gebhart/patrepeval huggingface dataset:
Pheromonal Regulation of Development in Saccharomyces cerevisiae (1981)

INTRODUCTION Mating of the two different haploid cell types of baker’s yeast Saccharomyces cerevisiae to form a diploid provides a relatively simple system for studying the biochemical basis of intercellular signaling and developmental control in eukaryotic cells. Conjugation occurs efficiently when cultures of opposite mating type are mixed but only exceedingly rarely when cultures of the same haploid cell type are mixed. Thus, there must be specific biochemical features that distinguish and define the mating type of a yeast cell and that mediate the intercellular interactions occurring between them to permit conjugation. Indeed, substantial progress has been made over the last 10 years in describing events in the mating process at the molecular level (for reviews, see Crandall 1977for reviews, see Crandall 1978; Crandall et al. 1977; Manney and Meade 1977; MacKay 1978; Goodenough 1980; Thorner 1980; Manney et al. 1981). One exciting outcome of these investigations is the demonstration that reciprocal exchange of diffusible oligopeptide pheromones is the intercellular stimulus that initiates the physiological changes in haploid cells that culminate in mating. In this paper, mating will be discussed in light of recent advances in our understanding of the cellular and molecular biology of yeast. Where possible, the identification and biochemical mode of action of cell-type-specific gene products that function in this developmental process will be emphasized, particularly the pivotal role of the mating pheromones. AN OVERVIEW OF MATING EVENTS A diagrammatic representation of the conjugation process is shown in Figure 1 and is based on the observations of a large number...
Improve E-Commerce Recommendation by Classification Tree and Fuzzy Sets (2016)

In order to enhance the performance of E-Commerce recommendation, a hybrid filtering approach based on the taxonomy of E-Commerce platform is put forward. The classification tree of products is used to find the users with similar shopping intention. The sparsity of user ratings, major problem for collaborative filtering, is overcome. A two-granularity user profile is built to reflect the customer's shopping interests. User profile is firstly described as a set of leaf nodes of the classification tree. Then, each category of the user profile is refined by the theory of fuzzy set. Fuzzy sets make user profile and item representation more accurate. At the same time, tags instead of key words extracted from item content, are used for the building of user profiles and representation of items. It overcomes the analysis difficulty and large calculation problems for content-based filtering.
Interfacial Adsorption and Aggregation Associated Changes in Secondary Structure of Human Calcitonin Monitored by ATR-FTIR Spectroscopy (1994)

The peptide hormone human calcitonin (hCT) has a marked tendency to aggregate in aqueous solutions, resulting in viscous and turbid dispersions consisting of long fibrils approximately 80 A in diameter. Both transmission (T-FTIR) and attenuated total reflection Fourier transform infrared (ATR-FTIR) experiments were applied on hCT adsorption and aggregation kinetics. By means of the surface sensitive ATR-FTIR spectroscopy at a hydrophobic/hydrophilic interface, early adsorption and aggregation steps of hCT could be followed in situ under real time conditions. Since the aggregation of hCT is associated with conformational changes, the secondary structure sensitive amide I'-band (D2O) could be used as a diagnostic marker. ATR-FTIR spectra recorded during the aggregation kinetics of hCT showed an increase of the amide I'-band intensity by a factor of 3.4, interpreted as pronounced adsorption of hCT molecules from bulk solution to the germanium plate. Furthermore, variations in the line shape of the amide I'-band were interpreted. At the beginning, hCT adopted a random coil conformation followed by distinct formations of alpha-helical and intermolecular parallel beta-sheet structures. Finally, the random coil content declined to 63%, whereas alpha and beta contents rose to 8% and 29%, respectively. From our kinetics results the alpha-structures were formed faster than the beta-structures. This was interpreted as an initial induction of amphiphilic helices during the adsorption process of hCT monomers. ATR-FTIR spectroscopy provides a sensitive analytical tool suggested to monitor interfacial adsorption and aggregation phenomena also of other peptides and proteins.
The Chemokine Monocyte Chemotactic Protein 1 Triggers Janus Kinase 2 Activation and Tyrosine Phosphorylation of the CCR2B Receptor (1998)

