gebhart/patrepeval huggingface dataset:
Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (2022)

In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArticle has been corrected to include the members and affiliations of the PCAWG Consortium in the main paper; the corrections have been made to the HTML version of the Article but not the PDF version. Additional corrections to affiliations have been made to the PDF and HTML versions of the original Article for consistency of information between the PCAWG list and the main paper.
Characteristic Classes and Zeroth Order Pseudodifferential Operators (2010)

We provide evidence for the conjecture that the Wodzicki-Chern classes vanish for all bundles with the group Z of invertible zeroth order pseudodifferential operators as structure group. In particular, we prove this vanishing if the structure group reduces to pseudodifferential operators with leading order symbol the identity. The leading order Chern classes are nonzero in general, and they detect elements of the de Rham cohomology groups of the classifying space BZ.
Resveratrol, from experimental data to nutritional evidence: the emergence of a new food ingredient (2013)

The polyphenol resveratrol is found notably in grapes and in a variety of medicinal plants. Recently, resveratrol has been suggested to have cardioprotective effects and to improve metabolic health by mimicking the effects of calorie restriction. Numerous animal and in vitro studies suggest that resveratrol could improve cardiovascular and metabolic health in humans. In view of this compelling preclinical evidence, several human studies investigating the effects of resveratrol on vascular and metabolic health have been initiated. Collectively, the animal, human epidemiological, and first human intervention studies support a role of resveratrol in vascular and metabolic health. This has led to the introduction of the first supplement and food products containing resveratrol and its emergence as a promising new health ingredient. Thus, supplementation with resveratrol may be included in nutritional and lifestyle programs aiming to reduce the risk of vascular and obesity-related problems.
<title>Standard (H.324M) compatible video decoding for mobile multimedia systems over error-prone channel</title> (1997)

Motivated by error-robust mobile multiplexer what was called H.223/Annex A, we investigate restriction of H.263 functionality in H.324 mobile terminals against error-prone channel. Although H.223/A employs strong error protection schemes such as rate compatible punctured convolutional code and automatic retransmission on request, it cannot detect errors is encoded video bit stream. In order to further increase the performance of the total H.324/M system, it is desirable to reduce functionality of H.263 so that H.263 decoder can easily locate errors in incoming H.263 stream, which cannot be made possible by H.223/A. We suggest one possible way to achieve H.263-compatible and reduced functionality incorporated with a new mobile multiplexer in wireless links aiming at enhancement of visual quality at receiver.
Determination of γ and−2βsfrom charmless two-body decays of beauty mesons (2014)

Using the latest LHCb measurements of time-dependent CP violation in the Bs0→K+K- decay, a U-spin relation between the decay amplitudes of Bs0→K+K- and B0→π+π- decay processes allows constraints to be placed on the angle γ of the unitarity triangle and on the Bs0 mixing phase -2βs. Results from an extended approach, which uses additional inputs on B0→π0π0 and B+→π+π0 decays from other experiments and exploits isospin symmetry, are also presented. The dependence of the results on the maximum allowed amount of U-spin breaking is studied. At 68% probability, the value γ=(63.5-6.7+7.2)° modulo 180° is determined. In an alternative analysis, the value -2βs=-0.12-0.16+0.14 rad is found. In both measurements, the uncertainties due to U-spin breaking effects up to 50% are included. © 2014 The Authors.
Spin-Dependent Resistivity at Transitions between Integer Quantum Hall States (2005)

The longitudinal resistivity at transitions between integer quantum Hall states in two-dimensional electrons confined to AlAs quantum wells is found to depend on the spin orientation of the partially filled Landau level in which the Fermi energy resides. The resistivity can be enhanced by an order of magnitude as the spin orientation of this energy level is aligned with the majority spin. We discuss possible causes and suggest a new explanation for the spikelike features observed at the edges of quantum Hall minima near Landau level crossings.
Methamphetamine Inhibits Antigen Processing, Presentation, and Phagocytosis (2008)

