gebhart/patrepeval huggingface dataset:
Pomegranate Fruit Extract Modulates UV-B–mediated Phosphorylation of Mitogen-activated Protein Kinases and Activation of Nuclear Factor Kappa B in Normal Human Epidermal Keratinocytes¶ (2005)

Excessive exposure of solar ultraviolet (UV) radiation, particularly its UV-B component, to humans causes many adverse effects that include erythema, hyperplasia, hyperpigmentation, immunosuppression, photoaging and skin cancer. In recent years, there is increasing use of botanical agents in skin care products. Pomegranate derived from the tree Punica granatum contains anthocyanins (such as delphinidin, cyanidin and pelargonidin) and hydrolyzable tannins (such as punicalin, pedunculagin, punicalagin, gallagic and ellagic acid esters of glucose) and possesses strong antioxidant and anti-inflammatory properties. Recently, we have shown that pomegranate fruit extract (PFE) possesses antitumor promoting effects in a mouse model of chemical carcinogenesis. To begin to establish the effect of PFE for humans in this study, we determined its effect on UV-B-induced adverse effects in normal human epidermal keratinocytes (NHEK). We first assessed the effect of PFE on UV-B-mediated phosphorylation of mitogen-activated protein kinases (MAPK) pathway in NHEK. Immunoblot analysis demonstrated that the treatment of NHEK with PFE (10-40 microg/mL) for 24 h before UV-B (40 mJ/cm(2)) exposure dose dependently inhibited UV-B-mediated phosphorylation of ERKl/2, JNK1/2 and p38 protein. We also observed that PFE (20 microg/mL) inhibited UV-B-mediated phosphorylation of MAPK in a time-dependent manner. Furthermore, in dose- and time-dependent studies, we evaluated the effect of PFE on UV-B-mediated activation of nuclear factor kappa B (NF-kappaB) pathway. Using Western blot analysis, we found that PFE treatment of NHEK resulted in a dose- and time-dependent inhibition of UV-B-mediated degradation and phosphorylation of IkappaBalpha and activation of IKKalpha. Using immunoblot analysis, enzyme-linked immunosorbent assay and electrophoretic mobility shift assay, we found that PFE treatment to NHEK resulted in a dose- and time-dependent inhibition of UV-B-mediated nuclear translocation and phosphorylation of NF-kappaB/p65 at Ser(536). Taken together, our data shows that PFE protects against the adverse effects of UV-B radiation by inhibiting UV-B-induced modulations of NF-kappaB and MAPK pathways and provides a molecular basis for the photochemopreventive effects of PFE.
Metabolic Fate of Menaquinone-4 in Dogs. (I). Absorption, Distribution, Metabolism and Excretion after a Single Oral Administration. (1997)

[14C]menaquinone-4, a therapeutic agent for osteoporosis, was administered orally to male dogs at a dose of 4 mg/kg, and the absorption, distribution, metabolism and excretion were investigated. 1. The plasma concentration of radioactivity reached the maximum level (Cmax) of 4540.4 ng eq./ml at 1 to 2 hours after administration and thereafter decreased slowly. At Tmax, the unchanged menaquinone-4 in the plasma corresponded to 79.6% of the total radioactivity. 2. Within 168 hours, 2.3 and 78.1% of the radioa ctivity was excreted into the urine and feces, respectively. Unchanged menaquinone-4 corresponded to 28.5% of the radioactivity in the feces excreted within 24 hours. 3. The liver (33164.0 ng eq./g) and spleen (12542.2 ng eq./g) showed much higher concentrations of radioactivity than the other tissues and plasma (2994.5 ng eq./ml) at 1.5 hours after administration. The concentration in bile (109392.1 ng eq./ml) was also high, suggesting that the menaquinone-4 was immediately excreted into the bile. The elimination of radioactivity from tissues was relatively slow compared to that from plasma. In bone tissues, the target organ of the drug, the marrow (1424.9 ng eq./g) and cancellous tissue (2465.7 ng eq./g) of thighbone and the marrow (3533.4 ng eq./g) of ribs showed levels as high as the plasma concentrations at 1.5 hours and were 2 to 3 times higher than that of the plasma at 24 hours after dosing. 4. The unchanged menaquinone-4 was the major form present in the plasma, liver, kidney, spleen, adrenal, adipose and cancellous tissue of thighbone at 1.5 hours after administration. The known metabolites, ω-COOH, K acid I and K acid II, were found in these tissues at 1.5 hours. In the adipose and cancellous tissue of thighbone, the unchanged menaquinone-4 was the major form up to 168 hours, while the relative amount of metabolites increased by 24 hours in the other tissues. Polar metabolites were found in the urine excreted within 24 hours and bile at 1.5 and 24 hours after administration. The unchanged menaquinone-4 was mainly found in the feces excreted within 24 hours. 5. The levels of radioactivity in the marrow and cancellous tissue of thighbone and the marrow of ribs at 1.5 and 24 hours after dosing (1.5 hours: 3.3−8.0×10-6 M, 24 hours: 1.9−3.1×10-6 M) were comparable to the pharmacologically effective concentrations of menaquinone-4 (10-6−10-5 M) in in vitro studies on bone formation. This finding suggests that menaquinone-4 distributes sufficiently into bone tissues after a single oral administration in dogs, and can be expected to maintain pharmacologically effective concentrations by repeated administration as a therapeutic agent for osteoporosis.
Comparison of Bovine, Simian and Human Rotavirus Structural Glycoproteins (1984)

