gebhart/patrepeval huggingface dataset:
Carbonylation Caused by Cigarette Smoke Extract Is Associated with Defective Macrophage Immunity (2010)

Oxidants in cigarette smoke inhibit pathogen recognition receptor function and phagocytosis, but the molecular basis of this inhibition remains obscure. We sought to identify the inhibitory mechanisms that impair alveolar macrophage function. Balb/c mice were acutely exposed to four cigarettes for 4 hours before treatment with intranasal LPS (1 μg). The mice exhibited significantly reduced airway neutrophilia and expression of TNF-α. Balb/c-derived MH-S alveolar macrophage cells exposed to cigarette smoke extract (CSE) displayed a similar inhibitory response to stimulation with LPS. The induction of inflammatory genes by recombinant (r) TNF-α (100 ng/ml) was also impaired by CSE. Because both pathways converge on NF-κB, the degradation of IκBα and the phosphorylation of p65 were assessed and shown to be blunted by CSE. CSE also blocked the activity of activator protein-1 (AP-1) by inhibiting p38 mitogen activated protein kinase (MAPK) in a reduced glutathione (GSH)-reversible manner. The induction of specific Toll-like receptor (TLR)-negative regulators (suppressor of cytokine signaling-1 [SOCS-1], interleukin-1 receptor associated kinase-M [IRAK-M], and IL-10) did not account for the impaired responses of TLRs. As free radical species are abundant in CSE and GSH restored function, a panel of oxidative/nitrosative stress markers was screened using immunocytochemistry. The panel identified protein carbonylation as the major CSE-inducible marker. Oxyblot analysis confirmed that CSE potently introduced carbonyl groups to many proteins in a dose-dependent and time-dependent manner that inversely correlated with the expression of TNF-α. The formation of pseudopodia was not prevented, but these membrane extensions were heavily carbonylated, and primary alveolar macrophages were also targeted for carbonylation. Oxidants in cigarette smoke drive a rapid, persistent, and global protein carbonylation that may represent a common pathway to altered immunity in disease.
Architecture and solution properties of hyperbranched polymers via the living radical mechanism (2002)

A novel route to hyperbranched polystyrenes (PSs) from N,N-diethylaminodithiocarbamoylmethylstyrene (DTCS) as an inimer by one-pot photopolymerization is presented. This polymerization proceeded by the self-addition living radical mechanism. Branched PSs were also prepared by living radical copolymerization of DTCS with styrene under UV irradiation. Two monomers (DTCS and styrene) showed equal reactivity towards both propagating species and the copolymer composition was the same as the comonomer composition. Both branching and the chain length of hyperbranched molecules could be controlled statistically by the feed monomer ratios. Hyperbranched poly(ethyl methacrylate)s (PEMAs) were also prepared by the self-addition living radical polymerization of 2-(N,N-diethylaminodithiocarbamoyl)ethyl methacrylate (DTCM). Copolymerizations of DTCS with maleic anhydride (MA) were carried out under UV irradiation. These reactivities showed strong alternation and the propagating copolymer radicals always proceeded with homopolymerization of 1 : 1 complexes formed between the donor and acceptor monomers. These hyperbranched polymers exhibited large amounts of photofunctional carbamate (DC) groups on the peripheral surface. Subsequently, amphiphilic hyperbranched-graft copolymers were derived by grafting from a hyperbranched PS macro-initiator with 1-vinyl-2-pyrrolidinone. These graft-hyperbranched copolymers were soluble in water and methanol. The dilute solution properties of such hyperbranched polymers were studied in detail.
Coexpression of MUC1 glycoprotein with multiple angiogenic factors in non-small cell lung cancer suggests coactivation of angiogenic and migration pathways. (2000)