The chemokines are a growing family of low m.w., 70- to 80-residue proinflammatory cytokines that operate by interacting with G protein-coupled receptors. Chemokines are involved in cell migration and in the activation of specific leukocyte subsets. Using the Mono Mac 1 monocytic cell line, we show that monocyte chemotactic protein 1 (MCP-1) triggers activation of the Janus kinase 2 (JAK2)/STAT3 pathway and CCR2 receptor tyrosine phosphorylation. Both Ca2+ mobilization and cell migration are blocked in Mono Mac 1 cells by tyrphostin B42, a specific JAK2 kinase inhibitor. Within seconds of MCP-1 activation, JAK2 phosphorylates CCR2 at the Tyr139 position and promotes JAK2/STAT3 complex association to the receptor. This MCP-1-initiated phosphorylation and association to JAK2 is also observed in CCR2B-transfected HEK293 cells. In contrast, when a CCR2B Tyr139Phe mutant is expressed in HEK293 cells, it is not phosphorylated in tyrosine and triggers neither JAK2/STAT3 activation nor Ca2+ mobilization in response to MCP-1. These results implicate the tyrosine kinase pathway in early chemokine signaling, suggesting a key role for this kinase in later events.
Structural basis of the TAL effector–DNA interaction (2012)

Phytopathogen transcription activator-like effectors (TALEs) bind DNA in a sequence specific manner in order to manipulate host transcription. TALE specificity correlates with repeat variable diresidues in otherwise highly stereotypical 34-35mer repeats. Recently, the crystal structures of two TALE DNA-binding domains have illustrated the molecular basis of the TALE cipher. The structures show that the TALE repeats form a right-handed superhelix that is wound around largely undistorted B-DNA to match its helical parameters. Surprisingly, repeat variable residue 1 is not in contact with the bases. Instead, it is involved in hydrogen bonding interactions that stabilize the overall structure of the protein. Repeat variable residue 2 contacts the top strand base and forms sequence-specific hydrogen bonds and/or van der Waals contacts. Very unexpectedly, bottom strand bases are exposed to solvent and do not make any direct contacts with the protein. This review contains a summary of TALE biology and applications and a detailed description of the recent breakthroughs that have provided insights into the molecular basis of the TALE code.
Photo-irradiation improved functional preservation of the isolated rat heart (1997)

Photo-irradiation improves functional recovery of the cold-stored rat heart possibly via conservation of ATP and antioxidant enzyme activity.
Identifying ligands at orphan GPCRs: current status using structure‐based approaches (2016)

GPCRs are the most successful pharmaceutical targets in history. Nevertheless, the pharmacology of many GPCRs remains inaccessible as their endogenous or exogenous modulators have not been discovered. Tools that explore the physiological functions and pharmacological potential of these 'orphan' GPCRs, whether they are endogenous and/or surrogate ligands, are therefore of paramount importance. Rates of receptor deorphanization determined by traditional reverse pharmacology methods have slowed, indicating a need for the development of more sophisticated and efficient ligand screening approaches. Here, we discuss the use of structure-based ligand discovery approaches to identify small molecule modulators for exploring the function of orphan GPCRs. These studies have been buoyed by the growing number of GPCR crystal structures solved in the past decade, providing a broad range of template structures for homology modelling of orphans. This review discusses the methods used to establish the appropriate signalling assays to test orphan receptor activity and provides current examples of structure-based methods used to identify ligands of orphan GPCRs. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc.
MM-wave tapered slot antennas on micromachined photonic bandgap dielectrics (2002)

