gebhart/patrepeval huggingface dataset:
Increased poly(ADP-ribosyl)ation of nuclear proteins in Alzheimer's disease (1999)

Experimental studies indicate that overactivation of the DNA repair protein poly(ADP-ribose) polymerase (PARP) in response to oxidative damage to DNA can cause cell death due to depletion of NAD+. Oxidative damage to DNA and other macromolecules has been reported to be increased in the brains of patients with Alzheimer's disease. In the present study we sought evidence of PARP activation in Alzheimer's disease by immunostaining sections of frontal and temporal lobe from autopsy material of 20 patients and 10 controls, both for PARP itself and for its end-product, poly(ADP-ribose). All of the brains had previously been subjected to detailed neuropathological examination to confirm the diagnosis of Alzheimer's disease or, in the controls, to exclude Alzheimer's disease-type pathology. Double immunolabelling for poly(ADP-ribose) and microtubule-associated protein 2 (MAP2), glial fibrillary-acidic protein (GFAP), CD68, A beta-protein or tau was used to assess the identity of the cells with poly(ADP-ribose) accumulation and their relationship to plaques and neurofibrillary tangles. Both PARP- and poly(ADP-ribose)-immunolabelled cells were detected in a much higher proportion of Alzheimer's disease (20 out of 20) brains than of control brains (5 out of 10) (P = 0.0018). Double-immunolabelling for poly(ADP-ribose) and markers of neuronal, astrocytic and microglial differentiation (MAP2, GFAP and CD68, respectively) showed many of the cells containing poly(ADP-ribose) to be neurons. Most of these were small pyramidal neurons in cortical laminae 3 and 5. A few of the cells containing poly(ADP-ribose) were astrocytes. No poly(ADP-ribose) accumulation was detected in microglia. Double-immunolabelling for poly(ADP-ribose) and tau or A beta-protein indicated that the cells with accumulation of poly(ADP-ribose) did not contain tangles and relatively few occurred within plaques. Our findings indicate that there is enhanced PARP activity in Alzheimer's disease and suggest that pharmacological interventions aimed at inhibiting PARP may have a role in slowing the progression of the disease.
A thymic stromal cell line supports in vitro development of surface IgM+ B cells and produces a novel growth factor affecting B and T lineage cells. (1994)

A thymic stromal cell line with a medullary phenotype (Z210R.1) supported the differentiation of surface IgM+ B cells when cocultured with fetal liver cells in vitro. Conditioned medium (CM) from this cell line supported the long-term growth of a B cell line (NAG8/7) isolated from cocultures and enhanced the proliferation of unfractionated thymocytes to suboptimal concentrations of anti-CD3 antibodies in vitro. Biological assays of the CM detected interleukin-7 (IL-7) but not IL-1, IL-2, IL-3, IL-4, IL-6, Steel factor (SCF), leukemia inhibitory factor (LIF), or macrophage or granulocyte colony-stimulating factors (M-CSF or G-CSF). The failure of recombinant IL-7 to maintain the long-term growth of NAG8/7 cells and the inability of anti-IL-7 antibodies to significantly affect the response of either NAG8/7 cells or thymocytes to CM suggested the presence of one or more other cytokines in the CM. Analysis of concentrated CM fractionated by anion exchange chromatography revealed a single peak of activity in the NAG8/7 assay with an elution profile that was distinct from IL-7. Two peaks of activity were detected in the thymocyte response to anti-CD3 antibodies; one corresponded to IL-7 and the other corresponded to the same fractions that stimulated NAG8/7 cells. The second peak of thymocyte stimulatory activity could not be inhibited by neutralizing anti-IL-7 antibodies. In addition to producing a cytokine with unique properties, this thymic stromal cell exhibits a functional homology to bone marrow or fetal liver stromal cells not previously appreciated.
Expression of Concern: Glycogen synthase kinase 3β (GSK3β) mediates 6‐ hydroxydopamine‐induced neuronal death (2004)

