gebhart/patrepeval huggingface dataset:
Leucine Zipper-mediated Homodimerization of the Adaptor Protein c-Cbl (1999)

The 120-kDa proto-oncogenic protein c-Cbl is a multidomain adaptor protein that is phosphorylated in response to the stimulation of a broad range of cell surface receptors and participates in the assembly of signaling complexes that are formed as a result of the activation of various signal transduction pathways. Several structural features of c-Cbl, including the phosphotyrosine-binding domain, proline-rich domain, and motifs containing phosphotyrosine and phosphoserine residues, mediate the association of c-Cbl with other components of these complexes. In addition to those domains that have been demonstrated to play a role in the binding of c-Cbl to other signaling molecules, c-Cbl also contains a RING finger motif and a putative leucine zipper. In this study, we demonstrate that the previously identified putative leucine zipper mediates the formation of Cbl homodimers. Using the yeast two-hybrid system, we show that deletion of the leucine zipper domain is sufficient to abolish Cbl homodimerization, while Cbl mutants carrying extensive N-terminal truncations retain the ability to dimerize with the full-length Cbl. The requirement of the leucine zipper for the homodimerization of Cbl was confirmed by in vitro binding assays, using deletion variants of the C-terminal half of Cbl with and without the leucine zipper domain, and in cells using Myc and green fluorescent protein (GFP) N-terminal-tagged Cbl variants. In cells, the deletion of the leucine zipper caused a decrease in both the tyrosine phosphorylation of Cbl and its association with the epidermal growth factor receptor following stimulation with epidermal growth factor, thus demonstrating a role for the leucine zipper in c-Cbl's signaling functions. Thus, the leucine zipper domain enables c-Cbl to homodimerize, and homodimerization influences Cbl's signaling function, modulating the activity of Cbl itself and/or affecting Cbl's associations with other signaling proteins in the cell.
Protection against murine disseminated candidiasis mediated by a Candida albicans-specific T-cell line (1993)

The role of T lymphocytes in disseminated candidiasis in a mouse model of irradiation-induced immunosuppression was investigated. A continuously cultured Candida albicans-specific T-cell line mediated protection of sublethally irradiated mice from disseminated candidiasis as measured by both the fungal load in the kidneys and mortality. These results are the first to demonstrate directly a role for antigen-specific T cells in the protective immune response against murine disseminated candidiasis.
Mass spectrometric evidence for the enzymatic mechanism of the depolymerization of heparin-like glycosaminoglycans by heparinase II (1998)

Heparin-like glycosaminoglycans, acidic complex polysaccharides present on cell surfaces and in the extracellular matrix, regulate important physiological processes such as anticoagulation and angiogenesis. Heparin-like glycosaminoglycan degrading enzymes or heparinases are powerful tools that have enabled the elucidation of important biological properties of heparin-like glycosaminoglycans in vitro and in vivo. With an overall goal of developing an approach to sequence heparin-like glycosaminoglycans using the heparinases, we recently have elaborated a mass spectrometry methodology to elucidate the mechanism of depolymerization of heparin-like glycosaminoglycans by heparinase I. In this study, we investigate the mechanism of depolymerization of heparin-like glycosaminoglycans by heparinase II, which possesses the broadest known substrate specificity of the heparinases. We show here that heparinase II cleaves heparin-like glycosaminoglycans endolytically in a nonrandom manner. In addition, we show that heparinase II has two distinct active sites and provide evidence that one of the active sites is heparinase I-like, cleaving at hexosamine-sulfated iduronate linkages, whereas the other is presumably heparinase III-like, cleaving at hexosamine-glucuronate linkages. Elucidation of the mechanism of depolymerization of heparin-like glycosaminoglycans by the heparinases and mutant heparinases could pave the way to the development of much needed methods to sequence heparin-like glycosaminoglycans.
Fabrication Process of Planarized Multi-Layer Nb Integrated Circuits (2005)

