(TCCC)5(TCCT)7, flanked by a CT-rich sequence. We analyzed polymorphisms of this microsatellite in 158 sporadic colorectal cancer, 143 matched normal adjacent tissues (NAT) and 150 health donors. Our results showed that this complex microsatellite was instable with polymorphic frequency of 77.2% in colorectal cancer, 52.4% in NAT and 54.7% in health donors (p<0.01) when compared to reference sequence. In the three tandem repeats, (TCCT)7 site was most polymorphic accounting for over 70.0% of polymorphisms in this complex microsatellite, followed by (TTCC)2 site for approximately 20%. Polymorphisms in (TCCC)5 was rare. Polymorphisms at the (TCCT)7 site were mainly insertions of 1 to 4 copies of TCCT (88.6%), and deletions occurred in about 6.4% of cases. The (TTCC)2 site was featured with one copy TTCC insertions. Pair-wise analyses between colorectal tumors and NAT revealed that 88 of 121 (72.7%) tumors displayed expansion, contraction or both in these tetranucleotide tandem repeats when compared to NAT. A cross-analysis with clinicopathological data of 158 colorectal cancers revealed that polymorphic alterations of the microsatellite associated with less lymphatic metastasis (p<0.001), and the colorectal cancer patients with polymorphic changes in this microsatellite demonstrated better survival (n=112, p=0.0058). Together these data suggest that this complex microsatellite is a potential prognostic marker of sporadic colorectal cancer.
salienShrink: Saliency-Based Wavelet Shrinkage

This paper describes salienShrink, a method to denoise images based on computing a map of salient coefficients in the wavelet domain and use it to improve common denoising algorithms. By salient, we refer to those coefficients that correspond mostly to pure signal and should therefore be preserved throughout the denoising procedure. We use a computationally efficient model to detect salient regions in the bands of the multiresolution wavelet transform. These regions are used to obtain a more accurate estimate of the noise level, improving the performance of existing well known shrinkage methods. Extensive experimental results on the BiShrink method show that the proposed method effectively enhances PSNR and improves the visual quality of the denoised images.
Promoting universal usability with multi-layer interface design

Increased interest in universal usability is causing some researchers to study advanced strategies for satisfying first-time as well as intermittent and expert users. This paper promotes the idea of multi-layer interface designs that enable first-time and novice users to begin with a limited set of features at layer 1. They can remain at layer 1, then move up to higher layers when needed or when they have time to learn further features. The arguments for and against multi-layer interfaces are presented with two example systems: a word processor with 8 layers and an interactive map with 3 layers. New research methods and directions are proposed.
Curated databases

Summary form only given. Scientists, notably biologists, are making increasing use of databases to publish both their data and their interpretation of data. These databases are valuable because of the human effort (curation) that goes into their construction and maintenance. They typically consist of a mixture of source data, metadata, annotations, and relevant data that has been extracted from other curated databases. Current database and data exchange technology does not serve database curation well. In this paper, the author addresses a number of issues connected with curated databases. Annotation of existing data now provides a new form of communication between scientists, but conventional database technology provides little support for attaching annotations. The author shows why new models of both data and query languages are needed. Closely related to annotation is provenance - archiving - is also important for verifying the basis of scientific research, yet few published scientific databases do a good job of archiving. Past "editions" of the database get lost. The author describes a system that allows frequent archiving and efficient retrieval with remarkably little space overhead. Finally the author argues that we need a new model of how curated databases are constructed. The idea that such databases are constructed as views of other data through conventional query and update languages is unhelpful, and that formulation of a "copy-and-paste" model of data construction may provide us with better curation tools.
Retrieval and classification of pneumoconiosis chest radiograph images using multiscale AM-FM methods

We propose the use of Amplitude-Modulation Frequency-Modulation (AM-FM) features for representing and retrieving X-Ray images with pneumoconiosis. The AM-FM features are estimated using multiscale filterbanks with wave-lengths related with the standard sizes for grading the level of opacities in X-Rays. The extracted AM-FM features represent opacity profusion in terms of instantaneous frequency (IF) and instantaneous amplitude (IA) features. Here, IF estimates in the medium and high scale frequencies can be used to capture early disease symptoms. AM-FM features from the low and medium scale frequencies are associated with advanced disease stages. We demonstrate the performance of the system in X-ray image retrieval and classification applications.
Characterization of 12 Novel Microsatellite Markers of Sogatella furcifera (Hemiptera: Delphacidae) Identified From Next-Generation Sequence Data

The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is a major pest of rice and has long-range migratory behavior in Asia. Microsatellite markers (simple sequence repeats) have been widely used to determine the origins and genetic diversity of insect pests. We identified novel microsatellite loci for S. furcifera samples collected from Laos, Vietnam, and three localities in Bangladesh from next-generation Roche 454 pyrosequencing data. Size polymorphism at 12 microsatellite loci was verified for 40 adult individuals collected from Shinan, South Korea. The average number of alleles per locus was 7.92. The mean values of observed (Ho) and expected heterozygosities (HE) were 0.615 and 0.757, respectively. These new microsatellite markers will be a resource for future ecological genetic studies of S. furcifera samples across more broad geographic regions in Asia and may assist in estimations of genetic differentiation and gene flow among populations for implementation of more effective management strategies to control this serious rice pest.
Auditing bone densitometry and fractures in children with chronic disease

