Miracle-dz/UniFAR-FTUs huggingface dataset:
Level oriented formal model for asynchronous circuit verification and its efficient analysis method

Using a level-oriented model for verification of asynchronous circuits helps users to easily construct formal models with high readability or to naturally model datapath circuits. On the other hand, in order to use such a model on large circuits, techniques to avoid the state explosion problem must be developed. This paper first introduces a level-oriented formal model based on time Petri nets, and then proposes its partial order reduction algorithm that prunes unnecessary state generation while guaranteeing the correctness of the verification.
SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)

Although yield trials for switchgrass (Panicum virgatum L.), a potentially high value biofuel feedstock crop, are currently underway throughout North America, the genetic tools for crop improvement in this species are still in the early stages of development. Identification of high-density molecular markers, such as single nucleotide polymorphisms (SNPs), that are amenable to high-throughput genotyping approaches, is the first step in a quantitative genetics study of this model biofuel crop species. We generated and sequenced expressed sequence tag (EST) libraries from thirteen diverse switchgrass cultivars representing both upland and lowland ecotypes, as well as tetraploid and octoploid genomes. We followed this with reduced genomic library preparation and massively parallel sequencing of the same samples using the Illumina Genome Analyzer technology platform. EST libraries were used to generate unigene clusters and establish a gene-space reference sequence, thus providing a framework for assembly of the short sequence reads. SNPs were identified utilizing these scaffolds. We used a custom software program for alignment and SNP detection and identified over 149,000 SNPs across the 13 short-read sequencing libraries (SRSLs). Approximately 25,000 additional SNPs were identified from the entire EST collection available for the species. This sequencing effort generated data that are suitable for marker development and for estimation of population genetic parameters, such as nucleotide diversity and linkage disequilibrium. Based on these data, we assessed the feasibility of genome wide association mapping and genomic selection applications in switchgrass. Overall, the SNP markers discovered in this study will help facilitate quantitative genetics experiments and greatly enhance breeding efforts that target improvement of key biofuel traits and development of new switchgrass cultivars.
Good Practices for Educational Software Engineering Projects

Recent publications indicate the importance of software engineering in the computer science curriculum. In this paper, we present the final part of software engineering education at University of Groningen in the Netherlands and Vaxjo University in Sweden, where student teams perform an industrial software development project. It furthermore presents the main educational problems encountered in such real-life projects and explains how this international course addresses these problems. The main contribution of this paper is a set of seven good practices for project based software engineering education.
Importance of Respiratory Viruses in Acute Otitis Media

SUMMARY Acute otitis media is usually considered a simple bacterial infection that is treated with antibiotics. However, ample evidence derived from studies ranging from animal experiments to extensive clinical trials supports a crucial role for respiratory viruses in the etiology and pathogenesis of acute otitis media. Viral infection of the upper respiratory mucosa initiates the whole cascade of events that finally leads to the development of acute otitis media as a complication. The pathogenesis of acute otitis media involves a complex interplay between viruses, bacteria, and the host’s inflammatory response. In a substantial number of children, viruses can be found in the middle-ear fluid either alone or together with bacteria, and recent studies indicate that at least some viruses actively invade the middle ear. Viruses appear to enhance the inflammatory process in the middle ear, and they may significantly impair the resolution of otitis media. Prevention of the predisposing viral infection by vaccination against the major viruses would probably be the most effective way to prevent acute otitis media. Alternatively, early treatment of the viral infection with specific antiviral agents would also be effective in reducing the occurrence of acute otitis media.
Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella

