Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptively Varying Modulus Blind Equalization Algorithm Using Fractionally-Spaced Equalizer

A new blind equalization scheme for QAM systems is proposed, which is referred to adaptively varying modulus algorithm based on SCA (A VSCA). The A VSCA changes the SCA from single modulus to multi-modulus for the characteristics of the QAM systems and then adapts the zero- error contours adaptively according to the decision of the equalizer output. Simulation using a fractionally-spaced equalizer for a typical voice-band communication channel and a practical microwave channel is evaluated to compare the proposed algorithm with the CMA, GSA and SCA. Theoretical analysis and simulation results demonstrate that A VSCA improves equalization performance by increasing the convergence speed and decreasing the residual inter-symbol interference.
Influence of host genes on HIV‐1 disease progression

The role of host genes in the course of HIV‐1 infection has been examined in different populations and among all major risk groups. Two extended human lymphocyte antigen (HLA) haplotypes, HLA A1‐Cw7‐B8‐DR3‐DQ2 and HLA A11‐Cw4‐B35‐DR1‐DQ1, are found to be associated with a faster progression to AIDS. The complement C4 factor and tumor necrosis factor genes of the major histocompatibility complex, as well as the mannose binding protein gene, have also been suggested to influence the outcome of AIDS. The recent discovery that chemokine receptors could serve as cofactors for HIV‐1 cell entry has prompted a search for polymorphisms in chemokine receptor genes. A 32 base pair inactivating deletion in the CCR5 gene and a point mutation within the CCR2b gene resulting in a conservative amino acid substitution have been examined and shown to be independently associated with delayed disease progression. Together, these observations strongly support a genetic component in AIDS pathogenesis. This article synthesizes the current state of knowledge about the influence of host genes on HIV‐1 disease progression. It provides a summary of all significant association studies reported so far. The role of the allelic polymorphism in these genes is discussed with regard to the immunopathogenesis of AIDS. —Roger, M. Influence of host genes on HIV‐1 disease progression. FASEB J. 12, 625–632 (1998)
The TAK1-NLK Mitogen-Activated Protein Kinase Cascade Functions in the Wnt-5a/Ca2+ Pathway To Antagonize Wnt/β-Catenin Signaling

ABSTRACT Wnt signaling controls a variety of developmental processes. The canonical Wnt/β-catenin pathway functions to stabilize β-catenin, and the noncanonical Wnt/Ca2+ pathway activates Ca2+/calmodulin-dependent protein kinase II (CaMKII). In addition, the Wnt/Ca2+ pathway activated by Wnt-5a antagonizes the Wnt/β-catenin pathway via an unknown mechanism. The mitogen-activated protein kinase (MAPK) pathway composed of TAK1 MAPK kinase kinase and NLK MAPK also negatively regulates the canonical Wnt/β-catenin signaling pathway. Here we show that activation of CaMKII induces stimulation of the TAK1-NLK pathway. Overexpression of Wnt-5a in HEK293 cells activates NLK through TAK1. Furthermore, by using a chimeric receptor (β2AR-Rfz-2) containing the ligand-binding and transmembrane segments from the β2-adrenergic receptor (β2AR) and the cytoplasmic domains from rat Frizzled-2 (Rfz-2), stimulation with the β-adrenergic agonist isoproterenol activates activities of endogenous CaMKII, TAK1, and NLK and inhibits β-catenin-induced transcriptional activation. These results suggest that the TAK1-NLK MAPK cascade is activated by the noncanonical Wnt-5a/Ca2+ pathway and antagonizes canonical Wnt/β-catenin signaling.
Simple extraction protocol for analysis of immunosuppressant drugs in whole blood.