Methamphetamine (Meth) is abused by over 35 million people worldwide. Chronic Meth abuse may be particularly devastating in individuals who engage in unprotected sex with multiple partners because it is associated with a 2-fold higher risk for obtaining HIV and associated secondary infections. We report the first specific evidence that Meth at pharmacological concentrations exerts a direct immunosuppressive effect on dendritic cells and macrophages. As a weak base, Meth collapses the pH gradient across acidic organelles, including lysosomes and associated autophagic organelles. This in turn inhibits receptor-mediated phagocytosis of antibody-coated particles, MHC class II antigen processing by the endosomal-lysosomal pathway, and antigen presentation to splenic T cells by dendritic cells. More importantly Meth facilitates intracellular replication and inhibits intracellular killing of Candida albicans and Cryptococcus neoformans, two major AIDS-related pathogens. Meth exerts previously unreported direct immunosuppressive effects that contribute to increased risk of infection and exacerbate AIDS pathology.
Ovariectomy Augments Hypertension Through Rho-Kinase Activation in the Brain Stem in Female Spontaneously Hypertensive Rats (2006)

Estrogen protects against increases in arterial pressure (AP) by acting on blood vessels and on cardiovascular centers in the brain. The mechanisms underlying the effects of estrogen in the brain stem, however, are not clear. The aim of the present study was to determine whether ovariectomy affects AP via the Rho/Rho-kinase pathway in the brain stem. We performed bilateral ovariectomy in 12-week-old female spontaneously hypertensive rats. AP and heart rate (HR), measured using radiotelemetry in awake rats, were increased in ovariectomized rats compared with control rats (mean AP: 163+/-3 versus 144+/-4 mm Hg; HR: 455+/-4 versus 380+/-6 bpm). Continuous intracisternal infusion of Y-27632 significantly attenuated the ovariectomy-induced increase in AP and HR (mean AP: 137+/-6 versus 163+/-3 mm Hg; HR: 379+/-10 versus 455+/-4 bpm). In addition, we confirmed the increase of Rho-kinase activity in the brain stem in ovariectomized rats, and the increase was attenuated by intracisternal infusion of Y-27632 via the phosphorylated ezrin, radixin, and moesin (ERM) family, which are Rho-kinase target proteins. Furthermore, angiotensin II type 1 receptor expression in the brain stem was significantly greater in ovariectomized rats than in control rats, and the increase was partially reduced by intracisternal infusion of Y-27632. In a separate group of animals, we confirmed that the serum and cerebrospinal fluid 17beta-estradiol concentrations decreased in ovariectomized rats. These results suggest that depletion of endogenous estrogen by ovariectomy, at least in part, induces hypertension in female spontaneously hypertensive rats via activation of the renin-angiotensin system and the Rho/Rho-kinase pathway in the brain stem.
Increased Corneal Epithelial Turnover Contributes to Abnormal Homeostasis in the Pax6+/− Mouse Model of Aniridia (2013)

We aimed to test previous predictions that limbal epithelial stem cells (LESCs) are quantitatively deficient or qualitatively defective in Pax6(+/-) mice and decline with age in wild-type (WT) mice. Consistent with previous studies, corneal epithelial stripe patterns coarsened with age in WT mosaics. Mosaic patterns were also coarser in Pax6(+/-) mosaics than WT at 15 weeks but not at 3 weeks, which excludes a developmental explanation and strengthens the prediction that Pax6(+/-) mice have a LESC-deficiency. To investigate how Pax6 genotype and age affected corneal homeostasis, we compared corneal epithelial cell turnover and label-retaining cells (LRCs; putative LESCs) in Pax6(+/-) and WT mice at 15 and 30 weeks. Limbal BrdU-LRC numbers were not reduced in the older WT mice, so this analysis failed to support the predicted age-related decline in slow-cycling LESC numbers in WT corneas. Similarly, limbal BrdU-LRC numbers were not reduced in Pax6(+/-) heterozygotes but BrdU-LRCs were also present in Pax6(+/-) corneas. It seems likely that Pax6(+/-) LRCs are not exclusively stem cells and some may be terminally differentiated CD31-positive blood vessel cells, which invade the Pax6(+/-) cornea. It was not, therefore, possible to use this approach to test the prediction that Pax6(+/-) corneas had fewer LESCs than WT. However, short-term BrdU labelling showed that basal to suprabasal movement (leading to cell loss) occurred more rapidly in Pax6(+/-) than WT mice. This implies that epithelial cell loss is higher in Pax6(+/-) mice. If increased corneal epithelial cell loss exceeds the cell production capacity it could cause corneal homeostasis to become unstable, resulting in progressive corneal deterioration. Although it remains unclear whether Pax6(+/-) mice have LESC-deficiency, we suggest that features of corneal deterioration, that are often taken as evidence of LESC-deficiency, might occur in the absence of stem cell deficiency if corneal homeostasis is destabilised by excessive cell loss.
Observation of columnar microstructure in lattice-matched InAlN/GaN grown by plasma assisted molecular beam epitaxy (2012)

