gebhart/patrepeval huggingface dataset:
Connective tissue growth factor(CCN2), a pathogenic factor in diabetic nephropathy. What does it do? How does it do it? (2009)

Connective tissue growth factor (CTGF/CCN2) is a member of the CCN family of matricellular proteins. Its expression is induced by a number of factors including TGF-beta. It has been associated with fibrosis in various tissues including the kidney. Diabetic nephropathy (DN) develops in about 30% of patients with diabetes and is characterized by thickening of renal basement membranes, fibrosis in the glomerulus (glomerulosclerosis), tubular atrophy and interstitial fibrosis, all of which compromise kidney function. This review examines changes in CTGF expression in the kidney in DN, the effects they have on glomerular mesangial and podocyte cells and the tubulointerstitium, and how these contribute to driving fibrotic changes in the disease. CTGF can bind to several other growth factors modifying their function. CTGF is also able to interact with receptors on cells, including integrins, tyrosine receptor kinase A (TrkA), low density lipoprotein receptor-related protein (LRP) and heparan sulphate proteoglycans. These interactions, the intracellular signalling pathways they activate, and the cellular responses evoked are reviewed. CTGF also induces the expression of chemokines which themselves have pharmacological actions on cells. CTGF may prompt some responses by acting through several different mechanisms, possibly simultaneously. For example, CTGF is often described as an effector of TGF-beta. It can promote TGF-beta signalling by binding directly to the growth factor, promoting its interaction with the TGF-beta receptor; by triggering intracellular signalling on binding the TrkA receptor, which leads to the transcriptional repression of Smad7, an inhibitor of the TGF-beta signalling pathway; and by binding to BMP-7 whose own signalling pathway opposing TGF-beta is inhibited, leading to enhanced TGF-beta signalling.
Orbital angular momentum of light and the transformation of Laguerre-Gaussian laser modes (1992)

Laser light with a Laguerre-Gaussian amplitude distribution is found to have a well-defined orbital angular momentum. An astigmatic optical system may be used to transform a high-order Laguerre-Gaussian mode into a high-order Hermite-Gaussian mode reversibly. An experiment is proposed to measure the mechanical torque induced by the transfer of orbital angular momentum associated with such a transformation.
Loss of E-Cadherin Promotes Ovarian Cancer Metastasis via α5-Integrin, which Is a Therapeutic Target (2008)

E-cadherin loss is frequently associated with ovarian cancer metastasis. Given that adhesion to the abdominal peritoneum is the first step in ovarian cancer dissemination, we reasoned that down-regulation of E-cadherin would affect expression of cell matrix adhesion receptors. We show here that inhibition of E-cadherin in ovarian cancer cells causes up-regulation of alpha(5)-integrin protein expression and transcription. When E-cadherin was blocked, RMUG-S ovarian cancer cells were able to attach and invade more efficiently. This greater efficiency could, in turn, be inhibited both in vitro and in vivo with an alpha(5)beta(1)-integrin-blocking antibody. When E-cadherin is silenced, alpha(5)-integrin is up-regulated through activation of an epidermal growth factor receptor/FAK/Erk1-mitogen-activated protein kinase-dependent signaling pathway and not through the canonical E-cadherin/beta-catenin signaling pathway. In SKOV-3ip1 ovarian cancer xenografts, which express high levels of alpha(5)-integrin, i.p. treatment with an alpha(5)beta(1)-integrin antibody significantly reduced tumor burden, ascites, and number of metastasis and increased survival by an average of 12 days when compared with IgG treatment (P < 0.0005). alpha(5)-Integrin expression was detected by immunohistochemistry in 107 advanced stage ovarian cancers using a tissue microarray annotated with disease-specific patient follow-up. Ten of 107 tissues (9%) had alpha(5)-integrin overexpression, and 39% had some level of alpha(5)-integrin expression. The median survival for patients with high alpha(5)-integrin levels was 26 months versus 35 months for those with low integrin expression (P < 0.05). Taken together, we have identified alpha(5)-integrin up-regulation as a molecular mechanism by which E-cadherin loss promotes tumor progression, providing an explanation for how E-cadherin loss increases metastasis. Targeting this integrin could be a promising therapy for a subset of ovarian cancer patients.
Efficient inhibition of HIV-1 replication in human immature monocyte-derived dendritic cells by purified anti–HIV-1 IgG without induction of maturation (2006)

