gebhart/patrepeval huggingface dataset:
A Survey on Software-Defined Networking (2014)

Emerging mega-trends (e.g., mobile, social, cloud, and big data) in information and communication technologies (ICT) are commanding new challenges to future Internet, for which ubiquitous accessibility, high bandwidth, and dynamic management are crucial. However, traditional approaches based on manual configuration of proprietary devices are cumbersome and error-prone, and they cannot fully utilize the capability of physical network infrastructure. Recently, software-defined networking (SDN) has been touted as one of the most promising solutions for future Internet. SDN is characterized by its two distinguished features, including decoupling the control plane from the data plane and providing programmability for network application development. As a result, SDN is positioned to provide more efficient configuration, better performance, and higher flexibility to accommodate innovative network designs. This paper surveys latest developments in this active research area of SDN. We first present a generally accepted definition for SDN with the aforementioned two characteristic features and potential benefits of SDN. We then dwell on its three-layer architecture, including an infrastructure layer, a control layer, and an application layer, and substantiate each layer with existing research efforts and its related research areas. We follow that with an overview of the de facto SDN implementation (i.e., OpenFlow). Finally, we conclude this survey paper with some suggested open research challenges.
Palladium‐Catalyzed β Arylation of Carboxylic Esters (2010)

Alter ego: In the presence of an appropriate palladium(0) catalyst, carboxylic esters underwent β arylation instead of the more common α-arylation reaction with aryl halides containing an ortho electronegative substituent (see scheme; Cy=cyclohexyl). An asymmetric version of the reaction gave the product with an enantiomeric ratio of up to 77:23.
Magnetic resonance imaging and spinal cord stimulation systems (1997)

In this manuscript, three patients with a neurostimulation system implant who underwent MRI scanning are presented. Possible hazards, effects of MR imaging and changes to the pulse generator's parameter settings are discussed. Concluded is that MRI can be safely used in certain selected circumstances. If the neurostimulator is in the anatomic region of the scanned area caution is recommended and images are likely to be affected.
Mosaicking images (2004)

Two methods of mosaicking images were developed, one for the simple case of a shift between two following images and another one for the general case. For the simple mosaicking, the error rate is acceptable for both cases of noisy or less noisy images. Owing to the fact that future generations of scouts would be provided with the 2.4 GHz transmission frequency, panoramic mosaics can be created with a high level of success. The operation is completely automated, and the execution time is close to three minutes for each mosaic. For the case of mosaicking images in general, the major problem is that the quality of the images given by the scout does not allow for choosing a small number of points for the Harris detector. This leads to long execution times. Furthermore, it is extremely hard to realize a panoramic vision by such a method because it is still unreliable without the intervention of an operator. Building 360/spl deg/ mosaics is not practical. Nevertheless, the general method can be used for creating precise mosaics of three consecutive images, thus providing wide-angle images. Image resulting from this operation represents 100/spl deg/ mosaics. Alas, the time of calculation is still a considerable four minutes.
Rapid and Simultaneous Characterization of Drug Conjugation in Heavy and Light Chains of a Monoclonal Antibody Revealed by High-Resolution Ion Mobility Separations in SLIM (2020)

Antibody-drug conjugates (ADCs) have recently gained traction in the biomedical community due to their promise for human therapeutics and an alternative to chemotherapy for cancer. Crucial metrics for ADC efficacy, safety, and selectivity are their drug-antibody ratios (DARs). However, DAR characterization (i.e., determining the average number of conjugated drugs on the antibody) through analytical methods remains challenging due to the heterogeneity of drug conjugation as well as the numerous post-translational modifications possible in the monoclonal antibody. Herein, we report on the use of high-resolution ion mobility spectrometry separations in structures for lossless ion manipulations coupled to mass spectrometry (SLIM IMS-MS) for the rapid and simultaneous characterization of the drug load profile (i.e., stoichiometric distribution of the number of conjugated drugs present on the mAb), determination of the weighted average DAR in both the heavy and light chains of a model antibody-drug conjugate, and calculation of the overall DAR of the ADC. After chemical reduction of the ADC and a subsequent 31.5 m SLIM IMS separation, the various drug-bound antibody species could be well resolved for both chains. We also show significantly higher resolution separations were possible for these large ions with SLIM IMS as compared to ones performed on a commercially available (1 m) drift tube IMS-MS platform. We expect high-resolution SLIM IMS separations will augment the existing toolbox for ADC characterization, particularly to enable the rapid optimization of DAR for a given ADC and thus better understand its potential toxicity and potency.
Tachyplesins Isolated from Hemocytes of Southeast Asian Horseshoe Crabs (Carcinoscorpius rotundicauda and Tachypleus gigas) (1990)

