Miracle-dz/UniFAR-FTUs huggingface dataset:
A Combination of Two Distinct in vitro Amplification Procedures for DNA Typing of HLA‐DRB and ‐DQB 1 Alleles

The differential hybridisation of oligonucleotide probes to polymerase chain reaction (PCR)‐amplified DNA has become a standard procedure for tissue typing. We describe a typing method in which differential ligation replaces differential hybridisation, which is a significant simplification of this strategy. After amplification by the PCR two labelled, sequence‐specific oligonucleotides hybridise, in the fluid phase, to one strand of heat‐denatured amplification product in juxtaposition. In the case of perfectly complementary sequences surrounding the gap, a thermostable ligase catalyses the ligation of the two oligonucleotides, otherwise they stay separated. The use of heat‐resistant ligase enables easy repetition of the denaturation‐annealing‐ligation cycle in a thermocycler. The ligation products are detected by an enzyme linked immunosorbent assay. We tested this typing approach in a model system, the characterisation of three functional alleles of HLA‐DRB 3 using three probe pairs. No discrepancies were observed in typing 100 individuals of known genotypes. A total of 33 probe pairs combined with generic and group‐specific amplification allowed the typing of alleles of HLA‐DRB and ‐DQB1 loci at low resolution. We confirmed ligation‐based typing results of 259 individuals with sequence‐based HLA‐DRB1 typing and HLA‐DQB1 typing using PCR with sequence‐specific primers (SSPs). In addition, more than 1,500 ligation‐based HLA‐DRB1 typings were concordant with SSP typing. Excellent signal‐to‐noise ratios in the enzyme‐linked immunosorbent assay make ligation‐based typing remarkably robust. The time requirement of 2.5 h post‐PCR enables practicable typing of putative organ donors. The whole procedure is more easily amenable to automation than methods based on differential hybridisation requiring additional incubators and extra handling for hybridisation and washing.
Petrology and Geochemistry of Mafic Lavas near Glacier Peak, North Cascades, Washington

Major element, trace element, and mineral compositions have been determined for four Quaternary mafic monogenetic cinder cones and flows south of Glacier Peak, a dacitic stratovolcano in the northern Cascade arc. The flows are the Whitechuck basalt, and the basaltic andesites of Indian Pass, Lightning Creek, and Dishpan Gap. Whitechuck has high concentrations of AI2O3 (> 18 wt.%) and low concentrations of K2O (< 0.45 wt.%) and shares similar trace element characteristics with high alumina olivine tholeiites reported in the central and southern Cascades. The three basaltic andesites are calcalkaline. Indian Pass and Lighting Creek have primitive compositions, with Mg# [100*Mg/(Mg+Fe*)] > 65, Cr > 200 ppm, and Ni > 100 ppm. Most samples have olivine in equilibrium with bulk rock compositions. Rb and Sr are relatively low in most flows, especially at Whitechuck and Dishpan Gap. Sr and La decrease with increasing Si02 in the Lightning Creek and Dishpan Gap cinder cones, indicating possible mixing with a Sr and La-poor felsic component represented by the most evolved Glacier Peak dacites. Petrographic observations of disequilibrium textures such as xenocrysts, xenoliths, quenched glass inclusions, and strongly-zoned phenocrysts in these two flows also indicate possible melting. All flows are enriched in large ion lithophile elements and light rare earth elements relative to high field strength elements, showing that the mantle beneath Glacier Peak has been fluxed by a hydrous subduction component. Ba/Nb ratios (-40-110) are highest for the three basaltic andesites, indicating that they had the greatest amount of subduction component enrichment. Nb and Ta abundances are highest at Indian Pass (Nb =~7 ppm) and lowest at Whitechuck (Nb = -2-3), indicating that Indian Pass and the other two basaltic andesites were produced by relatively low degree hydrous
Windowed multicarrier systems with minimum spectral leakage

