gebhart/patrepeval huggingface dataset:
Regulation of the biosynthesis of aminoacyl-transfer ribonucleic acid synthetases and of transfer ribonucleic acid in Escherichia coli. V. Mutants with increased levels of valyl-transfer ribonucleic acid synthetase (1979)

Spontaneous revertants of a temperature-sensitive Escherichia coli strain harboring a thermolabile valyl-transfer ribonucleic acid (tRNA) synthetase were selected for growth at 40 degrees C. Of these, a large number still contain the thermolabile valyl-tRNA synthetase. Three of these revertants contained an increased level of the thermolabile enzyme. The genetic locus, valX, responsible for the enzyme overproduction, is adjacent to the structural gene, valS, of valyl-tRNA synthetase. Determination (by radioimmunoassay) of the turnover rates of valyl-tRNA synthetase showed that the increased level of valyl-tRNA synthetase is due to new enzyme synthesis rather than decreased rates of protein degradation.
Role of renal nerves for the expression of renin in adult rat kidney (1994)

Utilizing a combination of mechanical and chemical unilateral denervation, we have examined the relevance of renal innervation for the expression of renin in kidneys of adult rats. Renal denervation led to a reduction by 57 +/- 4% of renin-containing areas in denervated kidneys as quantitated by morphometry of kidney sections immunoreactive against a polyclonal antirenin antibody. Preprorenin mRNA content in the denervated kidneys fell to 46 +/- 7% of the contralateral innervated kidneys. Treatment of rats with the beta 1-adrenoreceptor antagonist metoprolol (100 mg.kg-1.day-1) for 2 days decreased renal renin mRNA levels to 71% of control levels. Unilateral renal denervation led to a further decrease of renin mRNA levels also in metoprolol-treated animals to 60% of the values found in the contralateral kidneys. Hypotensive hemorrhage led to a 1.4-fold increase of renin mRNA in the kidneys of sham-treated animals. In unilaterally denervated rats renin mRNA increased to levels similar to those in sham-operated animals in both denervated and in contralateral innervated kidneys in response to bleeding. As a consequence, the ratio of abundance of renin mRNA in the denervated to the innervated kidneys rose to 86 +/- 7%. Pretreatment of the animals with metoprolol, on the other hand, prevented the rise of renin mRNA in response to hypotensive hemorrhage. Our findings suggest that in the adult organism renal neural input significantly contributes to the expression of renin under basal conditions, while it appears to be of less importance for stimulation of renin gene expression by severe blood loss.
Genome-wide Mapping of Protein-DNA Interactions by Chromatin Immunoprecipitation and DNA Microarray Hybridization (2003)

A critical part of understanding the mechanism and logic of cellular regulatory networks is understanding where enzymes and their regulatory proteins interact with the genome in vivo. From this, we can determine the genomic features that specify protein binding and simultaneously identify genes or other chromosomal elements whose function is affected by the binding. Recently, methods that combine well-established protocols for chromatin immunoprecipitations (1–6) with the surveying power of DNA microarrays have allowed researchers to create high-resolution, genomewide maps of the interaction between DNA-associated proteins and DNA (7–9). Many variations of the method have been published, but all contain the same basic steps (10): growth of cells, fixation, extract preparation, immunoprecipitation, fixation reversal, DNA purification, DNA amplification, microarray hybridization, and data analysis. The purpose here is to detail a single experimental method in yeast from start to finish, rather than to review all of the different protocols that have been used. The method described in this chapter worked for a particular set of DNA-associated proteins (Rap1p, Sir2p, Sir3p, and Sir4p), and their corresponding antibody-antigen interactions (8). Since the strength, specificity, and mechanism of antibody-antigen and protein-DNA association vary widely, this protocol should be viewed as a starting point, rather than an absolute procedure.
Cyclooxygenases: Structural, Cellular, and Molecular Biology (2000)

The prostaglandin endoperoxide H synthases-1 and 2 (PGHS-1 and PGHS-2; also cyclooxygenases-1 and 2, COX-1 and COX-2) catalyze the committed step in prostaglandin synthesis. PGHS-1 and 2 are of particular interest because they are the major targets of nonsteroidal anti-inflammatory drugs (NSAIDs) including aspirin, ibuprofen, and the new COX-2 inhibitors. Inhibition of the PGHSs with NSAIDs acutely reduces inflammation, pain, and fever, and long-term use of these drugs reduces fatal thrombotic events, as well as the development of colon cancer and Alzheimer's disease. In this review, we examine how the structures of these enzymes relate mechanistically to cyclooxygenase and peroxidase catalysis, and how differences in the structure of PGHS-2 confer on this isozyme differential sensitivity to COX-2 inhibitors. We further examine the evidence for independent signaling by PGHS-1 and PGHS-2, and the complex mechanisms for regulation of PGHS-2 gene expression.
Modeling of carrier mobility against carrier concentration in arsenic-, phosphorus-, and boron-doped silicon (1983)

