gebhart/patrepeval huggingface dataset:
Topographical and functional investigation of Escherichia coli penicillin-binding protein 1b by alanine stretch scanning mutagenesis (1997)

Penicillin-binding proteins (PBPs) are the targets of beta-lactam antibiotics. We have used a systematic five-alanine substitution method (called ASS [alanine stretch scanning] mutagenesis) to investigate the functional or structural role of various stretches of amino acids in the PBP1b of Escherichia coli. To probe the specific activity of each variant, the antibiotic discs assay was used with strain QCB1 (delta ponB) in the presence of cefaloridine, which totally inhibits the complementing action of PBP1a. This in vivo test has been combined with a quick and efficient in vitro test of the penicillin-binding activity of each of these variants with fluorescent penicillin. This approach has enabled us to show an unexpected role of the N-terminal and C-terminal tails of PBP1b. Moreover, we have established the correct position in PBP1b of the SMN motif that, with the SXXK and the KTG motifs, constitutes the signature of the penicilloyl serine transferases family. Finally, we have shown that the transglycosylase and the transpeptidase domains are separated by an inert linker region, where substitutions and insertions can be made without hindering the in vivo and in vitro activity of the protein.
Growth factors and cytokines in acute renal failure. (1997)

The mammalian kidney is susceptible to injury by ischemia/reperfusion and toxins, and regeneration after injury is characterized by hyperplasia and recovery of the damaged epithelial cells that line the tubules. Locally produced growth factors may serve as mediators of nephrogenesis and differentiation during renal development and of renal regeneration after acute injury. In cultured cells, administration of one or a mixture of growth factors to quiescent cells will initiate progression through the cell cycle and cell division. In the adult kidney, cell division normally is very low, but will increase up to 10-fold after acute injury. In addition to proliferation after lethal injury, there also is cellular repair in cells that have undergone sublethal injury. Recent studies indicate that growth factors inhibit programmed cell death in response to acute injury. Growth factors also may initiate or promote protein and lipid biosynthesis and provide an intracellular milieu that promotes cellular repair. In addition to cellular repair, growth factors also may be involved in the re-establishment of cell-extracellular matrix and cell-cell integrity. Finally, growth factors may limit injury by decreasing the factors that induce damage. Increased local renal expression of growth factors in response to acute injury include heparin binding epidermal growth factor (HB-EGF), hepatocyte growth factor (HGF), insulin-like growth factor-I (IGF-I), transforming growth factor-beta, parathyroid hormone-related peptide, and acidic fibroblast growth factor. In a number of experimental models of acute renal injury, administration of exogenous growth factors has been shown to accelerate both structural and functional recovery. Specifically, EGF, IGF-1, and HGF all have been shown to be effective in this regard. These studies are reviewed and potential therapeutic uses of growth factors and cytokines will be discussed.
II : 메시앙의 기독교 신앙과 음악적 표현에 관한 연구 (2000)

In the 20 century, Messiaen was one of the most representative composers who tried to deal with Christianity. His musical contents mostly have religious themes, subtitles. For that, Messiaen used his symbolic method explained in his preface to scores. Bas
A simple and effective model for electromagnetic bandgap structures embedded in printed circuit boards (2005)

Using a transmission-line model and considering a simple lumped-element substitute for the patch-via structure, a first-order, but detailed, quantitative and qualitative analysis of the filtering properties of a metallo-dielectric electromagnetic bandgap structure embedded in a printed circuit board is presented. This model is able to describe the resonant properties of the structure as well as its pass-band and stop-band regions.
Transforming growth factors: isolation of polypeptides from virally and chemically transformed cells by acid/ethanol extraction. (1980)