The transmitter output of OFDM or DMT systems with a rectangular window is known to have large spectral sidelobes. Windowing and pulse shaping have been proposed to reduce spectral leakage in the literature. If no extra cyclic prefix is available, windowing at the transmitter requires additional post-processing equalization at the receiver. In this paper, we design optimal windows with minimum spectral leakage. Moreover, we show that the post processing affects the SNR at the receiver and the resulting SNR can be given in a closed form. Furthermore, we demonstrate that we can have a good trade-off between SNR and spectral leakage.
Obtaining highly accurate topology estimates of evolutionary trees from very short sequences

The evolutionary history of a set of species is represented by a phylogenetic tree, in other words, by a rooted, leaf-labelled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees has long been considered one of the major challenges in systematic biology. None of the polynomial time methods developed by the theoretical computer science community has been shown to outperform the popular Neighbor-Joining method used by systematic biologists, with respect to topology estimation. (However, preliminary experiments indicate that two new variants of Neighbor-Joining, Bio-NJ and Weighbor, do exhibit improved performance.) In this paper, we present a simple polynomial time method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods. We analyze the performance of DCM-boosted distance methods under the general Markov model of evolution , and prove that, by using the DCM-boosted Bune-man method, for almost all trees, polylogarithmic length sequences suuce for complete accuracy with high probability , while polynomial length sequences always suuce. Our experimental study (based upon simulating sequence evolution on model trees, generating about 1000 datasets) con-rms these substantial reductions in error rates and extremely fast convergence rates. In particular, we report that DCM-boosted Neighbor-Joining has only 8% of the error of Neighbor-Joining under conditions that are adverse to Neighbor-Joining, and on some trees achieving acceptable error rates (less than 5% error in the topology estimation) from sequences of a few hundred nucleotides, while Neighbor-Joining needs more than 10K nucleotides to achieve the same level of accuracy. 1 Introduction The evolution of biomolecular sequences can be modeled as a Markov process operating on a rooted binary tree: A biomolecular sequence at the root of the tree \evolves down" the tree, with each edge of the tree introducing point mutations , thereby generating sequences at the leaves of the tree, each of the same length as the root sequence. The phylo-genetic tree reconstruction problem is to take the sequences that occur at the leaves of the tree, and infer, as accurately as possible, the tree that generated the sequences. The tree reconstruction problem has two objectives: rst, to recover the branching process, as represented by the rooted leaf-labelled topology of the evolutionary tree, and second, to estimate the parameters of the evolutionary process (the mutation probabilities on the edges of the tree, the rates of change across …
Graphene as Transparent Conductive Film for GaN-Based Vertical Cavity Surface Emitting Lasers

There is a need for lasers in the 370nm - 470nm spectrum (near ultraviolet - blue) for applications such as high storage, high resolution printers and biomedical applications. GaN-based vertical cavity surface emitting laser (VCSEL) is one interesting option due to the wide bandgap of the GaN and the 2D array capability and cost-effective production of VCSELs. Because of the high resistivity of p-GaN, these devices require the use of a transparent conductive film (TCF) to effectively laterally spread the current across the active region. The actual material used so far is ITO wish has problems related to the deposition technique and the constantly increasing price of the material. Graphene, a one atom layer thick (0.35 nm) graphite derivative 2D material, stands as a very good option due to its outstanding properties (high mobilities, high transmittance, etc.). In order to demonstrate the feasibility of replacing ITO with a graphene TCF the production, transfer, sheet resistance and contact resistivity to p-GaN have to be investigated and further developed. In this work a low-pressure cold-wall CVD reactor was used for reproducible production of large domains graphene films on 99.995% Cu foils of 50 µm. Different transfer techniques were assessed and reproducible graphene transfer was achieved by improving a recently developed method. The method is based on the separation of the graphene from the Cu foil by H2 bubbles formation on the surface of the Cu foil that was used as a cathode in an electrolytic cell with aqueous 0.25M NaOH solution. Different methods to improve the sheet resistance of the graphene were evaluated (artificially deposited dual layer films, doping with FeCl3, S1813 and PVA). Devices were created to characterize the mobility, sheet resistance, carrier concentration, maximum current densities and contact resistivity to p-GaN. A GaN-based LED using a graphene TCF was fabricated and showed efficient current spreading by the graphene based TCF. The results show that graphene is an interesting option for TCF however, more effort is needed to further improve the contact resistivity.
Developing a compassionate mind to enhance trauma-focused CBT with an adolescent female: a case study.

