gebhart/patrepeval huggingface dataset:
Signaling from E-cadherins to the MAPK Pathway by the Recruitment and Activation of Epidermal Growth Factor Receptors upon Cell-Cell Contact Formation (2000)

E-cadherins are well characterized cell surface molecules expressed in epithelial cells, which play a major role in cell adhesion through the establishment of calcium-dependent homophilic interactions at sites of cell-cell contacts. They are also integral components of morphogenetic programs controlling the maintenance of the structural and functional integrity of epithelia. Accumulated evidence indicates that the E-cadherin-mediated cell adhesion system is highly regulated from inside the cells by a number of intracellular signaling pathways. Recently available information suggests that E-cadherins may also play a role in the transduction of signals from the outside of the cell to the cytoplasm. However, the nature of the biochemical routes regulated by E-cadherins is still largely unknown. In this study, we set out to explore the possibility that E-cadherins may regulate the activity of MAPK, a key signaling pathway involved in cell fate decisions, upon the formation of cell-cell contacts among neighboring cells. By using an immortalized non-tumorigenic keratinocyte cell line, HaCat, as a model system, we provide evidence that the assembly of calcium-dependent adherens junctions leads to a rapid and remarkable increase in the state of activation of MAPK and that this event is mediated by E-cadherins. Furthermore, we found that E-cadherins stimulate the MAPK pathway through the ligand-independent activation of epidermal growth factor receptors and the consequent activation of a biochemical route leading to the stimulation of MAPKs. These findings suggest that E-cadherins can initiate outside-in signal transducing pathways through the engagement of tyrosine kinase receptors for epidermal growth factor, thus providing a novel molecular mechanism whereby these cell adhesion molecules may ultimately control the fate of normal and transformed epithelial cells.
Quorum regulation of luminescence in Vibrio fischeri. (1999)

Luminescence in Vibrio fischeri is controlled by a population density-responsive regulatory mechanism called quorum sensing. Elements of the mechanism include: LuxI, an acyl-homoserine lactone (acyl-HSL) synthase that directs synthesis of the diffusible signal molecule, 3-oxo-hexanoyl-HSL (V. fischeri autoinducer-1, VAI-1); LuxR, a transcriptional activator protein necessary for response to VAI-1; GroEL, which is necessary for production of active LuxR; and AinS, an acyl-HSL synthase that catalyzes the synthesis of octanoyl-HSL (VAI-2). The population density-dependent accumulation of VAI-1 triggers induction of lux operon (luxICDABEG; genes for luminescence enzymes and for LuxI) transcription and luminescence by binding to LuxR, forming a complex that facilitates the association of RNA polymerase with the luxoperon promoter. VAI-2, which apparently interferes with VAI-1 binding to LuxR, operates to limit premature luxoperon induction. Hierarchical control is imposed on the system by 3':5'-cyclic AMP (cAMP) and cAMP receptor protein (CRP), which are necessary for activated expression of luxR. Several non-lux genes in V. fischeri are controlled by LuxR and VAI-1. Quorum regulation in V. fischeri serves as a model for LuxI/LuxR-type quorum sensing systems in other gram-negative bacteria.
A Digital Television Sequence Store (1978)

This paper describes the capabilities and design of a new digital video system which permits a user to record and playback sequences, up to 80 s long, of digitized color television signal. In addition, a user may process the stored video via the associated computer and view the results. The above system, which is called the DVS (Digital Video Store), is intended as a simulation tool for investigating the effects of various video coding and processing algorithms.
Selective area growth of InP on InP precoated silicon substrate by hydride vapor phase epitaxy (2003)

Selective area growth of InP is carried out on an InP precoated [001] 2/spl deg/ off Si substrate in a low pressure hydride vapor phase epitaxy system under different gas phase supersaturation. Epitaxial lateral overgrowth can be formed on a Si/sub 3/N/sub 4/ mask under certain growth conditions, which has improved crystallographic quality of the InP seed layer. A crystallographic model is proposed to demonstrate the observed asymmetric growth profile of selective area growth.
Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation (2006)