The immunosuppressant drugs cyclosporine (cyclosporin A), tacrolimus, sirolimus, and everolimus are used to prevent organ rejection. Because commercial immunoassays are available only for cyclosporine and tacrolimus, HPLC (1)(2)(3), often in conjunction with mass spectrometry (MS or MS/MS) (4)(5)(6)(7), has been used to quantify these drugs. For MS/MS, sample preparation has often involved simple protein precipitation and solvent dissolution. Protocols have used zinc sulfate followed by acetonitrile (8), methanol (9), or acetone (10). Sometimes these reagents are premixed (11)(12)(13)(14). During in-house assay development we encountered several problems when zinc sulfate and acetonitrile were used. For example, many specimens clumped when blood was added to the zinc sulfate. Even after addition of acetonitrile and vortex-mixing, the clumps remained, necessitating manual dislodgement of the pellet. This occurred with lysed human blood specimens, lyophilized whole-blood controls (e.g., Bio-Rad Lyphochek), and College of American Pathologists proficiency testing specimens. We substituted methanol for acetonitrile with minor improvement. Another problem was that the recovery of sirolimus from whole blood using zinc sulfate followed by acetonitrile or methanol was <100% (9). In addition, the observed MS/MS responses for commercial calibrators and controls were often ∼30% higher than for human blood specimens. Here we present a new extraction protocol that improves absolute recoveries, provides excellent precision, and shows less ion suppression. Although the performance of this protocol for several immunosuppressants is described, we present example data only for sirolimus. We also describe a solid-phase extraction (SPE) that may be added to further enhance the cleanliness of extracts. For recovery and extraction experiments, we used cyclosporine from Novartis, tacrolimus from Fujisawa, and sirolimus from LC …
Constructive Discrepancy Minimization by Walking on the Edges

Minimizing the discrepancy of a set system is a fundamental problem in combinatorics. One of the cornerstones in this area is the celebrated six standard deviations result of Spencer (AMS 1985): In any system of n sets in a universe of size n, there always exists a coloring which achieves discrepancy 6√n. The original proof of Spencer was existential in nature, and did not give an efficient algorithm to find such a coloring. Recently, a breakthrough work of Bansal (FOCS 2010) gave an efficient algorithm which finds such a coloring. His algorithm was based on an SDP relaxation of the discrepancy problem and a clever rounding procedure. In this work we give a new randomized algorithm to find a coloring as in Spencer's result based on a restricted random walk we call Edge-Walk. Our algorithm and its analysis use only basic linear algebra and is “truly” constructive in that it does not appeal to the existential arguments, giving a new proof of Spencer's theorem and the partial coloring lemma.
Plasmonic photosensitization of a wide band gap semiconductor: converting plasmons to charge carriers.

A fruitful paradigm in the development of low-cost and efficient photovoltaics is to dope or otherwise photosensitize wide band gap semiconductors in order to improve their light harvesting ability for light with sub-band-gap photon energies. (1-8) Here, we report significant photosensitization of TiO2 due to the direct injection by quantum tunneling of hot electrons produced in the decay of localized surface-plasmon polaritons excited in gold nanoparticles (AuNPs) embedded in the semiconductor (TiO2). Surface plasmon decay produces electron-hole pairs in the gold. (9-15) We propose that a significant fraction of these electrons tunnel into the semiconductor's conduction band resulting in a significant electron current in the TiO2 even when the device is illuminated with light with photon energies well below the semiconductor's band gap. Devices fabricated with (nonpercolating) multilayers of AuNPs in a TiO2 film produced over 1000-fold increase in photoconductance when illuminated at 600 nm over what TiO2 films devoid of AuNPs produced. The overall current resulting from illumination with visible light is ∼50% of the device current measured with UV (ℏω>Eg band gap) illumination. The above observations suggest that plasmonic nanostructures (which can be fabricated with absorption properties that cover the full solar spectrum) can function as a viable alternative to organic photosensitizers for photovoltaic and photodetection applications.
A measurement‐based study of hardware support for object invocation

The object invocation paradigm is attractive for structuring distributed systems. Distributed object‐based operating systems view the resources of the system as a collection of objects. Object invocation is the primary mechanism in such systems, and is often used as a yardstick for measuring the system performance. However, existing systems of this flavour exhibit poor performance due to the mismatch between the requirements of the object invocation mechanism and the machine architecture. Through measurements of an existing object‐based kernel, we present a breakdown of the costs involved in implementing the object invocation mechanism. The measurements suggest architectural solutions to improve the performance of such systems. We present our preliminary studies towards providing hardware support for the object invocation mechanism.
Unsupervised learning of facial emotion decoding skills

