gebhart/patrepeval huggingface dataset:
Integrin function and regulation in development (2000)

Integrins are a large family of membrane receptors, consisting of alpha and beta subunits, that play a pivotal role in the interaction of cells with the extracellular matrix. Such interaction regulates the organization of cells in organs and tissues during development as well as cell differentiation and proliferation. We have shown that unfertilized oocytes express integrins that might be important during fertilization. We also analyzed nervous system and muscle tissue development showing that integrin expression is precisely regulated during organization of these tissues. The results indicate that two distinct integrin alpha subunits mediate the outgrowth of processes in nerve and glial cells. Alpha1 integrin, a laminin receptor, is up-regulated by nerve growth factor and other differentiation stimuli and is involved in neurite extension by nerve cells. In contrast, process extension by glial cells is likely to involve the alphaV integrin. Moreover, the latter integrin subunit is also transiently expressed in muscle of the embryo body where it localizes predominantly at developing myotendinous junctions. After birth this integrin disappears and is substituted by the alpha7 subunit. At the same time, important changes also occur in the expression of the associated beta subunit. In fact, the beta1A isoform which is expressed in fetal muscles, is substituted by beta1D. These isoforms are generated by alternative splicing and differ in only a few amino acid residues at the COOH terminus of the protein. This region of the molecule is exposed at the cytoplasmic face of the plasma membrane and is connected to the actin filaments. Our results show that beta1D, which is expressed only in striated muscle tissues, binds to both cytoskeletal and extracellular matrix proteins with an affinity higher than beta1A. Thus, beta1D provides a stronger link between the cytoskeleton and extracellular matrix necessary to support mechanical tension during muscle contraction. These results indicate that cells can regulate their interactions with the extracellular matrix by changing their expression of alpha integrin subunits and thus ligand specificity, or by more subtle changes involving alternative usage of different cytoplasmic domains. The important role of both alpha and beta integrin subunit cytoplasmic domains during development is further illustrated by the analysis of targeted mutations which we have generated by homologous recombination in mice.
Therapeutic Applications of Oligonucleotides (1992)

This review focuses strictly on the pharmacodynamic considerations of the use of oligonucleotides designed to interact with nucleic acids as therapeutics. The objectives are to place oligonucleotide therapeutics in the context of modern drug discovery and development and to summarize recent progress.
Collagen Cross-Linking Using Rose Bengal and Green Light to Increase Corneal Stiffness (2013)

RGX significantly increases cornea stiffness in a rapid treatment (≅12 minutes total time), does not cause toxicity to keratocytes and may be used to stiffen corneas thinner than 400 μm. Thus, RGX may provide an attractive approach to inhibit progression of keratoconus and other ectatic disorders.
Expression of neutral amino acid transporter ASCT2 in human prostate. (2003)

The neutral amino acid transporter ASCT2 has been associated with increased metabolism in malignant tumors. Its biological significance in tumor proliferation, progression, and its impact on cancer patients' survival remains largely unknown. Tissue microarray (TMA) technology was used to build arrays from 640 cases of radical prostatectomies (triplicate normal prostate, benign prostatic hyperplasia (BPH), and prostate adenocarcinoma (PCa)). Slides were immunostained with an antibody to ASCT2 and scored using a 0-3+ semi-quantitation scoring system for both intensity and percentage. Correlation of ASCT2 expression with patients' clinical and pathological variables was analyzed by the Spearman correlation test. Kaplan-Meier analysis and log rank test were used to determine the probability of disease recurrence. Cox regression model was also used for multivariate analysis. 497 PCa had accessible data. ASCT2 was localized in the cytoplasm of epithelial cells of normal prostate, BPH and PCa. High-level expression of ASCT2 was significantly higher in normal tissues (49%) as compared to BPH (25.8%) or cancer (25.3%) (p < 0.001). ASCT2 expression was weakly but significantly correlated with preoperative PSA (Pre-PSA), Gleason score (GS), lymph node status (LN) (p = 0.019). ASCT2 expression was significantly associated with shorter time to biochemical recurrence only on univariate analysis (p = 0.046). ASCT2 appears to be required for the glutamine metabolism in both nonmalignant and malignant prostate. ASCT2-positive PCa seems to be related to a more aggressive biological behavior. ASCT 2 seems to be involved in tumor progression.
Applications of nanopipettes in bionanotechnology (2009)