Nominally lattice matched InAlN/GaN was grown by plasma-assisted molecular beam epitaxy, and the intrinsic microstructure was investigated via x-ray diffraction, transmission electron microscopy, and atom probe tomography. The InAlN showed a cellular structure, which was comprised of ∼10 nm wide Al-rich cores and ∼1 nm In-rich InAlN intercellular boundaries. Despite the strong laterally non-uniform In distribution, both vertical and lateral lattices are unperturbed by the cellular structure, as evidenced by strong thickness fringes in on-axis ω−2θ high resolution x-ray diffraction scans, coherence lengths derived from on-axis (0002) and off-axis (101¯2) ω−2θ high resolution x-ray diffraction scans, and a modified Williamson-Hall analysis for on-axis reflections.
Effects of heat treatment atmosphere on the structure and activity of Pt3Sn nanoparticle electrocatalysts: a characterisation case study (2018)

Comprehensive identification of the phases and atomic configurations of bimetallic nanoparticle catalysts are critical in understanding structure-property relationships in catalysis. However, control of the structure, whilst retaining the same composition, is challenging. Here, the same carbon supported Pt3Sn catalyst is annealed under air, Ar and H2 resulting in variation of the extent of alloying of the two components. The atmosphere-induced extent of alloying is characterised using a variety of methods including TEM, XRD, XPS, XANES and EXAFS and is defined as the fraction of Sn present as Sn0 (XPS and XANES) or the ratio of the calculated composition of the bimetallic particle to the nominal composition according to the stoichiometric ratio of the preparation (TEM, XRD and EXAFS). The values obtained depend on the structural method used, but the trend air < Ar < H2 annealed samples is consistent. These results are then used to provide insights regarding the electrocatalytic activity of Pt3Sn catalysts for CO, methanol, ethanol and 1-butanol oxidation and the roles of alloyed Sn and SnO2.
A Generative Product-of-Filters Model of Audio (2013)

We propose the product-of-filters (PoF) model, a generative model that decomposes audio spectra as sparse linear combinations of "filters" in the log-spectral domain. PoF makes similar assumptions to those used in the classic homomorphic filtering approach to signal processing, but replaces hand-designed decompositions built of basic signal processing operations with a learned decomposition based on statistical inference. This paper formulates the PoF model and derives a mean-field method for posterior inference and a variational EM algorithm to estimate the model's free parameters. We demonstrate PoF's potential for audio processing on a bandwidth expansion task, and show that PoF can serve as an effective unsupervised feature extractor for a speaker identification task.
Flow-Based Detection of Bar Coded Particles (2005)

We have developed methods for flow control, electric field alignment, and readout of colloidal Nanobarcodes{copyright}. Our flow-based detection scheme leverages microfluidics and alternate current (AC) electric fields to align and image particles in a well-defined image plane. Using analytical models of the particle rotation in electric fields we can optimize the field strength and frequency necessary to align the particles. This detection platform alleviates loss of information in solution-based assays due to particle clumping during detection.
Gene expression profiling for mechanistic understanding of cellular aggregation in mammalian cell perfusion cultures (2012)