The causes of sporadic Parkinson's disease (PD) are poorly understood. 6-Hydroxydopamine (6-OHDA), a PD mimetic, is widely used to model this neurodegenerative disorder in vitro and in vivo; however, the underlying mechanisms remain incompletely elucidated. We demonstrate here that 6-OHDA evoked endoplasmic reticulum (ER) stress, which was characterized by an up-regulation in the expression of GRP78 and GADD153 (Chop), cleavage of procaspase-12, and phosphorylation of eukaryotic initiation factor-2 alpha in a human dopaminergic neuronal cell line (SH-SY5Y) and cultured rat cerebellar granule neurons (CGNs). Glycogen synthase kinase-3 beta (GSK3beta) responds to ER stress, and its activity is regulated by phosphorylation. 6-OHDA significantly inhibited phosphorylation of GSK3beta at Ser9, whereas it induced hyperphosphorylation of Tyr216 with little effect on GSK3beta expression in SH-SY5Y cells and PC12 cells (a rat dopamine cell line), as well as CGNs. Furthermore, 6-OHDA decreased the expression of cyclin D1, a substrate of GSK3beta, and dephosphorylated Akt, the upstream signaling component of GSK3beta. Protein phosphatase 2A (PP2A), an ER stress-responsive phosphatase, was involved in 6-OHDA-induced GSK3beta dephosphorylation (Ser9). Blocking GSK3beta activity by selective inhibitors (lithium, TDZD-8, and L803-mts) prevented 6-OHDA-induced cleavage of caspase-3 and poly(ADP-ribose) polymerase (PARP), DNA fragmentations and cell death. With a tetracycline (Tet)-controlled TrkB inducible system, we demonstrated that activation of TrkB in SH-SY5Y cells alleviated 6-OHDA-induced GSK3beta dephosphorylation (Ser9) and ameliorated 6-OHDA neurotoxicity. TrkB activation also protected CGNs against 6-OHDA-induced damage. Although antioxidants also offered neuroprotection, they had little effect on 6-OHDA-induced GSK3beta activation. These results suggest that GSK3beta is a critical intermediate in pro-apoptotic signaling cascades that are associated with neurodegenerative diseases, thus providing a potential target site amenable to pharmacological intervention.
Ubiquitin Cross-Reactive Protein is Released by the Bovine Uterus in Response to Interferon during Early Pregnancy1 (1996)

A 16-kDa protein has been identified that is secreted by the bovine endometrium in response to conceptus-derived interferon (IFN)-tau during early pregnancy. Because this uterine protein was similar in size to a human ubiquitin cross-reactive protein (hUCRP) that also was regulated by IFN, we suspected that they might be related. To test this hypothesis, uterine flushings, medium from cultured endometrium, and endometrial tissues were examined for the presence of ubiquitin-immunoreactive proteins. Immunoreacting proteins were detected through use of one-dimensional (1D)-PAGE and Western blotting with ubiquitin and hUCRP antiserum (1:500). A 16-kDa protein that cross-reacted with ubiquitin and hUCRP antisera was released by the endometrium and was present in uterine flushings from all Day 18 pregnant females examined (n = 12). The immunoreacting 16-kDa protein was absent in all nonpregnant females examined (n = 23). Regulation of this uterine protein by recombinant type I IFNs (rbIFN-tau, rbIFN-alpha, and roIFN-tau), using 0, 0.5, 5, and 25 nm of each IFN, was evaluated in nonpregnant (Day 12) heifers (n = 5) using 1D-PAGE and Western blotting. Release of the 16-kDa protein into medium was negligible in controls (0 nm IFN). For each IFN, a dose-dependent increase (p < 0.05) in release of the immunoreacting 16-kDa protein was noted. We conclude that the 16-kDa protein that is produced by the endometrium in response to IFN-tau during early pregnancy also shares epitopes with hUCRP and ubiquitin. The 16-kDa protein has been named bovine UCRP.
Lysophosphatidylcholine impairs endothelial barrier function through the G protein-coupled receptor GPR4 (2006)