At present, technical hurdles remain in probing biochemical processes in living cells and organisms at nanometre spatial resolution, millisecond time resolution and with high specificity and single-molecule sensitivity. Owing to its unique shape, size and electrical properties, the nanopipette has been used to obtain high-resolution topographic images of live cells under physiological conditions, and to create nanoscale features by controlled delivery of biomolecules. In the present paper, I discuss recent progress in the development of a family of new methods for nanosensing and nanomanipulation using nanopipettes.
Critical thickness enhancement of epitaxial SiGe films grown on small structures (2005)

This paper explores stress management in SiGe with two kinds of structures, namely, epitaxial SiGe films on small pillars and fins. In addition to the compliant substrate effect in the film/fin structures, the geometric effect in the film/pillar structures plays another important role in critical thickness enhancement. The stress-strain states of these two systems are calculated and the equilibrium critical thicknesses are predicted, using the work method, for different fin thicknesses, pillar radii, and Ge concentrations. Compared to conventional films grown on planar bulk substrates, the critical thicknesses for fin and pillar structures are increased significantly. SiGe films with various thicknesses and compositions were epitaxially grown around vertical fins and horizontal membranes with thicknesses as thin as 12nm to demonstrate the concepts. Cross-sectional transmission electron microscopy analysis showed that dislocation densities are much smaller than for films grown on bulk Si substrates. The dislocation density versus fin thickness also illustrated the expected trend.
Methionine Regeneration and Aminotransferases in Bacillus subtilis , Bacillus cereus , and Bacillus anthracis (2003)

The conversion of ketomethiobutyrate to methionine has been previously examined in a number of organisms, wherein the aminotransferases responsible for the reaction have been found to be members of the Ia subfamily (L. C. Berger, J. Wilson, P. Wood, and B. J. Berger, J. Bacteriol. 183:4421-4434, 2001). The genome of Bacillus subtilis has been found to contain no subfamily Ia aminotransferase sequences. Instead, the analogous enzymes in B. subtilis were found to be members of the If subfamily. These putative aspartate aminotransferases, the yugH, ywfG, ykrV, aspB, and patA gene products, have been cloned, expressed, and characterized for methionine regeneration activity. Only YkrV was able to convert ketomethiobutyrate to methionine, and it catalyzed the reaction only when glutamine was used as amino donor. In contrast, subcellular homogenates of B. subtilis and Bacillus cereus utilized leucine, isoleucine, valine, alanine, phenylalanine, and tyrosine as effective amino donors. The two putative branched-chain aminotransferase genes in B. subtilis, ybgE and ywaA, were also cloned, expressed, and characterized. Both gene products effectively transaminated branched-chain amino acids and ketoglutarate, but only YbgE converted ketomethiobutyrate to methionine. The amino donor preference for methionine regeneration by YbgE was found to be leucine, isoleucine, valine, phenylalanine, and tyrosine. The B. subtilis ybgE gene is a member of the family III of aminotransferases and falls in a subfamily designated here IIIa. Examination of B. cereus and Bacillus anthracis genome data found that there were no subfamily IIIa homologues in these organisms. In both B. cereus and B. anthracis, two putative branched-chain aminotransferases and two putative D-amino acid aminotransferases were discovered as members of subfamily IIIb. These four sequences were cloned from B. cereus, expressed, and characterized. Only the gene product from the sequence designated Bc-BCAT2 was found to convert ketomethiobutyrate to methionine, with an amino donor preference of leucine, isoleucine, valine, phenylalanine, and tyrosine. The B. anthracis homologue of Bc-BCAT2 was also cloned, expressed, and characterized and was found to be identical in activity. The aminooxy compound canaline was found to be an uncompetitive inhibitor of B. subtilis YbgE and also inhibited growth of B. subtilis and B. cereus in culture.
COLD-PCR: a new platform for highly improved mutation detection in cancer and genetic testing (2009)

