gebhart/patrepeval huggingface dataset:
Nitric oxide prevents 6‐hydroxydopamine‐induced apoptosis in PC12 cells through cGMP‐dependent PI3 kinase/Akt activation (2003)

Nitric oxide (NO) functions not only as an important signaling molecule in the brain by producing cGMP, but also regulates neuronal cell apoptosis. The mechanism by which NO regulates apoptosis is unclear. In this study, we demonstrated that NO, produced either from the NO donor S-nitroso-N-acetyl-d,l-penicillamine (SNAP) or by transfection of neuronal NO synthase, suppressed 6-hydroxydopamine (6-OHDA)-induced apoptosis in PC12 cells by inhibiting mitochondrial cytochrome c release, caspase-3 and -9 activation, and DNA fragmentation. This protection was significantly reversed by the soluble guanylyl cyclase inhibitor 1H-(1,2,4)-oxadiazole[4,3-a]quinoxalon-1-one, indicating that cGMP is a key mediator in NO-mediated anti-apoptosis. Moreover, the membrane-permeable cGMP analog 8-Br-cGMP inhibited 6-OHDA-induced apoptosis. These anti-apoptotic effects of SNAP and 8-Br-cGMP were suppressed by cGMP-dependent protein kinase G (PKG) inhibitor KT5823, indicating that PKG is a downstream signal mediator in the suppression of apoptosis by NO and cGMP. Both SNAP and 8-Br-cGMP induced endogenous Akt activation and Bad phosphorylation, resulting in the inhibition of Bad translocation to mitochondria; these effects were inhibited by KT5823 and the phosphatidylinositol 3-kinase (PI3K) inhibitors LY294002 and Wortmannin. Our data suggest that the NO/cGMP pathway suppresses 6-OHDA-induced PC12 cell apoptosis by suppressing the mitochondrial apoptosis signal via PKG/PI3K/Akt-dependent Bad phosphorylation.
Prenylation-dependent Association of Protein-tyrosine Phosphatases PRL-1, -2, and -3 with the Plasma Membrane and the Early Endosome (2000)

PRL-1, -2, and -3 represent a novel class of protein-tyrosine phosphatase with a C-terminal prenylation motif. Although PRL-1 has been suggested to be associated with the nucleus, the presence of three highly homologous members and the existence of a prenylation motif call for a more detailed examination of their subcellular localization. In the present study, we first demonstrate that mouse PRL-1, -2, and -3 are indeed prenylated. Examination of N-terminal epitope-tagged PRL-1, -2, and -3 expressed in transiently transfected cells suggests that PRL-1, -2, and -3 are present on the plasma membrane and intracellular punctate structures. Stable Chinese hamster ovary cells expressing PRL-1 and -3 in an inducible manner were established. When cells were treated with brefeldin A, PRL-1 and -3 accumulated in a collapsed compact structure around the microtubule-organizing center. Furthermore, PRL-1 and -3 redistributed into swollen vacuole-like structures when cells were treated with wortmannin. These characteristics of PRL-1 and -3 are typical for endosomal proteins. Electron microscope immunogold labeling reveals that PRL-1 and -3 are indeed associated with the plasma membrane and the early endosomal compartment. Expression of PRL-3 is detected in the epithelial cells of the small intestine, where PRL-3 is present in punctate structures in the cytoplasm. When cells are treated with FTI-277, a selective farnesyltransferase inhibitor, PRL-1, -2, and -3 shifted into the nucleus. Furthermore, a mutant form of PRL-2 lacking the C-terminal prenylation signal is associated with the nucleus. These results establish that the primary association of PRL-1, -2, and -3 with the membrane of the cell surface and the early endosome is dependent on their prenylation and that nuclear localization of these proteins may be triggered by a regulatory event that inhibits their prenylation.
Second-generation plasminogen activators (1987)

Journal Article Second-generation plasminogen activators Get access T.J.R. Harris T.J.R. Harris Molecular Biology, Celltech Ltd216 Bath Road, Slough SL1 4EN, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Protein Engineering, Design and Selection, Volume 1, Issue 6, 1987, Pages 449–458, https://doi.org/10.1093/protein/1.6.449 Published: 01 June 1987
Imitating driver behavior with generative adversarial networks (2017)

