Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic association mapping at the crossroads: which test and why? Overview and practical guidelines.

Until about a decade ago, genetic association testing essentially meant case control association analysis using genetic markers. Concerns about population stratification propelled family-based tests of association into widespread use and challenged the classic case control design. The literature now contains a vast collection of different family-based methods, most of which are based on the transmission/disequilibrium test (TDT). Some methods extend the original TDT to accommodate multiallelic markers, variable pedigree constellations, multiple loci, etc. Other methods go beyond the original design of the TDT to detect genetic association via haplotype sharing. Most recently, we have witnessed a revival of case control methods that control for population stratification. The purpose of this review is to help orient readers to the rapidly developing methods of association testing and enhance their understanding of the basic principles of these approaches. We present an overview of the development of genetic association tests, with practical guidelines on which test might be the most suitable for a given study.
Using MACS to Identify Peaks from ChIP‐Seq Data

Model‐based Analysis of ChIP‐Seq (MACS) is a command‐line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP‐Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor binding sites and histone modification–enriched regions if the ChIP‐Seq data, with or without control samples, are given. This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks. Furthermore, the basic ideas for the MACS algorithm and its appropriate usage are discussed. Curr. Protoc. Bioinform. 34:2.14. 1‐2.14. 14. © 2011 by John Wiley & Sons, Inc.
Solid solution GaSe1−xSx single crystals for THz generation

A table top source of coherent Terahertz (30-1000 μm) radiation, which is high power, narrow bandwidth, and broadly tunable, is high desired for applications in imaging, non-destructive testing (NDT), quantum, security and biomedical technologies. In spite of intensive research over many decades such a device remains elusive. Sulpher doped Gallium Selenide (GaSex−1Sx) solid solution ε-polytype crystals are an outstanding candidate for the efficient generation of radiation and tunability throughout the majority of the Terahertz (THz) regime; thanks to the prodigious linear and nonlinear optical properties of the Gallium Selenide (GaSe) parent crystal. Close control of doping and the crystal growth process enable the manufacture of superior quality nonlinear crystals, where the optical properties may be engineered and the mechanical properties vastly improved. Thus overcoming many of the physical issues that, despite its exceptional optical properties, have frustrated the widespread adoption of GaSe for laser frequency down conversion to the THz regime. In order to fully exploit the potential of GaSex−1Sx crystals and successfully design efficient sources for THz generation the optical properties of these crystals must be accurately determined and their transformation with doping well understood. The work in this thesis aims to accurately determine the optical properties of GaSe, Gallium Sulphide (GaS) and GaSex−1Sx crystals in the Far-Infrared and THz regimes to enable this exploitation. In the first phase of investigation we determine the linear refractive index (n) and absorption (α) coefficient for both the o and e waves in the THz regime (0.14.5 THz) using Terahertz Time Domain Spectroscopy (THz-TDS) for GaSe, and a dense set of GaSex−1Sx crystals (x = 0.05 0.11 0.22 0.29 0.44). Measurements of THz dispersion and absorption properties of GaS crystals are performed for the first time. The transformation of the optical properties of the crystals and their phonon structure is studied. We examine the sources of inaccuracy in the THzTDs measurements of high refractive index birefringent crystals and propose a set of criteria for the selection of adequate data. The nonlinear Figure of Merit (FOM) of available high quality GaSex−1Sx crystals is found to be an order of magnitude less than that predicted in the literature, with FOM = 19.8 for GaSe, FOM = 17 for GaSex−1Sx, on the other hand estimates for double doping with Sulphur and Aluminium predict significant enhanced of these FOM values, up to 5-10 times. In the second phase of investigation we examine the phonon band of the GaSe, GaS and GaSex−1Sx by FTIR and Raman spectroscopy. For the first time we determine the absorption coefficients of the main phonon peak in the set of GaSex−1Sx crystals. The transformation of the phonon band with doping is studied. In the third phase of investigation we attempt to determine the nonlinear optical properties deff and n2 of GaSe and GaSex−1Sx in the Far Infra-Red (FIR) and THz regimes using the Maker fringe and Z-scan methods on the FELIX free electron laser.
The development of tissue engineering corneal scaffold: which one the history will choose?