PCR is widely employed as the initial DNA amplification step for genetic testing and cancer biomarker detection. However, a key limitation of PCR-based methods, including real-time PCR, is the inability to selectively amplify low levels of variant alleles in a wild-type allele background. As a result, downstream assays are limited in their ability to identify subtle genetic changes that can have a profound impact on clinical decision-making and outcome or that can serve as cancer biomarkers. We developed COLD-PCR (co-amplification at lower denaturation temperature-PCR) [Li, Wang, Mamon, Kulke, Berbeco and Makrigiorgos (2008) Nat. Med. 14, 579-584], a novel form of PCR that amplifies minority alleles selectively from mixtures of wild-type and mutation-containing sequences irrespective of the mutation type or position on the sequence. Consequently, COLD-PCR amplification from genomic DNA yields PCR products containing high-prevalence variant alleles that can be detected. Since PCR constitutes a ubiquitous initial step for almost all genetic analysis, COLD-PCR provides a general platform to improve the sensitivity of essentially all DNA-variation detection technologies including Sanger sequencing, pyrosequencing, single molecule sequencing, mutation scanning, mutation genotyping or methylation assays. COLD-PCR combined with real-time PCR provides a new approach to boost the capabilities of existing real-time mutation detection methods. We replaced regular PCR with COLD-PCR before sequencing or real-time mutation detection assays to improve mutation detection-sensitivity by up to 100-fold and identified novel p53/Kras/EGFR (epidermal growth factor receptor) mutations in heterogeneous cancer samples that were missed by all existing methods. For clinically relevant micro-deletions, COLD-PCR enabled exclusive amplification and isolation of the mutants. COLD-PCR is expected to have diverse applications in the fields of biomarker identification and tracing, genomic instability, infectious diseases, DNA methylation testing and prenatal identification of fetal alleles in maternal blood.
Identification of a Novel Hypothalamic Neuropeptide Y Receptor Associated with Feeding Behavior (1996)

Neuropeptide Y (NPY) plays important roles in the central control of appetite and energy balance, but the receptor subtype responsible for this function has not been cloned. Here we report the cloning by expression of a novel NPY receptor subtype from a rat hypothalamus cDNA library. The novel receptor, referred to as the NPY Y5 receptor, has a transcript of approximately 2.6 kilobases with an open reading frame of 1335 base pairs that encodes a 445-amino acid protein. The amino acid sequence deduced from the rat Y5 cDNA clone shows only 30-33% identity to other NPY receptors, including Y1, Y2, and Y4/PP1. Using the rat Y5 receptor cDNA probe, the human homologue was obtained by low stringency hybridization. The human Y5 amino acid sequence has 88% identity to the rat Y5 receptor. Importantly, pharmacological analysis shows that the rat and human Y5 receptors have high affinity for the peptides that elicit feeding (e.g. NPY, PYY, (2-36)NPY, and (LP)NPY) and low affinity for nonstimulating peptides (e.g. (13-36)NPY and rat PP), suggesting that it is the NPY feeding receptor subtype.
Raf kinase as a target for anticancer therapeutics (2005)

The Ras-Raf-MEK-ERK (ERK) pathway is a logical therapeutic target because it represents a common downstream pathway for several key growth factor tyrosine kinase receptors which are often mutated or overexpressed in human cancers. Although considered mainly growth-promoting, in certain contexts, this pathway also seems to be apoptosis-suppressing. Several novel agents targeting this pathway have now been developed and are in clinical trials. One of the most interesting new agents is BAY 43-9006. Although initially developed as a Raf kinase inhibitor, it can also target several other important tyrosine kinases including VEGFR-2, Flt-3, and c-Kit, which contributes to its antiproliferative and antiangiogenic properties. To date, encouraging results have been seen with BAY 43-9006, particularly in renal cell cancers which are highly vascular tumors. This review will provide an overview of the ERK signaling pathway in normal and neoplastic tissue, with a specific focus on novel therapies targeting the ERK pathway at the level of Raf kinase.
Mast cell tumor necrosis factor α production is regulated by MEK kinases (1997)