We investigated the expression of MUC1 protein and its relationship to the microvessel density and the expression of thymidine phosphorylase, vascular endothelial growth factor (VEGF), VEGF-receptor KDR, basic fibroblast growth factor (bFGF), and bFGF-receptor (FGFR-2) in non-small cell lung cancer. Although MUC1 expression was found equally in poorly and highly vascularized tumors, a significant coexpression with multiple angiogenic factors and their receptors was noted (P = 0.0002, 0.03, 0.19, 0.10, and 0.01 for thymidine phosphorylase, VEGF, KDR, bFGF, and FGFR-2, respectively). In multiple regression analysis, both angiogenesis and MUC1 expression were independent prognostic variables. The present study suggests the existence of an early genetic event leading to the activation of both migration and angiogenesis pathways in non-small cell lung cancer.
Parameterized unit tests (2005)

Parameterized unit tests extend the current industry practice of using closed unit tests defined as parameterless methods. Parameterized unit tests separate two concerns: 1) They specify the external behavior of the involved methods for all test arguments. 2) Test cases can be re-obtained as traditional closed unit tests by instantiating the parameterized unit tests. Symbolic execution and constraint solving can be used to automatically choose a minimal set of inputs that exercise a parameterized unit test with respect to possible code paths of the implementation. In addition, parameterized unit tests can be used as symbolic summaries which allows symbolic execution to scale for arbitrary abstraction levels. We have developed a prototype tool which computes test cases from parameterized unit tests. We report on its first use testing parts of the .NET base class library.
A Description of Imperfections in Protein Crystals (1998)

An analysis is given of the contribution of various crystal imperfections to the rocking widths of reflections and the divergence of the diffracted beams. The crystal imperfections are the angular spread of the mosaic blocks in the crystal, the size of the mosaic blocks and the variation in cell dimensions between blocks. The analysis has implications for improving crystal perfection, defining data-collection requirements and for data-processing procedures. Measurements on crystals of tetragonal lysozyme at room temperature and 100 K were made in order to illustrate how parameters describing the crystal imperfections can be obtained. At 100 K, the dominant imperfection appeared to be a variation in unit-cell dimensions in the crystal.
Context-aware support for computer-supported ubiquitous learning (2004)

This paper describes a computer supported ubiquitous learning environment for language learning. This paper proposes two systems. The first is context-aware language-learning support system for Japanese polite expressions learning, which is called JAPELAS (Japanese polite expressions learning assisting system). This system provides learner the appropriate polite expressions deriving the learner's situation and personal information. The second system is called TANGO (Tag Added learNinG Objects) system, which detects the objects around learner using RFID tags, and provides the learner the educational information. This paper describes the preliminary evaluation of those two systems.
Dehydration and Hydration Ktnetics, Phase Change, Solubility and Dissolution Behavior of Fenoprofen Calcium (1995)

The role of water of hydration on the crystal structure, the solubility and the rate of dissolution of fenoprofen calcium dihydrate was examined. The rate of dehydration of fenoprofen calcium dihydrate at 0% relative humidity (R.H.) increased from 0.0400 to 0.7488 fraction dehydratedhour over a temperature range of 50°C to 80 °C and appeared to occur by a combination of diffusion and nucleation processes. The enthalpy of dehydration was 21.897 kcal/mole. Hydration of dehydrated fenoprofen calcium occurred rapidly at 100% R.H. X-ray powder diffraction analysis showed that the upon dehydration fenoprofen calcium dihydrate underwent a change in its crystal structure to form anhydrous fenoprofen calcium. The rate of dissolution of fenoprofen calcium dihydrate tablets at 37°C was not significantly different than that of tablets containing anhydrous fenoprofen. The enthalpies of solution (δHsol) of fenoprofen calcium dihydrate and anhydrous fenoprofen calcium were 2.0504 and 3.5583 kcaYmole respectively. The transition temperature at which the dihydrate and anhydrous fenoprofen had equal solubilities was approximately 59.91 °C.
L-Domain Flanking Sequences Are Important for Host Interactions and Efficient Budding of Vesicular Stomatitis Virus Recombinants (2005)

