gebhart/patrepeval huggingface dataset:
Negative feedback regulation of endothelial cell function by nitric oxide. (1993)

The objective of this study was to determine whether nitric oxide (NO) could function as a negative feedback modulator of endothelial cell function by inhibiting NO synthase in vascular endothelial cells. The rationale for this approach was a previous study from this laboratory, which revealed that NO inhibits neuronal NO synthase from rat cerebellum. In the present study, NO and NO-donor agents noncompetitively inhibited NO synthase derived from bovine aortic endothelial cells. Oxyhemoglobin blocked the inhibitory action of NO and by itself increased NO synthase activity. This finding suggests that NO acts as a negative feedback modulator of NO synthase. In intact aortic endothelial cells grown on microcarrier beads and perfused in a bioassay cascade system, pretreatment of cells with NO-donor agents caused a marked inhibition of endothelial NO biosynthesis in response to bradykinin and increased fluid shear or flow. When isolated bovine pulmonary arterial rings precontracted by phenylephrine were used, pretreatment of arterial rings with NO-donor agents diminished endothelium-dependent arterial relaxation involving the L-arginine-NO pathway without altering endothelium-independent relaxation to NO itself. On the basis of these studies, NO is suggested to play an important negative feedback regulatory role on endothelial NO synthase and, therefore, vascular endothelial cell function.
The multimode transform predictive coding paradigm (2003)

Presented is a new coding paradigm, multimode transform predictive coding (MTPC), which combines speech and audio coding principles in a single coding structure. The paradigm is an adaptive coding paradigm which automatically adjusts how different coding modules are used based on the input signal. This allows MTPC coders to robustly handle a wider range of signals than single configuration (mode) transform predictive coding (TPC) designs. A wideband MTPC coder design targeting two-way communication applications and bitrates from 13 to 40 kbit/s is also presented. Subjective absolute category rating test results on speech, speech in noise and music demonstrate that the performance at 16, 24 and 32 kbit/s meets or exceeds that of ITU-T Rec. G.722 at 48, 56 and 64 kbit/s respectively for many coding conditions. Subjective Reference-ABx (R-ABx) tests are also included to show the potential advantages of the multimode coder over a single mode TPC coder. Finally, possible improvements in the MTPC coder design for applications such as broadcasting, which are less sensitive to delay and encoder complexity, are discussed.
Roles of PLC-β2 and -β3 and PI3Kγ in Chemoattractant-Mediated Signal Transduction (2000)

The roles of phosphoinositide 3-kinase (PI3K) and phospholipase C (PLC) in chemoattractant-elicited responses were studied in mice lacking these key enzymes. PI3Kgamma was required for chemoattractant-induced production of phosphatidylinositol 3,4,5-trisphosphate [PtdIns (3,4,5)P3] and has an important role in chemoattractant-induced superoxide production and chemotaxis in mouse neutrophils and in production of T cell-independent antigen-specific antibodies composed of the immunoglobulin lambda light chain (TI-IglambdaL). The study of the mice lacking PLC-beta2 and -beta3 revealed that the PLC pathways have an important role in chemoattractant-mediated production of superoxide and regulation of protein kinases, but not chemotaxis. The PLC pathways also appear to inhibit the chemotactic activity induced by certain chemoattractants and to suppress TI-IglambdaL production.
Thermal imaging of spin Peltier effect (2016)

The Peltier effect modulates the temperature of a junction comprising two different conductors in response to charge currents across the junction, which is used in solid-state heat pumps and temperature controllers in electronics. Recently, in spintronics, a spin counterpart of the Peltier effect was observed. The 'spin Peltier effect' modulates the temperature of a magnetic junction in response to spin currents. Here we report thermal imaging of the spin Peltier effect; using active thermography technique, we visualize the temperature modulation induced by spin currents injected into a magnetic insulator from an adjacent metal. The thermal images reveal characteristic distribution of spin-current-induced heat sources, resulting in the temperature change confined only in the vicinity of the metal/insulator interface. This finding allows us to estimate the actual magnitude of the temperature modulation induced by the spin Peltier effect, which is more than one order of magnitude greater than previously believed.
Cell Adhesion in Animal Cell Culture: Physiological and Fluid-Mechanical Implications (2018)