Biofilm formation in Escherichia coli and other enteric bacteria involves the inverse regulation of the synthesis of flagella and biofilm matrix components such as amyloid curli fibres, cellulose, colanic acid and poly-N-acetylglucosamine (PGA). Physiologically, these processes reflect the transition from growth to stationary phase. At the molecular level, they are tightly controlled by various sigma factors competing for RNA polymerase, a series of transcription factors acting in hierarchical regulatory cascades and several nucleotide messengers, including cyclic-di-GMP. In addition, a surprisingly large number of small regulatory RNAs (sRNAs) have been shown to directly or indirectly modulate motility and/or biofilm formation. This review aims at giving an overview of these sRNA regulators and their impact in biofilm formation in E. coli and Salmonella. Special emphasis will be put on sRNAs, that have known targets such as the mRNAs of the flagellar master regulator FlhDC, the stationary phase sigma factor σS (RpoS) and the key biofilm regulator CsgD that have recently been shown to act as major hubs for regulation by multiple sRNAs.
Split-SAR ADCs: Improved Linearity With Power and Speed Optimization

This paper presents the linearity analysis of a successive approximation registers (SAR) analog-to-digital converters (ADC) with split DAC structure based on two switching methods: conventional charge-redistribution and Vcm-based switching. The static linearity performance, namely the integral nonlinearity and differential nonlinearity, as well as the parasitic effects of the split DAC, are analyzed hereunder. In addition, a code-randomized calibration technique is proposed to correct the conversion nonlinearity in the conventional SAR ADC, which is verified by behavioral simulations, as well as measured results. Performances of both switching methods are demonstrated in 90 nm CMOS. Measurement results of power, speed, and linearity clearly show the benefits of using Vcm-based switching.
On the recurrence coefficients of semiclassical Laguerre polynomials

It is known [L. Boelen, W. Van Assche, Proc. Amer. Math. Soc. 138 (2010), 1317–1331] that the coefficients of the three-term recurrence relation for orthogonal polynomials with respect to a semiclassical extension of the Laguerre weight satisfy a discrete Painlevé equation. By using the Toda system for the recurrence coefficients we show that this discrete equation can be obtained from a Bäcklund transformation of the fourth Painlevé equation.
A logarithmic upper bound on the minimum distance of turbo codes

We derive new upper bounds on the minimum distance, which turbo codes can maximally attain with the optimum interleaver of a given length. The new bounds grow approximately logarithmically with the interleaver length, and they are tighter than all previously derived bounds for medium-length and long interleavers. An extensive discussion highlights the impacts of the new bounds in the context of interleaver design and provides some new design guidelines.
The Emerging Biology of Autism Spectrum Disorders

Expression patterns of the diverse genes disrupted in autism spectrum disorders in the developing brain give a fresh perspective on the underlying biology. Autism spectrum disorders (ASD) are a genetically and phenotypically heterogeneous group of syndromes defined by fundamental impairments in social reciprocity and language development accompanied by highly restrictive interests and/or repetitive behaviors. Recent advances in genetics, genomics, developmental neurobiology, systems biology, monogenic neurodevelopment syndromes, and induced pluripotent stem cells (iPSC) are now offering remarkable insights into their etiologies and converging to provide a clear and immediate path forward from the bench to the bedside.
Truth Stranger Than Fiction