DNA methylation is a stable epigenetic mark for transcriptional gene silencing in diverse organisms including plants and many animals. In contrast to the well characterized mechanism of DNA methylation by methyltransferases, the mechanisms and function of active DNA demethylation have been controversial. Genetic evidence suggested that the DNA glycosylase domain-containing protein ROS1 of Arabidopsis is a putative DNA demethylase, because loss-of-function ros1 mutations cause DNA hypermethylation and enhance transcriptional gene silencing. We report here the biochemical characterization of ROS1 and the effect of its overexpression on the DNA methylation of target genes. Our data suggest that the DNA glycosylase activity of ROS1 removes 5-methylcytosine from the DNA backbone and then its lyase activity cleaves the DNA backbone at the site of 5-methylcytosine removal by successive beta- and delta-elimination reactions. Overexpression of ROS1 in transgenic plants led to a reduced level of cytosine methylation and increased expression of a target gene. These results demonstrate that ROS1 is a 5-methylcytosine DNA glycosylase/lyase important for active DNA demethylation in Arabidopsis.
Electrophilic substitution in indoles. Part 15. The reaction between methylenedi-indoles and p-nitrobenzenediazonium fluoroborate (1987)

p-Nitrobenzenediazonium fluoroborate (2 mol equiv.) reacts under aqueous conditions with 3,3′methylenedi-indole (9a) and N,N-dimethyl-3,3′-methylenedi-indole (9c) to give, in each instance, high yields of the corresponding 3-p-nitrophenylazoindoles (13a) and (13c). When 1 mol equiv. of diazonium salt is used, the methylenedi-indole (9a) gives < 1 mol equiv. of the 3-(p-nitrophenylazo)indole (13a) and some methylenedi-indole is recovered. In dry acetonitrile, 3,3′methylenedi-indole gives, with 1 mol equiv. of diazonium salt, a mixture of 3-(p-nitrophenylazo)indole (13a)(0.45 mol equiv.) and the unstable 3-(p-nitrophenylazo)-2,3′-methylenedi-indole (16a)(0.42 mol equiv.). The latter was also synthesized from indole-2,3-dione and chloroacetylindole via indol-2-yl, indol-3-yl, and 2,3′methylenedi-indole. Essentially similar results were obtained with N,N-dimethyl-3,3′-methylenedi-indole (9c) and the diazonium salt. The unsymmetrical compounds 3-indol-3-ylmethyl-1,2-dimethylindole (9d) and 3-indol-3-ylmethyl-2-methylindole (9e), with 2 mol equiv: of diazonium salt in aqueous solution, each give high yields of the two possible 3-p-nitrophenylazoindoles. With 1 mol equiv. of the diazonium salt only the 2-methyl-3-p-nitrophenylazo derivatives are obtained, together with 3,3′methylenedi-indole. In dry acetonitrile, with either 1 or 2 mol equiv. of diazonium salt, the unsymmetrical methylenedi-indoles each give only the 2-methyl-3-p-nitrophenylazoindoles. The displacement of an indolylmethyl residue from methylenedi-indoles by the diazonium salt, and the formation of the azo coupled rearrangement product (16a) provides firm evidence that azo coupling of 3-alkylindoles to give the 2,3-disubstituted indoles proceeds by initial attack at the 3-position followed by rearrangement, rather than by direct substitution at the 2-position.
Production of L-lactic acid from starch by recombinant Bacillus subtilis 1A304 (Φ105MU331) (2010)

Some 3D finite element systemic models are currently established and used to simulate the foot biomechanical state. However, during most of these 3D foot finite element static analyses, ligaments and plantar fascia are generally defined by connecting the corresponding attachment points on the bones, and the spaces between the bones are fused together by solid elements with given cartilage stiffness to simulate the connection of bones. This "connection of bones" takes the place of the real interactions between neighbored bones and enhances the structure of foot, which possibly leads to the result that the effects of ligaments and other soft tissues are completely replaced by the effect of articular cartilages. Thereby, ligaments and other soft tissues maybe not play an inherent role in the finite element analysis. The objective of this study was to estimate whether there exists the effect of ligaments and plantar fascia on the biomechanical behaviors of the foot tissue stress distribution and foot structure deformation during the balanced standing stance and static finite element analysis.
In vivo Diagnosis of Epidermal Growth Factor Receptor Expression using Molecular Imaging with a Cocktail of Optically Labeled Monoclonal Antibodies (2007)