Abundant evidence indicates that lysophosphatidylcholine (LPC) is proinflammatory and atherogenic. In the vascular endothelium, LPC increases permeability and expression of proinflammatory molecules such as adhesion molecules and cytokines. Yet, mechanisms by which LPC mediates these activities remain unclear and controversial. Recent evidence implicates involvement of a novel subfamily of G protein-coupled receptors (GPR4, G2A, OGR1, and TDAG8) that are sensitive to lysolipids and protons. We previously reported that one of these receptors, GPR4, is selectively expressed by a variety of endothelial cells and therefore hypothesize that the LPC-stimulated endothelial barrier dysfunction is mediated through GPR4. We developed a peptide Ab against GPR4 that detected GPR4 expression in transfected COS 7 cells and endogenous GPR4 expression in endothelial cells by Western blot. Endothelial cells infected with a retrovirus containing small interference RNA (siRNA) to GPR4 resulted in 40-50% decreased GPR4 expression, which corresponded with partial prevention of the LPC-induced 1) decrease in transendothelial resistance, 2) stress fiber formation, and 3) activation of RhoA. Furthermore, coexpression of the siRNA-GPR4 with a siRNA-resistant mutant GPR4 fully restored the LPC-induced resistance decrease. However, extracellular pH of <7.4 did not alter baseline or LPC-stimulated resistances. The results provide strong evidence that the LPC-mediated endothelial barrier dysfunction is regulated by endogenous GPR4 in endothelial cells and suggest that GPR4 may play a critical role in the inflammatory responses activated by LPC.
P2‐428: Methylthioninium chloride versus rivastigmine and their co‐administration efficacy in reversing scopolamine‐induced cognitive deficits in a pharmacological mouse model of Alzheimer's disease (2008)

The involvement of the cholinergic system in cognition as well as its role in age-related cognitive decline and Alzheimer disease (AD) has been extensively studied. Cholinergic enhancers, such as acetyl cholinesterase inhibitors (AChEIs), are used for temporary symptomatic treatment of AD. AChEIs, however, improve only certain symptoms and do so for a limited period, without affecting underlying disease progression. Methylthioninium chloride (MTC) is an inhibitor of tau aggregation and, in addition, has a broad range of potential biological actions, including antioxidant and metabolic-enhancing activities. We have examined its activity in relation to the AChEI, rivastigmine (Exelon®) MTC was tested for its anti-amnesic abilities in a pharmacological model of AD in which amnesia was induced by acute administration of scopolamine in wild-type mice. Their spatial learning and memory were tested in the water maze, a task that assesses hippocampal-dependent cognition, which is impaired in AD. MTC was administered after scopolamine either at a fully effective dose or at a sub-effective dose co-administered with rivastigmine. MTC, on a weight basis, was less toxic and more effective than rivastigmine when the drugs were administered singly after scopolamine. Although rivastigmine only reversed the scopolamine-induced deficits in learning, MTC reversed both short- and long-term memory in addition to the learning deficits. Co-administration of sub-effective doses of rivastigmine and MTC elicited a temporal synergy in reversing learning deficits and a full reversal of scopolamine-induced memory impairments at subefficacy doses for each drug individually. There were no non-specific side effects of MTC in this paradigm. The study indicates that MTC, in addition to its activity as a Tau Aggregation Inhibitor, also has symptomatic activity. It is able to reverse a pharmacological cholinergic deficit and is more affective in this respect than an established AChEI. When combined with the AChEI, the symptomatic efficacy of MTC was enhanced.
Coronavirus IBV: Structural Characterization of the Spike Protein (1983)

