gebhart/patrepeval huggingface dataset:
Low Cost Flywheel Energy Storage for a Fuel Cell Powered Transit Bus (2007)

This paper presents work that was performed to design a compact flywheel energy storage solution for a fuel cell powered transit bus with a focus on commercialization requirements. For hybrid vehicle applications, flywheels offer much higher power densities than conventional batteries. The presented design attempts to maximize the use of lower-cost technologies. The rotor relies primarily on steel for the flywheel structure, and emphasis is placed on size reduction for vehicle packaging advantages Simulations of bus configurations on measured routes was performed using PSAT to correctly size the flywheel energy storage system.
Jasmonate-Induced Nicotine Formation in Tobacco is Mediated by Tobacco COI1 and JAZ Genes (2008)

Biosynthesis of many plant alkaloids is enhanced by endogenous accumulation and exogenous application of jasmonates, but the general and specific signaling components are not well understood. In Arabidopsis, jasmonate-induced ZIM-domain-containing (JAZ) proteins have recently been found to be critical transcriptional repressors linking CORONATINE INSENSTIVE1 (COI1)-mediated jasmonate perception and jasmonate-regulated transcriptional regulation. Insect herbivory on tobacco leaves activates the jasmonate signaling pathway, leading to up-regulation of nicotine biosynthesis genes in roots. We show here that roots of COI1-silenced tobacco plants are insensitive to growth inhibition by methyl jasmonate, and do not activate nicotine biosynthesis genes after jasmonate treatment or wounding of leaves. Tobacco JAZ proteins appeared to be rapidly degraded after jasmonate treatment, whereas a C-terminally truncated form lacking the conserved Jas motif did not. When the non-degradable JAZ forms were expressed in tobacco hairy roots, jasmonate induction of nicotine biosynthesis was strongly inhibited. Formation of tobacco alkaloids in jasmonate-elicited tobacco BY-2 cells was also effectively suppressed by the COI1 RNAi (RNA interference) construct and by the dominant-negative truncated JAZ constructs. In addition, jasmonate-mediated induction of nicotine biosynthesis genes was diminished by treatment with a proteasome inhibitor MG132. These results indicate that jasmonate-triggered, COI1-mediated degradation of JAZ repressors activates transcriptional regulation of nicotine biosynthesis genes in tobacco roots.
Chemical synthesis of nitric oxide in the stomach from dietary nitrate in humans. (1997)

A very large and sustained increase in chemically derived gastric NO concentrations after an oral nitrate load was shown, which may be important both in host defence against swallowed pathogens and in gastric physiology.
Detecting pedestrians using patterns of motion and appearance (2003)

This paper describes a pedestrian detection system that integrates image intensity information with motion information. We use a detection style algorithm that scans a detector over two consecutive frames of a video sequence. The detector is trained (using AdaBoost) to take advantage of both motion and appearance information to detect a walking person. Past approaches have built detectors based on appearance information, but ours is the first to combine both sources of information in a single detector. The implementation described runs at about 4 frames/second, detects pedestrians at very small scales (as small as 20/spl times/15 pixels), and has a very low false positive rate. Our approach builds on the detection work of Viola and Jones. Novel contributions of this paper include: i) development of a representation of image motion which is extremely efficient, and ii) implementation of a state of the art pedestrian detection system which operates on low resolution images under difficult conditions (such as rain and snow).
Monoclonal antibody-defined epitope map of expressed rubella virus protein domains (1991)