To improve the operating speed and density of Nb single-flux-quantum integrated circuits, we developed an advanced fabrication process based on NEC's standard process. We fabricated planarized six-Nb-layer circuit structures using this advanced process. This new structure has four Nb wiring layers for greater design flexibility. To shield the magnetic field produced by the DC bias current, the DC bias power supply layer was placed under the groundplane. The critical current density of the Josephson junction was 10 kA/cm/sup 2/. We fabricated and tested more than 10 wafers and demonstrated that the six-layer circuits were successfully planarized. We also confirmed insulation between each Nb layer and the reliability of superconducting contacts. This planarization did not significantly degrade the junction characteristics. We measured small spreads in the critical current of less than 2%. These results demonstrated the effectiveness of this advanced process based on mechanical-polishing planarization.
Defining Cancer Cachexia in Head and Neck Squamous Cell Carcinoma (2007)

We have identified clinical characteristics and pathophysiologic mechanisms associated with cancer cachexia in a carefully defined population of patients with HNSCC. The data suggest that the acute-phase response and elevated IL-6 are associated with this complex disease state. We therefore hypothesize that IL-6 may represent an important therapeutic target for HNSCC patients with cancer cachexia.
The c-Jun N-Terminal Kinase Activator Dual Leucine Zipper Kinase Regulates Axon Growth and Neuronal Migration in the Developing Cerebral Cortex (2006)

Mammalian corticogenesis substantially depends on migration and axon projection of newborn neurons that are coordinated by a yet unidentified molecular mechanism. Dual leucine zipper kinase (DLK) induces activation of c-Jun N-terminal kinase (JNK), a molecule that regulates morphogenesis in various organisms. We show here, using gene targeting in mice, that DLK is indispensable for establishing axon tracts, especially those originating from neocortical pyramidal neurons of the cerebrum. Direct and quantitative analysis of radial migration of pyramidal neurons using slice culture and a time-lapse imaging system revealed that acceleration around the subplate was affected by DLK gene disruption and by administration of a JNK inhibitor. Phosphorylation of JNK substrates, including c-Jun and doublecortin, and of JNK itself at the activation loop were partially affected in brains of DLK-deficient mouse embryos. These data suggest that DLK plays a significant role in the coordinated regulation of radial migration and axon projection by modulating JNK activity.
Expression of a thyroid hormone-responsive recombinant gene introduced into adult mice livers by replication-defective adenovirus can be regulated by endogenous thyroid hormone receptor. (1994)

We constructed a recombinant adenovirus carrying the firefly luciferase gene driven by the thymidine kinase promoter and controlled by the palindromic thyroid hormone/retinoic acid-responsive element. The same adenovirus vector without the hormone-responsive element was used as control. Regulation of the luciferase gene expression was tested in pituitary-derived GH cells and hepatoma-derived HepG2 cells infected with the recombinant adenoviruses. Administration of triiodothyronine to GH cells and all-trans-retinoic acid to HepG2 cells resulted in 8.0 +/- 0.3-fold and 4.6 +/- 0.5-fold induction of luciferase activity, respectively. No significant increase was observed with the control adenovirus. Hormonal regulation was also examined in adult mice. Mice depleted of thyroid hormone were injected intravenously with the recombinant adenoviruses and given 4 times the replacement dose of triiodothyronine or vehicle only for 4 days. Hormone administration resulted in 4.2-fold increase of luciferase activity in liver homogenates. No significant effect was observed in animals injected with the control adenovirus. This recombinant adenovirus provides a new experimental system in the study of thyroid hormone and retinoic acid action and offers the potential to regulate by physiological means the expression of genes transferred for the purpose of therapy.
Enzyme interactions in heparan sulfate biosynthesis: Uronosyl 5-epimerase and 2- O -sulfotransferase interact in vivo (2001)