Dramatic improvements in the radiation properties of tapered slot antennas (TSA) integrated on high dielectric constant substrates have been achieved through micromachining techniques. A periodic hole structure was micromachined into the substrate converting it into a photonic bandgap material. The measured directivity of a 4/spl lambda//sub 0/ TSA on a 50 mil (1.27 mm) thick Duroid substrate (/spl epsiv//sub r/=10.5) was increased by 240% using micromachined holes with a hexagonal geometry. A similar improvement was observed when the process was performed at 30 GHz on a 14 mil (350 /spl mu/m) silicon wafer. We believe the technology can be scaled to 60 GHz and 94 GHz for communication systems, low-cost millimeter wave imaging arrays, and power combining systems.
Cancer cell immune escape and tumor progression by exploitation of anti-inflammatory and pro-inflammatory responses (2005)

Apoptotic cells can be eliminated by phagocytosis, which is mediated by antigen-presenting cells (APCs), such as macrophages and dendritic cells (DCs), through phosphatidylserine (PS) on apoptotic cells and phosphatidylserine receptor (PSR) on APCs. The phagocytosis of apoptotic cells by macrophages is strictly regulated by not only the inflammatory reaction, but also by an increase in anti-inflammatory factors such as IL-10, TGF-beta, and prostaglandin E2 (PGE2), leading to an anti-inflammatory situation, whereby apoptosis contributes to a noninflammatory response. However, because PS and PSR are expressed in cancer cells, shed soluble phosphatidylserine (sPS) can interact with the PS receptor on macrophages, which promotes an anti-inflammatory response to macrophages that may lead to immune escape. The sPS derived from cancer cells also reacts with the PSR on the cancer cells to produce IL-10, TGF-beta, and PGE2, which can cause suppression of anti-tumor immunity through the anti-inflammatory response to macrophages, which produces tumor-associated macrophages. Furthermore, sPS and TGF-beta inhibit the maturation of immature DCs, resulting in a functional inhibition of DCs. The potential roles of PS and PSR in cancer cells and macrophages in immune escape mediated by sPS and anti-inflammatory factors are discussed, which may explain their dual regulation of anti- and pro-inflammatory responses during tumor progression.
Membrane-bound IL-15 stimulation on peripheral blood natural kiler progenitors leads to the generation of an adherent subset co-expressing dendritic cells and natural kiler functional markers (2011)

Human peripheral blood natural killer progenitors represent a flexible, heterogeneous population whose phenotype and function are controlled by their membrane-bound IL-15. Indeed, reciprocal membrane-bond IL-15 trans-presentation commits these cells into NK differentiation, while membrane-bound IL-15 stimulation with its soluble ligand (sIL-15Rα) triggers a reverse signal (pERK1/2 and pFAK) that modifies the developmental program of at least two subsets of PB-NKPs. This treatment generates: i) the expansion of an immature NK subset growing in suspension; ii) the appearance of an unprecedented adherent non-proliferative subset with a dendritic morphology co-expressing marker, cytokines and functions typical of myeloid dendritic cells (CD1a(+)/BDCA1(+)/IL-12(+)) and NK cells (CD3-/NKp46(+)/ CD56(+)/IFNγ(+)). The generation of these putative NK/DCs is associated to the rapid inhibition of negative regulators of myelopoiesis (the transcription factors STAT6 and GATA-3) followed by the transient upregulation of inducers of myeloid development, such as the transcription factors (PU.1, GATA-1) and the anti-apoptotic molecule (MCL-1).
Targeting the urokinase plasminogen activator receptor with a monoclonal antibody impairs the growth of human colorectal cancer in the liver (2009)

uPAR MoAb therapy impaired CRC tumor growth in the liver in both small-volume and large-volume disease models.
Correlation of clonal T cell expansion with disease activity in systemic lupus erythematosus (1997)