Polypeptides characterized by their ability to confer a transformed phenotype on an untransformed indicator cell have been isolated directly from tumor cells growing both in culture and in the animal, by using an acid/ethanol extraction procedure. Assay of these polypeptides is based on their ability to induce normal rat kidney fibroblasts to form colonies in soft agar. Peptides from murine sarcoma virus-transformed mouse 3T3 cells grown in culture had the highest specific activity in this assay; peptides from sarcomas produced from these cells or from chemically induced transplantable bladder carcinomas of mice were one-third as active; and peptides from a chemically induced rat tracheal carcinoma had only one-tenth the activity. Treatment with either trypsin or dithiothreitol destroyed the activity of all of these materials. The properties of these intracellular polypeptides from both virally and chemically transformed cells are similar to those described for the sarcoma growth factors (SGFs) previously isolated from the conditioned medium of sarcoma virus-transformed mouse 3T3 cells, suggesting the definition of a class of transforming growth factors common to tumor cells of different origins. The transforming peptides from the cultured sarcoma virus-infected cells were separately by gel filtration into two fractions of apparent molecular weight 7000 and 10,000. The major fraction at molecular weight 7000 represented approximately 0.1% of the original cell protein and had a specific activity 50 times that of the original acid/ethanol extract.
Potentiometric digoxin antibody measurements with antigen-ionophore based membrane electrodes (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotentiometric digoxin antibody measurements with antigen-ionophore based membrane electrodesM. Y. Keating and G. A. RechnitzCite this: Anal. Chem. 1984, 56, 4, 801–806Publication Date (Print):April 1, 1984Publication History Published online1 May 2002Published inissue 1 April 1984https://pubs.acs.org/doi/10.1021/ac00268a048https://doi.org/10.1021/ac00268a048research-articleACS PublicationsRequest reuse permissionsArticle Views210Altmetric-Citations68LEARN 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 Get e-Alerts
On-chip high-speed sorting of micron-sized particles for high-throughput analysis (2005)

A new design of particle sorting chip is presented. The device employs a dielectrophoretic gate that deflects particles into one of two microfluidic channels at high speed. The device operates by focussing particles into the central streamline of the main flow channel using dielectrophoretic focussing. At the sorting junction (T- or Y-junction) two sets of electrodes produce a small dielectrophoretic force that pushes the particle into one or other of the outlet channels, where they are carried under the pressure-driven fluid flow to the outlet. For a 40 microm wide and high channel, it is shown that 6 microm diameter particles can be deflected at a rate of 300/s. The principle of a fully automated sorting device is demonstrated by separating fluorescent from non-fluorescent latex beads.
Anxiety disorders and suicidal behaviour: an update (2008)

Despite methodological issues preventing firm conclusions from being drawn in most cases, these findings should prompt clinicians to evaluate more specifically the impact of anxiety disorders on suicidal behaviour, particularly when they are co-morbid. Further research into treatment of anxiety disorders in relation to preventing suicide is required.
RNA Interference of Human Papillomavirus Type 18 E6 and E7 Induces Senescence in HeLa Cells (2003)

The human papillomavirus oncoproteins E6 and E7 promote cell proliferation and contribute to carcinogenesis by interfering with the activities of cellular tumor suppressors. We used a small interfering RNA molecule targeting the E7 region of the bicistronic E6 and E7 mRNA to induce RNA interference, thereby reducing expression of E6 and E7 in HeLa cells. RNA interference of E6 and E7 also inhibited cellular DNA synthesis and induced morphological and biochemical changes characteristic of cellular senescence. These results demonstrate that reducing E6 and E7 expression is sufficient to cause HeLa cells to become senescent.
Differentiation of the Gastric Mucosa III. Animal models of oxyntic atrophy and metaplasia (2006)

Gastric cancer in humans arises in the setting of oxyntic atrophy (parietal cell loss) and attendant hyperplastic and metaplastic lineage changes within the gastric mucosa. Helicobacter infection in mice and humans leads to spasmolytic polypeptide-expressing metaplasia (SPEM). In a number of mouse models, SPEM arises after oxyntic atrophy. In mice treated with the parietal cell toxic protonophore DMP-777, SPEM appears to arise from the transdifferentiation of chief cells. These results support the concept that intrinsic mucosal influences regulate and modulate the appearance of gastric metaplasia even in the absence of significant inflammation, whereas chronic inflammation is required for the further neoplastic transition.
Substratum Compliance Regulates Human Trabecular Meshwork Cell Behaviors and Response to Latrunculin B (2011)