Aggregation of baby hamster kidney (BHK) cells cultivated in perfusion mode for manufacturing recombinant proteins was characterized. The potential impact of cultivation time on cell aggregation for an aggregating culture (cell line A) was studied by comparing expression profiles of 84 genes in the extracellular adhesion molecules (ECM) pathway by qRT-PCR from 9 and 25 day shake flask samples and 80 and 94 day bioreactor samples. Significant up-regulation of THBS2 (4.4- to 6.9-fold) was seen in both the 25 day shake flask and 80 and 94 day bioreactor samples compared to the 9 day shake flask while NCAM1 was down-regulated 5.1- to 8.9-fold in the 80 and 94 day bioreactor samples. Subsequent comparisons were made between cell line A and a non-aggregating culture (cell line B). A 65 day perfusion bioreactor sample from cell line B served as the control for 80 and 94 day samples from four different perfusion bioreactors for cell line A. Of the 84 genes in the ECM pathway, four (COL1A1, COL4A1, THBS2, and VCAN) were consistently up-regulated in cell line A while two (NCAM1 and THBS1) were consistently down-regulated. The magnitudes of differential gene expression were much higher when cell lines were compared (4.1- to 44.6-fold) than when early and late cell line B samples were compared (4.4- to 6.9-fold) indicating greater variability between aggregating and non-aggregating cell lines. Based on the differential gene expression results, two mechanistic models were proposed for aggregation of BHK cells in perfusion cultures.
DOPA Residues Endow Collagen with Radical Scavenging Capacity** (2023)

Abstract Here we uncover collagen, the main structural protein of all connective tissues, as a redox‐active material. We identify dihydroxyphenylalanine (DOPA) residues, post‐translational oxidation products of tyrosine residues, to be common in collagen derived from different connective tissues. We observe that these DOPA residues endow collagen with substantial radical scavenging capacity. When reducing radicals, DOPA residues work as redox relay: they convert to the quinone and generate hydrogen peroxide. In this dual function, DOPA outcompetes its amino acid precursors and ascorbic acid. Our results establish DOPA residues as redox‐active side chains of collagens, probably protecting connective tissues against radicals formed under mechanical stress and/or inflammation.
Enhancement effect of ethanol on lipopolysaccharide-induced procoagulant status in human umbilical endothelial cells. (2009)

In spite of the inhibitory effects of ethanol (EtOH) on platelet function, soft blood clots are often observed in cadaveric blood in cases of sudden death after alcohol ingestion. In order to resolve this discrepancy, we have focused on the role of vascular endothelial cells. We tried to investigate the effects of EtOH and LPS on endothelial cells from various perspectives; thrombogenic factor (Von Willebrand factor, VWF), fibrinolytic factor (tissue plasminogen activator, tPA) and inflammatory factor (Interleukin-6, IL-6). Human umbilical vein endothelial cells (HUVECs) were incubated with various concentrations of EtOH (0-160 mM) with or without LPS. Treatment with EtOH and LPS increased VWF release from HUVECs without enhancement mRNA expression. Treatment with 40 mM of EtOH also increased IL-6 release from HUVECs without enhancement mRNA expression. Although EtOH inhibited LPS-induced IL-6 mRNA expression, 20 mM of EtOH still had an increasing effect on the release of IL-6. These doses of EtOH are consistent with a moderate drunkenness level in a normal person. On the other hand, mRNA expression and release reaction of tPA were not affected by EtOH and LPS addition. In conclusion, EtOH enhances procoagulant status via VWF release and IL-6 production cooperation with LPS and may contribute to soft blood clot formation in cadaveric blood.
Improved Rate Expression in the Quasi-Equilibrium Theory of Mass Spectra (1962)

An improved continuous approximation to the number of states of a collection of harmonic oscillators of different frequencies has been developed and applied to the quasi-equilibrium theory of mass spectra. The classical approximation previously used in this theory has been shown to be invalid at low energies. The difficulties in the application of the quasi-equilibrium theory of mass spectra are to a great extent resolved by the use of this more reasonable approximation.
An analysis of a modified point coordination function in IEEE 802.11 (2004)