Research on the mechanisms underlying human facial emotion recognition has long focussed on genetically determined neural algorithms and often neglected the question of how these algorithms might be tuned by social learning. Here we show that facial emotion decoding skills can be significantly and sustainably improved by practice without an external teaching signal. Participants saw video clips of dynamic facial expressions of five different women and were asked to decide which of four possible emotions (anger, disgust, fear, and sadness) was shown in each clip. Although no external information about the correctness of the participant’s response or the sender’s true affective state was provided, participants showed a significant increase of facial emotion recognition accuracy both within and across two training sessions two days to several weeks apart. We discuss several similarities and differences between the unsupervised improvement of facial decoding skills observed in the current study, unsupervised perceptual learning of simple visual stimuli described in previous studies and practice effects often observed in cognitive tasks.
Mek1 Kinase Is Regulated To Suppress Double-Strand Break Repair between Sister Chromatids during Budding Yeast Meiosis

ABSTRACT Mek1 is a meiosis-specific kinase in budding yeast which promotes recombination between homologous chromosomes by suppressing double-strand break (DSB) repair between sister chromatids. Previous work has shown that in the absence of the meiosis-specific recombinase gene, DMC1, cells arrest in prophase due to unrepaired DSBs and that Mek1 kinase activity is required in this situation to prevent repair of the breaks using sister chromatids. This work demonstrates that Mek1 is activated in response to DSBs by autophosphorylation of two conserved threonines, T327 and T331, in the Mek1 activation loop. Using a version of Mek1 that can be conditionally dimerized during meiosis, Mek1 function was shown to be promoted by dimerization, perhaps as a way of enabling autophosphorylation of the activation loop in trans. A putative HOP1-dependent dimerization domain within the C terminus of Mek1 has been identified. Dimerization alone, however, is insufficient for activation, as DSBs and Mek1 recruitment to the meiosis-specific chromosomal core protein Red1 are also necessary. Phosphorylation of S320 in the activation loop inhibits sister chromatid repair specifically in dmc1Δ-arrested cells. Ectopic dimerization of Mek1 bypasses the requirement for S320 phosphorylation, suggesting this phosphorylation is necessary for maintenance of Mek1 dimers during checkpoint-induced arrest.
Definition and Distribution Analysis of Glycoprotein B Gene Alleles of Human Herpesvirus 7

ABSTRACT As for other herpesviruses, glycoprotein B (gB) of human herpesvirus 7 (HHV-7) is believed to play a major role in virus infection and as a target of the host immunogenic response. Using nested PCR, we amplified the whole HHV-7 gB gene from 108 human peripheral blood mononuclear cell samples and studied its variability. By means of restriction fragment length polymorphism (RFLP) analysis, three distinct patterns, designated I, II, and III, were defined and detected at frequencies of 93, 5, and 2%, respectively. Determination of the nucleotide sequence allowed us to recognize five critical positions in the gB gene with six specific combinations of point changes at these positions. These combinations were gB alleles A, B, C, D, E, and F. Alleles D and E corresponded to RFLP patterns II and III, respectively, while the other four alleles corresponded to RFLP pattern I. Identical gB alleles were detected in serial samples as well as in paired samples of blood and saliva from the same individuals, except for one case. In contrast, the distribution of gB alleles differed according to the geographical origin of the human samples: C was the most frequent allele in both African and Caribbean samples, whereas F was the most frequent allele in European ones. Although none of the allele-specific nucleotide changes induced any modification at the protein level, the definition of gB alleles provided convenient viral markers for the study of both HHV-7 infections and human population genetics.
Experimental Observation of Nonlinear Traveling Waves in Turbulent Pipe Flow

Transition to turbulence in pipe flow is one of the most fundamental and longest-standing problems in fluid dynamics. Stability theory suggests that the flow remains laminar for all flow rates, but in practice pipe flow becomes turbulent even at moderate speeds. This transition drastically affects the transport efficiency of mass, momentum, and heat. On the basis of the recent discovery of unstable traveling waves in computational studies of the Navier-Stokes equations and ideas from dynamical systems theory, a model for the transition process has been suggested. We report experimental observation of these traveling waves in pipe flow, confirming the proposed transition scenario and suggesting that the dynamics associated with these unstable states may indeed capture the nature of fluid turbulence.
Population coding in sparsely connected networks of noisy neurons