Substratum compliance profoundly influenced HTM cell behaviors and modulated the response of HTM cells to Lat-B. The inclusion of substratum compliance that reflects healthy or glaucomatous HTM results in cell behaviors and responses to therapeutic agents in vitro that may more accurately reflect in vivo conditions.
Serologically assessed elastin degradation is related to force vital capacity in patients with IPF (2013)

Introduction: Elastin is a signature protein of the lungs and loss of elasticity is a pathological feature of a COPD and IPF. The pathogenesis involves an inflammatory response and tissue turnover mediated by proteases, especially matrix metalloprotease (MMP)-12, secreted by activated macrophages. Aim: We developed an optimized assay for the assessment of elastin degradation mediated by MMP-9 and MMP-12. The objective was to investigate the ability to non-invasively provide information in relation to lung function during pulmonary disease. Methods: Human insoluble lung elastin was in vitro cleaved for 2-169 hours by proteases and 400 fragments were identified by MS. A MMP-9 and -12 generated elastin neoepitope cleaved at the amino acid position 444 was chosen for monoclonal antibody generation for ELISA development. ELM was assessed in serum samples from a cohort of COPD (n=10), IPF (n=29) patients and healthy controls (n=11), stratified according to their forced vital capacity (FVC). Results: ELM was specific towards MMP-12 degraded lung elastin. ELM was related to disease in IPF patients with significant increased levels in IPF (p&lt;0.01) compared to controls. Furthermore, ELM was significantly correlated to individual FVC values in IPF patients (Spearman r=0.38, p=0.04). However, ELM was not elevated in mild COPD compared to controls Discussion: We showed that this novel marker of MMP-12 degraded elastin was able to diagnose IPF and that the ELM marker was correlated to FVC in IPF patients. Even though these findings need to be validated in larger clinical settings, the ELM marker described showed potential as marker of progression in IPF patients.
Phase II trial of vorinostat in combination with bortezomib in recurrent glioblastoma: a north central cancer treatment group study (2011)

Vorinostat, a histone deacetylase (HDAC) inhibitor, has shown evidence of single-agent activity in glioblastoma (GBM), and in preclinical studies, we have demonstrated significant synergistic cytotoxicity between HDAC inhibitors and proteasome inhibitors in GBM cell lines. We therefore conducted a phase II trial to evaluate the efficacy of vorinostat in combination with the proteasome inhibitor bortezomib in patients with recurrent GBM. Vorinostat was administered at a dose of 400 mg daily for 14 days of a 21-day cycle, and bortezomib was administered at a dose of 1.3 mg/m(2) intravenously on days 1, 4, 8, and 11 of the cycle. A total of 37 patients were treated, and treatment was well tolerated: grade 3, 4 nonhematologic toxicity occurred in 30% of patients and consisted mainly of fatigue (14%) and neuropathy (5%); grade 3, 4 hematologic toxicity occurred in 37% of patients and consisted of thrombocytopenia (30%), lymphopenia (4%), and neutropenia (4%). The trial was closed at the predetermined interim analysis, with 0 of 34 patients being progression-free at 6 months. One patient achieved a partial response according to the Macdonald criteria. The median time to progression for all patients was 1.5 months (range, 0.5-5.6 months), and median overall survival (OS) was 3.2 months. Patients who had received prior bevacizumab therapy had a shorter time to progression and OS, compared with those who had not. On the basis of the results of this phase II study, further evaluation of the vorinostat-bortezomib combination in GBM patients in this dose and schedule is not recommended.
Phorbol ester reduces constitutive nuclear NFχB and inhibits HIV-1 production in mature human monocytic cells (1992)