The structural glycoproteins of calf (BDV 486), human (Wa) and simian (SA11) rotaviruses were compared for sensitivity to endoglycosidase (Endo) H. The calf and human virus glycoproteins were reduced by approximately 5000 molecular weight in two equal stages. The simian rotavirus glycoprotein sustained only one 2500 molecular weight decrease. The effect of the host cell on the viral oligosaccharide composition was examined. Endo H digests of calf rotavirus 82-124 extracted from stool and its progeny propagated and [35S]methionine-labelled in MA104 cells were compared. Endo H had the same effects on the glycoproteins, indicating that the nature of the host cell does not affect the oligosaccharide composition of the virus glycoproteins.
Generic implementations of elliptic curve cryptography using partial reduction (2002)

Elliptic Curve Cryptography (ECC) is evolving as an attractive alternative to other public-key schemes such as RSA by offering the smallest key size and the highest strength per bit. The importance of ECC has been recognized by the US government and the standards bodies NIST and SECG. Standards for preferred elliptic curves over prime fields GF(p) and binary polynomial fields GF(2m) as well as the Elliptic Curve Digital Signature Algorithm (ECDSA) have been created. A security protocol based on ECC requires support for different curves representing different security levels. This is particularly true for server applications that are exposed to requests for secure connections with different parameters generated by a multitude of client devices. Reported implementations of ECC over GF(2m) typically choose to implement each curve as a special case so that modular reduction can be optimized, thus improving the overall performance. In contrast, this paper focuses on generic implementations of ECC point multiplication for arbitrary curves over GF(2m). We present a novel reduction algorithm that allows hardware and software implementations for variable field degrees m. Though not as high in performance as an implementation optimized for a specific curve, it offers an attractive solution to supporting infrequently used curves or curves not known at the time of the implementation.
TiO2hollow spheres with large amount of exposed (001) facets for fast reversible lithium storage (2010)

We report a simple approach for synthesizing uniform hollow spheres assembled from anatase TiO2 nanosheets with large amount of exposed (001) facets. These hierarchical TiO2 hollow spheres possessing a high specific surface area of 134.9 m2 g−1 manifest a high Coulombic efficiency for lithium extraction, excellent capacity retention, and superior rate behaviour owing to the hollow structure and unique crystal faceting of the building blocks.
Micheliolide overcomes KLF4-mediated cisplatin resistance in breast cancer cells by downregulating glutathione (2015)

Micheliolide (MCL) is a promising novel compound with broad-spectrum anticancer activity. However, little is known regarding its action and mechanism in breast cancer. To explore the potential therapeutic application of MCL as a chemosensitivity modulator, this study investigated the effects of MCL on cisplatin sensitivity in breast cancer and the underlying mechanisms. In the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cytotoxicity assay and a xenograft tumor model, MCL enhanced the cisplatin sensitivity of the breast cancer cell line MCF-7 both in vitro and in vivo. Treatment of MCF-7 cells with low-dose cisplatin (10 µM) was sufficient to enrich the proportion of ALDH(+) cells and upregulate Krüppel-like factor 4 (KLF4) expression. The results obtained from knockdown and overexpression experiments demonstrate that KLF4 is both necessary and sufficient to induce a cisplatin resistance phenotype in breast cancer cells. Furthermore, the glutathione (GSH) content was elevated in MCF-7 cells after overexpression of KLF4. KLF4-mediated resistance to cisplatin was found to be abrogated by treatment with buthionine sulfoximine, an inhibitor of GSH synthesis. MCL induced GSH depletion and severe cell death in KLF4-overexpressing MCF-7 cells following exposure to cisplatin. Therefore, these results suggest that MCL-mediated direct depletion of GSH represents a major mechanism in reversing KLF4-induced cisplatin resistance in MCF-7 cells.
Physical Properties of Carbon Nanotubes (1998)

