gebhart/patrepeval huggingface dataset:
Isolation of the cDNA encoding glycoprotein-2 (GP-2), the major zymogen granule membrane protein (1991)

GP-2, a 78-kDa glycoprotein, is the major component of zymogen granule membranes of the exocrine pancreas. We report the isolation of the cDNA encoding for GP-2 from a rat pancreatic lambda gt-11 cDNA library. The cDNA is 1921 base pairs in length with an open reading frame encoding for a protein of 530 amino acids containing eight potential N-glycosylation sites. It encompasses the amino terminus of the protein including the signal sequence as evidenced by in vitro transcription/translation experiments conducted in the presence of dog pancreas rough microsomes in which the protein underwent apparent core glycosylation. A hydrophobic stretch of amino acids is present at the carboxyl terminus which is likely to serve as a signal for attachment of a glycosyl phosphatidylinositol (GPI) membrane anchor as has been described for GP-2. When the cDNA was introduced into HeLa cells by transfection, the expressed protein was located on the cell surface and could be released by incubation of the cells with phosphatidylinositol-specific phospholipase C, confirming that it is GPI-linked. Upon searching through the GenBank database, the GP-2 amino acid sequence was found to have a 53% identity and 85% similarity to human uromodulin/Tamm-Horsfall protein (THP) over a 450-amino acid stretch that encompassed all 28 cysteines after the signal sequence of GP-2. Uromodulin/Tamm-Horsfall protein, an 85-kDa glycoprotein synthesized by the kidney, shares several characteristics with GP-2 in addition to its sequence similarity. Both are attached to the membrane by a GPI anchor, but are also released from the apical surface of their respective cells and subsequently form large aggregates. Together they may define a new gene family.
Update of Diagnostic Evaluation of Craniosynostosis with a Focus on Pediatric Systematic Evaluation and Genetic Studies (2016)

Most craniosynostoses are sporadic, but may have an underlying genetic basis. Secondary and syndromic craniosynostosis accompanies various systemic diseases or associated anomalies. Early detection of an associated disease may facilitate the interdisciplinary management of patients and improve outcomes. For that reason, systematic evaluation of craniosynostosis is mandatory. The authors reviewed systematic evaluation of craniosynostosis with an emphasis on genetic analysis.
Autonomous Microfluidic Capillary System (2002)

The transport of minute amounts of liquids using microfluidic systems has opened avenues for higher throughput and parallelization of miniaturized bio/chemical processes combined with a great economy of reagents. In this report, we present a microfluidic capillary system (CS) that autonomously transports aliquots of different liquids in sequence: liquids pipetted into the service port of the CS flow unidirectionally through the various sections of the CS, which comprises a 15-pL reaction chamber, into the capillary pump. A CS can thus be operated by simply delivering the different samples to its service port. The liquid transport concept presented here is advantageous because the pumping and valving functions are integrated into the device by means of capillary phenomena, and it therefore does not require any external power supply or control device. Thus, arrays of CSs can easily be formed by cloning a functional CS. Alternatively, the flow of liquids in CSs can also be interactively tuned if desired by (i) forcing the evaporating of liquid out of the capillary pumps and (ii) by contacting a secondary, removable capillary pump to the embedded ones. We illustrate the possibilities of CSs by conducting a surface immunoassay for a cardiac marker, within 25 min, on an area of 100 x 100 microm2, using 16 sequential filling steps.
Cooking flavor and texture of rice stored under different conditions. (1983)

Rice stored at 40°C and 80% relative humidity for 60 days, which was sensorially evaluated as old rice, showed a significant difference in cooking quality and texture of when cooked as compared with 4°C-stored rice. Free phenolic acids were detected in a larger amount in the 40°C-stored rice, and it is proposed that the increase of phenolic acids during storage may partly contribute to the cooking properties of old rice. GC analyses of the volatiles of cooked rice showed that a larger amount of pentanal, hexanal, heptanal, alkenals, ketones, 2-pentylfuran, 4-vinylphenol, etc., and a smaller amount of 1-pentanol, 1-hexanol, etc. were found in 40°C-stored rice than in 4°C-stored rice. The relationship between changes in these volatile components and the flavor of cooked old rice is also discussed.
Mutations in Salmonella Pathogenicity Island 2 (SPI2) Genes Affecting Transcription of SPI1 Genes and Resistance to Antimicrobial Agents (1998)