NF kappa B is a potent mediator of specific gene expression in human monocytes and has been shown to play a role in transcription of the HIV-1 genome in promonocytic leukemias. There is little information available on the response of NF kappa B to cytokines in normal human monocytes. We have used a 32P-labeled oligonucleotide derived from human immunodeficiency virus (HIV-1) long terminal repeat, which contains a tandem repeat of the NF kappa B binding sequence, as a probe in a gel retardation assay to study this transcription factor. Using this assay, we have detected NF kappa B in extracts of nuclei from normal human monocytes. Treatment of normal monocytes with 12-0-tetradecanoyl phorbol-13-acetate (TPA) for 4-24 h caused the complete disappearance of NF kappa B from nuclear extracts of monocytes. A similar result was obtained with the mature monocytic leukemia cell line THP-1. The constitutive transcription factor SP1 was unaffected by addition of TPA. The disappearance of NF kappa B from the nucleus was concentration dependent between 10 and 50 ng/ml of phorbol ester. In THP-1 cells, TPA also induced a new, faster-migrating NF kappa B species not induced in monocytes. Protein kinase C inhibitor staurosporine, but not cyclic nucleotide-dependent protein kinase inhibitor HA-1004, also dramatically reduced constitutive levels of nuclear NF kappa B. Finally, TPA addition to monocytes infected with HIV-1 inhibited HIV-1 replication, as determined by reverse transcriptase assays, in a concentration-dependent manner. These results are in striking contrast to the increase in nuclear NF kappa B and HIV-1 replication induced by phorbol esters in promonocytic leukemia cells U937 and HL-60, and emphasize the importance of studying cytokine regulation of HIV-1 in normal monocytes.
Tissue Engineering by Cell Transplantation Using Degradable Polymer Substrates (1991)

This paper reviews our research in developing novel matrices for cell transplantation using bioresorbable polymers. We focus on applications to liver and cartilage as paradigms for regeneration of metabolic and structural tissue, but review the approach in the context of cell transplantation as a whole. Important engineering issues in the design of successful devices are the surface chemistry and surface microstructure, which influence the ability of the cells to attach, grow, and function normally; the porosity and macroscopic dimensions, which affect the transport of nutrients to the implanted cells; the shape, which may be necessary for proper function in tissues like cartilage; and the choice of implantation site, which may be dictated by the total mass of the implant and which may influence the dimensions of the device by the available vascularity. Studies show that both liver and cartilage cells can be transplanted in small animals using this approach.
Crystallization of copolymers of ethylene glycol and diethylene glycol terephthalate (1961)

Abstract Rates of crystallization of polyethylene terephthalate and copolymers of ethylene glycol and diethylene glycol terephthalate were measured in the temperature range of 110 to 240°C.; this is the region of temperature in which the crystallization takes place at a measurable rate. It was found that the rate is defined by a modified Avrami type of equation over the entire temperature range of crystallization. Molecular motion, which limits crystallization at lower temperatures, was found to be a relaxation mechanism rather than simple viscous flow; to account for this, a modification of the Avrami type of equation was made. Data on copolymers of ethylene glycol and diethylene glycol terephthalate have shown that introduction of the longer chain yields a more flexible structure; hence at lower temperatures, where molecular motion is rate‐determining, the rate is increased. At higher temperatures introduction of the copolymer decreases the crystallization rate in the manner one would expect from the depression of the crystalline melting point.
Suspension of spherical particles in nematic solutions of disks and rods (1999)

We report on the behavior of colloidal spheres suspended in nematic solutions of rodlike (calamitic phase) and disklike (discotic phase) micelles. The particles form anisotropic structures that depend on the shape of the surrounding micelles. An analysis of these structures indicates that dipolar and quadrupolar elastic interactions are, respectively, observed in discotic and calamitic nematics. This shape dependency can be understood by considering the entropy driven alignment of the micelles at the surface of the particles.
Phase I Study of RO4929097, a Gamma Secretase Inhibitor of Notch Signaling, in Patients With Refractory Metastatic or Locally Advanced Solid Tumors (2012)

