Miracle-dz/UniFAR-FTUs huggingface dataset:
Signal Denoising With Random Refined Orthogonal Matching Pursuit

In this paper, an efficient sparse recovery algorithm called random refined orthogonal matching pursuit (RROMP) is proposed for signal denoising. Given a noisy signal, the RROMP algorithm first generates several sparse representations of it by applying a multi-selection strategy and a false discovery rate (FDR) control, instead of seeking the sparsest one. The multi-selection strategy accelerates the whole process of generating the representations, while the FDR control enables each representation to be competitive. Then the generated representations are averaged to form a more accurate estimate in the sense of mean-square-error (MSE). Our experiments on both synthetically generated signals and natural images demonstrate the superiority of the RROMP algorithm.
TAKES: a fast method to select features in the kernel space

Feature selection is an effective tool to deal with the "curse of dimensionality". To cope with the non-separable problem, feature selection in the kernel space has been investigated. However, previous study cannot adequately estimate the intrinsic dimensionality of the kernel space. Thus, it is difficult to accurately preserve the sketch of the kernel space using the learned basis, and the feature selection performance is affected. Moreover, the computing load of the algorithm reaches at least cubic with the number of training data. In this paper, we propose a fast framework to conduct feature selection in the kernel space. By designing a fast kernel subspace learning method, we automatically learn the intrinsic dimensionality and construct an orthogonal basis set of kernel space. The learned basis can accurately preserve the sketch of kernel space. Then backed by the constructed basis, we directly select features in kernel space. The whole proposed framework has a quadratic complexity with the number of training data, which is faster than existing kernel methods for feature selection. We evaluate our work under several typical datasets and find it not only preserves the sketch of the kernel space more accurately but also achieves better classification performance compared with many state-of-the-art methods.
Designing Pixel-Oriented Visualization Techniques: Theory and Applications

Visualization techniques are of increasing importance in exploring and analyzing large amounts of multidimensional information. One important class of visualization techniques which is particularly interesting for visualizing very large multidimensional data sets is the class of pixel-oriented techniques. The basic idea of pixel-oriented visualization techniques is to represent as many data objects as possible on the screen at the same time by mapping each data value to a pixel of the screen and arranging the pixels adequately. A number of different pixel-oriented visualization techniques have been proposed in recent years and it has been shown that the techniques are useful for visual data exploration in a number of different application contexts. In this paper, we discuss a number of issues which are important in developing pixel-oriented visualization techniques. The major goal of this article is to provide a formal basis of pixel-oriented visualization techniques and show that the design decisions in developing them can be seen as solutions of well-defined optimization problems. This is true for the mapping of the data values to colors, the arrangement of pixels inside the subwindows, the shape of the subwindows, and the ordering of the dimension subwindows. The paper also discusses the design issues of special variants of pixel-oriented techniques for visualizing large spatial data sets.
Identification of Highly Expressed Genes in Peripheral Blood T Cells from Patients with Atopic Dermatitis

Background: Analysis of genes that are differentially expressed in patients with atopic dermatitis (AD) and normal individuals will provide important information on the underlying molecular pathogenetic mechanisms of AD. Methods: Transcript of freshly isolated peripheral blood T cells from 59 individuals were analyzed with a fluorescent differential display (FDD) method. Ninety-two differentially expressed genes were identified in this manner. Additionally, real-time quantitative RT-PCR was employed to investigate the expression of the FDD-selected genes and also genes related to T cell function. Results: A number of genes, including CC chemokine receptor 4, T cell-specific tyrosine kinase (Emt/Itk), integrin β1, integrin α6, IQGAP1 and MAR/SAR DNA-binding protein (SATB1), were shown to be more highly expressed in patients with moderate and/or severe AD than in controls or patients with mild AD. Because the products of these upregulated genes influence chemotaxis, adhesion, migration and Th2 polarization, it is suggested that in more severe AD, circulating T cells may function differently in this regard. Several other genes, the role of which in T cell function is currently unknown, were also found to be differentially expressed in AD. These included the heat shock protein 40 and vasopressin-activated calcium-mobilizing receptor 1. Conclusion: The upregulated genes identified in this work may serve as useful markers for moderate to severe AD as opposed to normal or mild AD and also as markers indicating progression to more severe AD. Further functional characterization will provide a better understanding of the pathophysiology of circulating T cells in AD.
During the initiation of fermentation overexpression of hexokinase PII in yeast transiently causes a similar deregulation of glycolysis as deletion of Tps1