An expanded library of murine monoclonal antibodies (MAbs) was generated by infecting BALB/C mice with the Therien strain of rubella virus (RV) and selecting secreting hybrids by enzyme-linked immunosorbent assay (ELISA) using purified virion targets. A panel of plasmids containing specified RV cDNA fragments was also constructed by using a variety of strategies with pGE374- and pGE374-derived expression vectors. Hybrid RecA-RV-beta-galactosidase (LacZ)- or RecA-RV-truncated LacZ-containing proteins collectively representing the entire open reading frame of the structural proteins of RV were overexpressed in Escherichia coli. Bacterial lysates were then probed by ELISA with selected MAbs and by immunoblot following separation by electrophoresis under denaturing conditions. With this approach, MAbs that appeared to react with linear determinants defined epitopes localized within the following domains: MAbs C-1, C-2, and C-8 bind epitopes within the predicted amino-terminal 21 amino acids of the capsid region C9 to C29; MAb C-9 binds to a domain bounded by C64 and C97; MAbs E2-1 through E2-6 bind to the E2 glycoprotein backbone region from E2(1) to E2(115); MAbs E1-18 and E1-20 bind to the E1 glycoprotein region from E1(202) to E1(283). MAb E1-18 neutralizes RV infectivity; MAb E1-20 neutralizes infectivity and modestly inhibits hemagglutination. Analyses with selected synthetic peptides have confirmed several of the molecular domains deduced with the expressed proteins. These plasmid constructions and peptides have proven useful in beginning to unravel the molecular organization of several antigenic sites of this human pathogen.
Linkage of the Scrapie-associated Fibril Protein (PrP) Gene and Sinc Using Congenic Mice and Restriction Fragment Length Polymorphism Analysis (1987)

Sinc, with two alleles p7 and s7, is the major gene determining the incubation period of all strains of scrapie in mice. The major protein (PrP) of scrapie-associated fibrils is encoded by a cellular gene and we have used a cDNA copy of the hamster PrP mRNA to carry out restriction fragment length polymorphism (RFLP) analysis of different inbred mouse strains including VM(Sincp7) and VM(Sincs7) congenic mice. In VM(Sincp7) mice, a 5.5 kb XbaI fragment hybridized to the PrP cDNA sequence whereas VM(Sincs7) congenic mice had a 3.8 kb XbaI fragment. The VM X VM(Sincs7) congenic F1 mice had both the 5.5 kb and the 3.8 kb fragments. The Sincs7 donor mouse strain, C57BL, had the 3.8 kb fragment suggesting that the Sinc gene and the gene coding for PrP are linked, and could even be the same gene. Other Sincp7 inbred mice (IM and MB) had the 5.5 kb fragment but so too did some Sincs7 strains (RIII and VL), implying that the XbaI site polymorphism is not functionally involved in the difference between the two Sinc alleles. We have mapped the polymorphic XbaI site to the 3' flanking region of the PrP gene. TaqI and HhaI were also found to show polymorphisms in the inbred mouse strains studied. The apparent RFLP with HhaI may be a result of differences in methylation rather than in sequence.
Preeclampsia: The Role of Angiogenic Factors in Its Pathogenesis (2009)

Preeclampsia, a systemic syndrome of pregnancy clinically characterized by new onset of proteinuria and hypertension, is associated with significant morbidity and mortality to both mothers and fetuses. The pathogenesis of preeclampsia has been enigmatic; this review will focus on understanding the origins of this disorder. Preeclampsia originates in the placenta, starting with inadequate cytotrophoblast invasion and ending with widespread maternal endothelial dysfunction. Production of placental anti-angiogenic factors, specifically soluble fms-related tyrosine kinase 1 and soluble endoglin, have been shown to be upregulated in preeclampsia. These placental anti-angiogenic factors are released into the maternal circulation; their actions disrupt the maternal endothelium and result in hypertension, proteinuria, and the other systemic manifestations of preeclampsia. The molecular basis for placental dysregulation of these pathogenic factors remains unknown, remains unknown. Hypoxia is likely an important regulator. Other factors such as alterations in the renin-angiotensin-aldosterone axis, immune maladaption, excessive shedding of trophoblast debris, oxidative stress, and genetic factors likely contribute to the pathogenesis of the abnormal placentation. As of 2009, the only successful treatment for preeclampsia is delivery. No definitive preventive strategies have been identified. However, several of the recent observations related to phenotypic causality provide stimuli for the development of novel therapies.
Chondrocyte-mediated catabolism of aggrecan: aggrecanase-dependent cleavage induced by interleukin-1 or retinoic acid can be inhibited by glucosamine (1998)