The Salmonella typhimurium genome contains two pathogenicity islands (SPI) with genes encoding type III secretion systems for virulence proteins. SPI1 is required for the penetration of the epithelial layer of the intestine. SPI2 is important for the subsequent proliferation of bacteria in the spleens of infected hosts. Although most mutations in SPI2 lead to a strong reduction of virulence, they have different effects in vitro, with some mutants having significantly increased sensitivity to gentamicin and the antibacterial peptide polymyxin B. Previously we showed that certain mutations in SPI2 affect the ability of S. typhimurium to secrete SPI1 effector proteins and to invade cultured eukaryotic cells. In this study, we show that these SPI2 mutations affect the expression of the SPI1 invasion genes. Analysis of reporter fusions to various SPI1 genes reveals highly reduced expression of sipC, prgK, and hilA, the transcriptional activator of SPI1 genes. These observations indicate that the expression of one type III secretion system can be influenced dramatically by mutations in genes encoding a second type III secretion system in the same cell.
Paired analysis of TCRα and TCRβ chains at the single-cell level in mice (2010)

Characterizing the TCRα and TCRβ chains expressed by T cells responding to a given pathogen or underlying autoimmunity helps in the development of vaccines and immunotherapies, respectively. However, our understanding of complementary TCRα and TCRβ chain utilization is very limited for pathogen- and autoantigen-induced immunity. To address this problem, we have developed a multiplex nested RT-PCR method for the simultaneous amplification of transcripts encoding the TCRα and TCRβ chains from single cells. This multiplex method circumvented the lack of antibodies specific for variable regions of mouse TCRα chains and the need for prior knowledge of variable region usage in the TCRβ chain, resulting in a comprehensive, unbiased TCR repertoire analysis with paired coexpression of TCRα and TCRβ chains with single-cell resolution. Using CD8+ CTLs specific for an influenza epitope recovered directly from the pneumonic lungs of mice, this technique determined that 25% of such effectors expressed a dominant, nonproductively rearranged Tcra transcript. T cells with these out-of-frame Tcra mRNAs also expressed an alternate, in-frame Tcra, whereas approximately 10% of T cells had 2 productive Tcra transcripts. The proportion of cells with biallelic transcription increased over the course of a response, a finding that has implications for immune memory and autoimmunity. This technique may have broad applications in mouse models of human disease.
From Molecules to Crystal Engineering:  Supramolecular Isomerism and Polymorphism in Network Solids (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFrom Molecules to Crystal Engineering: Supramolecular Isomerism and Polymorphism in Network SolidsBrian Moulton and Michael J. ZaworotkoView Author Information Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, SCA 400, Tampa, Florida 33620 Cite this: Chem. Rev. 2001, 101, 6, 1629–1658Publication Date (Web):May 12, 2001Publication History Received6 September 2000Published online12 May 2001Published inissue 1 June 2001https://pubs.acs.org/doi/10.1021/cr9900432https://doi.org/10.1021/cr9900432research-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views21321Altmetric-Citations5872LEARN 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:Cavities,Chemical structure,Crystal structure,Ligands,Molecular structure Get e-Alerts
[Activation of complement by hemodialysis membrane]. (1989)