The formation of heparan sulfate occurs within the lumen of the endoplasmic reticulum-Golgi complex-trans-Golgi network by the concerted action of several glycosyltransferases, an epimerase, and multiple sulfotransferases. In this report, we have examined the location and interaction of tagged forms of five of the biosynthetic enzymes: galactosyltransferase I and glucuronosyltransferase I, required for the formation of the linkage region, and GlcNAc N-deacetylase/N-sulfotransferase 1, uronosyl 5-epimerase, and uronosyl 2-O-sulfotransferase, the first three enzymes involved in the modification of the chains. All of the enzymes colocalized with the medial-Golgi marker alpha-mannosidase II. To study whether any of these enzymes interacted with each other, they were relocated to the endoplasmic reticulum (ER) by replacing their cytoplasmic N-terminal tails with an ER retention signal derived from the cytoplasmic domain of human invariant chain (p33). Relocating either galactosyltransferase I or glucuronosyltransferase I had no effect on the other's location or activity. However, relocating the epimerase to the ER caused a parallel redistribution of the 2-O-sulfotransferase. Transfected epimerase was also located in the ER in a cell mutant lacking the 2-O-sulfotransferase, but moved to the Golgi when the cells were transfected with 2-O-sulfotransferase cDNA. Epimerase activity was depressed in the mutant, but increased upon restoration of 2-O-sulfotransferase, suggesting that their physical association was required for both epimerase stability and translocation to the Golgi. These findings provide in vivo evidence for the formation of complexes among enzymes involved in heparan sulfate biosynthesis. The functional significance of these complexes may relate to the rapidity of heparan sulfate formation.
The Dynamics of Real Estate Prices (1991)

Institute of University of I Business and V California at I Economic Research Berkeley FISHER CENTER FOR REAL ESTATE AND URBAN ECONOMICS p WORKING PAPER SERIES WORKING PAPER NO. 88-151 THE DYNAMICS OF REAL ESTATE PRICES” BY These papers are preliminary in nature: their purpose is to i?,E$Z‘£i.d?§2f§iZ?e”£ey BRADFORD CASE are nottobccited ortluotedin JOHN Mq QUIGLEY any publication without the ex- press permission of the author. WALTER A. HAAS SCHOOL OF BUSINESS
Noninvasive Whole-Genome Sequencing of a Human Fetus (2012)

Analysis of cell-free fetal DNA in maternal plasma holds promise for the development of noninvasive prenatal genetic diagnostics. Previous studies have been restricted to detection of fetal trisomies, to specific paternally inherited mutations, or to genotyping common polymorphisms using material obtained invasively, for example, through chorionic villus sampling. Here, we combine genome sequencing of two parents, genome-wide maternal haplotyping, and deep sequencing of maternal plasma DNA to noninvasively determine the genome sequence of a human fetus at 18.5 weeks of gestation. Inheritance was predicted at 2.8 × 10(6) parental heterozygous sites with 98.1% accuracy. Furthermore, 39 of 44 de novo point mutations in the fetal genome were detected, albeit with limited specificity. Subsampling these data and analyzing a second family trio by the same approach indicate that parental haplotype blocks of ~300 kilo-base pairs combined with shallow sequencing of maternal plasma DNA is sufficient to substantially determine the inherited complement of a fetal genome. However, ultradeep sequencing of maternal plasma DNA is necessary for the practical detection of fetal de novo mutations genome-wide. Although technical and analytical challenges remain, we anticipate that noninvasive analysis of inherited variation and de novo mutations in fetal genomes will facilitate prenatal diagnosis of both recessive and dominant Mendelian disorders.
Implementation of spectral phase interferometry for direct electric-field reconstruction with a simultaneously recorded reference interferogram (1999)

An improvement of the technique of spectral phase interferometry for direct electric-field reconstruction is presented. The possibility of simultaneously recording two interference spectra, one containing complete information on the spectral amplitude and the other containing complete information on the spectral phase, on a single one-dimensional detector is demonstrated. This is, to the author's knowledge, the only method that permits the complete characterization of an ultrashort light pulse with a single one-dimensional integrating detector and an algebraic inversion procedure.
Adhesion of human bifidobacterial strains to cultured human intestinal epithelial cells and inhibition of enteropathogen-cell interactions (1993)