This is an introductory textbook for graduate students and researchers from various fields of science who wish to learn about carbon nanotubes. The field is still at an early stage, and progress continues at a rapid rate. This book focuses on the basic principles behind the physical properties and gives the background necessary to understand the recent developments. Some useful computational source codes which generate coordinates for carbon nanotubes are also included in the appendix.
Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies (2009)

The restricted neutralization breadth of vaccine-elicited antibodies is a major limitation of current human immunodeficiency virus-1 (HIV-1) candidate vaccines. In order to permit the efficient identification of vaccines with enhanced capacity for eliciting cross-reactive neutralizing antibodies (NAbs) and to assess the overall breadth and potency of vaccine-elicited NAb reactivity, we assembled a panel of 109 molecularly cloned HIV-1 Env pseudoviruses representing a broad range of genetic and geographic diversity. Viral isolates from all major circulating genetic subtypes were included, as were viruses derived shortly after transmission and during the early and chronic stages of infection. We assembled a panel of genetically diverse HIV-1-positive (HIV-1(+)) plasma pools to assess the neutralization sensitivities of the entire virus panel. When the viruses were rank ordered according to the average sensitivity to neutralization by the HIV-1(+) plasmas, a continuum of average sensitivity was observed. Clustering analysis of the patterns of sensitivity defined four subgroups of viruses: those having very high (tier 1A), above-average (tier 1B), moderate (tier 2), or low (tier 3) sensitivity to antibody-mediated neutralization. We also investigated potential associations between characteristics of the viral isolates (clade, stage of infection, and source of virus) and sensitivity to NAb. In particular, higher levels of NAb activity were observed when the virus and plasma pool were matched in clade. These data provide the first systematic assessment of the overall neutralization sensitivities of a genetically and geographically diverse panel of circulating HIV-1 strains. These reference viruses can facilitate the systematic characterization of NAb responses elicited by candidate vaccine immunogens.
Microfluidic Patterning of Cells in Extracellular Matrix Biopolymers: Effects of Channel Size, Cell Type, and Matrix Composition on Pattern Integrity (2003)

The organization of cells within an extracellular matrix is critical to promote appropriate cellular interactions and tissue function in vivo. The ability to design and create biologically relevant cellular arrangements via microfluidic patterning on surfaces provides new capabilities for tissue engineering and biomimetics. The purpose of this article is to describe techniques using microfluidic patterning of three-dimensional biopolymer matrices to improve cellular pattern integrity and to provide microscale control over cellular microenvironments. Results demonstrated that the incorporation of extracellular matrix biopolymers in cell microfluidic patterning results in a more stable pattern of adherent human endothelial cells than patterning without matrix components after several days in vitro. This may be important for carrying out long-term biological experiments and tissue engineering in vitro. Moreover, chemical components in the patterned biopolymer matrices, such as collagen, chitosan, and fibronectin, influenced the ability of the matrices to control cell migration and pattern stability over time. Thus, microfluidic patterning of cells in extracellular matrix biopolymers was shown to be useful in patterning multiple cell types in well-defined three-dimensional geometries.
A 15&#x2013;40-GHz Frequency Reconfigurable RF MEMS Phase Shifter (2013)