A rat chondrosarcoma cell line and bovine cartilage explants have been used to study the control of aggrecan degradation by chondrocytes treated with interleukin-1 (IL-1) or retinoic acid (RA). Aggrecan fragment analysis with anti-neo-epitope antibodies suggests that aggrecanase (an as yet unidentified enzyme) is the only aggrecan-degrading proteinase active in these cultures. With rat cells, aggrecanase converts the aggrecan core protein into two major G1-domain-bearing products (60 kDa with a C-terminal Glu-373, and 220 kDa with a C-terminal Glu-1459). Both products were quantified on a standardized Western analysis system with a G1-specific antibody. Immunoblots were analysed by scanning densitometry and the sensitivity, linearity and reproducibility of the assay were established. With rat cells the aggrecanase response to IL-1 was optimal at about 2 mM glutamine, but was progressively inhibited at higher concentrations, with about 90% inhibition at 10 mM glutamine. Such inhibition by glutamine was not, however, observed with bovine explants. On the other hand, marked inhibition of aggrecanase-dependent cleavage was observed with both rat cells and bovine explants when d(+)-glucosamine was included at concentrations above 2 mM. Inhibition was apparently not due to cytotoxicity or interference with IL-1 signalling, since biosynthetic activity was not inhibited and inhibition of the aggrecanase response was also obtained when RA was used as the catabolic stimulator. Possible mechanisms for the inhibition of the aggrecanase response by glucosamine in chondrocytes treated with IL-1 or RA are discussed.
Synthese von Indol‐ und Carbazol‐Derivaten aus α‐Hydroxyketonen und aromatischen Aminen (1972)

Abstract Es werden die Anwendungsmöglichkeiten der Synthese von Indol‐ und Carbazol‐Derivaten durch Kondensation aromatischer Amine mit α‐Hydroxyketonen untersucht und die Struktur möglicher Isomere durch NMR‐Spektroskopie geklärt.
Colloidal silicon quantum dots: from preparation to the modification of self-assembled monolayers (SAMs) for bio-applications (2014)

Concerns over possible toxicities of conventional metal-containing quantum dots have inspired growing research interests in colloidal silicon nanocrystals (SiNCs), or silicon quantum dots (SiQDs). This is related to their potential applications in a number of fields such as solar cells, optoelectronic devices and fluorescent bio-labelling agents. The past decade has seen significant progress in the understanding of fundamental physics and surface properties of silicon nanocrystals. Such understanding is based on the advances in the preparation and characterization of surface passivated colloidal silicon nanocrystals. In this critical review, we summarize recent advances in the methods of preparing high quality silicon nanocrystals and strategies for forming self-assembled monolayers (SAMs), with a focus on their bio-applications. We highlight some of the major challenges that remain, as well as lessons learnt when working with silicon nanocrystals (239 references).
Site‐directed mutagenesis of the arginine‐glycine‐aspartic acid sequence in osteopontin destroys cell adhesion and migration functions (1995)

Osteopontin (OPN) is a secreted calcium-binding phosphoprotein produced in a variety of normal and pathological contexts, including tissue mineralization and cancer. OPN contains a conserved RGD (arg-gly-asp) amino acid sequence that has been implicated in binding of OPN to cell surface integrins. To determine whether the RGD sequence in OPN is required for adhesive and chemotactic functions, we have introduced two site-directed mutations in the RGD site of the mouse OPN cDNA, in which the RGD sequence was either deleted or mutated to RGE (arg-gly-glu). In order to test the effect of these mutations on OPN function, we expressed control and mutated mouse OPN in E. coli as recombinant glutathione-S-transferase (GST)-OPN fusion proteins. Control mouse GST-OPN was functional in cell adhesion assays, supporting attachment and spreading of mouse (malignant PAP2 ras-transformed NIH 3T3, and, to a lesser extent, normal NIH 3T3 fibroblasts) and human (MDA-MB-435 breast cancer, and normal gingival fibroblast) cells. In contrast, neither of the RGD-mutated OPN proteins ("delRGD" or "RGE") supported adhesion of any of the cell lines, even when used at high concentrations or for long assay times. GRGDS (gly-arg-gly-asp-ser) peptides inhibited cell adhesion to intact GST-OPN, as well as to fibronectin and vitronectin. In chemotaxis assays, GST-OPN promoted directed cell migration of both malignant (PAP2, MDA-MB-435) and normal (gingival fibroblast, and NIH 3T3) cells, while RGD-mutated OPN proteins did not. Together these results suggest that the conserved RGD sequence in OPN is required for the majority of the protein's cell attachment and migration-stimulating functions.
BCL-2 and MCL-1 Expression in Chinese Hamster Ovary Cells Inhibits Intracellular Acidification and Apoptosis Induced by Staurosporine (1996)