Since the 21st century, the development of corneal tissue engineering technology has been developing rapidly. With the progress of biomaterials, cell culture and tissue engineering technology, tissue engineering cornea has gained great development in both basic scientific research and clinical application. In particular, tissue engineered corneal scaffolds are the core components of tissue engineered corneas. It is the focus of current research on tissue engineering cornea to search for scaffolds with good biocompatibility, high safety and good biomechanical properties. In this paper, the recent research progress of tissue engineering corneal materials is reviewed.
The error exponent with delay for lossless source coding

In channel coding, reliable communication takes place at rates below capacity at the fundamental cost of end-to-end delay. Error exponents tell us how much faster convergence is when we settle for less rate. For lossless source coding, entropy takes the place of capacity and error exponents tell us how much faster convergence is when we use more rate. While in channel coding without feedback the block error exponent is a good proxy for studying the more fundamental tradeoff with fixed end-to-end delay, it is not so in source coding. Block-coding error exponents are quite conservative (despite being tight! ) when it comes to the tradeoff with delay. Nonblock codes can achieve much better performance with fixed delay and we present both the fundamental bound and how to achieve it in a delay-universal manner. The proof gives substance to Shannon's cryptic statement about how the duality between source and channel coding is like the duality between the past and the future.
Cost-effectiveness of coronary MDCT in the triage of patients with acute chest pain.

OBJECTIVE Patients at low risk for acute coronary syndrome (ACS) who present to the emergency department complaining of acute chest pain place a substantial economic burden on the U.S. health care system. Noninvasive 64-MDCT coronary angiography may facilitate their triage, and we evaluated its cost-effectiveness. MATERIALS AND METHODS A microsimulation model was developed to compare costs and health effects of performing CT coronary angiography and either discharging, stress testing, or referring emergency department patients for invasive coronary angiography, depending on their severity of atherosclerosis, compared with a standard-of-care (SOC) algorithm that based management on biomarkers and stress tests alone. RESULTS Using CT coronary angiography to triage 55-year-old men with acute chest pain increased emergency department and hospital costs by $110 and raised total health care costs by $200. In 55-year-old women, the technology was cost-saving; emergency department and hospital costs decreased by $410, and total health care costs decreased by $380. Compared with the SOC, CT coronary angiography-based triage extended life expectancy by 10 days in men and by 6 days in women. This translated into corresponding improvements of 0.03 quality-adjusted life years (QALYs) and 0.01 QALYs, respectively. The incremental cost-effectiveness ratio for CT coronary angiography was $6,400 per QALY in men; in women, CT coronary angiography was cost-saving. Cost-effectiveness ratios were sensitive to several parameters but generally remained in the range of what is typically considered cost-effective. CONCLUSION CT coronary angiography-based triage for patients with low-risk chest pain is modestly more effective than the SOC. It is also cost-saving in women and associated with low cost-effectiveness ratios in men.
Imatinib quantification in human serum with LC-MS3 as an effective way of protein kinase inhibitor analysis in biological matrices