TIM RODA: PHOTOGRAPHS GREG KUCERA GALLERY SEATTLE, WASHINGTON JANUARY 5-FEBRUARY 11, 2006 Tim Roda's second exhibition, on view at Greg Kucera Gallery in Seattle, Washington, exemplifies his continued development with staged familial narratives that marry theatre, domesticity, and fabricated realities. His intricately staged black-and-white photographs have remained focused on depictions of his immediate family and often convey tense dramatic moments between the characters. However, Roda's true sophistication lies in his surrealist tendencies, examining links between fantasy and reality. Furthermore, many images include a literal mirror, which supplies multiple perspectives of one character in the same scene. The reflections enliven an internally referential environment and expand photographic space and reality to include what is unseen or veiled. In Untitled #63 (2005), an image roughly two feet tall and three feet wide, Roda's son Ethan is bundled in winter attire and holds a pair of large lawn shears. The artist is sitting nearby wearing similar gear and a white costume beard. He is leaning over with one foot pressed firmly on the back end of a fabricated goose. (The sculptural components and sets utilized in Roda's photographs are often made from found or non-precious materials such as clay, wood, or paper.) One of his hands grips a knife, while the other has a tight clutch on the bird's neck. The boy passively places his sharp instrument on the neck of the goose and refrains from overt emotion--an element present in many of Roda's sitters. Even if the viewer is unaware of the real-life familial ties between the boy and the man, this theatrical scene communicates an undertone of domestic intimacy. Roda's family is central to the artist's photographs in both concept and creation. Young Ethan is captured in nearly all of the images, drawing a link to the artist's childhood. Roda explains, "A camera is used to record one moment of time that hovers between memories and constructed commentaries yet is a documentation of 'real time' events for me, my wife Allison and son Ethan. Although we three are the immediate subjects, the work is filled with metaphorical reverberations of my own memories of childhood and family traditions. " (1) His wife is essential to the process, since she also often releases the shutter. Roda's way of life and familial customs becomes intrinsic to his photographic process. In addition to depicting his family, Roda's images point toward a surrealist sentiment captured in his scenarios which meld familiar domestic scenes and peculiar environments. In particular, a correlation can be drawn to the artist Ralph Eugene Meatyard, who, like Roda, used friends and family members in his work, did not make images from double negatives, and was intrigued with creating otherworldly settings. …
Increasing robustness of LSB audio steganography using a novel embedding method

We present a novel high bit rate LSB audio watermarking method. The basic idea of the proposed LSB algorithm is watermark embedding that causes minimal embedding distortion of the host audio. Using the proposed two-step algorithm, watermark bits are embedded into higher LSB layers, resulting in increased robustness against noise addition or MPEG compression. Listening tests showed that the perceptual quality of watermarked audio is higher in the case of the proposed method than in the standard LSB method.
Implementation of MPEG-2 AAC on 16-bit Fixed-Point DSP

Efficient implementation of MPEG-2 advanced audio coding (AAC) decoder on low cost 16-bit fixed-point DSP needs some techniques to reduce the computational complexity. In this paper, we introduce an extra gain factor to adjust the value range of the spectrum data, and by adapting other techniques such as FFT, a low cost and high quality MPEG-2 AAC decoder is obtained
Detection, pathogenesis, and therapy of respiratory syncytial virus infections

Respiratory syncytial virus (RSV) infection is a major cause of serious lower respiratory disease in infancy and early childhood. The unique pathogenesis of lower respiratory illness due to RSV offers some intriguing clues to the role of the human immune system in both protection against and development of respiratory illness. More than any other virus, rapid diagnostic techniques have been especially successful in identifying RSV infection. Many of these techniques could be easily adaptable to diagnosis of influenza virus infection and other agents. Finally, ribavirin therapy of RSV infection represents one of the few instances in which antiviral therapy has been shown to be effective for respiratory illnesses. Fundamental observations in these areas in the case of RSV infection open up new and exciting pathways for investigation of respiratory infection due to other viral, chlamydial, and mycoplasmal agents.
PrAd: Enabling Privacy-Aware Location based Advertising

Smart phones and mobile devices have become more and more ubiquitous recently. This ubiquity gives chance for mobile advertising, especially location-based advertising, to develop into a very promising market. In many location-based advertising services, it is implied that service providers would obtain actual locations of users in order to serve relevant advertisements which are near users' current locations. However, this practice has raised a significant privacy concern as various private information of an user can be inferred based on her locations and trajectories. In this work, we propose PrAd, a location-based advertising model that appreciates users' location privacy; i.e. it never reveals their locations to any untrusted party. Our solution is conceptualized based on several state-of-the-art privacy preserving techniques such as data obfuscation, space encoding and private information retrieval (PIR). We especially introduce algorithmic modification to existing hardware-based PIR technique to make it more practical and thus suit real-time applications. Moreover, PrAd enables a correct billing mechanism among involved parties without revealing any individual sensitive information. Finally, we confirm the effectiveness of our proposed framework by evaluating its performance using a real world dataset.
A pr 2 01 1 A weighted configuration model and inhomogeneous epidemics