In the yeast Saccharomyces cerevisiae a novel control exerted by TPS1 (GGS1FDP1BYP1CIF1GLC6TSS1)‐encoded trehalose‐6‐phosphate synthase, is essential for restriction of glucose influx into glycolysis apparently by inhibiting hexokinase activity in vivo. We show that up to 50‐fold overexpression of hexokinase does not noticeably affect growth on glucose or fructose in wild‐type cells. However, it causes higher levels of glucose‐6‐phosphate, fructose‐6‐phosphate and also faster accumulation of fructose‐1,6‐bisphosphate during the initiation of fermentation. The levels of ATP and Pi correlated inversely with the higher sugar phosphate levels. In the first minutes after glucose addition, the metabolite pattern observed was intermediate between those of the tps1Δ mutant and the wild‐type strain. Apparently, during the start‐up of fermentation hexokinase is more rate‐limiting in the first section of glycolysis than phosphofructokinase. We have developed a method to measure the free intracellular glucose level which is based on the simultaneous addition of d‐glucose and an equal concentration of radiolabelled l‐glucose. Since the latter is not transported, the free intracellular glucose level can be calculated as the difference between the total d‐glucose measured (intracellular+periplasmic/extracellular) and the total l‐glucose measured (periplasmic/extracellular). The intracellular glucose level rose in 5 min after addition of 100 mm‐glucose to 0·5–2 mm in the wild‐type strain, ±10 mm in a hxk1Δ hxk2Δ glk1Δ and 2–3 mm in a tps1Δ strain. In the strains overexpressing hexokinase PII the level of free intracellular glucose was not reduced. Overexpression of hexokinase PII never produced a strong effect on the rate of ethanol production and glucose consumption. Our results show that overexpression of hexokinase does not cause the same phenotype as deletion of Tps1. However, it mimics it transiently during the initiation of fermentation. Afterwards, the Tps1‐dependent control system is apparently able to restrict properly up to 50‐fold higher hexokinase activity. © 1998 John Wiley & Sons, Ltd.
A novel gateway selection method to maximize the system throughput of Wireless Mesh Network deployed in disaster areas

Since Wireless Mesh Networks (WMNs) can be easily deployed without wirelines among wireless mesh routers, they allow us to quickly recover network access services in disaster areas even if the existing network infrastructures have been enormously destroyed by terrible earthquake, tsunami, and so on. However, the performance of wireless mesh networks is largely affected by many factors, e.g., wireless mesh routers' locations, channel assignment, transmission scheduling, etc. In particular, the method of selecting gateways which has a connection to external networks significantly impacts on the network performance when the topology and routing have been fixed in the wireless mesh network. In this paper, we suppose a wireless mesh network which consists of wireless mesh routers and a base station directly connected to external networks. The base station is located at the center of the wireless mesh network chooses a certain number of wireless mesh routers as gateways, and establishes a connection with each of them. Our goal is to easily and quickly find the candidate gateways that maximize the system throughput without solving a complex optimization problem which includes a large number of parameters and involves heavy computation load. The performance of the proposed scheme is evaluated by numerical analysis, and demonstrated through computer simulations. The results show that our proposed scheme can determine the appropriate candidate gateway with high accuracy when there is a certain variance in the amount of traffic generated by users at each wireless mesh router.
Impact on quality of life of botulinum toxin treatments for essential blepharospasm