The ability to accurately predict and simulate human driving behavior is critical for the development of intelligent transportation systems. Traditional modeling methods have employed simple parametric models and behavioral cloning. This paper adopts a method for overcoming the problem of cascading errors inherent in prior approaches, resulting in realistic behavior that is robust to trajectory perturbations. We extend Generative Adversarial Imitation Learning to the training of recurrent policies, and we demonstrate that our model rivals rule-based controllers and maximum likelihood models in realistic highway simulations. Our model both reproduces emergent behavior of human drivers, such as lane change rate, while maintaining realistic control over long time horizons.
Insertion of a Structural Domain of Interleukin (IL)-1β Confers Agonist Activity to the IL-1 Receptor Antagonist (1995)

We showed previously that replacement of Lys-145 in the IL-1 receptor antagonist (IL-1ra) with Asp resulted in an analog (IL-1ra K145D) with partial agonist activity. To identify additional amino acids that affect IL-1 bioactivity, we created second site mutations in IL-1ra K145D. Substitutions of single amino acids surrounding position 145 were made; none of these substitutions increased the bioactivity of IL-1ra K145D. However, the insertion of the beta-bulge (QGEESN) of IL-1 beta at the corresponding region of IL-1ra K145D resulted in a 3-4-fold augmentation of bioactivity. An additional increase in agonist activity was observed when the beta-bulge was co-expressed with a second substitution (His-54 --> Pro) in IL-1ra K145D. We also show that the bioactivity of both IL-1ra K145D and the triple mutant IL-1ra K145D/H54P/QGEESN is dependent on interaction with the newly cloned IL-1 receptor accessory protein.
Local cosine bases in two dimensions (1997)

We construct two-dimensional (2-D) local cosine bases in discrete time. Solutions are offered both for rectangular and nonrectangular lattices. In the case of nonrectangular lattices, the problem is solved by mapping it into a one-dimensional (1-D) equivalent problem.
Naturally occurring T-cell response against mutated p21 ras oncoprotein in pancreatic cancer. (2006)

Mutated p21 ras proteins (muRas) are present in approximately 90% of pancreatic adenocarcinomas and express mutants which can function as cancer-specific antigens. To evaluate the frequency and magnitude of the natural T-cell response against muRas in 19 HLA-A2-positive patients with muRas-positive pancreatic carcinomas, antigen-experienced T lymphocytes in fresh peripheral blood mononuclear cells were shown by IFN-gamma enzyme-linked immunospot using muRas peptides (5-21) that encompass both HLA class I (HLA-A2)- and class II-restricted (HLA-DRB1) epitopes. Six of 19 patients (32%) were found to have a specific T-cell response against individual mutation-specific ras(5-21) but not against other ras mutations or wild-type ras. In contrast, none of 19 healthy subjects had T cells specifically secreting IFN-gamma (P = 0.004). The T-cell response consisted of both CD8(+) and CD4(+) T cells but was dominated by CD8 T cells in three of four patients. MuRas(5-14) and muRas(6-14) were shown to specifically induce CD8(+) T-cell mediated cytotoxicity against HLA-A2-positive, muRas-bearing pancreatic carcinoma cells. The T-cell response was not correlated with prognostic or clinical variables such as tumor-node-metastasis status, stage, or survival. In conclusion, a natural T-cell response against muRas proteins that could be exploited for immunostimulatory therapeutic approaches has been shown in a significant proportion of patients with pancreatic cancer.
Extent of Linkage Disequilibrium in Holstein Cattle in North America (2008)

The success of fine-scale mapping and genomic selection depends mainly on the strength of linkage disequilibrium (LD) between markers and causal mutations. With Lewontin's measure of LD (known as D'), high levels of LD that extend over several million base pairs have been reported in livestock. However, this measure of LD can be strongly biased upward by small samples and by low allele frequencies. The aim of this study was to characterize the level and extent of LD in Holstein cattle in North America (Canada and the United States for purposes of this study) by using the squared correlation of the alleles at 2 loci (r(2)). The Affymetrix MegAllele GeneChip Bovine Mapping 10K single nucleotide polymorphism (SNP) array was used to genotype 821 bulls, from which 497 were used in the analysis of the extent of LD. A total of 5,564 SNP were used after filtering out SNP with more than 5% of Mendelian inconsistencies, with more than 20% missing genotypes, or with a minor allele frequency of less than 10%. Analysis of syntenic pairs revealed that useful LD (measured as r(2) > 0.3) occurred at distances shorter than 100 kb. Linkage disequilibrium decayed very rapidly, within a few hundred kilobase pairs. In addition, no substantial LD between unlinked loci was found. Using a sliding window analysis, we observed an irregular pattern of LD across the genome. These findings suggest that to capture useful LD, which is required for whole-genome fine mapping and genomic selection, a denser SNP map would be needed.
Effect of Adjuvant Chemotherapy on Integrity of Free Serum DNA in Patients with Breast Cancer (2008)