An in vivo imaging technique using an antibody cocktail simultaneously differentiated two tumors expressing distinct EGFRs and enabled an accurate characterization of each subtype.
Stimulation Of Nonspecific Resistance Against Aerogenic Viral And Bacterial Infections By Muramyl Dipeptide Combined With Trehalose Dimycolate (1986)

Stimulation Of Nonspecific Resistance Against Aerogenic Viral And Bacterial Infections By Muramyl Dipeptide Combined With Trehalose Dimycolate was published in Biological Properties of Peptidoglycan on page 401.
Cell-Mediated Immunity and the Outcome of Hepatitis C Virus Infection (2004)

The hepatitis C virus (HCV) infects approximately three percent of the world's population. Some individuals resolve the infection spontaneously, but the majority develop persistent viremia that often causes progressive liver disease. There is an emerging consensus that cellular immune responses are essential for spontaneous resolution of acute hepatitis C and long-term protection from persistent infection. This review focuses on the recent advances in understanding mechanisms of protective immunity and why they fail in most infected individuals. The distinct yet complementary role of CD4+ and CD8+ T lymphocytes in this process is highlighted.
Calcium signalling and control of cell proliferation by tyrosine kinase receptors (Review) (2002)

Most peptidic growth factors (GFs) that act as mitogens for different cell types bind to tyrosine kinase receptors (RTKs) and trigger complex intracellular signal transduction pathways finally leading to cell proliferation. Among the early events induced by GFs, cytosolic calcium increase plays a key role, and in particular calcium entry from extracellular medium appears to be a widespread signal. Even if a great amount of data has been provided during the last decades, several issues remain to be fully clarified: the nature of the calcium-permeable channels involved, their regulation by intracellular messengers, and the mechanisms underlying calcium-dependent cell proliferation. This review focuses on the relationship between calcium signals and angiogenesis, a process in which endothelial cell proliferation, mainly triggered by basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF), is a critical step.
Characterization of RNA helicase A as component of STAT6-dependent enhanceosome (2006)

Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated transcriptional activation by identifying STAT6 transcription activation domain (TAD) interacting nuclear proteins. The first of the identified proteins was coactivator protein p100, which regulates IL-4-induced transcription by connecting STAT6 with other transcriptional regulators. Here, we describe RNA helicase A (RHA) as a novel component of STAT6 transcriptosome. In vitro and in vivo experiments indicated that RHA did not directly interact with STAT6, but p100 protein was found to mediate the assembly of the ternary complex of STAT6-p100-RHA. In chromatin immunoprecipitation studies RHA together with p100 enhanced the binding of STAT6 on the human Igepsilon promoter after IL-4 stimulation. RHA enhanced the IL-4-induced transcription, and the participation of RHA in IL-4-regulated transcription was supported by RNAi experiments. Our results suggest that RHA has an important role in the assembly of STAT6 transcriptosome. As RHA is also known to interact with chromatin modifying proteins, the RHA containing protein complexes may facilitate the entry of transcriptional apparatus to the IL-4 responsive promoters.
Immunohistochemical analysis of the proapoptotic protein Par-4 in normal rat tissues. (1997)