This paper presents a novel frequency reconfigurable phase shifter using the RF microelectromechanical systems (MEMS) technology. The phase shifter is based on the triple-stub circuit topology composed of three stubs that are connected by two transmission lines that are all implemented as distributed MEMS transmission lines. The insertion phase of the circuit is controlled by changing the electrical lengths of the stubs and the connecting transmission lines, while having ideally zero reflection coefficient at all times. The phase shifter has theoretically no specific limits on the frequency; in other words, it can be reconfigured to work at any frequency between 15-40 GHz, with adjustable phase steps, while providing a constant time delay within a 2%-3% instantaneous bandwidth around any selected center frequency in the above-mentioned band. The phase shifter is fabricated monolithically using a surface micromachining process on a quartz substrate and occupies 10.8 mm × 5.9 mm. Measurement results show that the phase shifter has average phase error of 1.6 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> , 3.7 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> , and 4.7 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> , average insertion loss of 3.1, 5, and 8.2 dB and average return loss of 19.3, 15.8, and 13.7 dB at 15, 30, and 40 GHz, respectively. To the best of our knowledge, this paper demonstrates the first phase shifter in the literature that can work at any given frequency in a targeted band with adjustable phase steps.
The latest open-source video codec VP9 - An overview and preliminary results (2013)

Google has recently finalized a next generation open-source video codec called VP9, as part of the libvpx repository of the WebM project (http://www.webmproject.org/). Starting from the VP8 video codec released by Google in 2010 as the baseline, various enhancements and new tools were added, resulting in the next-generation VP9 bit-stream. This paper provides a brief technical overview of VP9 along with comparisons with other state-of-the-art video codecs H.264/AVC and HEVC on standard test sets. Results show VP9 to be quite competitive with mainstream state-of-the-art codecs.
Attachment of hyaluronan to metallic surfaces (2003)

Metal implants are in general not compatible with the tissues of the human body, and in particular, blood exhibits a severe hemostatic response. Herein we present results of a technique to mask the surface of metals with a natural biopolymer, hyaluronan (HA). HA has minimal adverse interactions with blood and other tissues, but attachment of bioactive peptides can promote specific biological interactions. In this study, stainless steel was cleaned and then surface-modified by covalent attachment of an epoxy silane. The epoxy was subsequently converted to an aldehyde functional group and reacted with hyaluronan through an adipic dihydrazide linkage, thus covalently immobilizing the HA onto the steel surface. Fluorescent labeling of the HA showed that the surface had a fairly uniform covering of HA. When human platelet rich plasma was placed on the HA-coated surface, there was no observable adhesion of platelets. HA derivatized with a peptide containing the RGD peptide sequence was also bound to the stainless steel. The RGD-containing peptide was bioactive as exemplified by the attachment and spreading of platelets on this surface. Furthermore, when the RGD peptide was replaced with the nonsense RDG sequence, minimal adhesion of platelets was observed. This type of controlled biological activity on a metal surface has potential for modulating cell growth and cellular interactions with metallic implants, such as vascular stents, orthopedic implants, heart valve cages, and more.
Recombinant secreted nonpancreatic phospholipase A2 induces a synovitis-like inflammation in the rat air pouch. (1994)

Only sPLA2 was able to exacerbate rat air pouch and its effect was unrelated to eicosanoid release.
Fc-galactosylation modulates antibody-dependent cellular cytotoxicity of therapeutic antibodies (2016)

The therapeutic activity of monoclonal antibodies can involve immune cell mediated effector functions including antibody-dependent cellular cytotoxicity (ADCC), an activity that is modulated by the structure of Fc-glycans, and in particular the lack of core fucose. The heterogeneity of these glycostructures and the inherent variability of traditional PBMC-based in vitro ADCC assays, have made it challenging to quantitatively assess the impact of other glycostructures on ADCC activity. We applied a quantitative NK cell based assay to generate a database consisting of Fc-glycostructure and ADCC data from 54 manufacturing batches of a CHO-derived monoclonal antibody. Explorative analysis of the data indicated that, apart from afucosylation, galactosylation levels could influence ADCC activity. We confirmed this hypothesis by demonstrating enhanced ADCC upon enzymatic hypergalactosylation of four different monoclonal antibodies derived using standard CHO manufacturing processes. Furthermore we quantitatively compare the effects of galactosylation and afucosylation in the context of glycan heterogeneity and demonstrate that while galactose can influence ADCC activity, afucosylation remains the primary driver of this activity.
Introduction: Recent Developments in Alkaline Phosphatase Research (1992)