The spike protein (S; surface projection) of avian infectious bronchitis virus (IBV) strain M41 comprises two glycopolypeptides, S1 (mol. wt. 90 X 10(3] and S2 (mol. wt. 84 X 10(3], in equimolar proportions. The apparent mol. wt. of S was calculated as 354 (+/- 17) X 10(3) following co-sedimentation with catalase in sucrose gradients. Incubation of radiolabelled IBV with urea resulted in the removal of most S1, but none of S2, from the virus particle. A similar result was obtained using low concentrations of SDS, although some nucleocapsid, but not matrix, protein was also released. 2% SDS alone was as effective as 2% SDS plus 2% 2-mercaptoethanol for the separation of S1 and S2 prior to SDS-polyacrylamide gel electrophoresis. Dithiothreitol did not remove S from virions but did decrease the buoyant density of the virus from 1.18 g/ml to 1.16 g/ml, and changed the configuration of S. It is concluded that IBV S protein is an oligomer comprising two copies of each of S1 and S2, although the possibility that there are three copies of each glycopolypeptide cannot be discounted. S is attached to the membrane by S2, while S1 has little or no contact with the membrane and may form the major part of the bulbous end of S. Interpeptide disulphide bonds do not occur in S, and the association of S1 and S2 is weak.
The virR gene, a member of a class of two-component response regulators, regulates the production of perfringolysin O, collagenase, and hemagglutinin in Clostridium perfringens (1994)

The perfringolysin O (theta-toxin) gene (pfoA) of Clostridium perfringens was cloned into an Escherichia coli-C. perfringens shuttle vector, and the pfoA gene was expressed in mutants of C. perfringens 13 which lacked the production of perfringolysin O. One group (SI117) could express the pfoA gene, and the other (SI112) could not. A mutation in the regulatory system for pfoA gene expression was suspected in SI112. A chromosomal DNA library constructed from strain 13 was transformed into strain SI112 to identify the regulatory gene(s) for the pfoA gene. Five strains of 10,000 transformants restored perfringolysin O production. All contained a 2.5-kb DNA fragment. This fragment activated the transcription of the pfoA gene and also restored the production of collagenase (kappa-toxin) and hemagglutinin in strain SI112. Deletion analysis showed that a 1.25-kb region was sufficient for the trans activity, and sequence analysis disclosed that open reading frame 2 (ORF2) was located in this region. A homology search for the deduced amino acid sequence revealed that ORF2 was homologous to a response regulator in a two-component signal transduction system. ORF2 was designated virR, and it is suggested that the virR gene plays an important role in the pathogenicity of C. perfringens.
TiO2−Graphene Nanocomposites for Gas-Phase Photocatalytic Degradation of Volatile Aromatic Pollutant: Is TiO2−Graphene Truly Different from Other TiO2−Carbon Composite Materials? (2010)

The nanocomposites of TiO(2)-graphene (TiO(2)-GR) have been prepared via a facile hydrothermal reaction of graphene oxide and TiO(2) in an ethanol-water solvent. We show that such a TiO(2)-GR nanocomposite exhibits much higher photocatalytic activity and stability than bare TiO(2) toward the gas-phase degradation of benzene, a volatile aromatic pollutant in air. By investigating the effect of different addition ratios of graphene on the photocatalytic activity of TiO(2)-GR systematically, we find that the higher weight ratio in TiO(2)-GR will decrease the photocatalytic activity. Analogous phenomenon is also observed for the liquid-phase degradation of dyes over TiO(2)-GR. In addition, the key features for TiO(2)-GR including enhancement of adsorptivity of pollutants, light absorption intensity, electron-hole pairs lifetime, and extended light absorption range have also been found in the composite of TiO(2) and carbon nanotubes (TiO(2)-CNT). These strongly manifest that TiO(2)-GR is in essence the same as other TiO(2)-carbon (carbon nanotubes, fullerenes, and activated carbon) composite materials on enhancement of photocatalytic activity of TiO(2), although graphene by itself has unique structural and electronic properties. Notably, this key fundamental question remains completely unaddressed in a recent report ( ACS Nano 2010 , 4 , 380 ) regarding liquid-phase degradation of dyes over the TiO(2)-GR photocatalyst. Thus, we propose that TiO(2)-GR cannot provide truly new insights into the fabrication of TiO(2)-carbon composite as high-performance photocatalysts. It is hoped that our work could avert the misleading message to the readership, hence offering a valuable source of reference on fabricating TiO(2)-carbon composites for their application as a photocatalyst in the environment cleanup.
Tuning Orbital Energetics in Arylene Diimide Semiconductors. Materials Design for Ambient Stability of n-Type Charge Transport (2007)