Prostate apoptosis response 4 (par-4) is a recently identified gene that encodes a transcription factor, Par-4, with a leucine zipper domain. Par-4 protein is constitutively expressed in various cell lines and is functionally required but not sufficient for apoptosis. Induction of Par-4 in cultured cells is found exclusively during apoptosis, and ectopic overexpression of Par-4 enhances the potency of apoptotic stimuli. Western or Northern blot analysis on mRNA or protein extracts, respectively, from rat organs revealed that the expression of Par-4 was ubiquitous and was not restricted to any specific organ(s). To further identify specific cell types that expressed Par-4, we performed an immunohistochemical analysis of the protein in paraffin-embedded sections of various organs from rats. Our findings indicated that consistent with its proapoptotic role, Par-4 is expressed in apoptotic granulosa cells of atretic ovarian follicles and in terminally differentiated cells, such as the cardiomyocytes, cerebellar Purkinje cells, and pyramidal cells of the hypothalamus. Moreover, testosterone ablation by castration of rats caused an early and transient induction of Par-4 in the ductal cells of the prostate that undergo apoptosis. By contrast, in tissues in which the cells could be visually differentiated from their mature counterparts, Par-4 expression was lowest in the mature cells. This was the case for epithelia of the mammary and the prostate gland in which the basal cells maintained higher protein levels of Par-4 than did the terminally differentiated ductal cells. Similarly, cells of the stratum corneum of the skin and cells on top of the duodenal villi stained less intensely for Par-4 as compared to the stem cells in the stratum basale and at the bottom of the crypts of Lieberkühn, respectively. It is possible that Par-4 has to be down-regulated for successful differentiation in these tissues. Taken together, the widespread expression of Par-4 in various adult cell types underscores the physiological importance of the protein. The observation of constitutive Par-4 expression in the stem cell compartments is inconsistent with the probability of apoptosis per se and can be extended to determine whether Par-4 plays a role in other cellular processes.
Chemical modification of hemoglobins: a study of conformation restraint by internal bridging. (1966)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Detection and delineation of CXCR-4 (fusin) as an entry and fusion cofactor for T-tropic [correction of T cell-tropic] HIV-1 by three different monoclonal antibodies. (1998)

A chemokine receptor, CXCR-4, has been identified as an entry cofactor for T cell line-tropic (T-tropic) HIV-1. To detect expression of CXCR-4 at the single cell level and dissect postbinding events of HIV-1 infection, we generated three mAbs against human CXCR-4. These mAbs inhibited SDF-1-induced intracellular Ca2+ mobilization, and one of the mAbs immunoprecipitated a specific 47-kDa component from CXCR-4+ cells. Flow cytometric analysis showed that most human cell lines examined expressed CXCR-4. A fraction of normal PBMC expressed CXCR-4, but neutrophils were negative. Two-color analysis revealed that the majority of T cells, virtually all B cells, and all monocytes expressed CXCR-4, while it was only weakly present on NK cells. Thus, expression of CXCR-4 is not ubiquitous but cell type specific in hemopoietic cells. The three mAbs were shown to suppress cell fusion mediated by envelope proteins of a T-tropic NL432 virus but not by those of an M-tropic JRCSF virus Likewise, they suppressed infection of NL432 but not that of an M-tropic NL162 virus. In both cases it was noted that the suppressive activity varied considerably among the mAbs. These data confirmed that CXCR-4 is directly involved in env-mediated entry and fusion of T-tropic HIV-1 and suggest that the epitopes on CXCR-4 recognized by the three mAbs may have different roles in interaction with the envelope proteins of T-tropic HIV-1.
Consumption of Wonderful Variety Pomegranate Juice and Extract by Diabetic Patients Increases Paraoxonase 1 Association with High-Density Lipoprotein and Stimulates Its Catalytic Activities (2008)

Association of paraoxonase 1 (PON1) with high-density lipoprotein (HDL) stabilizes the enzyme. In diabetic patients, PON1 dissociates from HDL and, as a consequence, is less biologically active. Our aim was to investigate the effects of Wonderful variety pomegranate juice (WPJ) and pomegranate polyphenol extract (WPOMxl) consumption on PON1 association with HDL in diabetic patients. Thirty patients with type 2 diabetes mellitus participated in the study. Ten male patients and 10 female patients received concentrated WPJ (50 mL/day for 4 weeks), while another group of 10 male patients received WPOMxl (5 mL/day for 6 weeks). There were no significant effects of WPJ or WPOMxl consumption on fasting blood glucose or hemoglobin A1c levels. After 4 weeks of WPJ consumption by male patients, basal serum oxidative stress was significantly decreased by 35%, whereas serum concentrations of thiol groups significantly increased by 25%. Moreover, HDL-associated PON1 arylesterase, paraoxonase, and lactonase activities increased significantly after WPJ consumption by 34-45%, as compared to the baseline levels. PON1 protein binding to HDL was significantly increased by 30% following WPJ consumption, and the enzyme became more stable. In male patients that consumed WPOMxl and in female patients that consumed PJ, a similar pattern was observed, although to a lesser extent. We conclude that WPJ as well as WPOMxl consumption by diabetic patients does not worsen their diabetic parameters. Furthermore, WPJ as well as WPOMxl consumption contribute to PON1 stabilization, increased association with HDL, and enhanced catalytic activities. These beneficial effects of pomegranate consumption on serum PON1 stability and activity could lead to retardation of atherosclerosis development in diabetic patients.
Endothelial NO Synthase Overexpression Inhibits Lesion Formation in Mouse Model of Vascular Remodeling (2001)