During mucosal HIV transmission, immature dendritic cells (DCs) present in the mucosa are among the first cellular targets of the virus. Previous studies have analyzed the inhibition of HIV-1 transfer from human mature DCs to T lymphocytes by neutralizing IgG, but so far no in vitro data regarding the capacity of antibodies to inhibit HIV-1 infection of immature DCs have been reported. Here, we found an increased HIV-inhibitory activity of monoclonal IgG and purified polyclonal IgG when immature monocyte-derived dendritic cells (iMDDCs) were used as target cells instead of autologous blood lymphocytes. We showed that FcgammaRII is involved in the mechanism for inhibiting HIV-1 infection of iMDDCs by IgG, whereas no induction of maturation was detected at concentrations of IgG that result in a 90% reduction of HIV replication. After induction of FcgammaRI expression on iMDDCs by IFN-gamma, an augmentation of the HIV-inhibitory activity of IgG, related to the expression of FcgammaRI, was observed. Taken together, our results demonstrate the participation of FcgammaRs in HIV-1 inhibition by IgG when iMDDCs are the targets. We propose that IgG is able to efficiently inhibit HIV-1 replication in iMDDCs and should be one of the components to be induced by vaccination.
Purification, characterization, assembly and crystallization of assembled alfalfa mosaic virus coat protein expressed in Escherichia coli (1996)

The coast protein of alfalfa mosaic virus (AMV) was cloned and expressed in Escherichia coli as a fusion protein containing a 37 amino acid extension with a (His)6 region for affinity purification. About half of the expressed recombinant coat protein (rCP) was soluble upon extraction and half was insoluble in inclusion bodies. Western blot analysis confirmed the identity of the rCP and protoplast infectivity assays indicated that the rCP was biologically active in an early event of AMV infection, called genome activation. The rCP assembled into T = 1 empty icosahedral particles, as described previously for native coat protein. Empty particles formed hexagonal crystals that diffracted X-rays to 5.5 A resolution. The crystals of trypsin-treated particles of rCP appear to be isomorphous with crystals of trypsin-treated particles of native coat protein, Spherical particles containing RNA assembled when the rCP was combined with in vitro transcripts of AMV RNA4, the smallest naturally encapsidated AMV RNA. Bacilliform particles that resembled native virions assembled when the rCP was combined with transcripts of RNA1, the largest genomic RNA.
Enhancer Control of Local Accessibility to V(D)J Recombinase (1997)

We have studied the role of transcriptional enhancers in providing recombination signal sequence (RSS) accessibility to V(D)J recombinase by examining mice carrying a transgenic human T-cell receptor (TCR) delta gene minilocus. This transgene is composed of unrearranged variable (Vdelta and Vdelta2), diversity (Ddelta3), joining (Jdelta1 and Jdelta3), and constant (Cdelta) gene segments. Previous data indicated that with the TCR delta enhancer (Edelta) present in the Jdelta3-Cdelta intron, V(D)J recombination proceeds stepwise, first V to D and then VD to J. With the enhancer deleted or mutated, V-to-D rearrangement is intact, but VD-to-J rearrangement is inhibited. We proposed that Edelta is necessary for J segment but not D segment accessibility and that J segment inaccessibility in the enhancerless minilocus resulted in the observed V(D)J recombination phenotype. In this study, we tested this notion by using ligation-mediated PCR to assess the formation of recombination-activating gene (RAG)-dependent double-strand breaks (DSBs) at RSSs 3' of Ddelta3 and 5' of Jdelta1. In five lines of mice carrying multicopy integrants of constructs that either lacked Edelta or carried an inactivated Edelta, the frequency of DSBs 5' of Jdelta1 was dramatically reduced relative to that in the wild type, whereas the frequency of DSBs 3' of Ddelta3 was unaffected. We interpret these results to indicate that Edelta is required for Jdelta1 but not Ddelta3 accessibility within the minilocus, and we conclude that enhancers regulate V(D)J recombination by providing local accessibility to the recombinase. cis-acting elements other than Edelta must maintain Ddelta3 in an accessible state in the absence of Edelta. The analysis of DSB formation in a single-copy minilocus integrant indicates that efficient DSB formation at the accessible RSS 3' of Ddelta3 requires an accessible partner RSS, arguing that RSS synapsis is required for DSB formation in chromosomal substrates in vivo.
Robust Plasmon Waveguides in Strongly Interacting Nanowire Arrays (2008)