It has been proposed that T cell activation may play an important role in the pathogenesis of systemic lupus erythematosus (SLE). In order to examine this hypothesis, we assessed the whole degree of clonal accumulation of T cells using RT-PCR and subsequent single-strand conformation polymorphism (SSCP) analysis. The analysis of the beta chain of the TCR revealed little clonotypic T cell expansion in the peripheral blood of lupus patients in remission, whereas in patients with active disease many dominant T cell clonal expansions without any distinct V beta bias were observed. The alteration in the number of T cell clones correlated well with disease activities, since these T cell expansions decreased as patients had improved. Furthermore, similar but more intense accumulations of T cell clones were found in pleural and pericardial effusions of patients with lupus serositis. Some of these identical expanded clonotypes were observed irrespective of the lesions and the times of sampling, and some of them were identical to those observed in the peripheral blood. These results suggest that the T cell clonal expansions correlate with the disease activities and that the expansion might contribute to the pathogenic lesion formation in SLE.
Cell surface antigen CD109 is a novel member of the α2 macroglobulin/C3, C4, C5 family of thioester-containing proteins (2002)

Cell surface antigen CD109 is a glycosylphosphatidylinositol (GPI)-linked glycoprotein of approximately 170 kd found on a subset of hematopoietic stem and progenitor cells and on activated platelets and T cells. Although it has been suggested that T-cell CD109 may play a role in antibody-inducing T-helper function and it is known that platelet CD109 carries the Gov alloantigen system, the role of CD109 in hematopoietic cells remains largely unknown. As a first step toward elucidating the function of CD109, we have isolated and characterized a human CD109 cDNA from KG1a and endothelial cells. The isolated cDNA comprises a 4335 bp open-reading frame encoding a 1445 amino acid (aa) protein of approximately 162 kd that contains a 21 aa N-terminal leader peptide, 17 potential N-linked glycosylation sites, and a C-terminal GPI anchor cleavage-addition site. We report that CD109 is a novel member of the alpha 2 macroglobulin (alpha 2M)/C3, C4, C5 family of thioester-containing proteins, and we demonstrate that native CD109 does indeed contain an intact thioester. Analysis of the CD109 aa sequence suggests that CD109 is likely activated by proteolytic cleavage and thereby becomes capable of thioester-mediated covalent binding to adjacent molecules or cells. In addition, the predicted chemical reactivity of the activated CD109 thioester is complement-like rather than resembling that of alpha 2M proteins. Thus, not only is CD109 potentially capable of covalent binding to carbohydrate and protein targets, but the t(1/2) of its activated thioester is likely extremely short, indicating that CD109 action is highly restricted spatially to the site of its activation.
Developing Non-GMO Tobacco Cultivars with Lower Alkaloid Content Using a Reverse Genetics Strategy. (2011)

LOPEZ, HARRY O. Developing Non-GMO Tobacco Cultivars with Lower Alkaloid Content Using a Reverse Genetics Strategy.(Under the direction of Ralph E. Dewey.)Nicotiana tabacum L. produces alkaloids such as nicotine that are not only responsible for the pharmacological effects of tobacco products, but also serve in the formation of nitrosated compounds which have been shown to be carcinogenic.These compounds are known as tobacco-specific-nitrosamines (TSNAs), the carcinogenic properties of which have been documented in numerous mammalian studies.Considerable interest has been shown in the development of tobacco lines (and products) with low alkaloid content.Although the value of low alkaloid-containing tobaccos is subject to debate, potential advantages for such plants include: (1) reductions in TSNA levels;(2) possible reduced potential for addictiveness; (3) utilization in smoking cessation products; and (4) as the preferred platform for "biopharming" applications.The availability of reduced alkaloid tobaccos may be of increasing importance in the future, as the FDA is now responsible for the regulation of tobacco products, including the authority to mandate future products to contain lower levels of nicotine.In an attempt to develop tobacco plants that produce lower alkaloid levels, we used a reverse genetic strategy to inhibit the expression of key genes in the alkaloid biosynthetic pathway.Initially, chemical mutagenesis was used to develop a population of tobacco plants with mutations randomly distributed throughout the genome.Primers were then designed for the specific PCR amplification of exons from PMT, A622 and BBL, three genes whose role in alkaloid synthesis had been previously documented, or suggested.Bioinformatic tools allowed the identification of five isoforms for PMT, two isoforms for A622 and four isoforms for BBL.Primers were further developed for specificity against the
Spectroscopic study of Si-based quantum wells with neighbouring confinement structure (1997)