Journal Article Introduction: Recent Developments in Alkaline Phosphatase Research Get access M E De Broe, M E De Broe University Hospital, Department of Nephrology and Hypertension, Antwerp, Belgium Search for other works by this author on: Oxford Academic Google Scholar D W Moss D W Moss University Hospital, Department of Nephrology and Hypertension, Antwerp, Belgium Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 38, Issue 12, 1 December 1992, Page 2485, https://doi.org/10.1093/clinchem/38.12.2485 Published: 01 December 1992
ACAM2000: a newly licensed cell culture-based live vaccinia smallpox vaccine (2008)

The studies with ACAM2000 indicate that it closely matches the safety of Dryvax in both non-clinical and clinical trials. ACAM2000 met two of the four primary surrogate efficacy end point criteria established for the Phase III clinical trials. Concern over the incidence of myopericarditis with ACAM2000 and Dryvax exists. So far the cardiac events seem to be self-limited. There are no pediatric safety data for ACAM2000. Overall, clinical trial results were sufficient to convince the FDA that ACAM2000 is a suitable replacement for Dryvax in the event of bioterrorism involving variola (smallpox).
The Matrix Coalescent and an Application to Human Single-Nucleotide Polymorphisms (2002)

The "matrix coalescent" is a reformulation of the familiar coalescent process of population genetics. It ignores the topology of the gene tree and treats the coalescent as a Markov process describing the decay in the number of ancestors of a sample of genes as one proceeds backward in time. The matrix formulation of this process is convenient when the population changes in size, because such changes affect only the eigenvalues of the transition matrix, not the eigenvectors. The model is used here to calculate the expectation of the site frequency spectrum under various assumptions about population history. To illustrate how this method can be used with data, we then use it in conjunction with a set of SNPs to test hypotheses about the history of human population size.
Conformational plasticity of RNA for target recognition as revealed by the 2.15 Å crystal structure of a human IgG–aptamer complex (2010)

Aptamers are short single-stranded nucleic acids with high affinity to target molecules and are applicable to therapeutics and diagnostics. Regardless of an increasing number of reported aptamers, the structural basis of the interaction of RNA aptamer with proteins is poorly understood. Here, we determined the 2.15 Å crystal structure of the Fc fragment of human IgG1 (hFc1) complexed with an anti-Fc RNA aptamer. The aptamer adopts a characteristic structure fit to hFc1 that is stabilized by a calcium ion, and the binding activity of the aptamer can be controlled many times by calcium chelation and addition. Importantly, the aptamer-hFc1 interaction involves mainly van der Waals contacts and hydrogen bonds rather than electrostatic forces, in contrast to other known aptamer-protein complexes. Moreover, the aptamer-hFc1 interaction involves human IgG-specific amino acids, rendering the aptamer specific to human IgGs, and not crossreactive to other species IgGs. Hence, the aptamer is a potent alternative for protein A affinity purification of Fc-fusion proteins and therapeutic antibodies. These results demonstrate, from a structural viewpoint, that conformational plasticity and selectivity of an RNA aptamer is achieved by multiple interactions other than electrostatic forces, which is applicable to many protein targets of low or no affinity to nucleic acids.
Spectroscopic studies of the multiple binding modes of a trimethine-bridged cyanine dye with DNA (2003)

The interaction between DNA and a benzothiazole-quinoline cyanine dye with a trimethine bridge (TO-PRO-3) results in the formation of three noncovalent complexes. Unbound TO-PRO-3 has an absorption maximum (lambda(max)) of 632 nm, while the bound dyes (with calf thymus DNA) have electronic transitions with lambda(max) = 514 nm (complex I), 584 nm (complex II) and 642 nm (complex III). The blue shifts in the electronic transitions and the bisignate shape of the circular dichroism bands indicate that TO-PRO-3 aggregates with DNA. Complex I has a high dye:base pair stoichiometry, which does not depend on base sequence or base modifications. The bound dyes exhibit strong interdye coupling, based on studies with a short oligonucleotide and on enhanced resonance scattering. From thermal dissociation studies, the complex is weakly associated with DNA. Studies with poly(dGdC)2 and poly(dIdC)2 and competitive binding with distamycin demonstrate that complex II is bound in the minor groove. This complex stabilizes the helix against dissociation. For complex III, the slightly red-shifted electronic transition and the stoichiometry are most consistent with intercalation. Using poly(dAdT)2, the complexes have the following dye mole fractions (X(dye)): X(dye) = 0.65 (complex I), 0.425 (complex II) and 0.34 (complex III).