purpose To determine the impact on quality of life of Botulinum toxin therapy for essential blepharospasm. methods A cross-sectional study was undertaken using the Glasgow Benefit Inventory, in the form of a postal questionnaire, to assess the subjective patient benefit of Botulinum toxin treatments for essential blepharospasm in 44 consecutive patients attending a specialist Botulinum toxin clinic. (The Glasgow Benefit Inventory generates a score from −100 (maximum harm) through 0 (no effect) to +100 (maximum benefit) for the intervention under investigation. ) The Wilcoxon signed-ranks test was used to test the significance of the total scores and subdomain scores. results A high response rate of 36 out of 44 (81.8%) was achieved. The median total benefit score was +29.2 (97.1% CI = 16.7 to 38.9, p < 0.0001). The median subdomain scores were: general +43.8 (97.1% CI = 20.8 to 54.2, p < 0.0001), social 0.0 (97.1% CI = 0.0 to 16.7, p = 0.0019) and physical 0.0 (97.1% CI = 0.0 to 0.0, p = 0.4810). conclusions This study demonstrates significant quality of life benefit from Botulinum toxin therapy for essential blepharospasm, and justifies continued treatment.
Enhanced mutagenesis parallels enhanced reactivation of herpes virus in a human cell line.

U.v. irradiation of human NB‐E cells results in enhanced mutagenesis and enhanced reactivation of u.v. ‐irradiated H‐1 virus grown in those cells (Cornelis et al., 1982). This paper reports a similar study using herpes simplex virus (HSV) in NB‐E cells. The mutation frequency of HSV (resistance of virus plaque formation to 40 micrograms/ml iododeoxycytidine) increased approximately linearly with exposure of the virus to u.v. radiation. HSV grown in unirradiated cells gave a slope of 1.8 X 10(‐5)m2/J, with 3.2 X 10(‐5)m2/J for HSV grown in cells irradiated (3 J/m2) 24 h before infection. There was no evidence for mutagenesis of unirradiated virus by irradiated cells, as seen with H‐1 virus. Enhanced reactivation of irradiated HSV in parallel cultures increased virus survival, manifested as a change in slope of the final component of the two‐component survival curve from a D0 of 27 J/m2 in unirradiated cells to 45 J/m2 in irradiated cells. Thus, enhanced mutagenesis and enhanced reactivation occurred for irradiated HSV in NB‐E cells. The difference in the enhanced mutagenesis of HSV (dependent on damaged DNA sites) and of H‐1 virus (primarily independent of damaged DNA sites) is discussed in terms of differences in DNA polymerases.
Medical Image Registration by GSA Optimized Matching Algorithm

The primary contribution of this research is the development of computational frameworks that tackle in a general and principled way the problems arising in the construction of an image registration system. A novel algorithm for image features matching is used in terms of evolutionary algorithms. We have efficiently used the gravitational search algorithm (GSA) to match image features by tuning the rotational angle of image. The complete work is divided into three modules: edge detection, features extraction and features matching. After studying previous work on this, we used the effective phase congruency method for the edge detection to avoid non uniform illumination problem occurred in detection of edges. The requirement of features extraction is that matching points which don’t change even after change in angle of rotation of image. So we used scale invariant features transform (SIFT) method to extract features and finally we purposed the tuned matching algorithm which can work for almost every type of image. Our features matching using GSA algorithm tune the rotational angle of test image and set it to an optimum angle so that it can best match with the reference image.
Demand Response Management via Real-Time Electricity Price Control in Smart Grids