BACKGROUND Shame and disgust are often associated with posttraumatic stress disorder (PTSD) following interpersonal traumas such as sexual assault. It has been suggested that individuals with high levels of shame might do less well in standard cognitive behavioural (CBT) interventions. AIMS To see whether applying compassion-focused therapy and developing a compassionate mind can enhance trauma-focused CBT in an adolescent with high levels of shame and disgust the way it has been shown to within the adult population. METHOD This single case study describes how trauma-focused CBT was enhanced by compassionate mind training. It details work using this approach with an adolescent female experiencing shame and disgust-based flashbacks. Treatment was provided for 20 sessions over 8 months. Symptoms of PTSD, depression and self-criticism, as well as the ability to self-soothe/reassure, were measured at assessment/start of treatment, mid- and end of treatment. RESULTS Clinically significant reductions in PTSD, depressive, shame and self-attacking symptoms were found between assessment and completion of treatment. Clinically significant increases in self-reassurance were also reported. Following treatment, symptoms of PTSD and depression were sub-clinical. CONCLUSION This case study suggests that developing a compassionate mind alongside trauma-focused CBT may be beneficial to adolescents experiencing shame and disgust with consideration for the young person's level of development and personal circumstances.
On-Disk Data Processing: Issues and Future Directions

In this paper, we present a survey of "on-disk" data processing (ODDP). ODDP, which is a form of near-data processing, refers to the computing arrangement where the secondary storage drives have the data processing capability. Proposed ODDP schemes vary widely in terms of the data processing capability, target applications, architecture and the kind of storage drive employed. Some ODDP schemes provide only a specific but heavily used operation like sort whereas some provide a full range of operations. Recently, with the advent of Solid State Drives, powerful and extensive ODDP solutions have been proposed. In this paper, we present a thorough review of architectures developed for different on-disk processing approaches along with current and future challenges and also identify the future directions which ODDP can take.
Statistical Inferences by Gaussian Markov Random Fields on Complex Networks

Gaussian Markov random fields are applied to many statistical inferences. Probabilistic models of statistical inferences are constructed in the concept of Bayesian statistics and have some network structures. In the present paper, we analyze the statistical performance of the statistical inferences in Gaussian Markov random fields on some complex networks including scale free networks. We discuss efficiency of scale free networks for statistical inferences of Gauss Markov random fields.
A Wide Temperature, Radiation Tolerant, CMOS-Compatible Precision Voltage Referencefor Extreme Radiation Environment Instrumentation Systems

Many design techniques have been incorporated into modern CMOS design practices to improve radiation tolerance of integrated circuits. Annular-gate NMOS structures have been proven to be significantly more radiation tolerant than the standard, straight-gate variety. Many circuits can be designed using the annular-gate NMOS and the inherently radiation tolerant PMOS. Bandgap reference circuits, however, typically require p-n junction diodes. These p-n junction diodes are the dominating factor in radiation degradation in bandgap reference circuits. This paper proposes a different approach to bandgap reference design to alleviate the radiation susceptibility presented by the p-n junction diodes.
Exterior ows at low Reynolds numbers: concepts, solutions, and applications

We discuss uid structure interaction for exterior ows, for Reynolds numbers ranging from about one to several thousand. New applications demand a better quantitative understanding of the details of such ows, and this has stimulated a revival of interest in this topic. Astonishingly, in spite of the apparent simplicity of low Reynolds number ows, their precise prediction turns out to be numerically demanding even with today's computers. On the basis of simple examples we review the progress that has been made over the recent years in the analysis of such problems through a combined use of techniques from asymptotic analysis, symbolic computation, and computational uid dynamics, and discuss open problems which one should be able to solve with the techniques presented here.
Modeling the Atmospheric Boundary Layer Wind Response to Mesoscale Sea Surface Temperature Perturbations