It is not known how chemotherapy-induced cell death influences the size distribution of circulating free DNA (cf-DNA) in serum or plasma of cancer patients. In the present study, we investigated the integrity of cf-DNA during adjuvant systemic therapy in patients (n= 41) with invasive breast cancer. Sera taken at the beginning and the end of the adjuvant chemotherapy were comparatively analyzed for the integrity of cf-DNA. The assay was based on quantification of shorter and longer fragments representing apoptotic or non-apoptotic DNA from abundant genomic ALU repeats by quantitative real-time PCR. The ratio of longer to shorter fragments showed the integrity of free serum DNA. During chemotherapy, in half of the patients (51.2%), total DNA levels increased, but decreased in the other half. The distribution of the DNA integrity in the whole patient group after the systemic therapy (median 0.31) did not significantly differ from that at the beginning (median 0.29, P= 0.39). However, in the subgroups, the variation of the DNA integrity was related to the course of the total DNA level. In the subgroup with an increasing DNA level, the median DNA integrity was elevated from 0.27 to 0.39 (P= 0.005), whereas in the group with a decrease it declined from 0.34 to 0.28 (P= 0.044). Our results show that longer fragments released from non-apoptotic cells are the main contributors to increasing DNA levels during adjuvant systemic therapy. This information might be helpful in evaluating the response of patients to adjuvant systemic therapy.
Porphycene—a Novel Porphin Isomer (1986)

Examination of the porhyrins from the viewpoint of the “annulene chemist” has led to the discovery of the novel, simple porphin isomer porphycene 2. The path from conception to the synthesis of the molecule was surprisingly short. 2 is formed as a stable compound upon McMurry reaction of 1.
RNase1 prevents the damaging interplay between extracellular RNA and tumour necrosis factor-α in cardiac ischaemia/reperfusion injury (2014)

Despite optimal therapy, the morbidity and mortality of patients presenting with an acute myocardial infarction (MI) remain significant, and the initial mechanistic trigger of myocardial "ischaemia/reperfusion (I/R) injury" remains greatly unexplained. Here we show that factors released from the damaged cardiac tissue itself, in particular extracellular RNA (eRNA) and tumour-necrosis-factor α (TNF-α), may dictate I/R injury. In an experimental in vivo mouse model of myocardial I/R as well as in the isolated I/R Langendorff-perfused rat heart, cardiomyocyte death was induced by eRNA and TNF-α. Moreover, TNF-α promoted further eRNA release especially under hypoxia, feeding a vicious cell damaging cycle during I/R with the massive production of oxygen radicals, mitochondrial obstruction, decrease in antioxidant enzymes and decline of cardiomyocyte functions. The administration of RNase1 significantly decreased myocardial infarction in both experimental models. This regimen allowed the reduction in cytokine release, normalisation of antioxidant enzymes as well as preservation of cardiac tissue. Thus, RNase1 administration provides a novel therapeutic regimen to interfere with the adverse eRNA-TNF-α interplay and significantly reduces or prevents the pathological outcome of ischaemic heart disease.
KESTREL: a powerful method for identifying the physiological substrates of protein kinases (2005)

The identification of all the substrates of every protein kinase is one of the major challenges of post-genomic research. Here we review a powerful method for tackling this problem that we have developed over the last 5 years. The method has so far been used to identify novel substrates for eight different protein kinases, demonstrating that it is of general utility. Importantly, the method can be used to identify distinct physiological substrates of protein kinases, such as PKB (protein kinase B) and SGK (serum- and glucocorticoid-induced kinase), that are closely related in structure and have similar specificity determinants.
RFID-ENABLED CAPABILITIES AND THEIR IMPACT ON HEALTHCARE PROCESS PERFORMANCE (2010)