We have reviewed the general forces through which cells interact with substrata in their first nonspecific contact. The complex, fast-emerging biology of specific cell adhesion and the structure of the extracellular matrix were reviewed in substantial detail, and the most updated conceptual model of biological cell adhesion was assembled from past efforts and new literature data. The chemistries of the various possible substrata for cell adhesion have been reviewed extensively in the past, and here only a brief summary was presented, with particular emphasis on the materials for traditional and porous microcarriers. The fascinating molecular and cellular implications of cell adhesion were reviewed in detail to establish that cell adhesion and the extracellular matrix provide more than structural support for the cells and their assemblies, and that in fact they constitute fundamental regulators of cell function, metabolism, and differentiation. We reviewed the fluid-mechanical mechanisms of cell damage in microcarrier systems and provided experimental evidence for the importance of the cell-adhesion quality in the ability of cells to withstand fluid forces in bioreactors. We provided evidence that the interplay of cell adhesion and fluid forces is likely to produce cell responses more complex than that of simple life and death, and we suggested that such responses are awaiting investigation and exploration for new applications and culturing possibilities. We also reviewed the experimental evidence on the importance of cell adhesion in cell and microcarrier aggregation and discussed the implications of such aggregation on the culturing environment and the operation of bioreactors. Finally, we discussed the possible implications of cell adhesion as it relates to the developing field of tissue engineering, using the example of bone marrow culture, which involves a large variety of cells and constitutes one of the most complex cell culture systems.
Adaptive Inertia Caused by Hidden Pleiotropic Effects (1997)

Pleiotropic effects among quantitative characters are believed to be extensive and universal, although their actual amount and pattern remains to be determined. Theoretical studies have shown that pleiotropic effects can influence the dynamics of a character under stabilizing selection and mutation through genetic correlations as well as hidden pleiotropic effects. It is further known that pleiotropic effects on fitness can cause an apparent stabilizing selection for an otherwise neutral character. The response to directional selection also depends on genetic correlations to other characters via correlated selection responses and deleterious side effects. In this paper we analyze a class of models for the adaptation of complex organisms based on three assumptions: (1) pleiotropic effects among characters are extensive, even in the absence of genetic correlations (hidden pleiotropic effects); (2) directional selection only acts on one or a small number of characters simultaneously (mosaic evolution); (3) the remaining characters are either neutral or under stabilizing selection. We show that the response to directed natural selection is strongly influenced by hidden pleiotropic effects on a second uncorrelated character which is under stabilizing selection. The hidden pleiotropic effects are inducing apparent stabilizing selection which interacts with the directional selection acting on the first character. The apparent stabilizing selection is mediated through the dynamics of the genetic variance associated with a change in the mean genotypic value. The result can be either inhibitory or accelerating, depending on the frequency of the alleles. The inhibitory effect can even completely prevent a response to directional selection if apparent stabilizing selection is strong compared to directional selection. In finite populations, the asymptotic rate of evolution is also influenced by hidden pleiotropic effects. This is mostly caused by a reduction of the asymptotic genetic variance maintained by mutation under sustained directional selection. It is concluded that hidden pleiotropic effects lead to adaptive inertia even in the absence of genetic correlations.
Monolithically Integrated Multilayer Silicon Nitride-on-Silicon Waveguide Platforms for 3-D Photonic Circuits and Devices (2018)

In this paper, we review and provide additional details about our progress on multilayer silicon nitride (SiN)-on-silicon (Si) integrated photonic platforms. In these platforms, one or more SiN waveguide layers are monolithically integrated onto a Si photonic layer. This paper focuses on the development of three-layer platforms for the O- and SCL-bands for very large-scale photonic integrated circuits requiring hundreds or thousands of waveguide crossings. Low-loss interlayer transitions and ultralow-loss waveguide crossings have been demonstrated, along with bilevel and trilevel grating couplers for fiber-to-chip coupling. The SiN and Si passive devices have been monolithically integrated with high-efficiency optical modulators, photodetectors, and thermal tuners in a single photonic platform.
Transcriptional gene expression profiling of small cell lung cancer cells. (2003)