AbstractThe wind speed response to mesoscale SST variability is investigated over the Agulhas Return Current region of the Southern Ocean using the Weather Research and Forecasting (WRF) Model and the U.S. Navy Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) atmospheric model. The SST-induced wind response is assessed from eight simulations with different subgrid-scale vertical mixing parameterizations, validated using Quick Scatterometer (QuikSCAT) winds and satellite-based sea surface temperature (SST) observations on 0.25° grids. The satellite data produce a coupling coefficient of sU = 0.42 m s−1 °C−1 for wind to mesoscale SST perturbations. The eight model configurations produce coupling coefficients varying from 0.31 to 0.56 m s−1 °C−1. Most closely matching QuikSCAT are a WRF simulation with the Grenier–Bretherton–McCaa (GBM) boundary layer mixing scheme (sU = 0.40 m s−1 °C−1), and a COAMPS simulation with a form of Mellor–Yamada parameterization (sU = 0.38 m s−1 °C−1). Model rankings.
Hepatitis C Virus Fails To Activate NF-κB Signaling in Plasmacytoid Dendritic Cells

ABSTRACT Plasmacytoid dendritic cells (pDCs) respond to viral infection by production of alpha interferon (IFN-α), proinflammatory cytokines, and cell differentiation. The elimination of hepatitis C virus (HCV) in more than 50% of chronically infected patients by treatment with IFN-α suggests that pDCs can play an important role in the control of HCV infection. pDCs exposed to HCV-infected hepatoma cells, in contrast to cell-free HCV virions, produce large amounts of IFN-α. To further investigate the molecular mechanism of HCV sensing, we studied whether exposure of pDCs to HCV-infected hepatoma cells activates, in parallel to interferon regulatory factor 7 (IRF7)-mediated production of IFN-α, nuclear factor kappa B (NF-κB)-dependent pDC responses, such as expression of the differentiation markers CD40, CCR7, CD86, and tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and secretion of the proinflammatory cytokines TNF-α and interleukin 6 (IL-6). We demonstrate that exposure of pDCs to HCV-infected hepatoma cells surprisingly did not induce phosphorylation of NF-κB or cell surface expression of CD40, CCR7, CD86, or TRAIL or secretion of TNF-α and IL-6. In contrast, CpG-A and CpG-B induced production of TNF-α and IL-6 in pDCs exposed to the HCV-infected hepatoma cells, showing that cell-associated virus did not actively inhibit Toll-like receptor (TLR)-mediated NF-κB phosphorylation. Our results suggest that cell-associated HCV signals in pDCs via an endocytosis-dependent mechanism and IRF7 but not via the NF-κB pathway. In spite of IFN-α induction, cell-associated HCV does not induce a full functional response of pDCs. These findings contribute to the understanding of evasion of immune responses by HCV.
Discrete Nonnegative Spectral Clustering

Spectral clustering has been playing a vital role in various research areas. Most traditional spectral clustering algorithms comprise two independent stages (e.g., first learning continuous labels and then rounding the learned labels into discrete ones), which may cause unpredictable deviation of resultant cluster labels from genuine ones, thereby leading to severe information loss and performance degradation. In this work, we study how to achieve discrete clustering as well as reliably generalize to unseen data. We propose a novel spectral clustering scheme which deeply explores cluster label properties, including discreteness, nonnegativity, and discrimination, as well as learns robust out-of-sample prediction functions. Specifically, we explicitly enforce a discrete transformation on the intermediate continuous labels, which leads to a tractable optimization problem with a discrete solution. Besides, we preserve the natural nonnegative characteristic of the clustering labels to enhance the interpretability of the results. Moreover, to further compensate the unreliability of the learned clustering labels, we integrate an adaptive robust module with $\ell _{2,p}$ loss to learn prediction function for grouping unseen data. We also show that the out-of-sample component can inject discriminative knowledge into the learning of cluster labels under certain conditions. Extensive experiments conducted on various data sets have demonstrated the superiority of our proposal as compared to several existing clustering approaches.
Hybrid No-Reference Quality Metric for Singly and Multiply Distorted Images