Arrays of parallel metallic nanowires are shown to provide a tunable, robust, and versatile platform for plasmon interconnects, including high-curvature turns with minimum signal loss. The proposed guiding mechanism relies on gap plasmons existing in the region between adjacent nanowire pairs and multiwire arrays. We focus on square and circular silver nanowires in silica, which we demonstrate to perform much better than previous schemes in terms of a relevant figure of merit measuring the degree of allowed integration. Our work provides the tools for designing plasmon-based interconnects and achieving a high degree of integration with minimum cross talk between adjacent plasmon guides, which should be relevant ingredients for future multiplexed biosensors.
A small-molecule, nonpeptide CCR5 antagonist with highly potent and selective anti-HIV-1 activity (1999)

The beta-chemokine receptor CCR5 is considered to be an attractive target for inhibition of macrophage-tropic (CCR5-using or R5) HIV-1 replication because individuals having a nonfunctional receptor (a homozygous 32-bp deletion in the CCR5 coding region) are apparently normal but resistant to infection with R5 HIV-1. In this study, we found that TAK-779, a nonpeptide compound with a small molecular weight (Mr 531.13), antagonized the binding of RANTES (regulated on activation, normal T cell expressed and secreted) to CCR5-expressing Chinese hamster ovary cells and blocked CCR5-mediated Ca2+ signaling at nanomolar concentrations. The inhibition of beta-chemokine receptors by TAK-779 appeared to be specific to CCR5 because the compound antagonized CCR2b to a lesser extent but did not affect CCR1, CCR3, or CCR4. Consequently, TAK-779 displayed highly potent and selective inhibition of R5 HIV-1 replication without showing any cytotoxicity to the host cells. The compound inhibited the replication of R5 HIV-1 clinical isolates as well as a laboratory strain at a concentration of 1.6-3.7 nM in peripheral blood mononuclear cells, though it was totally inactive against T-cell line-tropic (CXCR4-using or X4) HIV-1.
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT) (2006)

In both normal and pathological states, cells respond rapidly to environmental cues by synthesizing new proteins. The selective identification of a newly synthesized proteome has been hindered by the basic fact that all proteins, new and old, share the same pool of amino acids and thus are chemically indistinguishable. We describe here a technology, based on the cotranslational introduction of azide groups into proteins and the chemoselective tagging of azide-labeled proteins with an alkyne affinity tag, to separate and identify, specifically, the newly synthesized proteins in mammalian cells. Incorporation of the azide-bearing amino acid azidohomoalanine is unbiased, not toxic, and does not increase protein degradation. As a first demonstration of the method, we report the selective purification and identification of 195 metabolically labeled proteins with multidimensional liquid chromatography in-line with tandem MS. Furthermore, in combination with leucine-based mass tagging, candidates were immediately validated as newly synthesized proteins. The identified proteins, synthesized in a 2-h window, possess a broad range of biochemical properties and span most functional gene ontology categories. This technology makes it possible to address the temporal and spatial characteristics of newly synthesized proteomes in any cell type.
Long-term Therapy for Heart Failure With Continuous Ambulatory Peritoneal Dialysis (1985)

This article reports the treatment with continuous ambulatory peritoneal dialysis of a patient with intractable congestive heart failure secondary to an ischemic cardiomyopathy. Although the use of peritoneal dialysis to treat refractory heart failure is not new, the advent of an effective continuous peritoneal dialysis system has allowed its use over prolonged periods of time. The two-year treatment interval described herein represents the longest reported application of this technique, to the best of our knowledge.
Asymmetric synthesis of optically active β-substituted ketones by highly enantioselective catalytic conjugate addition of dialkylzinc reagents to enones using a catalyst system of nickel(II)-chiral ligand–achiral ligand in acetonitrile/toluene (1989)

Highly enantioselective conjugate addition of dialkylzinc reagents to aryl substituted enones using Ni(II)-bipyridyl–chiral ligand in acetonitrile (MeCN)/toluene as an in situ prepared catalyst system affords β-substituted ketones in up to 90% enantiomeric excess (e.e.).
Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G (2012)