Thirteen human bifidobacterial strains were tested for their abilities to adhere to human enterocyte-like Caco-2 cells in culture. The adhering strains were also tested for binding to the mucus produced by the human mucus-secreting HT29-MTX cell line in culture. A high level of calcium-independent adherence was observed for Bifidobacterium breve 4, for Bifidobacterium infantis 1, and for three fresh human isolates from adults. As observed by scanning electron microscopy, adhesion occurs to the apical brush border of the enterocytic Caco-2 cells and to the mucus secreted by the HT29-MTX mucus-secreting cells. The bacteria interacted with the well-defined apical microvilli of Caco-2 cells without cell damage. The adhesion to Caco-2 cells of bifidobacteria did not require calcium and was mediated by a proteinaceous adhesion-promoting factor which was present both in the bacterial whole cells and in the spent supernatant of bifidobacterium culture. This adhesion-promoting factor appeared species specific, as are the adhesion-promoting factors of lactobacilli. We investigated the inhibitory effect of adhering human bifidobacterial strains against intestinal cell monolayer colonization by a variety of diarrheagenic bacteria. B. breve 4, B. infantis 1, and fresh human isolates were shown to inhibit cell association of enterotoxigenic, enteropathogenic, diffusely adhering Escherichia coli and Salmonella typhimurium strains to enterocytic Caco-2 cells in a concentration-dependent manner. Moreover, B. breve 4 and B. infantis 1 strains inhibited, dose dependently, Caco-2 cell invasion by enteropathogenic E. coli, Yersinia pseudotuberculosis, and S. typhimurium strains.
Rapid Method of Converting Primary Amides to Nitriles and Nitriles to Primary Amides by ZnCl2using Microwaves under Different Reaction Conditions (2007)

Abstract A rapid and facile method for the conversion of primary amides to nitriles using inexpensive and readily available ZnCl2 in aqueous acetonitrile and their regeneration using ZnCl2–H2O–THF in the presence of acetamide under microwave irradiation in good yields is reported. The reactions go to completion within a minute.
The tyrosine repressor negatively regulates aroH expression in Escherichia coli (1991)

The levels of the tryptophan-sensitive isoenzyme of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase of Escherichia coli, encoded by the aroH gene, were elevated in tyrR and/or trpR mutants. The effect of tyrR and trpR lesions on aroH expression was confirmed by using a lacZ reporter system. The mutational elimination of either repressor led to a threefold increase in beta-galactosidase.
A Trust Model Using Fuzzy Logic In Wireless Sensor Network (2008)

Adapting various sensor devices to communicate within sensor networks empowers us by providing range of possibilities. The sensors in sensor networks need to know their measurable belief of trust for efficient and safe communication. In this paper, we suggested a trust model using fuzzy logic in sensor network. Trust is an aggregation of consensus given a set of past interaction among sensors. We applied our suggested model to sensor networks in order to show how trust mechanisms are involved in communicating algorithm to choose the proper path from source to destination.
[Morphological changes and prion accumulation in the cerebellar cortex in Creutzfeldt-Jacob disease]. (2008)

Histological sections of the cerebellar cortex taken from 5 patients with Creutzfeldt-Jacob disease (CJD), including 3 patients with sporadic form, were comparatively studied. The rate of pathological alterations as well as localization of prion protein (PrP) deposits greatly varied in these two groups of patients. The intensity of neural loss, damage of glial cells and accumulation of PrP increased in parallel to the duration of the disease. In nvCJD, all layers of the cerebellum, the granular layer in particular, were affected to give rise to diffuse deposits of PrP and immature amyloid plaques. Vacuolization was less pronounced and occurred predominantly in the molecular layer in all patients.
A Mus dunni cell line that lacks sequences closely related to endogenous murine leukemia viruses and can be infected by ectropic, amphotropic, xenotropic, and mink cell focus-forming viruses (1984)

A Mus dunni cell line has been developed that is permissive for all four classes of murine leukemia viruses (MuLV): ecotropic, amphotropic, xenotropic, and mink cell focus-forming viruses. The M. dunni cells contain fewer MuLV-related sequences than do feral or domestic mouse, rat, or mink cells. Infection of the line by ecotropic MuLV induces a distinct cytopathic effect, and the cells can be readily transfected by MuLV DNA. The M. dunni line has been used to isolate an endogenous MuLV from the SC-1 feral mouse cell line.
Application of the Polymerase Chain Reaction to the Detection of Plant Pathogens (1996)