In recent years, hospitals have begun to invest in RFID systems to control costs, reduce errors, and improve quality of care. Despite the transformative impact that RFID may have in healthcare settings, few studies have examined how and why this change may occur. The purpose of this study is to systematically understand how RFID can transform work practices and address cost, safety, and quality of care issues, most notably in inventory management. We leverage a sociomateriality framework to explore the causal linkages that connect the material properties of RFID with the behavioral changes that are observed through its use. By linking the material properties of RFID with innovations in existing practices, we provide a data-driven account of how and why RFID is useful in this setting. In doing so, we also contribute to recent work by IS scholars who argue for a reconfiguration of conventional assumptions regarding the role of technology in contemporary organizations. By adopting this perspective, we recast the issue of whether or not IT matters, and instead offer interesting and useful insight into how and why it does.
Amyloid-β Deposition Is Associated with Decreased Hippocampal Glucose Metabolism and Spatial Memory Impairment in APP/PS1 Mice (2004)

In Alzheimer disease (AD) patients, early memory dysfunction is associated with glucose hypometabolism and neuronal loss in the hippocampus. Double transgenic (Tg) mice co-expressing the M146L presenilin 1 (PS1) and K670N/M671L, the double "Swedish" amyloid precursor protein (APP) mutations, are a model of AD amyloid-beta deposition (Abeta) that exhibits earlier and more profound impairments of working memory and learning than single APP mutant mice. In this study we compared performance on spatial memory tests, regional glucose metabolism, Abeta deposition, and neuronal loss in APP/PS1, PS1, and non-Tg (nTg) mice. At the age of 2 months no significant morphological and metabolic differences were detected between 3 studied genotypes. By 8 months, however, APP/PS1 mice developed selective impairment of spatial memory, which was significantly worse at 22 months and was accompanied by reduced glucose utilization in the hippocampus and a 35.8% dropout of neurons in the CA1 region. PS1 mice exhibited a similar degree of neuronal loss in CA1 but minimal memory deficit and no impairment of glucose utilization compared to nTg mice. Deficits in 22 month APP/PS1 mice were accompanied by a substantially elevated Abeta load, which rose from 2.5% +/- 0.4% at 8 months to 17.4% +/- 4.6%. These findings implicate Abeta or APP in the behavioral and metabolic impairments in APP/PS1 mice and the failure to compensate functionally for PS1-related hippocampal cell loss.
HIV protease inhibitors: effects on viral maturation and physiologic function in macrophages (1994)

Human immunodeficiency virus (HIV), the retrovirus believed to be the cause of acquired immunodeficiency syndrome (AIDS), infects a variety of CD4+ cells, including lymphocytes and cells of the monocyte/macrophage lineage. Encoded in the HIV genome are several precursor proteins that must undergo proteolytic cleavage to yield functional proteins. The gag precursor protein of HIV (p55) is cleaved by a virally encoded aspartate protease (HIV protease). Because cleavage of p55 is required for viral maturation and infectivity, inhibition of HIV protease is an attractive target for therapy designed to block the progression of HIV infection. Inhibitors of HIV protease from a variety of chemical classes have been synthesized and antiviral activity has been demonstrated in lymphocytes and cells from the monocyte/macrophage lineage. A few HIV protease inhibitors have progressed to the clinic and some have shown promise in early trials. There are, however, several important issues that will affect the development of a successful HIV protease inhibitor, including cell and tissue distribution and immunotoxicity. These issues are tissue distribution and immunotoxicity. These issues are discussed, with an emphasis on the complexities posed by cells of the monocyte/macrophage lineage.
Perfluorocyclobutane‐Based Arylamine Hole‐Transporting Materials for Organic and Polymer Light‐Emitting Diodes (2002)