Tachyplesins and their analogs are antimicrobial peptides composed of 17 or 18 amino acid residues present abundantly in acid extracts of hemocyte debris of horseshoe crabs. We purified here tachyplesin isopeptides from hemocytes of two species of Southeast Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus gigas, and determined their amino acid sequences. The major tachyplesin isolated from both species was identified, respectively, as tachyplesin I, which had previously been found in hemocytes of the Japanese horseshoe crab (Tachypleus tridentatus). The yield from both species was very high (more than 70 mg per 100 g wet weight of hemocytes), i.e., comparable with that from T. tridentatus. In addition to tachyplesin I, a new tachyplesin isopeptide, named tachyplesin III, was also isolated from T. gigas hemocytes, in which an arginine replaced the 15th lysine of tachyplesin I. The carboxyl-terminal residue of the isolated tachyplesins I and III was confirmed, respectively, to be an arginine alpha-amide by chemical analysis. Furthermore, a tachyplesin peptide derivative with a carboxyl-terminal extension of glycine-lysine was newly found in the hemocytes of C. rotundicauda. It appeared to be an intermediate derived from a tachyplesin precursor during processing to the mature form.
Carboxy SNARF-4F as a Fluorescent pH Probe for Ensemble and Fluorescence Correlation Spectroscopies (2005)

The optical spectroscopic properties of 1,4(and 5)-benzenedicarboxylic acid, 2-[10-(dimethylamino)-4-fluoro-3-oxo-3H-benzo[c]xanthen-7-yl] (carboxy SNARF-4F), a commercial promising fluorescent pH probe, are investigated in buffered aqueous solutions in the 5.6-8.2 pH range by steady-state and time-resolved spectroscopy. A multiexponential global analysis of the picosecond time-resolved data is performed. The nonprotonated A species decays monoexponentially (0.73 ns), while the protonated species AH decays following a biexponential law with time constants of 0.40 and 1.87 ns. A kinetic scheme is proposed to explain the observations, which involves AH in equilibrium with a species denoted Y. The nature of Y is discussed in terms of a possible structural change in the molecule producing the lactone form, although the formation of a hydrogen-bonded complex to the solvent cannot be ruled out. Finally, the ability of the dye to probe pH at the single-molecule level is explored using fluorescence correlation spectroscopy.
High efficiency current-mode class-D amplifier with integrated resonator (2004)

This paper shows that current mode class-D (CMCD) amplifiers with integrated parallel LC resonator can achieve high efficiency at RF frequencies. In contrast to the conventional class-D amplifier, output shunt capacitance discharge loss is eliminated in a CMCD amplifier topology by satisfying the zero voltage switching (ZVS) condition. To reduce parasitic resistance, bondwires are utilized to implement a high Q inductor in the LC resonator. An experimental CMCD amplifier with collector efficiency of 78.5% at output power of 29.5dBm (0.89W) is demonstrated using GaAs HBTs at 700 MHz.
Proapoptotic and antiapoptotic markers in cutaneous T-cell lymphoma skin infiltrates and lymphomatoid papulosis (2001)

Journal Article Proapoptotic and antiapoptotic markers in cutaneous T‐cell lymphoma skin infiltrates and lymphomatoid papulosis Get access H. Nevala, H. Nevala Department of Dermatology and Venereal Diseases, Helsinki University Central Hospital, PO Box 160, 00029 HUS, Helsinki, Finland Search for other works by this author on: Oxford Academic Google Scholar L. Karenko, L. Karenko Department of Dermatology and Venereal Diseases, Helsinki University Central Hospital, PO Box 160, 00029 HUS, Helsinki, Finland Search for other works by this author on: Oxford Academic Google Scholar L. Väkevä, L. Väkevä Department of Dermatology and Venereal Diseases, Helsinki University Central Hospital, PO Box 160, 00029 HUS, Helsinki, Finland Search for other works by this author on: Oxford Academic Google Scholar A. Ranki A. Ranki Department of Dermatology and Venereal Diseases, Helsinki University Central Hospital, PO Box 160, 00029 HUS, Helsinki, Finland Professor Annamari Ranki.E‐mail: Annamari.Ranki@hus.fi Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 145, Issue 6, 1 December 2001, Pages 928–937, https://doi.org/10.1046/j.1365-2133.2001.04523.x Published: 01 December 2001
Ordered structures of molecular bottlebrushes (1997)