This chapter will focus on polymerase chain reaction (PCR)-based techniques applied to plant pathogens. Readers are also referred to the chapter by Kate J. Wilson on the subject of molecular approaches to the field ecology of microorganisms.
Late Domain Function Identified in the Vesicular Stomatitis Virus M Protein by Use of Rhabdovirus-Retrovirus Chimeras (1999)

Little is known about the mechanisms used by enveloped viruses to separate themselves from the cell surface at the final step of budding. However, small sequences in the Gag proteins of several retroviruses (L domains) have been implicated in this process. A sequence has been identified in the M proteins of rhabdoviruses that closely resembles the PPPPY motif in the L domain of Rous sarcoma virus (RSV), an avian retrovirus. To evaluate whether the PPPY sequence in vesicular stomatitis virus (VSV) M protein has an activity analogous to that of the retroviral sequence, M-Gag chimeras were characterized. The N-terminal 74 amino acids of the VSV (Indiana) M protein, including the PPPY motif, was able to replace the L domain of RSV Gag and allow the assembly and release of virus-like particles. Alanine substitutions in the VSV PPPY motif severely compromised the budding activity of this hybrid protein but not that of another chimera which also contained the RSV PPPPY sequence. We conclude that this VSV sequence is functionally homologous to the RSV L domain in promoting virus particle release, making this the first example of such an activity in a virus other than a retrovirus. Both the RSV and VSV motifs have been shown to interact in vitro with certain cellular proteins that contain a WW interaction module, suggesting that the L domains are sites of interaction with unknown host machinery involved in virus release.
Dielectrophoretic Segregation of Different Human Cell Types on Microscope Slides (2005)

A new method for preparing cells for microscopic examination is presented in which cell mixtures are fractionated by dielectrophoretic forces and simultaneously collected into characteristic zones on slides. The method traps cells directly from the suspending medium onto the slide, reducing cell loss. Furthermore, it exploits differences in the dielectric properties of the cells, which sensitively reflect their morphology. Because different cell types are trapped in characteristic zones on the slide, the technique represents an advance over existing methods for slide preparation, such as centrifugation and smears where cells are randomly distributed. In particular, the new method should aid in the detection of rare and anomalous cell subpopulations that might otherwise go unnoticed against a high background of normal cells. As well as being suitable for traditional microscopic examination and automated slide scanning approaches, it is compatible with histochemical and immunochemical techniques, as well as emerging molecular and proteomic methods. This paper describes the rationale and design of this so-called electrosmear instrumentation and shows experimental results that verify the theory and applicability of the method with model cell lines and normal peripheral blood subpopulations.
The Photo-Erasable Memory Switching Effect of Ag Photo-Doped Chalcogenide Glasses (1973)

Abstract The electric conductivity of the chalcogenide glass increased with an increase in the amount of Ag which had been photo-doped. By applying the electric field to the electrodes which were set on the surface of the Ag photo-doped chalcogenide glass film, a conductive path was grown from the cathode to the anode. As a result of the connection of the electrodes with the path, the electric resistance of the cell abruptly decreased (ON state). The path was made of the metal silver reduced by electrolysis and was diminished by irradiation with light. As the path was erased, the cell was turned into the resistant state (OFF state). The cycles were repeatable many times. There was a delay time (td) in turning the cell from the OFF to the ON state by applying the electric field (E). It was empirically described by the following equation for the Ag photo-doped chalcogenide glasses: t_d=aexp(-b·E)
Indoor DS-CDMA system deployment and performance with successive interference cancellation (2004)

Using a Monte-Carlo analysis and measured propagation data, investigation has been conducted into whether the deployment of a multi-floor indoor DS-CDMA system is influenced by the use of successive interference cancellation. The results show that the cancellation of inter-cell interference influences the optimal system deployment strategy whereas the cancellation of intra-cell interference does not.