ABSTRACT Vesicular stomatitis virus (VSV) possesses a PPPY and a PSAP motif within the matrix (M) protein. The PPPY motif has significant L-domain activity in BHK-21 cells, whereas the PSAP motif does not. Since the core PSAP motif alone is insufficient to provide L-domain activity, we modified upstream or downstream amino acids flanking the PSAP core motif to determine their effect on L-domain activity. VSV recombinants were recovered that contained single or multiple amino acid mutations in upstream or downstream sequences flanking the PSAP core. Recombinant viruses were examined for growth kinetics, budding efficiency, and functional interactions with host proteins. We demonstrate that the composition of amino acids surrounding the L-domain core motifs are critical for efficient L-domain activity and for interactions with host proteins in the context of a VSV infection.
A Novel Metalloproteinase, Almelysin, from a Marine Bacterium,<i>Alteromonas</i>sp. No. 3696: Purification and Characterization (1997)

We have discovered a novel metalloproteinase, which has high activity at low temperatures, from the culture supernatant of a marine bacterium. The strain was identified as Alteromonas sp. No. 3696. The metalloproteinase, named almelysin, was purified to homogeneity from the cultured supernatant at 10 degrees C by two column chromatographies. About 20 mg of purified almelysin was obtained from 18.4 liters of the culture supernatant. The molecular mass of almelysin was estimated to be 28 kDa by SDS-PAGE and the isoelectric point was 4.3. The optimum pH for activity of almelysin was pH 8.5-9.0 and 6.5 using casein and (7-methoxycoumarin-4-yl)acetyl(MOCAc)-Pro-Leu-Gly-Leu-(N3- [2,4-dinitrophenyl]-L-2,3-diaminopropionyl) [A2pr(Dnp)]-Ala-Arg-NH2 as substrates, respectively. Almelysin was stable between pH 7.5-8.0 and below 40 degrees C. The optimum temperature for the activity was observed to be 40 degrees C using both casein and MOCAc-Pro-Leu-Gly-Leu-A2pr(Dnp)-Ala-Arg-NH2 as substrates. The activity of almelysin was inhibited by such metallo chelators as EDTA and o-phenanthroline, while talopeptin, phosphoramidon, and SMPI, typical metalloproteinase inhibitors, had no effect. Almelysin primarily cleaved the Ala14-Leu15 bond and Phe24-Phe25 bond, and secondarily the Tyr16-Leu17 bond in oxidized insulin B-chain. However, almelysin could not cleave the His5-Leu6, His10-Leu11, and Gly23-Phe24 bonds, which were cleaved by other metalloproteinases. These results indicate that the substrate specificity of almelysin is different from other metalloproteinases. Interestingly, Alteromonas sp. No. 3696 strain produced another proteinase as well as almelysin at 25 degrees C.
Computational differential geometry tools for surface interrogation, fairing, and design (2006)

This thesis presents a set of new mesh processing methods which are based on computational differential geometry techniques. The underlying idea of the methods consists of using proper discrete approximations of differential surface properties. The methods developed in the thesis contribute to the areas of curvature feature detection, mesh parameterization, fair mesh generation, mesh denoising, and free-form and variational mesh deformations. Comparisons of the developed methods with several state-of-the-art techniques and algorithms are done. The results of numerous numerical experiments demonstrate significant advantages of the proposed methods over conventional techniques. Applications of the methods are discussed and demonstrated. The main contributions of the thesis are as follows: Similarity-based Mesh Denoising. A new, powerful, and high quality feature preserving mesh/soup denoising technique and a new scheme for comparing different mesh/soup smoothing methods are proposed. The technique is based on a similarity-weighted averaging procedure and a new and robust similarity measuring scheme. Fair Mesh Generation via Elastica. A new numerical scheme for generating fair meshes is developed. Applications to shape restoration are considered. The scheme is build upon a discrete approximation of Willmore row. A tangent speed component is introduced to the discrete Willmore row in order to improve the quality of the evolving mesh and to increase computational stability. Fast and Robust Detection of Feature Lines on Meshes. A new, fast, and robust crest line detection method is developed. Applications to feature-adaptive mesh simplification and segmentation are considered. A novel thresholding scheme and a simple new formula for computing directional curvature derivatives are also introduced. Fast Low-Stretch Mesh Parameterization. A new, fast, simple, and valid low-stretch mesh parameterization scheme and its application for efficient remeshing are proposed by using a moving mesh approach. The scheme is based on a weighted quasi-conformal parameterization which equalizes the local stretch distribution. Particularly, the scheme does not generate regions of undesirable high anisotropic stretch. Free-Form Skeleton-driven Mesh Deformations. A new and powerful approach for generating natural-looking large-scale mesh deformations is proposed. An interesting feature of the approach consists of preserving original shape thickness. New self-intersection fairing schemes are also developed. Multiresolutional and variational extensions of the approach are considered.
Time‐ and media‐dependent secondary carotenoid accumulation in <i>Haematococcus pluvialis</i> (2008)