New carrier mobility data for both arsenic- and boron-doped silicon are presented in the high doping range. The data definitely show that the electron mobility in As-doped silicon is significantly lower than in P-doped silicon for carrier concentrations higher than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . By integrating these data with those previously published, empirical relationships able to model the carrier mobility against carrier concentration in the whole experimental range examined to date (about eight decades in concentration) for As-, P-, and B-doped silicon are derived. Different parameters in the expression for the n-type dopants provide differentiation between the electron mobility in As-and in P-doped silicon. Finally, it is shown that these new expressions, once implemented in the SUPREM II process simulator, lead to reduced errors in the simulation of the sheet resistance values.
Thrombolysis of peripheral graft occlusion in patients with hypertension. (1996)

The objective of this study was to evaluate the effect of hypertension on the use of thrombolytic therapy in patients with occluded synthetic peripheral bypass grafts. Thrombolysis with urokinase was performed in 44 cases of occluded lower extremity bypass grafts. The cases were divided into two groups: Group I consisted of patients currently being treated for hypertension. Group II consisted of patients without a history of hypertension. A comparison of pre- or intra-lytic data revealed that there was no significant difference in each group. Complications occurred in 15 (32.6%) out of 46 cases. There was no significant increase in complication when the risk factors were compared. In Group I, the one, two, and three year patency rates were 42.7%, 23.0%, and 7.7% and the limb salvage rates were 93.3%, 73.9%, and 73.9% for one, two, and three years respectively. The Group II patency rates were 70.6%, 41.6%, and 41.6% and the limb salvage rates were 94.1%, 86.9%, and 86.9%. The patency rate was significantly reduced when Group I was compared to Group II (p < 0.05). There was no statistically significant difference in limb salvage rates between Groups I and II. In conclusion, hypertension is one of the important risk factors that reduce the patency rate after thrombolytic therapy in patients with peripheral arterial bypass graft.
Lyophilization-induced reversible changes in the secondary structure of proteins. (1995)

Changes in the secondary structure of some dozen different proteins upon lyophilization of their aqueous solutions have been investigated by means of Fourier-transform infrared spectroscopy in the amide III band region. Dehydration markedly (but reversibly) alters the secondary structure of all the proteins studied, as revealed by both the quantitative analysis of the second derivative spectra and the Gaussian curve fitting of the original infrared spectra. Lyophilization substantially increases the beta-sheet content and lowers the alpha-helix content of all proteins. In all but one case, proteins become more ordered upon lyophilization.
The study of the interaction of human mesenchymal stem cells and monocytes/macrophages with single‐walled carbon nanotube films (2006)

Abstract The influence of single‐walled carbon nanotube (SWCNT) films on two different human cell types was investigated: primary mesenchymal stem cells (MSC) and the monocytes/macrophages cell line THP‐1, the focus being on the metabolic activity of these cells. The SWCNT were free of impurity as was confirmed by Raman and VIS‐NIR spectroscopy. No surfactant was used to minimize the effect of other agents on the behavior of the cells. The results obtained on SWCNT films were compared to those measured on carbon fibers (CF). The metabolic activity of the investigated cell types cultured on SWCNT film was only slightly reduced (about 20%), while carbon fibers led to a much stronger decrease (about 40%). The reaction of the cells depended on the cell number, with more cells showing less metabolic inhibition. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p185HER2/neu monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment. (1998)

The use of rhuMAb HER2 in combination with CDDP in patients with HER2/neu-overexpressing metastatic breast cancer results in objective clinical response rates higher than those reported previously for CDDP alone, or rhuMAb HER2 alone. In addition, the combination results in no apparent increase in toxicity. Finally, the pharmacology of rhuMAb HER2 was unaffected by coadministration with CDDP.
Age‐related telomere length dynamics in peripheral blood mononuclear cells of healthy cynomolgus monkeys measured by Flow FISH (2002)