Incubation of normal human serum with hemodialysis membranes in vitro resulted in conversion of C3 which was detected by crossed immunoelectrophoresis. In addition, formation of C3d was also observed, as was detected by double-decker rocket immunoelectrophoresis. Furthermore, breakdown products of complement (iC3b, C4d & Bb) in plasma samples were measured by ELISA. The microassay plates were coated with monoclonal antibodies which bind specifically to human iC3b, C4d and Bb, respectively, while the plasma samples were drawn from five polycystic kidney patients during initial hemodialysis. As a result, the iC3b and Bb levels in plasma were seen to increase during hemodialysis but the C4d levels revealed no significant changes. It was also observed that the Bb levels in patients undergoing hemodialysis were significantly higher than those in various renal and collagen diseases. Terminal complement complex (TCC) was not present in detectable amounts in normal human serum when measured by ELISA. However, incubation of normal human serum with hemodialysis membranes in vitro resulted in detection of TCC. TCC was present in the same plasma samples drawned from the five polycystic kidney patients during initial hemodialysis. It is suggestive that activation of complement by hemodialysis membrane is predominantly mediated through the alternative pathway and products such as TCC and anaphylatoxin are formed by this activation.
Indoor navigation system using image and sensor data processing on a smartphone (2012)

The navigation and mobile positioning paradigm has been an active research topic in the past two decades. The proliferation of mobile devices equipped with inertial sensors able to detect phone motion lead to an increase in research and product development in the field of personal locating technologies. Within this scenario, this paper proposes a combined technique for the estimation of user's position in indoor environments, which only relies on sensors of a commercial smartphone, without the active aid of external infrastructures. The smartphone's video camera is used to identify known keypoints, named anchors previously identified and geo-referenced in the building map. A SURF algorithm is employed for quick and effective detection of image features independently from the viewpoint. The accelerometers and the compass of the smartphone are used to estimate the amount of steps and the direction in which the user is moving by performing statistical data processing. Heading data is compensated taking into account the relative position of the smartphone with respect to the user. Experiments have been carried out in a real scenario showing the effectiveness of the proposed solutions.
Action of FR901228, a Novel Antitumor Bicyclic Depsipeptide Produced byChromo-bacterium violaceumNo. 968, on Ha-rasTransformed NIH3T3 Cells (1994)

FR901228, a novel antitumor antibiotic, reversed the transformed morphology of the Ha-ras transformants, Ras-1 cells, and inhibited their growth. The reduction of c-myc expression was observed in FR901228-treated Ras-1 cells by RNA dot-blot hybridization. This reduction of c-myc expression and morphological reversion of the transformed cells to normal were correlated with growth inhibition (G0/G1 arrest in cell cycle).
PCA3: A Molecular Urine Assay for Predicting Prostate Biopsy Outcome (2008)

PCA3 is independent of prostate volume, serum prostate specific antigen level and the number of prior biopsies. The quantitative PCA3 score correlated with the probability of positive biopsy. Logistic regression results suggest that the PCA3 score could be incorporated into a nomogram for improved prediction of biopsy outcome. The results of this study provide further evidence that PCA3 is a useful adjunct to current methods for prostate cancer diagnosis.
Experimental Autoimmune Encephalomyelitis Induction in Genetically B Cell–deficient Mice (1996)

Experimental autoimmune encephalomyelitis (EAE) is an animal model for autoimmune central nervous system disease mediated by CD4 T cells. To examine the role of B cells in the induction of EAE, we used B10.PL (I-Au) mice rendered deficient in B cells by deletion of their mu chain transmembrane region (B10.PLmicroMT). By immunizing B10.PL and B10.PLmicroMT mice with the NH-terminal myelin basic protein encephalitogenic peptide Ac1-11, we observed no difference in the onset or severity of disease in the absence of mature B cells. There was, however, a greater variation in disease onset, severity, and especially of recovery in the B cell-deficient mice compared to controls. B10.PLmicroMT mice rarely returned to normal in the absence of B cells. Taken together, our data suggest that B cells do not play a role in the activation of encephalitogenic T cells, but may contribute to the immune modulation of acute EAE. The mechanisms to explain these effects are discussed.
A visible (AlGa)As heterostructure laser grown by molecular beam epitaxy (1981)