RO4929097 was well tolerated at 270 mg on schedule A and at 135 mg on schedule B; the safety of schedule C has not been fully evaluated. Further studies are warranted on the basis of a favorable safety profile and preliminary evidence of clinical antitumor activity.
Absolute Gene Expression Patterns of Thioredoxin and Glutaredoxin Redox Systems in Mouse (2003)

This work provides the first absolute expression patterns of genes coding for all known components of both thioredoxin (Trx) and glutaredoxin (Grx) systems in mouse: Trx1, Trx2, Grx1, Grx2, TrxR1, TrxR2, thioredoxin/glutathione reductase, and glutathione reductase. We devised a novel assay that, combining the advantages of multiplex and real-time PCR, streamlines the quantitation of the actual mRNA copy numbers in whole-animal experiments. Quantitations reported establish differences among adult organs and embryonic stages, compare mRNA decay rates, explore the significance of alternative mRNA isoforms derived from TrxR1 and Grx2 genes, and examine the time-course expression upon superoxide stress promoted by paraquat. Collectively, these quantitations show: i) unique expression profiles for each transcript and mouse organ examined, yet with some general trends like the higher amounts of mRNA species coding for thioredoxins than those coding for the reductases that control their redox states and activities; ii) continuous expression during embryogenesis with outstanding up-regulations of Trx1 and TrxR1 mRNAs in specific temporal sequences; iii) drastic differences in mRNA stability, liver decay rates range from 2.8 h (thioredoxin/glutathione reductase) to >/= 35 h (Trx1 and Trx2), and directly correlate with mRNA steady-state values; iv) testis-specific differences in the amounts (relative to total isoforms) of transcripts yielding the mitochondrial Grx2a and 67-kDa TrxR1 variants; and v) coordinated up-regulation of TrxR1 and glutathione reductase mRNAs in response to superoxide stress in an organ-specific manner. Further insights into in vivo roles of these redox systems should be gained from more focused studies of the mechanisms underlying the vast differences reported here at the transcript level.
Tetr Hybrid Transcription Factors Report Cell Signaling and Are Inhibited by Doxycycline (2005)

We developed a bigenic reporter system composed of a hybrid transcription factor that combines the regulatory and activation domains of either Elk-1 or cyclic AMP-responsive element binding protein (CREB) with the DNA binding, dimerization, and regulatory domains from a synthetic variant of the bacterial Tet repressor (TetR). The novel hybrid transcription factor TetR-Elk-1 was regulated by MAPK ERK kinase 1 (MEK-1) overexpression, and TetR-CREB was regulated by protein kinase A (PKA) overexpression or elevation of cyclic AMP levels. These hybrid transcription factors could be useful reporters of cell signaling pathways because, unlike previous GAL4 hybrid reporters, TetR hybrid transcription factors are inhibited by the administration of doxycycline. We validated this system in cell culture transfection experiments utilizing luciferase assays to monitor reporter gene expression and Western blot analysis to monitor transcription factor expression and phosphorylation levels. This system may be useful in creating temporally restricted windows of response to cell signaling and may be of value in the advancement of methods used to study signal transduction.
Gettering of metals by voids in silicon (1995)

The gettering efficiency of copper and platinum by cavities formed in silicon after high dose helium implantation and thermal processing has been investigated. The formation of helium bubbles and their evolution into cavities has been investigated by transmission electron microscopy; the measured values of void density, diameter and the width of the void layer can be interpreted by assuming a simple coalescence model. Metal impurities intentionally introduced in silicon by ion implantation are efficiently gettered inside these cavities, probably due to the large amount of unsatured bonds at the void internal surface. Processing at temperatures higher than 1000oC causes a release of the trapped metal atoms which can be gettered again by repeating the process. The method is demonstrated on real devices such as large area diodes (a particle detector) and bipolar transistors. The capability to localize in depth and across the wafer surface on the gettering sites allows the development of a new gettering engineering.