Multiple physiological and pharmacological stimuli induce cells to die by apoptosis. In many cases, this apoptosis is inhibited by BCL-2, suggesting the involvement of a common regulatory pathway. One frequent characteristic of apoptosis is the digestion of DNA into oligonucleosome-length fragments. Intracellular acidification and increased intracellular calcium have been variously implicated in activating the endonuclease responsible for this DNA digestion. To explore the involvement of these potential signals in endonuclease activation, we have analyzed three Chinese hamster ovary cell lines: a parental line, one expressing a cDNA encoding BCL-2, and the third expressing the BCL-2 family member MCL-1. Apoptosis was induced with the protein kinase inhibitor staurosporine and intracellular pH and calcium were measured by flow cytometry. We found that both MCL-1 and BCL-2 inhibited DNA digestion compared to the parent cell line, although BCL-2 was more potent in this regard. Concurrent with DNA digestion, we observed intracellular acidification; MCL-1 and BCL-2 inhibited intracellular acidification to an extent commensurate with their ability to inhibit DNA digestion. In contrast, staurosporine caused a dose-dependent increase in intracellular calcium in all three cell lines, demonstrating that intracellular free calcium levels did not correlate with the induction of apoptosis. These results suggest that BCL-2 and MCL-1 may regulate a pathway for intracellular pH homeostasis during apoptotic cell death.
Peptide and Protein Mimetics Inhibiting Amyloid β-Peptide Aggregation (2008)

Protein misfolding is related to some fatal diseases including Alzheimer's disease (AD). Amyloid beta-peptide (Abeta) generated from amyloid precursor protein can aggregate into amyloid fibrils, which are known to be a major component of Abeta deposits (senile plaques). The fibril formation of Abeta is typical of a nucleation-dependent process through self-recognition. Moreover, during fibrillization, several metastable intermediates such as soluble oligomers, including Abeta-derived diffusible ligands (ADDLs) and Abeta*56, are produced, which are thought to be the most toxic species to neuronal cells. Therefore, construction of molecules that decrease the Abeta aggregates, including soluble oligomers, protofibrils, and amyloid fibrils, might further our understanding of the mechanism(s) behind fibril formation and enable targeted drug discovery against AD. To this aim, various peptides and peptide derivatives have been constructed using the "Abeta binding element" based on the structural models of Abeta amyloid fibrils and the mechanisms of self-assembly. The central hydrophobic amino acid sequence, LVFF, of Abeta is a key sequence to self-assemble into amyloid fibrils. By combination of this core sequence with a hydrophobic or hydrophilic moiety, such as cholic acid or aminoethoxy ethoxy acetic acid units, respectively, good inhibitors of Abeta aggregation can be designed and synthesized. A peptide, LF, consisting of the sequence Ac-KQKLLLFLEE-NH 2, was designed based on the core sequence of Abeta but with a simplified amino acid sequence. The LF peptide can form amyloid-like fibrils that efficiently coassemble with mature Abeta1-42 fibrils. The LF peptide was also observed to immediately transform the soluble oligomers of Abeta1-42, which are thought to pose toxicity in AD, into amyloid-like fibrils. On the other hand, two Abeta-like beta-strands with a parallel orientation were embedded in green fluorescent protein (GFP), comprised of a beta-barrel structure, to make pseudo-Abeta beta-sheets on its surface. The GFP variant P13H binds to Abeta1-42 and inhibits Abeta1-42 oligomerization effectively in a substoichiometric condition. Thus, molecules capable of binding to Abeta can be designed based on structural similarities with the Abeta molecule. The peptide and protein mimetics based on the structural features of Abeta might lead to the development of drug candidates against AD.
Targeted delivery of large fusion protein into hippocampal neurons by systemic administration (2010)

Targeted delivery of proteins into the hippocampus has not yet been achieved. Here, we show that systemic administration of the β-galactosidase, fused to a 43-amino-acid peptide derived from rabies virus glycoprotein (RVG), results in targeted delivery of the fusion protein into the hippocampal neurons. This approach may enable the development of protein therapy for neurodegenerative diseases, such as Alzheimer's disease. This result may open new possibilities in using neurotropic virus glycoprotein-derived peptides for targeted delivery of therapeutic molecules into local brain regions.
A soluble class II cytokine receptor, IL-22RA2, is a naturally occurring IL-22 antagonist (2001)