Mast cells synthesize and secrete specific cytokines and chemokines which play an important role in allergic inflammation. Aggregation of the high-affinity Fc receptor (FcɛRI) for immunoglobulin E (IgE) in MC/9 mouse mast cells stimulates the synthesis and secretion of tumor necrosis factor α (TNF-α). FcɛRI aggregation activates several sequential protein kinase pathways, leading to increased activity of extracellular signal-regulated kinases (ERKs), c-Jun amino-terminal kinases (JNKs), and the p38 mitogen-activated protein (MAP) kinase. Inhibition of ERKs with the compound PD 098059 had little effect on FcɛRI-stimulated TNF-α production. Aggregation of FcɛRI stimulated MEK kinase 1 (MEKK1) activity, which activates JNK kinase (JNKK), the kinase that phosphorylates and activates JNKs. Expression of activated MEKK1 (ΔMEKK1) in MC/9 cells strongly stimulated JNK activity but only weakly stimulated p38 activity, and it induced a large activation of TNF-α promoter-regulated luciferase gene expression. Inhibitory mutant JNK2 expressed in MC/9 cells significantly blunted FcɛRI stimulation of TNF-α promoter-driven luciferase expression. Wortmannin, an inhibitor of phosphatidylinositol 3-kinase, diminished FcɛRI-mediated TNF-α synthesis, significantly blunted JNK activation and TNF-α promoter-driven luciferase expression, and only weakly inhibited p38 kinase activation. Inhibition of NFκB activation resulting from ΔMEKK1 expression or FcɛRI stimulation did not affect TNF-α promoter-driven luciferase expression. Our findings define a MEKK-regulated JNK pathway activated by FcɛRI that regulates TNF-α production in mast cells.
The sustained-release behavior and in vitro and in vivo transfection of pEGFP-loaded core-shell-structured chitosan-based composite particles (2014)

Novel submicron core-shell-structured chitosan-based composite particles encapsulated with enhanced green fluorescent protein plasmids (pEGFP) were prepared by complex coacervation method. The core was pEGFP-loaded thiolated N-alkylated chitosan (TACS) and the shell was pH- and temperature-responsive hydroxybutyl chitosan (HBC). pEGFP-loaded TACS-HBC composite particles were spherical, and had a mean diameter of approximately 120 nm, as measured by transmission electron microscopy and particle size analyzer. pEGFP showed sustained release in vitro for >15 days. Furthermore, in vitro transfection in human embryonic kidney 293T and human cervix epithelial cells, and in vivo transfection in mice skeletal muscle of loaded pEGFP, were investigated. Results showed that the expression of loaded pEGFP, both in vitro and in vivo, was slow but could be sustained over a long period. pEGFP expression in mice skeletal muscle was sustained for >60 days. This work indicates that these submicron core-shell-structured chitosan-based composite particles could potentially be used as a gene vector for in vivo controlled gene transfection.
Potent Antigen-specific Immune Responses Stimulated by Codelivery of CpG ODN and Antigens in Degradable Microparticles (2007)

CpG ODN stimulates a TH1 response through its receptor Toll-like receptor 9 (TLR9). TLR9 is a receptor that is found intracellularly. Microparticles are efficiently internalized by dendritic cells (DCs) and macrophages and would thus be an ideal delivery vehicle for CpG ODN to reach its target site thereby enhancing the TH1 response to an antigen also encapsulated in the microparticle. Here, we show that careful control over fabrication parameters can produce biodegradable microparticles with predictable size distributions, surface morphology, and shape. Entrapment efficiencies of the model antigen OVA ranged from 19% to 23% with an average loading of 10 microg/mg of microparticles. For CpG ODN, these values were 33% to 35%, which corresponded to an average loading of 8.5 microg/mg of microparticles. The microparticles release CpG ODN and OVA in a burst followed by sustained release profile. At the highest concentration of microparticles incubated with a pure DC cell line, 92% of DCs had internalized microparticles by 16 hours, confirming that DCs efficiently take up the microparticles. Microparticles are capable of inducing DC maturation as determined by up-regulation of CD80 and CD86 markers. Although the presence of CpG ODN in the microparticles did not impact on the phenotype of the DCs, it was necessary for DCs to induce activation of antigen-specific T cells as indicated by interferon-gamma production. Microparticles entrapping both antigen and CpG ODN induced significantly higher amounts of anti-OVA antibody production than other preparations such as the soluble OVA and CpG ODN (P<0.01) and stimulated stronger IgG2a production than delivery of microparticles entrapping antigen alone. We conclude that co-encapsulating immunostimulatory CpG ODN and antigen in degradable microparticles is an effective approach to enhancing development of a TH1 immune response.
Affinity for the cognate monoclonal antibody of synthetic peptides derived from selection by phage display (2000)