Visible (AlGa)As double-heterostructure lasers with a 200-Å Al0.17Ga0.83As active layer have been prepared by molecular beam epitaxy. The diodes lase at ∼7520 Å and have an average pulsed threshold current density Jth of 810A/cm2, which agrees for the first time with the value calculated from first principles without adjustable parameters by Casey, Jr., in the very thin active-layer regime. The far-field half-power full-width ϑd in the direction perpendicular to the junction plane is as narrow as 11 °. The temperature coefficient T0 of the temperature dependence of threshold is 110 K.
Six putative two-component regulatory systems isolated from Lactococcus lactis subsp. cremoris MG1363 The GenBank accession numbers for the sequences of the six 2CSs and surrounding ORFs determined in this work are AF172649, AF176556, AF178425, AF172650, AF176557 and AF176809 for systems A–F, respectively. (2000)

The genetic elements specifying six putative two-component regulatory systems (2CSs) were identified on the chromosome of Lactococcus lactis MG1363. These 2CSs appear to represent distinct loci, each containing a histidine kinase and response-regulator-encoding gene pair. Transcriptional analysis of the six 2CSs was performed either by generating transcriptional fusions to a reporter gene or by primer extension. Two of the systems appeared to be expressed constitutively at a high level, whilst the remaining four exhibited growth-phase-dependent expression. Insertional mutagenesis established that the two constitutively expressed 2CSs are necessary for normal cell growth and/or survival. Mutational analysis of the remaining four systems revealed that they are implicated in susceptibility to extreme pH, osmotic or oxidative conditions, or the regulation of phosphatase activity in L. lactis.
Atomic Layer Epitaxy Growth of TiN Thin Films from Til4 and  NH 3 (1998)

TiN thin films were grown by atomic layer epitaxy using titanium tetraiodide () and ammonia () as precursors. The films were characterized with Rutherford backscattering spectrometry, time‐of‐flight elastic recoil detection analysis, energy dispersive X‐ray spectroscopy, X‐ray diffraction, scanning electron microscopy, and resistivity measurements. Both the growth rate and film quality were markedly dependent on the growth temperature. As the temperature was increased from 400 to 500°C the growth rate increased from 0.12 to 0.30 Å/cycle, and the resistivity decreased from 380 to 70 μΩ cm. Also, the oxygen content decreased with increasing temperature being about 10 atom % in the films grown at 475 to 500°C. The iodine contents were below 0.5 atom %.
Substrate specificity of eukaryotic signal peptidase. Site-saturation mutagenesis at position -1 regulates cleavage between multiple sites in human pre (delta pro) apolipoprotein A-II. (1988)

We have previously described a novel mutant of human preproapolipoprotein A-II (pre(delta pro)apoA-II) in which the wild-type 18-amino acid-long signal sequence (Gly18 decreases) was functionally redefined to 20 amino acids in length (Ala 20 decreases). We have used this mutant as a model preprotein to probe the substrate specificity of eukaryotic signal peptidase. Site-saturation mutagenesis was performed resulting in the substitution of 13 different amino acids (acidic, basic, aromatic, hydrophobic, and small-neutral) for Ala20 (or position -1). The effects of these substitutions were assessed using an in vitro transcription/translation/microsomal membrane processing system. NH2-terminal sequence analysis of the 13 mutant proteins demonstrated that amino acids which occupy position -1 in a signal peptide are critical in establishing a good context for signal peptidase cleavage and that two or more potential sites of cleavage may compete for recognition by signal peptidase.
Serotype Distribution and Antimicrobial Resistance of Streptococcus pneumoniae Isolates Causing Systematic Infections in Spain, 1979-1989 (1990)

Serotypes and antibiotic susceptibilities were determined for 2,197 Streptococcus pneumoniae strains isolated from patients with systemic infections over an 11-year period. The predominant serogroups and serotypes, in order of decreasing frequency, were 3, 6, 23, 19, 9, 1, 5, 8, 7, 14, 4, and 15; these types accounted for more than 75% of the strains studied. Altogether, 93% of the pneumococci belonged to groups or types included in the 23-valent pneumococcal vaccine. Overall, 65.5% of pneumococci were resistant to one or more drugs. The incidence of penicillin-resistant pneumococci rose from 6% in 1979 to 44% in 1989, and the degree of penicillin resistance also increased throughout the study. Overall, the resistance rates were 28% for penicillin, 56% for tetracycline, 43% for chloramphenicol, and 5% for erythromycin. Seventy-one pneumococcal isolates resistant to all four antibiotics tested were found. The prevalence of pneumococcal resistance in Spain is, as far as we know, among the highest published to date.
Prediction of biologically significant components from microarray data:Independently Consistent Expression Discriminator (ICED) (2002)