In this review 'molecular bottlebrushes' are flexible polymers densely loaded with equally flexible side chains. Interest in these structures arises from the possibility of lyotropic behaviour in dilute solution in a good solvent, as well as the possibility of highly ordered microphase-separated states in the melt. In addition, supramolecular chemistry has led to alternative and often much simpler ways of synthesizing complex polymer architectures. Here we will concentrate on molecular bottlebrushes obtained by hydrogen bonding between homopolymers and end-functionalized oligomers, and address their complex phase behaviour. Particular attention will be given to the possibility of lyotropic behaviour and to the role of the reversibility of the noncovalent bonding. The coupling between micro- and macrophase separation and the possibility of various Lifshitz points will also be discussed.
NOD1 ligand administration restores optimal steady-state hematopoiesis in germ-free mice (2016)

Abstract The microbiota is required for optimal hematopoiesis. When compared to specific-pathogen free (SPF) mice, germ free (GF) animals display decreased numbers of hematopoietic stem cells (HSC), common myeloid progenitors (CMP) and common lymphoid progenitors (CLP) in bone marrow. Muropeptides produced by both gram-negative and gram-positive bacteria are important agonists of the innate immune response and are recognized by the intracellular pattern-recognition receptors NOD1 and NOD2. In the present study, we examined both direct and indirect effects of NOD signaling on hematopoietic homeostasis. While stimulation with NOD1 or NOD2 ligands had no effect on survival/proliferation of HSC, CMP and CLP in vitro, exposure of bone marrow-derived stroma cells (BMSC) to NOD1, but not NOD2, ligand induced expression of the differentiation factors SCF, IL-7, IL-3, Thpo and IL-6. Interestingly LPS, which is known to act directly on hematopoietic precursors, selectively induced only IL-6 in BMSC. To test the effects of NOD1 ligand in vivo, we compared groups of GF animals with and without peroral NOD1 ligand administration. NOD1 ligand treatment restored to normal levels serum concentrations of SCF, Thpo and IL-6, as well as the numbers of HSC, CMP and CLP in bone marrow. Taken together, these findings demonstrate that NOD1 ligand induces BMSC to produce cytokines that regulate the size of the major hematopoietic precursor pools. Thus, NOD1 signaling appears to be a major factor underlying the requirement for the microbiota in the maintenance of steady-state hematopoiesis. This work was supported by the Intramural Research Program of the National Institute of Allergy and Infectious diseases.
A New View of Electrochemistry at Highly Oriented Pyrolytic Graphite (2012)

Major new insights on electrochemical processes at graphite electrodes are reported, following extensive investigations of two of the most studied redox couples, Fe(CN)(6)(4-/3-) and Ru(NH(3))(6)(3+/2+). Experiments have been carried out on five different grades of highly oriented pyrolytic graphite (HOPG) that vary in step-edge height and surface coverage. Significantly, the same electrochemical characteristic is observed on all surfaces, independent of surface quality: initial cyclic voltammetry (CV) is close to reversible on freshly cleaved surfaces (>400 measurements for Fe(CN)(6)(4-/3-) and >100 for Ru(NH(3))(6)(3+/2+)), in marked contrast to previous studies that have found very slow electron transfer (ET) kinetics, with an interpretation that ET only occurs at step edges. Significantly, high spatial resolution electrochemical imaging with scanning electrochemical cell microscopy, on the highest quality mechanically cleaved HOPG, demonstrates definitively that the pristine basal surface supports fast ET, and that ET is not confined to step edges. However, the history of the HOPG surface strongly influences the electrochemical behavior. Thus, Fe(CN)(6)(4-/3-) shows markedly diminished ET kinetics with either extended exposure of the HOPG surface to the ambient environment or repeated CV measurements. In situ atomic force microscopy (AFM) reveals that the deterioration in apparent ET kinetics is coupled with the deposition of material on the HOPG electrode, while conducting-AFM highlights that, after cleaving, the local surface conductivity of HOPG deteriorates significantly with time. These observations and new insights are not only important for graphite, but have significant implications for electrochemistry at related carbon materials such as graphene and carbon nanotubes.
Selective inhibition of antigen-specific T lymphocyte proliferation by acute ethanol exposure: the role of impaired monocyte antigen presentation capacity and mediator production (1993)