A global gene expression analysis using oligonucleotide microarrays was performed on many human small cell lung cancer (SCLC) cell lines in cell culture and/or as xenografts. The expression was compared with the expression profiles of 18 normal tissues. In a hierarchical cluster analysis the cell lines clustered distinctly from normal tissues and grouped into four clusters. One cluster consisted of two related cell lines and was markedly different from the other SCLC cell lines, whereas the rest of the clusters grouped together. Two subclusters contained the classical SCLC types and one subcluster the variant SCLC type, thus identifying many genes with differential expression between the two variants of SCLC. All of the xenografts clustered closest to the cell lines from which they originated and had the same expression levels as the cells grown in culture for the majority of genes. The analysis confirmed the high expression of many genes identified previously as highly expressed in SCLC cells including neuroendocrine markers, oncogenes, and genes involved in cell proliferation and division. The analysis furthermore identified a number of molecules not identified previously as expressed in SCLC. Several of these are expressed in low or undetectable amounts in the majority of normal tissues and, therefore, are potential targets for new therapeutic approaches. By including the published array profiles of six ressected SCLC tumors from Bhattacharjee et al. (A. Bhattacharjee et al., Proc. Natl. Acad. Sci. USA, 98: 13790-13795, 2001.), the analysis revealed that most of the novel potential targets expressed by SCLC cell lines and xenografts were also expressed in the tumors. This analysis demonstrates the value of using cell lines and xenografts for expression profiling, when a limited quantity of tumor material is available.
Tests of a Silica Aerogel Cerenkov Detector to be Used in the European Hybrid Spectrometer (1981)

An 18 module Cerenkov detector with a total sensitive area of 2.3 m /sup 2/ having silica aerogel as radiator is being tested in a particle beam at CERN PS. The modules having a sensitive area of 23*55 cm/sup 2/ give typically a Cerenkov signal for beta =1 particles of 12 photoelectrons for silica aerogel of refractive index 1.03 and a thickness of 15 cm. (0 refs).
Field-Modulated Carrier Transport in Carbon Nanotube Transistors (2002)

We have investigated the electrical transport properties of carbon nanotube field-effect transistors as a function of channel length, gate dielectric film thickness, and dielectric material. Our experiments show that the bulk properties of the semiconducting carbon nanotubes do not limit the current flow through the metal/nanotube/metal system. Instead, our results can be understood in the framework of gate and source-drain field induced modulation of the nanotube band structure at the source contact. The existence of one-dimensional Schottky barriers at the metal/nanotube interface determines the device performance and results in an unexpected scaling behavior.
Identification of Serum Soluble ST2 Receptor as a Novel Heart Failure Biomarker (2003)

Serum soluble ST2 is a novel biomarker for neurohormonal activation in patients with heart failure. In patients with severe chronic NYHA class III to IV heart failure, the change in ST2 levels is an independent predictor of subsequent mortality or transplantation.
Control of the Gastrointestinal Tract by Enteric Neurons (1994)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
A Chitinase-like Protein in the Lung and Circulation of Patients with Severe Asthma (2007)

YKL-40 is found in increased quantities in the serum and lungs in a subgroup of patients with asthma, in whom expression of chitinase in both compartments correlates with the severity of asthma. The recovery of YKL-40 from these patients indicates either a causative or a sentinel role for this molecule in asthma.
Distillation as a Defense to Adversarial Perturbations Against Deep Neural Networks (2016)