Abstract Background: As imatinib gained a lot of attention in the field of medicine, appropriate methods are needed for drug analysis. LC-MS/MS combined with complex sample preparation and column enrichment is usually the method of choice when high sensitivity is necessary. The application of LC-MS3 in imatinib quantification has not been discussed in the literature. Methods: An LC-MS3 imatinib quantification method was developed and validated in human serum. The sample preparation was based on the liquid-liquid extraction of 50 μL human serum. Chromatographic separation was performed using a Luna 5 μm C18 (2) 100 A, 150 mm×2 mm column and the elution was done using a mobile phase consisting of A (H2O/methanol=95/5, v/v) and B (H2O/methanol=3/97, v/v), both with 10 mM ammonium acetate and 0.1% acetic acid. Results: The conditions applied resulted in a limit of detection/quantification value of 0.14/0.45 ng/mL reached without a sophisticated sample preparation technique or enrichment column application. It could be demonstrated that MS3 detection is a very effective way of sensitive imatinib quantification. Further, it could be stated that the strategy presented can be very useful for a sensitive analysis of other protein kinase inhibitors, because their molecule structure is appropriate for MS3 detection. Conclusions: The presented analytical strategy is an effective way of protein kinase inhibitor analysis in human serum.
Therapeutic Effects of Human Amniotic Fluid-Derived Stem Cells on Renal Interstitial Fibrosis in a Murine Model of Unilateral Ureteral Obstruction

Interstitial fibrosis is regarded as the main pathway for the progression of chronic kidney disease (CKD) and is often associated with severe renal dysfunction. Stem cell-based therapies may provide alternative approaches for the treatment of CKD. Human amniotic fluid-derived stem cells (hAFSCs) are a novel stem cell population, which exhibit both embryonic and mesenchymal stem cell characteristics. Herein, the present study investigated whether the transplantation of hAFSCs into renal tissues could improve renal interstitial fibrosis in a murine model of unilateral ureteral obstruction (UUO). We showed that hAFSCs provided a protective effect and alleviated interstitial fibrosis as reflected by an increase in microvascular density; additionally, hAFSCs treatment beneficially modulated protein levels of vascular endothelial growth factor (VEGF), hypoxia inducible factor-1α (HIF-1α) and transforming growth factor-β1 (TGF-β1). Therefore, we hypothesize that hAFSCs could represent an alternative, readily available source of stem cells that can be applied for the treatment of renal interstitial fibrosis.
Feature and distribution normalization schemes for statistical mismatch reduction in reverberant speech recognition

Reverberant noise has been a major concern in speech recognition systems. Many speech recognition systems, even with state-of-art features, fail to respond to reverberant effects and the recognition rate deteriorates. This paper explores the significance of normalization strategies in reducing statistical mismatches for robust speech recognition in reverberant environment. Most normalization works focused only on ambient noise and have yet been experimented on reverberant noise. In addition, we propose a new approach for the odd order cepstral moment normalization which is computationally more efficient and reduces the convergence rate in the algorithm. The proposed method is experimentally justified and corroborated by the performance of other normalization schemes. The results emphasize the significance of reducing statistical mismatches in feature space for reverberant speech recognition.
A Monitoring System Based on Embedded Internet Technology for Embedded Devices

A monitoring system based on the embedded Internet technology for embedded devices is designed and implemented. The Browser/Server mode is adopted in this monitoring system and the realization technologies of an embedded Web server, which includes a thin TCP/IP stack, an embedded file system and a device gateway, are discussed in details. The way of embedding the Web server in the device makes it possible for numerous embedded devices to be connected to the Internet. The results of system performance testing show that the system can meet most of the embedded Internet applications demands and the purposes of online access, control and management the embedded devices using a standard Web browser over the Internet can be realized.
Heparanase-Induced GEF-H1 Signaling Regulates the Cytoskeletal Dynamics of Brain Metastatic Breast Cancer Cells