Telomere length is a good biomarker to study the cellular senescence as well as aging of an organism, because it regulates the replicative capacity of vertebrate somatic cells. To demonstrate age-related telomere length dynamics in the peripheral blood mononuclear cells (PBMC) of the cynomolgus monkey, we introduced a novel method of measuring telomere length by fluorescence in situ hybridization with a Peptide Nucleic Acid (PNA) labelled probe and flow cytometry (Flow FISH). A highly significant correlation was observed between the intensity of telomere-specific fluorescence by Flow FISH and telomere length by Southern blot analysis (R = 0.923, n = 22). The intensity of telomere fluorescence in PBMC significantly decreased with age in 55 monkeys aged from 0 to 34 years and this decrease corresponded to the loss of 62.7 base pairs per year (R = - 0.52, P < 0.00004). We also analysed the expression of naive cell-associated markers, CD28, CD62L and CD45RA/CD62L in T lymphocytes of 47 cynomolgus monkeys. An age-related increase in the CD28- subset was observed in CD8+ T lymphocytes in monkeys less than 11 years old and in CD4+ T lymphocytes in monkeys over 23 years old, respectively. The percentage of CD62L+ subsets was significantly decreased with age in both CD4+ (R = - 0.55) and CD8+ T lymphocytes (R = - 0.73). From the comparison of telomere length among PBMC, CD62L+ and CD62L- T lymphocytes, it was clearly evident that loss of naive subsets results in the shortening of telomere length in vivo. These results show that this method can be applicable to studying the turnover and precursor-progeny of PBMC in cynomolgus monkeys as an animal model of aging.
Optimization of Recombinant Adeno-Associated Virus-Mediated Expression for Large Transgenes, Using a Synthetic Promoter and Tandem Array Enhancers (2015)

The packaging capacity of recombinant adeno-associated viral (rAAV) vectors limits the size of the promoter that can be used to express the 4.43-kb cystic fibrosis transmembrane conductance regulator (CFTR) cDNA. To circumvent this limitation, we screened a set of 100-mer synthetic enhancer elements, composed of ten 10-bp repeats, for their ability to augment CFTR transgene expression from a short 83-bp synthetic promoter in the context of an rAAV vector designed for use in the cystic fibrosis (CF) ferret model. Our initial studies assessing transcriptional activity in monolayer (nonpolarized) cultures of human airway cell lines and primary ferret airway cells revealed that three of these synthetic enhancers (F1, F5, and F10) significantly promoted transcription of a luciferase transgene in the context of plasmid transfection. Further analysis in polarized cultures of human and ferret airway epithelia at an air-liquid interface (ALI), as well as in the ferret airway in vivo, demonstrated that the F5 enhancer produced the highest level of transgene expression in the context of an AAV vector. Furthermore, we demonstrated that increasing the size of the viral genome from 4.94 to 5.04 kb did not significantly affect particle yield of the vectors, but dramatically reduced the functionality of rAAV-CFTR vectors because of small terminal deletions that extended into the CFTR expression cassette of the 5.04-kb oversized genome. Because rAAV-CFTR vectors greater than 5 kb in size are dramatically impaired with respect to vector efficacy, we used a shortened ferret CFTR minigene with a 159-bp deletion in the R domain to construct an rAAV vector (AV2/2.F5tg83-fCFTRΔR). This vector yielded an ∼17-fold increase in expression of CFTR and significantly improved Cl(-) currents in CF ALI cultures. Our study has identified a small enhancer/promoter combination that may have broad usefulness for rAAV-mediated CF gene therapy to the airway.
Intracellular receptors for activated protein kinase C. Identification of a binding site for the enzyme (1991)

Protein kinase C (PKC) isozymes comprise a family of cytosolic enzymes that translocate to different intracellular sites on activation. We have recently characterized at least two intracellular receptor proteins for PKC (termed RACKs for receptors for activated C-kinase) in the Triton-insoluble material of the particulate fraction from neonatal rat heart. Here, we identify a sequence that appears to resemble the PKC binding site on these RACKs. A peptide (peptide I) with the sequence KGDYEKILVALCGGN bound PKC, and binding was markedly increased in the presence of PKC activators. Furthermore, peptide I inhibited PKC binding to RACKs in a dose-dependent manner. These data suggest that these RACKs have a common PKC binding sequence. Since peptide I inhibited PKC binding to RACKs in vitro, it may be a useful tool to inhibit PKC translocation and subsequent function in vivo.
Neodymium:yttrium aluminum garnet laser irradiation with low pulse energy: a potential tool for the treatment of peri‐implant disease (2006)

Bacterial contamination may seriously compromise successful implant osteointegration in the clinical practice of dental implantology. Several methods for eliminating bacteria from the infected implants have been proposed, but none of them have been shown to be an effective tool in the treatment of peri-implantitis. In the present study, we investigated the efficacy of pulsed neodymium:yttrium aluminum garnet laser irradiation (Nd:YAG) in achieving bacterial ablation while preserving the surface properties of titanium implants. For this purpose, suspensions of Escherichia coli or Actinobacillus (Haemophilus) actinomycetemcomitans were irradiated with different laser parameters, both streaked on titanium implants, and in broth medium. It was found, by light and atomic force microscopy, that Nd:YAG laser, when used with proper working parameters, was able to bring about a consistent microbial ablation of both aerobic and anaerobic species, without damaging the titanium surface.
Identification and Functional Characterization of theLactococcus lactisCodY-Regulated Branched-Chain Amino Acid Permease BcaP (CtrA) (2006)