The AID/APOBEC family of enzymes in higher vertebrates converts cytosines in DNA or RNA to uracil. They play a role in antibody maturation and innate immunity against viruses, and have also been implicated in the demethylation of DNA during early embryogenesis. This is based in part on reported ability of activation-induced deaminase (AID) to deaminate 5-methylcytosines (5mC) to thymine. We have reexamined this possibility for AID and two members of human APOBEC3 family using a novel genetic system in Escherichia coli. Our results show that while all three genes show strong ability to convert C to U, only APOBEC3A is an efficient deaminator of 5mC. To confirm this, APOBEC3A was purified partially and used in an in vitro deamination assay. We found that APOBEC3A can deaminate 5mC efficiently and this activity is comparable to its C to U deamination activity. When the DNA-binding segment of AID was replaced with the corresponding segment from APOBEC3A, the resulting hybrid had much higher ability to convert 5mC to T in the genetic assay. These and other results suggest that the human AID deaminates 5mC's only weakly because the 5-methyl group fits poorly in its DNA-binding pocket.
Studies on the development of natural immunity to poliomyelitis in Louisiana. V. Passive transfer of polioantibody from mother to fetus, and natural decline and disappearance of antibody in the infant. (1960)

Maternal, umbilical cord, and serially-collected infant blood samples, were available incidental to the “Louisiana Study” of natural infection with polioviruses. By means of the simultaneous titration of series of these specimens, the passive transfer of circulating maternal antibody to the infant and the decline in the infant of the maternally-derived antibody were investigated by the neutralization test. Sixty-six maternal cord blood pairs permitted observation on 188 typespecific comparisons, and showed that the titer of humoral antibody varies, in general, very little within each pair, but that there is a greater tendency for type 3 transfer to be inefficient as compared with types 1 and 2. However, specific transfer inefficiency of any antibody type may be associated with individual women. Since the antibody comparison possessed by children at birth is a function of maternal titer and since the passively acquired antibody gradually disappears, the percentage of seropositive infants in a population gradually diminishes with postpartum age. In this highly endemic area, over 50% of infants were seronegative, at a serum dilution of 1:10, against any one antibody type, by 3 months of age. The implications of this finding to early vaccination were discussed. The half-life for passive polioantibody was calculated by a study of the mean titer of antibody at successive monthly intervals of infants born of mothers with various antibody levels. The decline was found to be exponential in nature and not to vary appreciably or consistently with maternal titer. The half-life of the passive antibody was found to be approximately 25 days.
Cytokines in proliferative diabetic retinopathy and proliferative vitreoretinopathy (1995)

We determined whether interleukin-8, monocyte chemotactic protein-1, and macrophage-colony stimulating factor are present in the vitreous of patients with proliferative diabetic retinopathy (PDR) or proliferative vitreoretinopathy (PVR). The levels of these cytokines were measured by specific enzyme-linked immunoassays in vitreous from 30 patients with PDR, 13 patients with PVR, and 26 control individuals, including 10 cadaver eyes and 16 patients with idiopathic macular holes, idiopathic macular puckers, vitreous hemorrhages, or uncomplicated retinal detachments. Detectable levels of interleukin-8 were found in 90% of vitreous samples of patients with PDR, 85% with PVR, and 58% of control samples. IL-8 was significantly increased in PDR (mean +/- SEM; 25.0 +/- 5.3 ng/ml; p = 0.01), but not in PVR (11.9 +/- 3.9 ng/ml; p = 0.50) compared to control human vitreous (8.5 +/- 2.5 2.5 ng/ml). MCP-1 was detected in 90% of vitreous samples of patients with PDR, 92% with PVR, and 81% of control samples. MCP-1 was significantly increased in PDR (6.2 +/- 0.9 ng/ml, p = 0.001) and PVR (7.7 +/- 2.5 ng/ml, p = 0.001) over the levels in control vitreous (1.2 +/- 0.2 ng/ml). M-CSF was detected in 94% of vitreous samples of patients with PDR, 88% with PVR, and 92% from control vitreous. M-CSF was significantly elevated in PDR (32.3 +/- 8.3 ng/ml, p = 0.03), but not in PVR (23.6 +/- 12.8 ng/ml, p = 0.4) compared to control (10.7 +/- 3.5 ng/ml). Our results suggest that IL-8, MCP-1, and M-CSF participate in the pathogenesis of PDR and PVR.
CELLULAR AND MOLECULAR CHARACTERISTICS OF BASAL CELLS IN AIRWAY EPITHELIUM (2001)