This study examines the relationship between population coding and spatial connection statistics in networks of noisy neurons. Encoding of sensory information in the neocortex is thought to require coordinated neural populations, because individual cortical neurons respond to a wide range of stimuli, and exhibit highly variable spiking in response to repeated stimuli. Population coding is rooted in network structure, because cortical neurons receive information only from other neurons, and because the information they encode must be decoded by other neurons, if it is to affect behavior. However, population coding theory has often ignored network structure, or assumed discrete, fully connected populations (in contrast with the sparsely connected, continuous sheet of the cortex). In this study, we modeled a sheet of cortical neurons with sparse, primarily local connections, and found that a network with this structure could encode multiple internal state variables with high signal-to-noise ratio. However, we were unable to create high-fidelity networks by instantiating connections at random according to spatial connection probabilities. In our models, high-fidelity networks required additional structure, with higher cluster factors and correlations between the inputs to nearby neurons.
Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution.

UNLABELLED The contribution of whole-genome doubling to chromosomal instability (CIN) and tumor evolution is unclear. We use long-term culture of isogenic tetraploid cells from a stable diploid colon cancer progenitor to investigate how a genome-doubling event affects genome stability over time. Rare cells that survive genome doubling demonstrate increased tolerance to chromosome aberrations. Tetraploid cells do not exhibit increased frequencies of structural or numerical CIN per chromosome. However, the tolerant phenotype in tetraploid cells, coupled with a doubling of chromosome aberrations per cell, allows chromosome abnormalities to evolve specifically in tetraploids, recapitulating chromosomal changes in genomically complex colorectal tumors. Finally, a genome-doubling event is independently predictive of poor relapse-free survival in early-stage disease in two independent cohorts in multivariate analyses [discovery data: hazard ratio (HR), 4.70, 95% confidence interval (CI), 1.04-21.37; validation data: HR, 1.59, 95% CI, 1.05-2.42]. These data highlight an important role for the tolerance of genome doubling in driving cancer genome evolution. SIGNIFICANCE Our work sheds light on the importance of whole-genome–doubling events in colorectal cancer evolution. We show that tetraploid cells undergo rapid genomic changes and recapitulate the genetic alterations seen in chromosomally unstable tumors. Furthermore, we demonstrate that a genome-doubling event is prognostic of poor relapse-free survival in this disease type.
Relationships in Large-Scale Graph Computing

In 2009 Grzegorz Czajkowski from Google's system infrastructure team has published an article which didn't get much attention in the SEO community at the time. It was titled "Large-scale graph computing at Google" and gave an excellent insight into the future of Google's search. This article highlights some of the little known facts which lead to transformation of Google's algorithm in the last two years.
Insights on the Impact of Physical Impairments in Full-Body Motion Gesture Elicitation Studies

Elicitation studies are becoming recently popular methodology to investigate novel gestural interfaces. Yet, little is known about possible factors that may influence this type of studies. To our knowledge, this paper is the first to investigate the impact of physical impairments in full-body motion gesture elicitation studies. Our study was conducted with 20 healthy and 12 arm and/or hand impaired voluntary participants undergoing rehabilitation. In total, 1,707 gestures were logged, analyzed, and paired with think-aloud data for 27 referents performed with and without imposed physical constrains. Our findings supported by observational analyses aim to reveal the challenges to achieve a single canonical gesture set, the most popular strategies for defining gestures, the variation of physical body engagement with full-body motion gestures, and the tendency towards personalized and hybrid gestures. Our results add to few existing research papers aiming for better understanding of potential shortcomings of end-user interaction elicitation.
The Cambridge Handbook of Computational Psychology: Putting the Pieces Together Again

4 What are the functions of vision? 5 4.1 The importance of mobile hands . 6 4.2 Seeing processes, affordances and empty spaces . 8 4.3 Seeing without recognising objects . 9 4.4 Many developmental routes to related cognitive competences . 10 4.5 The role of perception in ontology extension . 10
Exploring the Complexity of Layout Parameters in Tournaments and Semicomplete Digraphs