The optical properties of a neighbouring confinement structure (NCS), a promising candidate for a Si-based light emitter, were systematically investigated by using continuous-wave and time-resolved photoluminescence (PL) spectroscopy. An NCS consists of a single pair of a tensilely strained Si layer, a quantum well (QW) for electrons, and a compressively strained layer, a QW for holes, embedded between relaxed layers. Intense PL with an enhanced no-phonon (NP) line was clearly observed from NCS in spite of the indirect band structure in real and k-spaces. The quantum confinement effect was clearly observed by varying the well width, showing that the enhanced NP lines do come from the expected transitions of the NCS. Post-growth annealing was found to lead to selective quenching of the NP line compared to its transverse optical phonon replica (TO). Time-resolved PL study clarified that the radiative lifetime of the annealed sample increases with increasing temperature, while that of the as-grown sample shows no significant change at low temperatures (<40 K). These results were reasonably explained by considering that the exciton localization at the heterointerface is the controlling mechanism for the NP enhancement observed at low temperatures in the as-grown NCS. The idea was supported by the increase of the critical temperature for exciton delocalization by using a pure-Si/pure-Ge pair as the active layers, which is considered to construct a deep localization potential through the interface roughness.
Screening Mixtures by Affinity NMR (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTScreening Mixtures by Affinity NMRMengfen Lin, Michael J. Shapiro, and James R. WareingView Author Information Department of Analytics, Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901, and Metabolic and Cardiovascular Diseases, Preclinical Research, Novartis Pharmaceuticals Corporation, 59 Rt. 10, East Hanover, New Jersey 07936 Cite this: J. Org. Chem. 1997, 62, 25, 8930–8931Publication Date (Web):December 12, 1997Publication History Received30 June 1997Published online12 December 1997Published inissue 1 December 1997https://pubs.acs.org/doi/10.1021/jo971183jhttps://doi.org/10.1021/jo971183jbrief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views517Altmetric-Citations77LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Ethers,Mixtures,Molecules,Organic acids,Receptors Get e-Alerts
Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems (2020)

Abstract: Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale. One Sentence Summary In situ sequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.
Live Bivalent Vaccine for Parainfluenza and Influenza Virus Infections (2005)

Influenza and human parainfluenza virus infections are of both medical and economical importance. Currently, inactivated vaccines provide suboptimal protection against influenza, and vaccines for human parainfluenza virus infection are not available, underscoring the need for new vaccines against these respiratory diseases. Furthermore, to reduce the burden of vaccination, the development of multivalent vaccines is highly desirable. Thus, to devise a single vaccine that would elicit immune responses against both influenza and parainfluenza viruses, we used reverse genetics to generate an influenza A virus that possesses the coding region for the hemagglutinin/neuraminidase ectodomain of parainfluenza virus instead of the influenza virus neuraminidase. The recombinant virus grew efficiently in eggs but was attenuated in mice. When intranasally immunized with the recombinant vaccine, all mice developed antibodies against both influenza and parainfluenza viruses and survived an otherwise lethal challenge with either of these viruses. This live bivalent vaccine has obvious advantages over combination vaccines, and its method of generation could, in principle, be applied in the development of a "cocktail" vaccine with efficacy against several different infectious diseases.
Flupenthixol Decanoate in Schizophrenia (1974)

The anti-psychotic properties of flupenthixol have been described by Gottfries (1971) and Gross and Kaltenback (1965), and its antidepressant action by Reiter (1969), Merskey (1971), and Hall and Coleman (1973). It is available in the form of its decanoate in oil (‘Depixol’) as a depot injection.