The data described herein utilized ICED to analyze the large AML/ALL training and test data set (Golub et al., 1999, Science, 286, 531-537) in addition to a smaller data set consisting of an animal model of the childhood neurodegenerative disorder, Batten disease, generated for this study. Both of the analyses presented herein have correctly predicted biologically relevant perturbations that can be used for disease classification, irrespective of sample size. Furthermore, the results have provided candidate proteins for future study in understanding the disease process and the identification of potential targets for therapeutic intervention.
Separable portions of the CD2 cytoplasmic domain involved in signaling and ligand avidity regulation. (1993)

Effective T cell immune responses require the molecular interplay between adhesive and signaling events mediated by the T cell receptor for antigen (TCR) and other cell surface coreceptor molecules. In this report, we have distinguished between the role of regulated adhesion and transmembrane signaling in coreceptor function using the T cell glycoprotein CD2. By binding its ligands on antigen-presenting cell (APC), CD2 serves both to initiate signal transduction events and to promote cellular adhesion. Furthermore, the avidity of CD2 for one ligand, CD58 (LFA-3), is regulated by TCR signaling. We have expressed wild type CD2 and a series of mutated CD2 molecules in an antigen-specific murine T cell hybridoma. Structure-function studies using these stably transfected cell lines identify two structurally and functionally distinct regions of the 116 amino acid (aa) cytoplasmic domain. One region is required for CD2-mediated signal transduction, and a separate COOH-terminal 21 aa portion is required for CD2 activity regulation. Cell lines expressing CD2 molecules lacking the cytoplasmic segment required for CD2-initiated IL-2 production retain the ability to upregulate CD2 avidity. Conversely, cell lines expressing CD2 mutants lacking the cytoplasmic segment required for avidity regulation retain the ability to initiate CD2-specific signaling. In antigen-specific T cell responses, basal binding of CD2 to its ligands enhances antigen responsiveness only minimally, whereas regulated avidity and transmembrane signaling are both required for optimal coreceptor function. Taken together, these studies demonstrate the independent contributions of regulated adhesion and intracellular signaling in CD2 coreceptor function.
Osteopontin: An Interfacial Extracellular Matrix Protein in Mineralized Tissues (1996)

Among the noncollagenous matrix proteins found in mineralized tissues (MTs), colloidal-gold immunocytochemistry has demonstrated that the ultrastructural distribution of osteopontin (OPN) is unique in that this protein preferentially accumulates at MT interfaces. In bone, OPN is present as a major component of cell- and matrix-matrix interfacial structures termed laminae limitantes and cement lines, respectively. Here, we review the implications of this distinct, interfacial tissue distribution as it relates to the properties and functional motifs of OPN (e.g. RGD, polyAsp, phosphorylation) in different MTs, and more specifically, how it pertains to current theory on the cellular and extracellular matrix (ECM) events associated with bone remodeling. The production of OPN as one of the earliest, and latest, secretory activities of the osteoblast lineage is discussed, together with a consideration of the role of OPN in cement lines and laminae limitantes in bone and in other normal, pathological and healing MTs such as teeth, kidney stones, bone wound healing and implant osseointegration. Further to its ability to influence cell dynamics, calcification and possibly tissue cohesion in MTs, it is proposed that OPN in cement lines may also promote adhesion between apposing substrata. With regard to this latter function, it is suggested that the molecular interactions within, and biomechanical properties of, such an OPN-rich interfacial zone may be important in minimizing strain-induced fatigue damage and microcrack propagation in bone and across other MT interfaces.