Heparanase is the only mammalian endoglycosidase which has been widely implicated in cancer because of its capability to degrade heparan sulfate chains of heparan sulfate proteoglycans (HSPG). Specifically, the cell surface HSPG syndecan-1 and -4 (SDC1 and SDC4) are modulators of growth factor action, and SDC4 is implicated in cell adhesion as a key member of focal adhesion complexes. We hypothesized that extracellular heparanase modulates brain metastatic breast cancer (BMBC) cell invasiveness by affecting cytoskeletal dynamics, SDC4 carboxy-terminal–associated proteins, and downstream targets. We used two independently derived human BMBC cell systems (MB-231BR and MB-231BR3), which possess distinct cellular morphologies and properties. Highly aggressive spindle-shaped 231BR3 cells changed to a round cell morphology associated with expression of the small GTPase guanine nucleotide exchange factor-H1 (GEF-H1). We showed that GEF-H1 is a new component of the SDC4 signaling complex in BMBC cells. Treatment with heparanase resulted in regulation of the SDC4/protein kinase C α axis while maintaining a constitutive GEF-H1 level. Third, GEF-H1 knockdown followed by cell exposure to heparanase caused a significant regulation of activities of Rac1 and RhoA, which are GEF-H1 targets and fundamental effectors in cell plasticity control. Fourth, L-heparanase augmented expression of β1 integrin in BMBC cells and of vascular cell adhesion molecule 1 (VCAM1; the major β1 integrin receptor) in human brain microvascular endothelial cells. Finally, using a newly developed blood–brain barrier in vitro model, we show that BMBC cell transmigration was significantly reduced in GEF-H1 knockdown cells. These findings implicate heparanase in mechanisms of cytoskeletal dynamics and in the cross-talk between tumor cells and vascular brain endothelium. They are of relevance because they elucidate molecular events in the initial steps leading to BMBC onset and capturing distinct roles of latent and active heparanase in the brain microenvironment. Mol Cancer Res; 10(6); 689–702. ©2012 AACR.
The regulation of E2F by pRB-family proteins.

Much has been written about the functions of the E2F transcription factor and the product of the retinoblastoma tumor suppressor gene (pRB). These proteins have been described in terms that vary from ‘‘master regulators of cell cycle and differentiation’’ to ‘‘peripheral factors that lie outside the core cell cycle machinery. ’’ Most often, pRB and E2F are described in short and simple terms as opposing molecules that control the G1to Sphase transition. There is an element of truth in each of these descriptions. E2Fand pRB-family proteins clearly play important roles in cell proliferation and differentiation. The extent to which they are master regulators or peripheral factors is a question of semantics, and these terms tell us more about the writer than the proteins. Perhaps the most important development in the E2F literature is the appreciation that E2F and pRB are not unique molecules with functions that can be defined in black and white terms. Instead, E2F and pRB represent families of related proteins that have diverse and occasionally contradictory activities. We now know a great deal about E2F complexes and pRB-family proteins and the emerging picture defies a one-line explanation. The fascinating variety of activities ascribed to various E2F complexes challenges us to place these into context and to find the right perspective. This review is presented into two sections. The first section summarizes the tremendous progress into the composition and properties of E2F and the many interactions that coordinately regulate E2F-dependent transcription. The rapid growth in the size of the E2F literature hides the fact that several fundamental questions have not been fully answered. Because of this, the second section of this review details five unresolved issues that have been highlighted by recent publications. It is impossible to cover all of the relevant E2F literature in a single review and readers are referred to reviews by Farnham (1995); Sardet et al. (1997); Helin (1998); and Yamasaki (1998) for a comprehensive survey.
Business process in supply chain integration in sugar and ethanol industry

Purpose – Despite the increasing interests in supply chain management (SCM) within academy and industrial environment, there is still a lack of academic literature concerning topics such as methodologies to guide and support supply chain integration. The paper aims to discuss these issues. Design/methodology/approach – This article presents the application of a diagnosis method in a Brazilian company from the sugar and ethanol industry to identify the level of supply chain integration. The diagnosis method is based on Cooper, Lambert and Pagh reference model for SCM. The method involves nine referential axes established from the eighth key business processes of the reference model. Findings – It was pre-tested and supplemented with findings from interviews with academics and practitioners. Additionally, an illustration application was conducted in three relevant companies. Originality/value – The application results were useful for refining the method that can be considered as a diagnosis instrument to pe.
Multiscale finite element analyses on mechanical properties of graphene-reinforced composites