In a retrospective analysis of bone densitometry scans performed in an audit of 576 children with chronic disease, lean-mass-adjusted bone mineral content (BMC) for the total body and the lumbar spine was marginally lower in children with fractures. However, the predictive ability of different bone mineral densities (BM) and BMC cut-offs to identify fracture risk in children with chronic disease needs to be tested for specific disease conditions in larger prospective studies.
Multi-agents based distributed-energy-resource management for intelligent microgrid with potential game algorithm

This paper presents a multi-agent (MAS) solution to the energy management in microgrid. An introduction and analysis of the system, including the structure of microgrid, characteristics of MAS and the potential game theory, are presented firstly. Then, micro models of agents for each component are proposed. The MAS is shown of having attributes of distribution, heterogeneity, autonomous, dynamism and openness. And then, the overall model of MAS and the process of optimization are presented in the next part. Potential game theory is introduced which applying as the distributed optimization method embedded in each micro agent model. Finally, the MAS for microgrid is formulated and implemented by the JADE platform. A scenario case study on the MAS and its testing process are included in the paper.
The efficient computation of polyhedral invariant sets for linear systems with polytopic uncertainty

In this paper the concept of maximal admissable set (MAS), introduced by Gilbert et al. (1991) for linear time-invariant systems, is extended to linear systems with polytopic uncertainty under linear state feedback. It is shown that by constructing a tree of state predictions using the vertices of the uncertainty polytope and by imposing state and input constraints on these predictions, a polyhedral robust invariant set can be constructed. The resulting set is proven to be the maximal admissable set. The number of constraints defining the invariant set is shown to be finite if the closed loop system is quadratically stable (i.e. has a quadratic Lyapunov function). An algorithm is also proposed that efficiently computes the polyhedral set without exhaustively exploring the entire prediction tree. This is achieved through the formulation of a more general invariance condition than that proposed in Gilbert et al. (1991) and by the removal of redundant constraints in intermediate steps. The efficiency and correctness of the algorithm is demonstrated by means of a numerical example.
Common Industry Format Usability Tests

A Common Industry Format for usability test reports is currently being agreed between major software suppliers and purchasers in an initiative co-ordinated by NIST. The objective is to raise the profile of usability in the procurement process, and to demonstrate the consequent benefits of acquiring products with increased usability. For the reports to be useful, they should contain reliable measures of usability. This requires a carefully designed evaluation procedure and use of appropriate metrics. BACKGROUND Usability will only be taken seriously when it is part of the acceptance criteria for a product, and this requires a means to specify usability goals and assess their achievement. In many organisations usability is ignored because there are no objective criteria for usability when developing and procuring products. A Common Industry Format for usability test reports is currently being agreed between major American software suppliers and purchasers in an initiative supported by NIST (the US National Institute of Standards and Technology) (Blanchard, 1998), and in co-operation with ACM SIGCHI. Although it is not at this stage intended to be the basis for a formal standard, material from relevant standards (such as ISO 9241-11) has been incorporated where appropriate. In making purchase decisions, companies and organisations have traditionally had little indication of how usable a product would be, how productive its users will be, or how much training and support its users would need. The situation has made it difficult to compare products, to plan for support, or estimate total cost of ownership. The goals of the NIST initiative are to: • Encourage software suppliers to work more closely with consumer organisations to understand the needs of the users. • Develop a common usability reporting format for sharing usability data with consumer organisations. • Conduct a pilot study to determine how well the usability reporting format works and to determine the value of using this information for software procurement. The scheme is due to be published and start pilot testing in early 1999. The information in this paper is based on the draft report format which is in the process of being finalised. AUDIENCE The CIF is intended to be used by usability professionals within supplier organisations to generate reports that can be used by consumer organisations. The CIF is also meant to be used by consumer organisations to verify that a particular report is CIF compliant. The CIF report is intended for two types of readers: • Technical professionals and managers who are using the test results to make procurement decisions. • Human factors or other usability professionals in consumer organisations who are evaluating both the technical merit of usability tests and the usability of the products.
Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of “modern” human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations.
The Chemoattractant Receptor-like Protein C5L2 Binds the C3a des-Arg77/Acylation-stimulating Protein*