A simple digraph is semicomplete if for any two of its vertices u and v, at least one of the arcs (u,v) and (v,u) is present. We study the complexity of computing two layout parameters of semicomplete digraphs: cutwidth and optimal linear arrangement (Ola). We prove the following: • Both parameters are NP-hard to compute and the known exact and parameterized algorithms for them have essentially optimal running times, assuming the Exponential Time Hypothesis. • The cutwidth parameter admits a quadratic Turing kernel, whereas it does not admit any polynomial kernel unless NP ⊆ coNP/poly. By contrast, Ola admits a linear kernel. These results essentially complete the complexity analysis of computing cutwidth and Ola on semicomplete digraphs (with respect to standard parameters). Our techniques also can be used to analyze the sizes of minimal obstructions for having a small cutwidth under the induced subdigraph relation.
Smith ScholarWorks Smith ScholarWorks

Most Recent bryozoan species are encrusting sheets, and many of these colonies have densely packed feeding zooids. In this study, I tested whether tight packing of feeding zooids affects food capture. Colonies of a bryo-zoan with an encrusting sheet form ( Membranipora mem-branacea ) were dissected to produce individuals whose feeding zooids were (1) closely packed, (2) more widely spaced, or (3) isolated. For each type, rates of particle ingestion were measured in still water and in a freestream velocity of 2.7 cm s (cid:1) 1 . Ingestion rate increased when zooids were closest together, probably because of reduced reﬁltra-tion and increased feeding current strength farther from the lophophores. The mean incurrent velocity within 0.02 cm above the center of the lophophore was 0.28 cm s (cid:1) 1 regardless of zooid spacing; however, when the incurrent velocity was measured more than 0.1 cm from the lophophores, zooids that were close together or spaced one zooid’s width apart had signiﬁcantly faster incurrent velocities than single zooids. Flow visualization suggests that isolated zooids and those spaced far apart reﬁlter more water than zooids that are close together. These results along with the observed trend of increased zooid integration over evolutionary time suggest that the beneﬁts of increasing coordination out-weigh the consequences of intrazooid competition.
Patterned expression of BDNF and NT-3 in the retina and anterior segment of the developing mammalian eye.

PURPOSE The neurotrophins brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) are hypothesized to play an important role in vertebrate eye development because of their patterned expression in the developing and adult neuroretina, their regulated response to retinal and optic nerve injury, and the effects of altered neurotrophin signaling on retinal development. To further characterize the role of these neurotrophins in mammalian eye development and maintenance, the pattern of expression of BDNF and NT-3 was analyzed in the developing and mature mouse eye. METHODS Using mouse strains in which the reporter gene lacZ, encoding the enzyme beta-galactosidase, was targeted to either the BDNF or NT-3 locus, the expression of BDNF and NT-3 in the eyes of mice heterozygous for these mutations was analyzed by enzyme histochemistry during embryogenesis, postnatal development, and adulthood. RESULTS BDNF and NT-3 expression were first observed in the inner and outer segments of the developing optic cup at embryonic days 10.5 to 11.5. As the retina matured, BDNF expression was restricted to retinal ganglion cells and a subset of cells in the inner nuclear layer (INL), whereas NT-3 expression was confined to a small subset of cells in the INL and ganglion cell layer. Both neurotrophins were expressed within the developing retinal pigment epithelium. In the anterior segment, BDNF and NT-3 were expressed at high levels in the developing and mature ciliary epithelium. In the lens and cornea, however, these neurotrophins displayed distinct patterns of expression during development and adulthood. BDNF expression was found in the lens epithelium, immature trabecular meshwork, corneal endothelium, and corneal epithelium, whereas NT-3 expression was confined to the corneal epithelium. CONCLUSIONS BDNF and NT-3 exhibit different, yet overlapping, patterns of expression during the development and differentiation of the mouse eye. In addition to the neuroretina, the spatiotemporal expression of BDNF and NT-3 may play an important role in the development and maintenance of the lens, ciliary body, trabecular meshwork, and cornea.