NO produced by endothelial NO synthase (eNOS) plays important roles in the regulation of vascular tone and structure. The purpose of this study was to clarify the role of eNOS-derived NO on vascular remodeling by use of eNOS-transgenic (eNOS-Tg) mice. The common carotid artery was ligated just proximal to the carotid bifurcation. Four weeks later, the proximal carotid artery of the ligation site was histologically examined. In this vascular remodeling model, the endothelium remains uninjured, but neointimal and medial thickening occurs in combination with a reduction in vascular diameter at the proximal portion of the ligation. At 4 weeks after ligation, the respective neointimal and medial areas in wild-type mice were 17 200+/-1100 and 24 300+/-1500 microm(2), whereas both were reduced to 8000+/-1900 (P:<0.01) and 18 400+/-700 microm(2) (P:<0.01) in eNOS-Tg mice (n=8). Total vascular area was not different between the 2 genotypes. N:(G)-Nitro-L-arginine methyl ester treatment increased neointimal and medial areas to the same extent in both genotypes. Leukocyte infiltration was observed in the luminal side of the vessel, but the number of infiltrating cells was significantly attenuated in eNOS-Tg mice compared with wild-type mice. This reduction of leukocyte infiltration in eNOS-Tg mice was associated with reduced expressions of intracellular adhesion molecule-1 and vascular cellular adhesion molecule-1 on the endothelium. In conclusion, chronic eNOS overexpression in the endothelium reduced leukocyte infiltration and inhibited neointimal formation and medial thickening. Our data provide the evidence for the regulatory role of NO from the endothelium on vascular structure integrity.
Intrastriatal adrenal medulla grafts in rats (1986)

Rats with rotational behavior consequent to unilateral lesions of the substantia nigra have been proposed for an experimental model of Parkinson's disease. Adrenal medulla or embryonic substantia nigra grafts in the lateral ventricle of these animals reduce this rotational behavior. For application to primate and human subjects, it may be necessary to implant tissue directly into the parenchyma of the corpus striatum rather than into the ventricle in order to achieve a sufficient distribution of the grafted tissues and increase the efficacy of the grafts. In the present study, the properties of intraparenchymal adrenal medulla grafts were investigated. Grafts were obtained from both young (4 to 5 weeks old) and aging (22 to 24 months old) donor rats. Much of the implanted tissue did not survive, although 200 chromaffin cells per recipient rat were found to have survived for at least 6 months. All of the surviving cells developed process-like cytoplasmic extensions, although these processes did not appear to have reinnervated host brain tissue. Grafts from both young and aging donor rats prevented a slight deterioration in the performance of a sensory neglect test that was observed in a control group that received grafts of sciatic nerve. There was also a tendency that did not reach statistical significance for grafts from young (but not from aging) donors to decrease apomorphine-induced rotational behavior. It is concluded that, although the corpus striatum does not appear to provide a particularly favorable environment for the implantation of adrenal medulla grafts, striatal implants of adrenal medulla might become a promising procedure if a means of improving the survival of these tissues could be developed.
Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing (2015)

Our approach underlines the power and limitations of two commonly used next-generation sequencers for the analysis of influenza virus gene diversity. We conclude that the Illumina MiSeq platform is better suited for detecting variant sequences whereas the Ion Torrent PGM platform has a shorter turnaround time. The data analysis pipeline that we propose here will also help to standardize variant calling in small RNA genomes based on next-generation sequencing data.