This paper proposes a real-time pricing scheme that reduces the peak-to-average load ratio through demand response management in smart grid systems. The proposed scheme solves a two-stage optimization problem. On one hand, each user reacts to prices announced by the retailer and maximizes its payoff, which is the difference between its quality-of-usage and the payment to the retailer. On the other hand, the retailer designs the real-time prices in response to the forecasted user reactions to maximize its profit. In particular, each user computes its optimal energy consumption either in closed forms or through an efficient iterative algorithm as a function of the prices. At the retailer side, we develop a Simulated-Annealing-based Price Control (SAPC) algorithm to solve the non-convex price optimization problem. In terms of practical implementation, the users and the retailer interact with each other via a limited number of message exchanges to find the optimal prices. By doing so, the retailer can overcome the uncertainty of users' responses, and users can determine their energy usage based on the actual prices to be used. Our simulation results show that the proposed real-time pricing scheme can effectively shave the energy usage peaks, reduce the retailer's cost, and improve the payoffs of the users.
The Hipparcos transit data: What, why and how? ?

The Hipparcos Transit Data are a collection of partially reduced, fully calibrated observations of (mostly) double and multiple stars obtained with the ESA Hipparcos astrometry satellite. The data are publicly available, as part of the CD-ROM set distributed with the Hipparcos and Tycho Catalogues (ESA SP{1200, 1997), for about a third of the Hipparcos Catalogue entries including all confirmed or suspected non-single stars. The Transit Data consist of signal modulation parameters derived from the individual transits of the targets across the Hipparcos focal grid. The Transit Data permit re-reduction of the satellite data for individual objects, using arbitrarily complex object models in which time-variable photometric as well as geometric characteristics may be taken into account. We describe the structure and contents of the Transit Data files and give examples of how the data can be used. Some of the applications use standard astronomical software: Difmap or AIPS for aperture synthesis imaging, and GaussFit for detailed model fitting. Fortran code converting the data into formats suitable for these application programs has been made public in order to encourage and facilitate the use of Hipparcos Transit Data.
Compute-Compress-and-Forward: Exploiting Asymmetry of Wireless Relay Networks

Compute-and-forward (CF) harnesses interference in a wireless network by allowing relays to compute combinations of source messages. The computed message combinations at relays are correlated, and so directly forwarding these combinations to a destination generally incurs information redundancy and spectrum inefficiency. To address this issue, we propose a novel relay strategy, termed compute-compress-and-forward (CCF). In CCF, source messages are encoded using nested lattice codes constructed on a chain of nested coding and shaping lattices. A key difference of CCF from CF is an extra compressing stage inserted in between the computing and forwarding stages of a relay, so as to reduce the forwarding information rate of the relay. The compressing stage at each relay consists of two operations: first to quantize the computed message combination on an appropriately chosen lattice (referred to as a quantization lattice), and then to take modulo on another lattice (referred to as a modulo lattice). We study the design of the quantization and modulo lattices and propose successive recovering algorithms to ensure the recoverability of source messages at destination. Based on that, we formulate a sum-rate maximization problem that is in general an NP-hard mixed integer program. A low-complexity algorithm is proposed to give a suboptimal solution. Numerical results are presented to demonstrate the superiority of CCF over the existing CF schemes.
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios

MOTIVATION Whole-genome and -exome sequencing on parent-offspring trios is a powerful approach to identifying disease-associated genes by detecting de novo mutations in patients. Accurate detection of de novo mutations from sequencing data is a critical step in trio-based genetic studies. Existing bioinformatic approaches usually yield high error rates due to sequencing artifacts and alignment issues, which may either miss true de novo mutations or call too many false ones, making downstream validation and analysis difficult. In particular, current approaches have much worse specificity than sensitivity, and developing effective filters to discriminate genuine from spurious de novo mutations remains an unsolved challenge. RESULTS In this article, we curated 59 sequence features in whole genome and exome alignment context which are considered to be relevant to discriminating true de novo mutations from artifacts, and then employed a machine-learning approach to classify candidates as true or false de novo mutations. Specifically, we built a classifier, named De Novo Mutation Filter (DNMFilter), using gradient boosting as the classification algorithm. We built the training set using experimentally validated true and false de novo mutations as well as collected false de novo mutations from an in-house large-scale exome-sequencing project. We evaluated DNMFilter's theoretical performance and investigated relative importance of different sequence features on the classification accuracy. Finally, we applied DNMFilter on our in-house whole exome trios and one CEU trio from the 1000 Genomes Project and found that DNMFilter could be coupled with commonly used de novo mutation detection approaches as an effective filtering approach to significantly reduce false discovery rate without sacrificing sensitivity. AVAILABILITY The software DNMFilter implemented using a combination of Java and R is freely available from the website at http://humangenome.duke. edu/software.
A TIRF Microscopy Technique for Real-time, Simultaneous Imaging of the TCR and its Associated Signaling Proteins