ABSTRACT A new multiscale simulation method for analyzing the mechanical properties of graphene-reinforced composites is proposed. The atomistic and the macroscopic scales are combined in the proposed finite element modeling approach. In the nanoscale analysis, a space frame structure of graphene is selected, the carbon atoms are described as nodes, and the carbon–carbon covalent bonds are represented with nanoscale beams. The macroscopic homogeneous isotropic model of the matrix and the interface is included in the representative volume element of the composites. The effect of graphene volume fraction and different inclined angles on the mechanical properties of the composites is investigated under axial tension. The simulation results showed that with the increase in the graphene volume fraction, the Young's modulus of the composites was increased significantly. The Young's modulus of the composites was highly dependent on the size of graphene. The stress transfer in the interface of the composites was also analyzed using this multiscale approach.
A Novel Approach of Mining Frequent Sequential Pattern from Customized Web Log Preprocessing

Millions of visitors interact daily with web sites around the world. The several kinds of data have to be organized in a manner that they can be accessed by several users effectively and efficiently. Web mining is the extraction of exciting and constructive facts and inherent information from artifacts or actions related to the WWW. Web usage mining is a kind of data mining method that can be useful in recommending the web usage patterns with the help of users’ session and behavior. Web usage mining includes three process, namely, preprocessing, pattern discovery and pattern analysis. After the completion of these three phases the user can find the required usage patterns and use this information for the specific needs. Web usage mining requires data abstraction for pattern discovery. This dataion for pattern discovery. This data abstraction is achieved through dataion is achieved through data preprocessing. Experiments have proved that advanced data preprocessing technique can enhanced the quality of data preprocessing results. To capture users’ web access behavior, one promising approach is web usage mining which discovers interesting and frequent user access patterns from web logs. Sequential Web page Access pattern mining has been a focused theme in data mining research for over a decade with wide range of applications. The aim of discovering frequent sequential access (usage) patterns in Web log data is to obtain information about the navigational behavior of the users. This can be used for advertising purposes, for creating dynamic user profiles etc. In this paper we survey about the Sequential Pattern Mining
Callus Cultures of Arabidopsis

Protoplasts are plant cells lacking cell walls. They can be generated from stationary callus cultures derived from Arabidopsis thaliana seedlings. After treatment of the callus with cellulase and pectinase, protoplasts are inoculated with viral RNAs using polyethylene glycol. After various times postinoculation, total RNA is extracted and subjected to electrophoresis on nondenaturing agarose gels for further analysis. Stationary callus cultures are simpler to maintain than more traditional suspension cultures and yield high‐quality, uniform protoplasts. Protoplasts prepared in this fashion can also be used for uptake of DNA.
Simultaneous template optimization and mask assignment for DSA with multiple patterning

Block Copolymer Directed Self-Assembly (DSA) is a promising technique to print contacts/vias for the 10nm technology node and beyond. By using hybrid lithography that cooperates DSA with multiple patterning, multiple masks are used to print the DSA templates and then the templates can be used to guide the self-assembly of the block copolymer. In this paper, we propose approaches to solve the simultaneous template optimization and mask assignment problem for DSA with multiple patterning. We verified in experiments that our approaches remarkably outperform the state of the art work in reducing the manufacturing cost.
Data vs. Decision Fusion in the Category Theory Framework

In this paper we first formally define the notions of data fusion and decision fusion. Then we formulate a theorem that decision fusion is a special case of data fusion. We show the meaning of this theorem on a simple example of edge detection. Edge detection can be done in two ways: by first fusing the original images and then detecting edges in the fused image (data fusion) or by first detecting edges in each image separately and then fusing the results (decision fusion) of edge detection in the decision fusion block. We show, first in general and then on the edge detection example, that decision fusion can be viewed as a special case of data fusion. To the designer of an information fusion system this means that the choice of the decision fusion approach over data fusion in any specific case needs to be supported by some additional consideration, for instance the computational complexity of the fusion algorithm.