A random graph model with prescribed degree distribution and degree dependent edge weights is introduced. Each vertex is independently equipped with a random number of half-edges and each half-edge is assigned an integer valued weight according to a distribution that is allowed to depend on the degree of its vertex. Half-edges with the same weight are then paired randomly to create edges. An expression for the threshold for the appearance of a giant component in the resulting graph is derived using results on multi-type branching processes. The same technique also gives an expression for the basic reproduction number for an epidemic on the graph where the probability that a certain edge is used for transmission is a function of the edge weight. It is demonstrated that, if vertices with large degree tend to have large (small) weights on their edges and if the transmission probability increases with the edge weight, then it is easier (harder) for the epidemic to take off compared to a randomized epidemic with the same degree and weight distribution. A recipe for calculating the probability of a large outbreak in the epidemic and the size of such an outbreak is also given. Finally, the model is fitted to three empirical weighted networks of importance for the spread of contagious diseases and it is shown that R0 can be substantially overor underestimated if the correlation between degree and weight is not taken into account.
Characterization of TP53 mutations in clonal cytopenia of undetermined significance

of 24-h urinary prednisolone excretion and a modest association with the daily prednisolone dose, in keeping with considerable inter-subject pharmacokinetic variability. Twenty-4h urinary prednisolone excretion is considered to reflect the overall exposure to prednisolone. Previously, it has been shown that prednisolone dose-dependently inhibits the release of interleukin-6 (IL-6) which is known to induce hepcidin expression. We had no data available on IL-6 levels to assess whether effects on IL-6 is the mechanism behind the association of prednisolone with hepcidin. The possible role of prednisolone as a direct hepcidin antagonist and possible mechanisms linking prednisolone with hepcidin need to be delineated in more detail in future studies. The major strength of this report is the large cohort of RTRs with availability of concurrent 24-h urinary prednisolone excretion and hepcidin data. Limitations are that it comprises a single center study, and that we cannot exclude the possibility of residual confounding. In conclusion, lower serum hepcidin levels are related to higher 24-h urinary prednisolone excretion in RTRs independent of clinically relevant covariates. Our findings extend earlier data concerning effects of other (synthetic) steroids on hepcidin regulation, and provide a rationale to more precisely delineate direct or indirect effects of glucocorticoids on hepcidin regulation. From a clinical perspective, our findings lend support to the possibility that prednisolone may be regarded as a hitherto unappreciated hepcidin antagonist.
Fuzzy logic Supply Chain Agility Assessment methodology

Supply Chain Agility Assessment has been considered as one of the most important issues in world class manufacturing research study. The environmental issue as well as speed, variety, flexibility and integration in production line come along with customer relationship and mass customization concept should come to light in today¿s research study. To achieve the competitive edge, companies must align with suppliers and customers to streamline operations, as well as agility characteristic beyond individual companies. Consequently agile supply chain (ASC) is considered as a dominant competitive advantage. However, so far a little effort has been made to build ASC assessment methodology in recent years. Therefore, due to ambiguity of agility assessment, we have constructed a fuzzy rule based system, considering agility capabilities such as Responsiveness, competency, flexibility and Quickness to evaluate agility in supply chains. This evaluation helps managers to perform gap analysis between existent agility level and the desired one.
The Role of the Carcinoembryonic Antigen Receptor in Colorectal Cancer Progression