Randomized peptide sequences displayed at the surface of filamentous phages are often used to select antibody ligands. The selected sequences are generally further used in the form of synthetic peptides; however, as such, their affinity for the selecting antibody is extremely variable and factors influencing this affinity have not been fully deciphered. We have used an f88.4 phage-displayed peptide library to identify ligands of mAb 11E12, an antibody reactive to human cardiac troponin I. A majority of the sequences thus selected showed a (T/A/I/L) EP(K/R/H) motif, homologous to the Y-TEPH motif identified by multiple peptide synthesis as the critical motif recognized by mAb 11E12 in the peptide epitope. A set of 15-mer synthetic peptides derived from the phage-selected sequences was used in BIACORE to characterize their interaction with mAb 11E12. Most peptides exhibited affinities in the 7-26 nM range. These affinities represented, however, only 1.9-7. 5% of the affinity of the 15-mer peptide epitope. In circular dichroism experiments, the peptide epitope showed a propensity to have some stabilized conformation, whereas a low-affinity peptide selected by phage-display did not. To try to decipher the molecular basis of this difference in affinity, new peptides were prepared by grafting the N- or the C-terminal sequence of the peptide epitope to the Y-TEPK motif of a low-affinity peptide selected by phage-display. These hybrid peptides showed marked increases both in affinity (as assessed using BIACORE) and in inhibitory potency (as assessed in competition ELISA), compared with the parent sequence. Thus, the sequences flanking the motif, although not containing critical residues, convey some determinants necessary for high affinity. The affinity of a given peptide strongly depends on its capacity to maintain the antigenically reactive structure it has on the phage, implying that it is impossible to predict whether high- or low-affinity peptides will be obtained from phage display.
Quantitative analysis of cocaine in solid mixtures using Raman spectroscopy and chemometric methods (2000)

Near-infrared (785 nm) excitation was used to obtain Raman spectra from a series of 33 solid mixtures containing cocaine, caffeine and glucose (9.8–80.6% by weight cocaine), which were then analysed using chemometric methods. Principal component analysis of the data was employed to ascertain what factors influenced the spectral variation across the concentration range. It was found that 98% of the spectral variation was accounted for by three principal components. Analysis of the score and loadings plots for these components showed that the samples can be clearly classified on the basis of cocaine concentration. Discrimination on the basis of caffeine and glucose concentrations was also possible. Quantitative calibration models were generated using partial least-squares algorithms which predicted the concentration of cocaine in the solid mixtures containing caffeine and glucose from the Raman spectrum with a root mean standard error of prediction (RMSEP) of 4.1%. Caffeine and glucose concentrations were estimated with RMSEPs of 5.2 and 6.6%, respectively. These measurements demonstrate the feasibility of using near-IR Raman spectroscopy for rapid quantitative characterization of illegal narcotics. Copyright © 2000 John Wiley & Sons, Ltd.
Plasma-induced damage in GaN-based light emitting diodes (2007)

The effects of plasma induced damage in different conditions of ICP and PECVD processes on LEDs were presented. For ICP mesa etch, in an effort to confirm the effects of dry etch damage on the optical properties of p-type GaN, a photoluminescence (PL) measurement was investigated with different rf chuck power. It was founded the PL intensity of the peak decreased with increasing DC bias and the intensity of sample etched at a higher DC bias of -400V is less by two orders of magnitude than that of the as-grown sample. Meanwhile, In the I-V curve for the etched samples with different DC biases, the reverse leakage current of higher DC bias sample was obviously degraded than the lower one. In addition, plasma induced damage was also inevitable during the deposition of etch masks and surface passivation films by PECVD. The PL intensity of samples deposited with different powers sharply decreased when the power was excessive. The PL spectra of samples deposited under the fixed condition with the different processing time were measured, indicating the intensity of sample deposited with a lower power did not obviously vary after a long time deposition. A two-layer film was made in order to improve the compactness of sparse dielectric film deposited with a lower power.