The orphan receptor C5L2 has recently been described as a high affinity binding protein for complement fragments C5a and C3a that, unlike the previously described C5a receptor (CD88), couples only weakly to Gi-like G proteins (Cain, S. A., and Monk, P. N. (2002) J. Biol. Chem. 277, 7165–7169). Here we demonstrate that C5L2 binds the metabolites of C4a and C3a, C4a des-Arg77, and C3a des-Arg77 (also known as the acylation-stimulating protein or ASP) at a site distinct from the C5a binding site. The binding of these metabolites to C5L2 does not stimulate the degranulation of transfected rat basophilic leukemia cells either through endogenous rat G proteins or when co-transfected with human Gα16. C3a des-Arg77/ASP and C3a can potently stimulate triglyceride synthesis in human skin fibroblasts and 3T3-L1 preadipocytes. Here we show that both cell types and human adipose tissue express C5L2 mRNA and that the human fibroblasts express C5L2 protein at the cell surface. This is the first demonstration of the expression of C5L2 in cells that bind and respond to C3a des-Arg77/ASP and C3a. Thus C5L2, a promiscuous complement fragment-binding protein with a high affinity site that binds C3a des-Arg77/ASP, may mediate the acylation-stimulating properties of this peptide.
Functional Broadside Tests with Minimum and Maximum Switching Activity

Functional broadside tests were defined as broadside tests that detect target faults using only states that the circuit can visit during functional operation. With functional broadside tests, the peak switching activity and current demands during fast capture cycles can be guaranteed not to exceed those of functional operation, avoiding overtesting due to current demands that cannot be met. Therefore, functional broadside tests make it possible to explore tests with different switching activities as a way to maximize defect detection. For example, a test with a higher switching activity exercises more circuit lines, and is thus likely to activate and detect more defects. In addition, the maximum switching activity under functional broadside tests can be used as an upper bound on the switching activity that can be allowed for other types of tests. Tests with low switching activity may be preferred during wafer testing. Motivated by these applications, we study the range of switching activity possible for the functional broadside tests that detect a target fault, considering transition faults. We use the results to evaluate (low-power) standard broadside test sets.
Starchart: Hardware and software optimization using recursive partitioning regression trees

Graphics processing units (GPUs) are in increasingly wide use, but significant hurdles lie in selecting the appropriate algorithms, runtime parameter settings, and hardware configurations to achieve power and performance goals with them. Exploring hardware and software choices requires time-consuming simulations or extensive real-system measurements. While some auto-tuning support has been proposed, it is often narrow in scope and heuristic in operation. This paper proposes and evaluates a statistical analysis technique, Starchart, that partitions the GPU hardware/software tuning space by automatically discerning important inflection points in design parameter values. Unlike prior methods, Starchart can identify the best parameter choices within different regions of the space. Our tool is efficient - evaluating at most 0.3% of the tuning space, and often much less - and is robust enough to analyze highly variable real-system measurements, not just simulation. In one case study, we use it to automatically find platform-specific parameter settings that are 6.3× faster (for AMD) and 1.3× faster (for NVIDIA) than a single general setting. We also show how power-optimized parameter settings can save 47W (26% of total GPU power) with little performance loss. Overall, Starchart can serve as a foundation for a range of GPU compiler optimizations, auto-tuners, and programmer tools. Furthermore, because Starchart does not rely on specific GPU features, we expect it to be useful for broader CPU/GPU studies as well.
The Electromagnetic Articulography Mandarin Accented English (EMA-MAE) corpus of acoustic and 3D articulatory kinematic data

There is a significant need for more comprehensive electromagnetic articulography (EMA) datasets that can provide matched acoustics and articulatory kinematic data with good spatial and temporal resolution. The Marquette University Electromagnetic Articulography Mandarin Accented English (EMA-MAE) corpus provides kinematic and acoustic data from 40 gender and dialect balanced speakers representing 20 Midwestern standard American English L1 speakers and 20 Mandarin Accented English (MAE) L2 speakers, half Beijing region dialect and half are Shanghai region dialect. Three dimensional EMA data were collected at a 400 Hz sampling rate using the NDI Wave system, with articulatory sensors on the midsagittal lips, lower incisors, tongue blade and dorsum, plus lateral lip corner and tongue body. Sensors provide three-dimensional position data as well as two-dimensional orientation data representing the orientation of the sensor plane. Data have been corrected for head movement relative to a fixed reference sensor and also adjusted using a biteplate calibration system to place the data in an articulatory working space relative to each subject's individual midsagittal and maxillary occlusal planes. Speech materials include isolated words chosen to focus on specific contrasts between the English and Mandarin languages, as well as sentences and paragraphs for continuous speech, totaling approximately 45 minutes of data per subject. A beta version of the EMA-MAE corpus is now available, and the full corpus is in preparation for public release to help advance research in areas such as pronunciation modeling, acoustic-articulatory inversion, L1-L2 comparisons, pronunciation error detection, and accent modification training.
Adaptive nonlinearity for collisions in complex rod assemblies

We develop an algorithm for the efficient and stable simulation of large-scale elastic rod assemblies. We observe that the time-integration step is severely restricted by a strong nonlinearity in the response of stretching modes to transversal impact, the degree of this nonlinearity varying greatly with the shape of the rod. Building on these observations, we propose a collision response algorithm that adapts its degree of nonlinearity. We illustrate the advantages of the resulting algorithm by analyzing simulations involving elastic rod assemblies of varying density and scale, with up to 1.7 million individual contacts per time step.