IL-22 is an IL-10 homologue that binds to and signals through the class II cytokine receptor heterodimer IL-22RA1/CRF2-4. IL-22 is produced by T cells and induces the production of acute-phase reactants in vitro and in vivo, suggesting its involvement in inflammation. Here we report the identification of a class II cytokine receptor designated IL-22RA2 (IL-22 receptor-alpha 2) that appears to be a naturally expressed soluble receptor. IL-22RA2 shares amino acid sequence homology with IL-22RA1 (also known as IL-22R, zcytor11, and CRF2-9) and is physically adjacent to IL-20Ralpha and IFN-gammaR1 on chromosome 6q23.3-24.2. We demonstrate that IL-22RA2 binds specifically to IL-22 and neutralizes IL-22-induced proliferation of BaF3 cells expressing IL-22 receptor subunits. IL-22RA2 mRNA is highly expressed in placenta and spleen by Northern blotting. PCR analysis using RNA from various tissues and cell lines showed that IL-22RA2 was expressed in a range of tissues, including those in the digestive, female reproductive, and immune systems. In situ hybridization revealed the dominant cell types expressing IL-22RA2 were mononuclear cells and epithelium. Because IL-22 induces the expression of acute phase reactants, IL-22RA2 may play an important role as an IL-22 antagonist in the regulation of inflammatory responses.
Deletion of Gtl2 , imprinted non-coding RNA, with its differentially methylated region induces lethal parent-origin-dependent defects in mice (2009)

The cluster of imprinted genes located in the Dlk1-Dio3 domain spanning 1 Mb plays an essential role in controlling pre- and postnatal growth and differentiation in mice and humans. The failure of parent-of-origin-dependent gene expression in this domain results in grave disorders, leading to death in some cases. However, little is known about the role of maternally expressed non-coding RNAs (ncRNAs) including many miRNAs and snoRNAs in this domain. In order to further understand the role of these ncRNAs, we created Gtl2-mutant mice harboring a 10 kb deletion in exons 1-5. The mutant mice exhibited a very unique inheritance mode: when the deletion was inherited from the mother (Mat-KO), the pups were born with normal phenotypes; however, all of them died within 4 weeks after birth, probably due to severely hypoplastic pulmonary alveoli and hepatocellular necrosis. Mice carrying the paternal deletion (Pat-KO) showed severe growth retardation and perinatal lethality. Interestingly, the homozygous mutants (Homo-KO) survived and developed into fertile adults. Our results show that these phenotypes occur due to altered expression of the Dlk1-Dio3 cluster genes including miRNAs and snoRNAs via the cis and trans effects.
A 1-Year Study of Brimonidine Twice Daily in Glaucoma and Ocular Hypertension (1997)

Brimonidine is safe and effective in lowering IOP in glaucomatous eyes. Brimonidine provides a sustained long-term ocular hypotensive effect, is well tolerated, and has a low rate of allergic response.
Negative Immune Regulator Tim-3 Is Overexpressed on T Cells in Hepatitis C Virus Infection and Its Blockade Rescues Dysfunctional CD4 + and CD8 + T Cells (2009)

A number of emerging molecules and pathways have been implicated in mediating the T-cell exhaustion characteristic of chronic viral infection. Not all dysfunctional T cells express PD-1, nor are they all rescued by blockade of the PD-1/PD-1 ligand pathway. In this study, we characterize the expression of T-cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) in chronic hepatitis C infection. For the first time, we found that Tim-3 expression is increased on CD4(+) and CD8(+) T cells in chronic hepatitis C virus (HCV) infection. The proportion of dually PD-1/Tim-3-expressing cells is greatest in liver-resident T cells, significantly more so in HCV-specific than in cytomegalovirus-specific cytotoxic T lymphocytes. Tim-3 expression correlates with a dysfunctional and senescent phenotype (CD127(low) CD57(high)), a central rather than effector memory profile (CD45RA(negative) CCR7(high)), and reduced Th1/Tc1 cytokine production. We also demonstrate the ability to enhance T-cell proliferation and gamma interferon production in response to HCV-specific antigens by blocking the Tim-3-Tim-3 ligand interaction. These findings have implications for the development of novel immunotherapeutic approaches to this common viral infection.