Ethanol consumption is associated with impaired immunity. Our data demonstrate that even a single dose of a biologically relevant concentration (25-150 mM) of ethanol can down-regulate antigen-specific T lymphocyte proliferation. In contrast, ethanol augmented mitogen-induced T cell proliferation, suggesting that its inhibitory effect on antigen-specific T cell proliferation was due to its effects on monocytes (m phi s) rather than on T cells. The immunodepressive effects of ethanol on m phi antigen-presenting cell (APC) capacity were manifested whether alcohol treatment was limited to the antigen uptake-processing period only or was present during the entire period of antigen presentation. These inhibitory effects of ethanol were also evident on both the high-antigen-presenting, Fc gamma RI-negative (-31 +/- 17%), and low-antigen-presenting, Fc gamma RI-positive (-42 +/- 15%) m phi subpopulations. Further analysis demonstrated that ethanol inhibits the production of interleukin-1 beta (IL-1 beta) and induces transforming growth factor beta (TGF-beta) and prostaglandin E2 (PGE2), monocyte-derived mediators that can affect T cell proliferation. Ethanol resulted in a dose-dependent down-regulation of secreted and cell-associated IL-1 beta protein as well as IL-1 beta mRNA levels induced by adherence or bacterial stimulation. The causal relationship between decreased m phi IL-1 beta production, elevated TGF-beta levels, and the decreased m phi APC capacity was further substantiated when exogenous IL-1 beta protein or anti-TGF-beta neutralizing antibody prevented the down-regulatory effect of ethanol on antigen-specific T cell proliferation. Utilizing a cyclooxygenase inhibitor, we also demonstrated that the ethanol-induced decrease in m phi APCs is not mediated by enhanced PGE2 production.
Modeling Human Head Tissues Using Fourth-Order Debye Model in Convolution-Based Three-Dimensional Finite-Difference Time-Domain (2014)

A fourth order Debye model is derived using genetic algorithms to represent the dispersive properties of the 17 tissues that form the human head. The derived model gives accurate estimation of the electrical properties of those tissues across the frequency band from 0.1 GHz to 3 GHz that can be used in microwave systems for head imaging. A convolution-based three-dimensional finite-difference time-domain (3D-FDTD) formulation is implemented for modeling the electromagnetic wave propagation in the dispersive head tissues whose frequency dependent properties are represented by the derived fourth-order Debye model. The presented results show that the proposed 3D-FDTD and fourth-order Debye model can accurately show the electromagnetic interaction between a wide band radiation and head tissues with low computational overhead and more accurate results compared with using multi-pole Cole-Cole model.
Acuity recovery and cone pigment regeneration after a bleach in patients with retinitis pigmentosa and rhodopsin mutations. (1999)

A slowing of foveal visual acuity recovery and cone pigment regeneration, which are related to each other, can occur in patients with retinitis pigmentosa, due to a rod-specific gene defect.
Tubulin-G protein interactions involve microtubule polymerization domains (1991)

It has been suggested that elements of the cytoskeleton contribute to the signal transduction process and that they do so in association with one or more members of the signal-transducing G protein family. Relatively high-affinity binding between dimeric tubulin and the alpha subunits of Gs and Gi1 has also been reported. Tubulin molecules, which exist in solution as alpha beta dimers, have binding domains for microtubule-associated proteins as well as for other tubulin dimers. This study represents an attempt to ascertain whether the association between G proteins and tubulin occurs at one of these sites. Removal of the binding site for MAP2 and tau from tubulin by subtilisin proteolysis did not influence the association of tubulin with G protein, as demonstrated in overlay studies with [125I]tubulin. A functional consequence of that association, the stable inhibition of synaptic membrane adenylyl cyclase, was also unaffected by subtilisin treatment of tubulin. However, ring structures formed from subtilisin-treated tubulin were incapable of effecting such inhibition. Stable G protein-tubulin complexes were formed, and these were separated from free tubulin by Octyl-Sepharose chromatography. Using this methodology, it was demonstrated that assembled microtubules bound G protein quite weakly compared with tubulin dimers. The alpha subunit of Gi1 and, to a lesser extent, that of Go were demonstrated to inhibit microtubule polymerization. In aggregate, these data suggest that dimeric tubulin binds to the alpha subunits of G protein at the sites where it binds to other tubulin dimers during microtubule polymerization. Interaction with signal-transducing G proteins, thus, might represent a role for tubulin dimers which is independent of microtubule formation.
CysLT1 receptor is a target for extracellular nucleotide-induced heterologous desensitization: a possible feedback mechanism in inflammation (2005)