Basal cells exist as a separate layer of cells covering most of the airway basal lamina. In this central position, they can interact with columnar epithelium, neurons, basement membrane, and the underlying mesenchymal cells. In addition, they interact with inflammatory cells, lymphocytes and dendritic cells. These interactions take place in the lateral intercellular space between basal cells. In this central position basal cells become a very important part of the epithelial-mesenchymal trophic unit of larger airways. In this review it is shown that basal cells may function as progenitor cells of airway epithelium and have a role in attachment of columnar epithelium with the basement membrane. They also have the potential to function in regulation of neurogenic inflammation, the inflammatory response, transepithelial water movement, oxidant defense of the tissue and formation of the lateral intercellular space. Other characteristics of basal cells were not clearly associated with a particular function. The functions for basal cells listed attempt to explain the presence of recently identified molecules in basal cells of airway epithelium. It should be pointed out that specific studies have not been carried out which test the relationship between the molecular functions we describe in this review and the basal cell in airway epithelium.
The Retinal Pigment Epithelial-specific 11-cis Retinol Dehydrogenase Belongs to the Family of Short Chain Alcohol Dehydrogenases (1995)

We have isolated and partially characterized a 32-kDa membrane-associated protein (p32), which forms a complex with p63, an abundant membrane protein in bovine retinal pigment epithelium. The sequence of a cDNA clone for p32 revealed an open reading frame encoding 318 amino acid residues. Several hydrophobic regions could be identified, suggesting that p32 is an integral membrane protein. A search of data bases identified p32 as a member of the superfamily of short chain alcohol dehydrogenases. Transcripts for p32 were specifically expressed in retinal pigment epithelium. Overexpression of p32 in Cos cells produced a membrane-bound stereospecific 11-cis retinol dehydrogenase, active in the presence of NAD+ as cofactor but not in the presence of NADP. We propose that p32 is the stereospecific 11-cis retinol dehydrogenase, which catalyzes the final step in the biosynthesis of 11-cis retinaldehyde, the universal chromophore of visual pigments.
Electronic state characterization of SiOx thin films prepared by evaporation (2005)

Si O x thin films with different stoichiometries from SiO1.3 to SiO1.8 have been prepared by evaporation of silicon monoxide in vacuum or under well-controlled partial pressures of oxygen (P&amp;lt;10−6Torr). These thin films have been characterized by x-ray photoemission and x-ray-absorption spectroscopies, this latter at the Si K and L2,3 absorption edges. It has been found that the films prepared in vacuum consists of a mixture of Si3+ and Si+ species that progressively convert into Si4+ as the partial pressure of oxygen during preparation increases. From this spectroscopic analysis, information has been gained about the energy distribution of both the full and empty states of, respectively, the valence and conduction bands of SiOx as a function of the O∕Si ratio. The characterization of these films by reflection electron energy-loss spectroscopy (REELS) has provided further evidences about their electronic structure (band gap and electronic states) as a function of the oxygen content. The determination of the plasmon energies by REELS has also shown that the films prepared by evaporation in vacuum consist of a single phase which is characterized by a density (1.7gcm−3) lower than that of SiO2 (i.e., 2.2gcm−3) or Si (i.e., 2.4gcm−3). The optical properties (n and k) of the films as a function of the O∕Si content have been deduced from the analysis of REELS spectra in the energy range from 4to20eV. It has been also shown that the O∕Si ratio in the films and several spectroscopic parameters such as the Auger parameter or the energy of bulk plasmons present a linear relationship and that this linear dependence can be used for a rapid characterization of SiOx materials. By contrast, the band-gap energy changes differently with the O∕Si ratio, following a smooth linear increase from about 3.8eV for SiO1.3 to ca. 5.0eV for SiO1.7 and a jump up to 8.7eV for SiO2. These results indicate that the random-bonding model does not apply to thin films prepared by evaporation under our experimental conditions. Other distributions of Sin+ states can be induced if the films are excited with an external source such as heat or photon irradiation. In this case the electronic properties vary and the previous linear correlations as a function of the oxygen content do not hold any longer.