The green microalgae Haematococcus pluvialis synthesizes secondary carotenoids after exposure to environmental stress, a process that is used for the biotechnological production of astaxanthin (Ax). This study reports, for the first time, the medium-dependent changes in the carotenoid pattern throughout the cultivation process as well as the exact composition of carotenoids and their fatty acid mono- and diesters using LC-MS. Secondary carotenoid formation started immediately upon exposure to nutrient depletion and high light conditions. Ax and its corresponding mono- and diesters were detected simultaneously. After 15 days of cultivation, no significant changes were detected in carotenoid composition; however, the ratio between carotenoid mono- and diesters still varied. Main carotenoids were identified as Ax linolenate and Ax oleate, but also five adonirubin and one lutein monoester were detected. The influence of three different autotroph media was studied on carotenoid content, which reached a maximum 16.1 mg/g dry weight. The results indicate that media composition has an influence on the ratio of Ax mono- to diester but not on the qualitative composition of secondary carotenoids in H. pluvialis. Beside the pathway via echinenone, canthaxanthin and adonirubin the results indicate that Ax biosynthesis takes place via another route: from beta-carotene via beta-cryptoxanthin, zeaxanthin and adonixanthin.
Evidence that Spinach Leaves Express Calreticulin but Not Calsequestrin (1995)

The presence of either calreticulin (CR) or calsequestrin (CS-like proteins in spinach (Spinacia oleracea L.) leaves has been previously described. Here we report the purification from spinach leaves of two highly acidic (isoelectric point 5.2) Ca(2+)-binding proteins of 56 and 54 kD by means of DEAE-cellulose chromatography followed by phenyl-Sepharose chromatography in the presence of Zn(2+) (i.e., under experimental conditions that allowed the purification of CR from human liver). On the other hand, we failed to identify any protein sharing with animal CS the ability to bind to phenyl-Sepharose in the absence of Ca(2+). Based on the N-terminal amino acid sequence, the 56- and 54-kD spinach Ca(2+)-binding proteins were identified as two distinct isoforms of CR. Therefore, we conclude that CR, and not CS, is expressed in spinach leaves. The 56-kD spinach CR isoform was found to be glycosylated, as judged by ligand blot techniques with concanavalin A and affinity chromatography with concanavalin A-Sepharose. Furthermore, the 56-kD CR was found to differ from rabbit liver CR in amino acid sequence, peptide mapping after partial digestion with Staphylococcus aureus V8 protease, pH-dependent shift of electrophoretic mobility, and immunological cross-reactivity with an antiserum raised to spinach CR, indicating a low degree of structural homology with animal CRs.
Arrest of the proliferation of renal and prostate carcinomas of human origin by inhibition of mitochondrial protein synthesis. (1986)