Clinical and experimental data suggest that carcinoembryonic antigen (CEA, CD66e, CEACAM-5) plays a key role in the formation of hepatic metastasis from colorectal and other types of epithelial cancers. The molecular events involved in CEA-induced metastasis have yet to be defined. Our group first cloned the gene (CEAR) for CEA-binding protein from the surface of fixed liver macrophages, (Kupffer cells). In this study to further elucidate the role of CEAR in colorectal cancer progression, its expression in colorectal cancer cells was suppressed by short hairpin RNAs (shRNAs) in CEA-overexpressing and CEA - negative MIP-101 colorectal cancer cell lines. The data show that targeted suppression of endogenous CEAR in tumor cells resulted in changes in cell invasiveness. RT-PCR data indicated reduced levels of E-cadherin, Snail, MMP-2, and Oct-4 in the clones with suppressed CEAR suggesting a role in the epithelial mesenchymal transition. The comparative analysis of tumorigenic activity to the liver of the cell lines with suppressed CEAR has also been conducted using an intrasplenic injection model in immuno-deficient mice. This data shows a decrease in tumor progression associated with CEAR suppression. In summary the results of this study revealed a novel role for CEAR gene in the regulation of colorectal cancer cell invasiveness and progression.
Optimization of the Economy of an Oil-Producing Country

A dynamic socioeconomic model of a small oil-producing country has been set up, based on a two-sector economy (oil sector and non-oil sector) and including population dynamics, internal consumption, and external investment. With the aid of a computer program, the model can be used to optimize the rates of oil production and investment in oil production. The criterion used for optimization is the present value of future income (including the worth of remaining oil reserves in the ground). Comparative results for a 50-year period are obtained, showing that optimum oil production peaks in the first 10-year period and drops gradually. The optimality of this production pattern is almost unaffected by different planning parameters, while the optimal schedule for investment in the oil sector is sensitive to other planning parameter choices.
Conformal flattening of non-planar surface

This paper presents an approach that uses conformal mapping to flattening a 3D surface to 2D plane. We propose an algorithm by traversing the mesh in a region growing way. The algorithm is greedy and begins with a seed triangle which can be chosen freely. In each operation, we develop a piecewise linear mapping function that is conformal. In addition, at first step, we initialize the planar triangle which corresponding to the seed triangle. The initialization ensures that the seed triangle flattening process produce no distortion. And in other steps, we reduce the distortion by unifying the vertices in the plane. Our approach is efficient and fast enough.
800 MHz-band low noise low distortion Si-MMIC front-end using BJT/MOSFET LNA and MOSFET mixer

Both low noise and low distortion characteristics are strongly desired for cellular terminal receiver application. In the case of Si-MMIC, BJT has superior feature in its low noise performance and MOSFET has it in low distortion performance. By using BJT amplifier as the 1st stage of LNA and MOSFET as the 2nd stage of LNA and a down mixer, both low noise and low distortion performance is achieved. The fabricated Si-MMIC front-end, which contains two-stage LNA and down mixer and LO amplifier, performs 3.7 dB NF, 16.7 dB conversion gain and -15.5 dBm IIP/sub 3/ with 3V/13.7 mA d.c. power and -10 dBm LO power.
Light Propagation Maps on Parallel Graphics Architectures

Light going through a participating medium like smoke can be scattered or absorbed by every point in the medium. To accurately render such a medium we must compute the radiance resulting at every point inside the medium because of these physical effects, which have been modeled by the radiative transfer equation. Computing the radiance at any point inside a participating medium amounts to numerically solving this radiative transport equation. Discrete Ordinate Method (DOM) is a widely used solution method. DOM is computationally intensive. Fattal [Fat09] proposed Light Propagation Maps (LPM) to expedite DOM computation. In this paper we propose a streaming based parallelization of LPM to run on SIMD graphics hardware. Our method is fast and scalable. We report more than 20x speed improvement by using our method as compared to Fattal’s original method. Using our approach we are able to render 64x64x64 dynamic volumes with multiple scattering of light at interactive speed on complex lighting, and are able to render volumes of any size independent of the GPU memory capability.