Since the point coordination function (PCF) in the IEEE 802.11 is based on a centralized polling protocol, some bandwidth is wasted due to the polling overheads and also due to null packets that are issued in case a polled station does not have any data to transmit. In order to reduce this waste and increase the channel utilization, we have proposed a modified version of the standard PCF. The modified PCF uses a distributed polling protocol (DPP) as the access mechanism for the uplink transmission of real-time traffic. The transmission period in the modified PCF consists of a distributed polling protocol period (DPPP) which is controlled by the DPP and the real-time traffic downlink period (KTDP). Our proposal further includes a technique for dealing with the hidden station problem for use together with the proposed modification. In this paper, an analysis is done to compare the performance of the modified PCF with the standard PCF in terms of number of supportable stations in a contention-free period (CFP) and the channel efficiency. The analytical results show that the modified PCF can support a much higher number of stations than the standard PCF. In addition, the channel efficiency of the modified PCF is better under the assumption that there is no hidden station in the system. The results imply that the channel utilization of the modified PCF is better than the standard PCF.
Rapid Laser Pulse Synthesis of Supported Metal Nanoclusters with Kinetically Tunable Size and Surface Density for Electrocatalytic Hydrogen Evolution (2020)

Matrix-supported metal nanoclusters (1–10 nm) with unique size- and shape-dependent properties have drawn attention for their potential applications in electronics, catalysis, energy storage, and sensors. However, synthesis of matrix-supported ultrasmall nanoclusters at high concentration and in an unaggregated state is challenging. Here we demonstrate a rapid laser pulse technique to in situ fabricate ultrasmall metal nanoclusters supported on a carbon nanofiber (CNF) matrix with kinetically controllable size and surface density. A rapid laser pulse heating on the metal precursor incorporated CNF matrix triggers the fast nucleation and growth of metal nanoclusters, and a subsequent ultrafast quenching freezes them onto the CNF structure. We find that a shorter laser pulse enables the formation of metal nanoclusters with higher number densities and smaller sizes while longer laser pulse leads to the further growth of metal nanoclusters and the achievement of their equilibrium shape. A characteristic time analysis suggests that the growth of metal nanoclusters is dominated by surface diffusion and sintering, and Ostwald ripening is mainly involved at the early stage of nanocluster formation. We also demonstrate that the catalytic performance of CNF matrix supported metal nanoclusters toward electrocatalytic hydrogen evolution is enhanced for metal nanoclusters with a smaller size and higher number density. This work provides a promising approach for rapid and scalable fabrication of ultrasmall, high-density metal nanoclusters, and nanocluster-based devices.
A Subband Space Constrained Beamformer incorporating Voice Activity Detection (2006)

This paper introduces a new subband adaptive space constrained beamforming structure for use in hands-free speech enhancement applications. The scheme incorporates a space constrained source model and voice activity information through the integration of a voice activity detector (VAD). The VAD information is used to estimate noise covariance information during non-speech periods and to optimally estimate the source power spectral density (PSD), which is used to provide a spectrally optimized constraint on the source. The proposed structure is evaluated in a real car environment, yielding results which compare well to the optimal Wiener solution where full knowledge of the source is known.
Rapid tracking of small displacements with ultrasound (2006)

Time-delay estimators, such as normalized cross correlation and phase-shift estimation, form the computational basis for elastography, blood flow measurements, and acoustic radiation force impulse (ARFI) imaging. This paper examines the performance of these algorithms for small displacements (less than half the ultrasound pulse wavelength). The effects of noise, bandwidth, stationary echoes, kernel size, downsampling, interpolation, and quadrature demodulation on the accuracy of the time delay estimates are measured in terms of bias and jitter. Particular attention is given to the accuracy and resolution of the displacement measurements and to the computational efficiency of the algorithms. In most cases, Loupas' two-dimensional (2-D) autocorrelator performs as well as the gold standard, normalized cross correlation. However, Loupas' algorithm's calculation time is significantly faster, and it is particularly suited to operate on the signal data format most commonly used in ultrasound scanners. These results are used to implement a real-time ARFI imaging system using a commercial ultrasound scanner and a computer cluster. Images processed with the algorithms are examined in an ex vivo liver ablation study.