Abstract A series of in‐situ thermally polymerizable hole‐transporting materials based on the triarylamine‐containing perfluorocyclobutanes (PFCBs) have been developed and characterized. Electrochemical studies reveal that the energy level of the highest occupied molecular orbital (HOMO) for these materials is between –5.1 and –5.3 eV, which is a good match for the work function of indium tin oxide (ITO), a commonly used anode for organic and polymeric light‐emitting diodes. UV‐vis absorption, photo‐ and electro‐luminescence spectral studies indicate that aggregates are formed during the thermal polymerization. The PFCB‐based materials are very robust after polymerization, which enables the fabrication of multilayer polymer light‐emitting diodes. Highly efficient organic and polymer LEDs are demonstrated using these materials as the hole‐transporting layer, illustrating the superb performance of the PFCB‐based polymers.
Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene Duplications (2009)

Phylogenomic analyses show that gene and genome duplication events have led to the diversification of transcription factor gene families throughout the evolutionary history of land plants and that gene duplications have played an important role in shaping regulatory networks influencing key phenotypic characters including floral development and flowering time. A molecular evolutionary investigation of the mode and tempo of selection acting on the angiosperm MADS box AP1/SQUA, AP3/PI, AG/AGL11, and SEP gene subfamilies revealed site-specific patterns of shifting evolutionary constraint throughout angiosperm history. Specific positions in the four canonical MADS box gene regions, especially K domains and C-terminal regions of all four of these MADS box gene subfamilies exhibited clade-specific shifts in selective constraint following concerted duplication events. Moreover, the frequency of site-specific shifts in constraint was correlated with gene duplications and early angiosperm diversification. We hypothesize that coevolution among interacting MADS box proteins may be responsible for simultaneous increases in the ratio of nonsynonymous to synonymous substitutions (dN/dS = ω) early in angiosperm history and following concerted duplication events.
Chiral Ansa Metallocenes with Cp Ring-Fused to Thiophenes and Pyrroles:  Syntheses, Crystal Structures, and Isotactic Polypropylene Catalysts (2001)

Syntheses, crystal structures, and polymerization data for new isospecific metallocenes (heterocenes) having cyclopentenyl ligands b-fused to substituted thiophenes (Tp) and pyrroles (Pyr) are reported. The C2- and C1-symmetric heterocenes are dimethylsilyl bridged, have methyl groups adjacent to the bridgehead carbon atoms, and have aryl substituents protruding in the front. rac-Me2Si(2,5-Me2-3-Ph-6-Cp[b]Tp)2ZrCl2/MAO (MAO = methyl alumoxanes) is the most active metallocene catalyst for polypropylene reported to date. rac-Me2Si(2,5-Me2-3-Ph-6-Cp[b]Tp)2ZrCl2 and rac-Me2Si(2,5-Me2-1-Ph-4-Cp[b]Pyr)2ZrCl2 have the same structure, and the former is 6 times more active, produces half the total enantiofacial errors, and is 3.5 times less regiospecific in propylene polymerizations at the same conditions. rac-Me2Si(2-Me-4-Ph-1-Ind)2ZrCl2/MAO is 3.5 times lower in activity than rac-Me2Si(2,5-Me2-3-Ph-6-Cp[b]Tp)2ZrCl2 catalyst, and while the former is the more stereospecific and the less regiospecific, the sum of these two enantioface errors is the same for both species. Fine-tuning the heterocene sterics by changing selected hydrogen atoms on the ligands to methyl groups influenced their catalyst activities, stereospecificites, regiospecificites, and isotactic polypropylene (IPP) Mw. Thus, both substituting a hydrogen atom adjacent to the phenyl ring with a methyl group on an azapentalenyl ligand system and replacing one and then two hydrogens on the phenyl ring with methyls on thiopentalenyl ligands provided increased polymer Tm and Mw with increasing ligand bulk. Polymer molecular weights are sensitive to and inversely proportional to MAO concentration, and the catalyst activities increase when hydrogen is added for molecular weight control. The polymer Tm values with the thiopentalenyls as TIBAL/[Ph3C][B(C6F5)4] systems were higher than with MAO as catalyst activator. A racemic C1, pseudo-meso complex with a hybrid dimethylsilyl-bridged 2-Me-4-Ph-1-Ind/2,5-Me2-4-Ph-1-Cp[b]Pyr ligand produced the first sample of IPP with all the steric pentad intensities fitting the enantiomorphic site control model. Speculative mechanistic considerations are offered regarding electronic effects of the heteroatoms and steric effects of the ligand structures, the preferred phenyl torsion angles, and anion effects.