The results described in this paper demonstrate that proliferation arrest by low concentrations of tetracyclines, which has previously been shown in experiments with animal tumor systems, can also be achieved in tumor systems of human origin. Tetracyclines specifically inhibit mitochondrial protein synthesis. Prolonged and continuous impairment of protein synthesis inside the mitochondria leads to reduction of the cellular concentration of the polypeptide products which are coded and synthesized within mitochondria. These products are part of the oxidative phosphorylative system of the cell. Long-term tetracycline treatment leads to a decrease of oxidative ATP-generating capacity as monitored by cytochrome c oxidase activity. This may cause severe energetic or metabolic disturbances which explain the proliferation arrest observed. Proliferation arrest, provided that mitochondrial protein synthesis is blocked effectively, is found in vitro as well as in vivo. It is shown that the effect of doxycycline is not limited to cytostasis; prolonged doxycycline treatment is clearly cytotoxic for the tumor cells.
AMBIX - A SUGGESTED AMBISONICS FORMAT (2011)

Ambisonics is a 3D audio surround rendering and representation approach based on spherical harmonics with loud-speaker independent transmission channels. Although it was developed in the seventies and the techniques are well known, there are disagreements how to normalize, store and exchange Ambisonic data. This paper’s mission is to propose a standard for the Ambisonics community and it should be seen as an encouragement to use the proposed convention, in order to facilitate exchange and communication. This standard is named ambiX (Ambisonics exchangeable). For the case that mixed order or reduced Ambisonic signal sets are beneficial, the format includes a simple matrix- named &quot;adaptor matrix&quot;. This matrix can be freely configured to re-order, complete, re-normalize, or embed the transmitted or stored audio channels to a default set of periphonic Ambisonic signals. It is advocated as extended format, because it enables new techniques to reduce the Ambisonic signal set utilizing prior knowledge about restricted surround geometries like hemispherical or circular. Providing a default periphonic decoder for all surround geometries ensures universal applicability, while inspection tools for the adaptor matrix are advanced means for optimal decoding. IEM provides a small &quot;proof of concept &quot; implementation of tools to write, read audio data and the adaptor matrix, as well tools to analyze the adaptor matrix graphically to select the best decoder for given files.
The Neuroimmune Interface in Prion Diseases (2000)

Prion diseases are fatal neurodegenerative disorders of animals and humans. Here we address the role of the immune system in the spread of prions from peripheral sites to the central nervous system and its potential relevance to iatrogenic prion disease.
HardCoRe-NAS: Hard Constrained diffeRentiable Neural Architecture Search (2021)

Realistic use of neural networks often requires adhering to multiple constraints on latency, energy and memory among others. A popular approach to find fitting networks is through constrained Neural Architecture Search (NAS), however, previous methods enforce the constraint only softly. Therefore, the resulting networks do not exactly adhere to the resource constraint and their accuracy is harmed. In this work we resolve this by introducing Hard Constrained diffeRentiable NAS (HardCoRe-NAS), that is based on an accurate formulation of the expected resource requirement and a scalable search method that satisfies the hard constraint throughout the search. Our experiments show that HardCoRe-NAS generates state-of-the-art architectures, surpassing other NAS methods, while strictly satisfying the hard resource constraints without any tuning required.
Analysis of a Ubiquitous Promoter Element in a Primitive Eukaryote: Early Evolution of the Initiator Element (1999)

Typical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protist Trichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examined T. vaginalis genes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found in T. vaginalis protein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.
Entanglement swapping with independent sources over an optical-fiber network (2017)

Establishing entanglement between two remote systems by the method of entanglement swapping is an essential step for a long-distance quantum network. Here we report a field-test entanglement swapping experiment with two independent telecommunication band entangled photon-pair sources over an optical fiber network in Hefei. The two sources are located at two nodes that are $12.5\phantom{\rule{4pt}{0ex}}\mathrm{km}$ apart and the Bell-state measurement is performed at a third location which is connected to the two source nodes with 14.7-km and 10.6-km optical fibers, respectively. The observed average visibility is $79.9\ifmmode\pm\else\textpm\fi{}4.8%$, which is sufficient for the violation of Bell inequalities. Furthermore, with the swapped entanglement, we demonstrate a source-independent quantum key distribution, which is also immune to any detection attacks at the measurement site.