Deep learning algorithms have been shown to perform extremely well on many classical machine learning problems. However, recent studies have shown that deep learning, like other machine learning techniques, is vulnerable to adversarial samples: inputs crafted to force a deep neural network (DNN) to provide adversary-selected outputs. Such attacks can seriously undermine the security of the system supported by the DNN, sometimes with devastating consequences. For example, autonomous vehicles can be crashed, illicit or illegal content can bypass content filters, or biometric authentication systems can be manipulated to allow improper access. In this work, we introduce a defensive mechanism called defensive distillation to reduce the effectiveness of adversarial samples on DNNs. We analytically investigate the generalizability and robustness properties granted by the use of defensive distillation when training DNNs. We also empirically study the effectiveness of our defense mechanisms on two DNNs placed in adversarial settings. The study shows that defensive distillation can reduce effectiveness of sample creation from 95% to less than 0.5% on a studied DNN. Such dramatic gains can be explained by the fact that distillation leads gradients used in adversarial sample creation to be reduced by a factor of 1030. We also find that distillation increases the average minimum number of features that need to be modified to create adversarial samples by about 800% on one of the DNNs we tested.
Distributed Dual Ascent Algorithm for Steiner Problems in Networks (2013)

Abstract. Steiner Problems in undirected or directed graphs are often used to model multicast routing problems. The directed case being particularly suitable to situations where most of the trafic has a single source. Sequential Steiner heuristics are not convenient in that context, since one can not assume that a central node has complete information about the topology and the state of a large wide area network. This work presents a distributed version of the Dual Ascent Heuristic proposed by Wong, known for its remarkable good practical results, lower and upper bounds, in both undirected and directed Steiner problems. The distributed Dual Ascent has worst case complexities of O(|V | 2) time and O(|T |.|V | 2) messages. Experimental results are also presented, showing the eficiency of the proposed algorithm. 1.
Traffic matrix estimation (2002)

Very few techniques have been proposed for estimating traffic matrices in the context of Internet traffic. Our work on POP-to-POP traffic matrices (TM) makes two contributions. The primary contribution is the outcome of a detailed comparative evaluation of the three existing techniques. We evaluate these methods with respect to the estimation errors yielded, sensitivity to prior information required and sensitivity to the statistical assumptions they make. We study the impact of characteristics such as path length and the amount of link sharing on the estimation errors. Using actual data from a Tier-1 backbone, we assess the validity of the typical assumptions needed by the TM estimation techniques. The secondary contribution of our work is the proposal of a new direction for TM estimation based on using choice models to model POP fanouts. These models allow us to overcome some of the problems of existing methods because they can incorporate additional data and information about POPs and they enable us to make a fundamentally different kind of modeling assumption. We validate this approach by illustrating that our modeling assumption matches actual Internet data well. Using two initial simple models we provide a proof of concept showing that the incorporation of knowledge of POP features (such as total incoming bytes, number of customers, etc.) can reduce estimation errors. Our proposed approach can be used in conjunction with existing or future methods in that it can be used to generate good priors that serve as inputs to statistical inference techniques.
Manipulating Polysulfide Conversion with Strongly Coupled Fe3O4 and Nitrogen Doped Carbon for Stable and High Capacity Lithium–Sulfur Batteries (2018)

Abstract Li–S batteries are among the most promising energy storage technologies but their commercialization faces substantial challenges, largely due to difficulties in controlling their reaction pathways under practical conditions. Here, the synthesis of strongly coupled Fe 3 O 4 and N‐doped carbon directly in flexible carbon cloth is demonstrated, as well as their novel use for hosting sulfur with outstanding performance for Li–S batteries. It is discovered that the synergistic effects of Fe 3 O 4 and N‐carbon bring strong adsorption toward lithium polysulfide, and ensure nearly complete conversion of short‐chain polysulfide to Li 2 S during discharge. The Li 2 S solids generated on these novel hosts are extremely reactive and can be readily charged back to S without a noticeable overpotential. The critical roles of Fe 3 O 4 and N‐doped carbon are studied and direct correlations are established between their surface concentration/crystallinity and the Li 2 S 4 to Li 2 S conversion capacity. This novel manipulation of polysulfide conversion allows to fabricate freestanding and flexible sulfur cathodes that deliver a specific capacity of 1316 mAh g −1 at 0.1C and stable cycling for 1000 cycles at 0.2C under a high sulfur loading of ≈4.7 mg cm −2 .
An Approach to Multiplexing an Immunosorbent Assay with Antibody−Oligonucleotide Conjugates (2010)