Signaling is initiated through the T Cell Receptor (TCR) when it is engaged by antigenic peptide fragments bound by Major Histocompatibility Complex (pMHC) proteins expressed on the surface of antigen presenting cells (APCs). The TCR complex is composed of the ligand binding TCRαβ heterodimer that associates non-covalently with CD3 dimers (the εδ and εγ heterodimers and the ζζ homodimer)1. Upon engagement of the receptor, the CD3 ζ chains are phosphorylated by the Src family kinase, Lck. This leads to the recruitment of the Syk family kinase, Zap70, which is then phosphorylated and activated by Lck. After that, Zap70 phosphorylates the adapter proteins LAT and SLP76, initiating the formation of the proximal signaling complex containing a large number of different signaling molecules2. The formation of this complex eventually results in calcium and Ras-dependent transcription factor activation and the consequent initiation of a complex series of gene expression programs that give rise to T cell differentiation2. TCR signals (and the resulting state of differentiation) are modulated by many other factors, including antigen potency and crosstalk with co-stimulatory/co-inhibitory, chemokine, and cytokine receptors 3-4. Studying the spatial and temporal organization of the proximal signaling complex under various stimulation conditions is, therefore, key to understanding the TCR signaling pathway as well as its regulation by other signaling pathways. One very useful model system to study signaling initiated by the TCR at the plasma membrane in T cells is glass-supported lipid bilayers, as described previously5-6. They can be utilized to present antigenic pMHC complexes, adhesion, and co-stimulatory molecules to T cells-serving as artificial APCs. By imaging the T cells interacting with the lipid bilayer using total internal reflection fluorescence microscopy (TIRFM), we can restrict the excitation to within 100 nm of the space between the glass and the cell surface 7-8. This allows us to image primarily the signaling events occurring at the plasma membrane. As we are interested in imaging the recruitment of signaling proteins to the TCR complex, we describe a two-camera TIRF imaging system wherein the TCR, labeled with fluorescent Fab (fragment antigen binding) fragments of the H57 antibody (purified from hybridoma H57-597, ATCC, ATCC Number:HB-218) which is specific for TCRβ, and signaling proteins, tagged with GFP, may be imaged simultaneously and in real time. This strategy is necessary due to the highly dynamic nature of both the T cells and of the signaling events that are occurring at the TCR. This imaging modality has allowed researchers to image single ligands 9-11 as well as recruitment of signaling molecules to activated receptors and is an excellent system to study biochemistry in-situ12-16.
Fabrication of Micro-lens Arrays Based on Ink-jet Printing and Photolithographic Hole Templates for Integral Imaging 3-D Display

In this paper, we present a fabrication technique of micro-lens arrays (MLAs) for integral imaging 3-D display, which combines photolithographic hole templates and ink-jet printing. Laser 3-D microscope and a homemade setup have been used for the characterization of MLAs. The results show that precisely aligned MLAs can be obtained using holes arrays as templates. By controlling the driving voltage at different steps, the distance between nozzle and substrate, as well as the number of liquid droplets, MLAs with smooth morphology, different sizes, good repeatability of geometry parameters, great uniformity of focusing, and good converging performance can be achieved. For demonstration, MLAs with curvature and focal length of MLAs of 255.9 and 501.77 μm are applied for the reconstructions in integral imaging 3-D display, exhibiting good reconstruction performance.