In a typical image communication system, the visual signal presented to the end users may undergo the steps of acquisition, compression and transmission which cause the artifacts of blurring, quantization and noise. However, the researches of image quality assessment (IQA) with multiple distortion types are very limited. In this paper, we first introduce a new multiply distorted image database (MDID2013), which is composed of 324 images that are simultaneously corrupted by blurring, JPEG compression and noise injection. We then propose a new six-step blind metric (SISBLIM) for quality assessment of both singly and multiply distorted images. Inspired by the early human visual model and recently revealed free energy based brain theory, our method works to systematically combine the single quality prediction of each emerging distortion type and joint effects of different distortion sources. Comparative studies of the proposed SISBLIM with popular full-reference IQA approaches and start-of-the-art no-reference IQA metrics are conducted on five singly distorted image databases (LIVE, TID2008, CSIQ, IVC, Toyama) and two newly released multiply distorted image databases (LIVEMD, MDID2013). Experimental results confirm the effectiveness of our blind technique. MATLAB codes of the proposed SISBLIM algorithm and MDID2013 database will be available online at http://gvsp.sjtu. edu.cn/.
A Novel Fuzzy Linear Feature Extraction for Hyperspectral Image Classification

In this paper, a novel fuzzy linear discriminant analysis feature extraction method has been proposed for classifying hyperspectral image data. We used the fuzzification mechanism proposed by Keller, et al. to discover samples close to the class boundary or not, and different weights are assigned on samples when estimating the within-class and between-class scatter matrix. The effectiveness of the proposed feature extraction scheme as compared to nonparametric weighted feature extraction (NWFE) and linear discriminant analysis (LDA) is demonstrated using Washington DC Mall data, and achieve a satisfactory performance.
Ouabain‐induced changes in MAP kinase phosphorylation in primary culture of rat cerebellar cells

Cardiotonic steroid (CTS) ouabain is a well‐established inhibitor of Na,K‐ATPase capable of inducing signalling processes including changes in the activity of the mitogen activated protein kinases (MAPK) in various cell types. With increasing evidence of endogenous CTS in the blood and cerebrospinal fluid, it is of particular interest to study ouabain‐induced signalling in neurons, especially the activation of MAPK, because they are the key kinases activated in response to extracellular signals and regulating cell survival, proliferation and apoptosis. In this study we investigated the effect of ouabain on the level of phosphorylation of three MAPK (ERK1/2, JNK and p38) and on cell survival in the primary culture of rat cerebellar cells. Using Western blotting we described the time course and concentration dependence of phosphorylation for ERK1/2, JNK and p38 in response to ouabain. We discovered that ouabain at a concentration of 1 μM does not cause cell death in cultured neurons while it changes the phosphorylation level of the three MAPK: ERK1/2 is phosphorylated transiently, p38 shows sustained phosphorylation, and JNK is dephosphorylated after a long‐term incubation. We showed that ERK1/2 phosphorylation increase does not depend on ouabain‐induced calcium increase and p38 activation. Changes in p38 phosphorylation, which is independent from ERK1/2 activation, are calcium dependent. Changes in JNK phosphorylation are calcium dependent and also depend on ERK1/2 and p38 activation. Ten‐micromolar ouabain leads to cell death, and we conclude that different effects of 1‐μM and 10‐μM ouabain depend on different ERK1/2 and p38 phosphorylation profiles. Copyright © 2016 John Wiley & Sons, Ltd.
Dynamic assignment of tasks to mobile robots in presence of obstacles

Assignment of tasks to robots in multi-robot system has been under intensive investigation over last years. The method which does not use any explicit communication, but applies a simple model of signal emission and propagation in the environment is presented in this paper. The environment model included obstacles that are to be avoided by the robots. Usability and interesting features of the method are shown on the basis of simulation experiments and their results. The approach enables management of robots movement between locations of tasks and assignment of robots to tasks without explicit communication.