Structural and electronic criteria for ambient stability in n-type organic materials for organic field-effect transistors (OFETs) are investigated by systematically varying LUMO energetics and molecular substituents of arylene diimide-based materials. Six OFETs on n+-Si/SiO2 substrates exhibit OFET response parameters as follows: N,N'-bis(n-octyl)perylene-3,4:9,10-bis(dicarboximide) (PDI-8): mu = 0.32 cm2 V(-1) s(-1), Vth = 55 V, I(on)/I(off) = 10(5); N,N'-bis(n-octyl)-1,7- and N,N'-bis(n-octyl)-1,6-dibromoperylene-3,4:9,10-bis(dicarboximide) (PDI-8Br2): mu = 3 x 10(-5) cm2 V(-1) s(-1), Vth = 62 V, I(on)/I(off) = 10(3); N,N'-bis(n-octyl)-1,6,7,12-tetrachloroperylene-3,4:9,10-bis(dicarboximide) (PDI-8Cl4): mu = 4 x 10(-3) cm2 V(-1) (s-1), Vth = 37 V, I(on)/I(off) = 10(4); N,N'-bis(n-octyl)-2-cyanonaphthalene-1,4,5,8-bis(dicarboximide) (NDI-8CN): mu = 4.7 x 10(-3) cm2 V(-1) s(-1), Vth = 28, I(on)/I(off) = 10(5); N,N'-bis(n-octyl)-1,7- and N,N'-bis(n-octyl)-1,6-dicyanoperylene-3,4:9,10-bis(dicarboximide) (PDI-8CN2): mu = 0.13 cm2 V(-1) s(-1), Vth = -14 V, I(on)/I(off) = 10(3); and N,N'-bis(n-octyl)-2,6-dicyanonaphthalene-1,4,5,8-bis(dicarboximide) (NDI-8CN2): mu = 0.15 cm2 V(-1) s(-1), Vth = -37 V, I(on)/I(off) = 10(2). Analysis of the molecular geometries and energetics in these materials reveals a correlation between electron mobility and substituent-induced arylene core distortion, while Vth and I(off) are generally affected by LUMO energetics. Our findings also indicate that resistance to ambient charge carrier trapping observed in films of N-(n-octyl)arylene diimides occurs at a molecular reduction potential more positive than approximately -0.1 V (vs SCE). OFET threshold voltage shifts between vacuum and ambient atmosphere operation suggest that, at E(red1) < -0.1 V, the interfacial trap density increases by greater than approximately 1 x 10(13) cm(-2), while, for semiconductors with E(red1) > -0.1 V, the trap density increase is negligible. OFETs fabricated with the present n-type materials having E(red1) > -0.1 V operate at conventional gate biases with minimal hysteresis in air. This reduction potential corresponds to an overpotential for the reaction of the charge carriers with O2 of approximately 0.6 V. N,N'-1H,1H-Perfluorobutyl derivatives of the perylene-based semiconductors were also synthesized and used to fabricate OFETs, resulting in air-stable devices for all fluorocarbon-substituted materials, despite generally having E(red1) < -0.1 V. This behavior is consistent with a fluorocarbon-based O2 barrier mechanism. OFET cycling measurements in air for dicyanated vs fluorinated materials demonstrate that energetic stabilization of the charge carriers results in greater device longevity in comparison to the OFET degradation observed in air-stable semiconductors with fluorocarbon barriers.
Ray casting of multiple volumetric datasets with polyhedral boundaries on manycore GPUs (2009)