Early detection of cancer biomarkers provides clinically valuable information. While the conventional enzyme-linked immunosorbent assay (ELISA) has been routinely used for individual cancer markers, methods for simultaneous determination of multiple markers within a single sample are still in demand. Here, we present a novel oligonucleotide-linked immunosorbent assay (OLISA) with a multiplexing capability on the same microwell plate-based system as in ELISA. Employing a DNA oligonucleotide that is covalently conjugated to the detection antibody and a complementary RNA oligonucleotide which is appended with a fluorophore and a quencher, degradation of the RNA in the DNA-RNA duplex by RNase H is exploited for fluorescent signal generation. Iterative cycles of DNA-RNA duplexation and subsequent degradation of the RNA in the duplex by RNase H further lead to amplification of the detection signal in OLISA. Moreover, the use of antibody-oligonucleotide conjugates enables multiplexing of OLISA, which is successfully demonstrated by tethering DNA molecules to detection antibodies and by performing assays for three common cancer markers including α-fetoprotein, prostate-specific antigen, and carcinoembryonic antigen. With the simple procedure and reliable detection performance, the developed multiplex OLISA has a wide potential for use in analysis of a panel of biomarkers in clinical diagnostics.
Cytomics—New technologies: Towards a human cytome project (2004)

Abstract Background Molecular cell systems research (cytomics) aims at the understanding of the molecular architecture and functionality of cell systems (cytomes) by single‐cell analysis in combination with exhaustive bioinformatic knowledge extraction. In this way, loss of information as a consequence of molecular averaging by cell or tissue homogenisation is avoided. Progress The cytomics concept has been significantly advanced by a multitude of current developments. Amongst them are confocal and laser scanning microscopy, multiphoton fluorescence excitation, spectral imaging, fluorescence resonance energy transfer (FRET), fast imaging in flow, optical stretching in flow, and miniaturised flow and image cytometry within laboratories on a chip or laser microdissection, as well as the use of bead arrays. In addition, biomolecular analysis techniques like tyramide signal amplification, single‐cell polymerase chain reaction (PCR), and the labelling of biomolecules by quantum dots, magnetic nanobeads, or aptamers open new horizons of sensitivity and molecular specificity at the single‐cell level. Data sieving or data mining of the vast amounts of collected multiparameter data for exhaustive multilevel bioinformatic knowledge extraction avoids the inadvertent loss of information from unknown molecular relations being inaccessible to an a priori hypothesis. Challenge It seems important to address the challenge of a human cytome project using hypothesis‐driven molecular information collection from disease associated cell systems, supplemented by systematic and exhaustive knowledge extraction. This will allow the description of the molecular setup of normal and abnormal cell systems within a relational knowledge system, permitting the standardised discrimination of abnormal cell states in disease. As one of the consequences, individualised predictions of further disease course in patients (predictive medicine by cytomics) by characteristic discriminatory data patterns will permit individualised therapies, identification of new pharmaceutical targets, and establishment of a standardised framework of relevant molecular alterations in disease. This special issue of Cytometry , on new technologies in cytomics, focuses on prominent examples of this presently fast‐moving scientific field, and represents one of the preconditions for the formulation of a human cytome project. © 2004 Wiley‐Liss, Inc.
IgM rheumatoid factor and the inhibition of covalent binding of C4b to IgG in immune complexes. (1993)

Work by other investigators has shown that IgM-rheumatoid factors (IgM-RF's) can impede complement-mediated inhibition of immune precipitation. We examined the binding of complement component C4b to radiolabelled IgG in model immune complexes and demonstrate that IgM-RF's are capable of reducing the covalent binding of C4b to 125I-IgG in the complexes. Reduced binding to IgG, however, may not be accompanied by binding of C4b to IgM-RF's within the complex, as we also demonstrate that IgM-RF's are relatively poor at C4b capture compared with normal IgM.