Both cysteinyl-leukotrienes and extracellular nucleotides mediate inflammatory responses via specific G-protein-coupled receptors, the CysLT and the P2Y receptors, respectively. Since these mediators accumulate at sites of inflammation, and inflammatory cells express both classes of receptors, their responses are likely to be crossregulated. We investigated the molecular basis of desensitization and trafficking of the CysLT1 receptor constitutively and transiently expressed in the human monocyte/macrophage-like U937 or COS-7 cells in response to LTD4 or nucleotides. Exposure to agonist induced a rapid homologous desensitization of the CysLT1 receptor [as measured by the reduction in the maximal agonist-induced intracellular cytosolic Ca2+ ([Ca2+]i) transient], followed by receptor internalization (as assessed by equilibrium binding and confocal microscopy). Activation of P2Y receptors with ATP or UDP induced heterologous desensitization of the CysLT1 receptor. Conversely, LTD4-induced CysLT1 receptor activation had no effect on P2Y receptor responses, which suggests that the latter have a hierarchy in producing desensitizing signals. Furthermore, ATP/UDP-induced CysLT1 receptor desensitization was unable to cause receptor internalization, induced a faster recovery of CysLT1 functionality and was dependent upon protein kinase C. By contrast, homologous desensitization, which is probably dependent upon G-protein-receptor kinase 2 activation, induced a fast receptor downregulation and, accordingly, a slower recovery of CysLT1 functionality. Hence, CysLT1 receptor desensitization and trafficking are differentially regulated by the CysLT1 cognate ligand or by extracellular nucleotides. This crosstalk may have a profound physiological implication in the regulation of responses at sites of inflammation, and may represent just an example of a feedback mechanism used by cells to fine-tune their responses.
Statistical Retinal OCT Appearance Models (2014)

More than 20.000 OCT scans of over 1000 patients retrieved from the Vienna Reading Center (VRC) database were used as a basis for the generation of the synthetic data set. The scans were grouped by vendor (Spectralis OCT, Heidelberg Engineering and Cirrus HD-OCT, Carl Zeiss Meditec) and for each scan the internal limiting membrane (ILM) and retinal pigment epithelium (RPE) segmentation of the device specific software where extracted. The thickness profile (i.e. distance between ILM and RPE) was calculated and regions with missing or implausible thickness values were excluded automatically. After estimating the foveal position, the polar coordinates relative to the macular center were calculated for each A-scan. By grouping spatially close A-scans with same thickness values, an appearance model for each position and thickness was estimated (Fig. 2). A mathematical model of the thickness map was constructed (Fig. 1) and used to select corresponding A-scans out of the appearance model. The A-scans of the final synthetic volume were interpolated using a weighted circular neighborhood in order to avoid artifacts introduced due to the spatial grouping of the source A-scans. Fig. 1 left: thickness map of mildly pathologic eye, right: mathematical model of the thickness map
The reusable holdout: Preserving validity in adaptive data analysis (2015)

Misapplication of statistical data analysis is a common cause of spurious discoveries in scientific research. Existing approaches to ensuring the validity of inferences drawn from data assume a fixed procedure to be performed, selected before the data are examined. In common practice, however, data analysis is an intrinsically adaptive process, with new analyses generated on the basis of data exploration, as well as the results of previous analyses on the same data. We demonstrate a new approach for addressing the challenges of adaptivity based on insights from privacy-preserving data analysis. As an application, we show how to safely reuse a holdout data set many times to validate the results of adaptively chosen analyses.