We present a new GPU-based rendering system for ray casting of multiple volumes. Our approach supports a large number of volumes, complex translucent and concave polyhedral objects as well as CSG intersections of volumes and geometry in any combination. The system (including the rasterization stage) is implemented entirely in CUDA, which allows full control of the memory hierarchy, in particular access to high bandwidth and low latency shared memory. High depth complexity, which is problematic for conventional approaches based on depth peeling, can be handled successfully. As far as we know, our approach is the first framework for multivolume rendering which provides interactive frame rates when concurrently rendering more than 50 arbitrarily overlapping volumes on current graphics hardware.
Local Parallel Computation of Stochastic Completion Fields (1997)

We describe a local parallel method for computing the stochastic completion field introduced in the previous article (Williams and Jacobs, 1997). The stochastic completion field represents the likelihood that a completion joining two contour fragments passes through any given position and orientation in the image plane. It is based on the assumption that the prior probability distribution of completion shape can be modeled as a random walk in a lattice of discrete positions and orientations. The local parallel method can be interpreted as a stable finite difference scheme for solving the underlying Fokker-Planck equation identified by Mumford (1994). The resulting algorithm is significantly faster than the previously employed method, which relied on convolution with large-kernel filters computed by Monte Carlo simulation. The complexity of the new method is O (n 3 m), while that of the previous algorithm was O(n 4 m 2 (for an n × n image with m discrete orientations). Perhaps most significant, the use of a local method allows us to model the probability distribution of completion shape using stochastic processes that are neither homogeneous nor isotropic. For example, it is possible to modulate particle decay rate by a directional function of local image brightnesses (i.e., anisotropic decay). The effect is that illusory contours can be made to respect the local image brightness structure. Finally, we note that the new method is more plausible as a neural model since (1) unlike the previous method, it can be computed in a sparse, locally connected network, and (2) the network dynamics are consistent with psychophysical measurements of the time course of illusory contour formation.
cDNA sequences of two inducible T-cell genes. (1989)

We have previously described a set of human T-lymphocyte-specific cDNA clones isolated by a modified differential screening procedure. Apparent full-length cDNAs containing the sequences of 14 of the 16 initial isolates were sequenced and were found to represent five different species of mRNA; three of the five species were identical to previously reported cDNA sequences of preproenkephalin, T-cell-replacing factor, and a serine esterase, respectively. The other two species, 4-1BB and L2G25B, were inducible sequences found in mRNA from both a cytolytic T-lymphocyte and a helper T-lymphocyte clone and were not previously described in T-cell mRNA; these mRNA sequences encode peptides of 256 and 92 amino acids, respectively. Both peptides contain putative leader sequences. The protein encoded by 4-1BB also has a potential membrane anchor segment and other features also seen in known receptor proteins.
Synthesis of clustered D-GalNAc (Tn) and D-Galβ(1→3)GalNAc (T) antigenic motifs using a pentaerythritol scaffold (1996)

The tris(aminoethyl) and triamino derivatives of pentaerythritol have been used as scaffolds or templates for the attachment of immunologically relevant carbohydrates such as D-Galβ(1→3)GalNAc (T) and GalNAc (Tn), through amide linkages with the respective α-glycolyl and α-N-acetyl-L-serinyl glycosides. These clustered glycosidic motifs are intended as haptens for use in the preparation of tumor specific carbohydrate antigens and vaccines. Key words: glycoside synthesis, 2-thiopyridyl carbonate, glycosyl donors and glycopeptide motifs
The physics of block copolymers (1999)

1. Introduction 2. Melt Phase Behaviour of Block Copolymers 3. Block Copolymers in Dilute Solution 4. Block Copolymers in Semidilute and Concentrated Solutions 5. Solid State Structure of Block Copolymers 6. Blends Containing Block Copolymers Appendix: The Self Consistent Field Theory