Transcriptome analyses have previously revealed that a gene encoding the putative amino acid transporter CtrA (YhdG) is one of the major targets of the pleiotropic regulator CodY in Lactococcus lactis and Bacillus subtilis. The role of ctrA in L. lactis was further investigated with respect to both transport activity as well as CodY-mediated regulation. CtrA is required for optimal growth in media containing free amino acids as the only amino acid source. Amino acid transport studies showed that ctrA encodes a secondary amino acid transport system that is specific for branched-chain amino acids (BCAAs) (isoleucine, leucine, and valine) and methionine, which is in disagreement with its previously proposed function (a cationic amino acid transporter), which was assigned based on homology. We propose to rename CtrA BcaP, for branched-chain amino acid permease. BcaP is a member of a group of conserved transport systems, as homologs are widely distributed among gram-positive bacteria. Deletion of bcaP resulted in the loss of most of the BCAA uptake activity of L. lactis, indicating that BcaP is the major BCAA carrier of this organism. Deletion of bcaP together with a second (putative) BCAA permease, encoded by brnQ, further reduced the viability of the strain. DNA microarray analysis showed that deletion of bcaP predominantly affects genes belonging to the regulons of the transcriptional regulator CodY, which is involved in global nitrogen metabolism and needs BCAAs for its activation, and of CmbR, which is involved in sulfur amino acid metabolism.
An Efficient Wireless Sensor Network for Precision Agriculture (2012)

Wireless sensor network consists of many node with capability of sensing, computation, and wireless communications. The wireless sensor network technologies are increasingly being implemented for modern precision agriculture monitoring. The privileges of wireless sensor network in agriculture are for several causes: high performance, increase the production efficiency while decreasing cost, low-power consumption and collected distributed data.
A metallo-supramolecular approach to a half-subtractor (2008)

The tetraamine dinucleating ligand L, which bears naphthalene moieties at both ends, behaves as a combinatorial logic circuit for a molecular half-subtractor in the presence of ZnII ions.
Probiotics for treatment of Clostridium difficile-associated colitis in adults (2008)

There is insufficient evidence to recommend probiotic therapy as an adjunct to antibiotic therapy for C. difficile colitis. There is no evidence to support the use of probiotics alone in the treatment of C. difficile colitis.
Adsorption of Trichoderma reesei CBHI and Thermomonospora fusca E₅ cellulases on model solid surfaces (1998)

approved: Michelle K. Bothwell In this research, the interfacial behavior of Trichoderma reesei CBHI and Thermomonospora fusca E5 cellulases were studied at synthetic surfaces. For this purpose, colloidal silica and polystyrene particles were used to prepare cellulase-particle suspensions that were analyzed by several solution-phase techniques. These included circular dichroism spectroscopy, size exclusion chromatography and filtration, and a spectrophotometric assay for cellulase activity. All techniques were performed in the presence and absence of particles. Circular dichroism spectroscopy (CD) and size exclusion chromatography showed, however, that binding did not occur between either cellulase and silica, presumably because silica is hydrophilic and negatively charged. Binding did occur between each cellulase and polystyrene, most likely mediated through hydrophobic associations. Cellulase-polystyrene complexes were not analyzed using CD because of high light absorption by the polystyrene nanoparticles. Upon adsorption to polystyrene, the activity of the E5 dropped about 95% relative to that of the free enzyme. While this substantial loss in activity may have been the result of binding being mediated through the catalytic domain, strong evidence supporting the thought that adsorption occurs through hydrophobic associations, mediated through the binding domain, suggests that structural or steric factors were partly responsible for the loss. Redacted for Privacy
Towards Retinoid Therapy for Alzheimers Disease (2009)

Alzheimer's disease(AD) is associated with a variety of pathophysiological features, including amyloid plaques, inflammation, immunological changes, cell death and regeneration processes, altered neurotransmission, and age-related changes. Retinoic acid receptors (RARs) and retinoids are relevant to all of these. Here we review the pathology, pharmacology, and biochemistry of AD in relation to RARs and retinoids, and we suggest that retinoids are candidate drugs for treatment of AD.
Immunohistochemical demonstration of growth factors, TGF-alpha, TGF-beta, IGF-I and neu oncogene product in benign and malignant human breast tissues. (1990)

The expression of growth factors, TGF-alpha, TGF-beta, IGF-I and neu oncogene product was studied immunohistochemically in the tissue of 120 benign and malignant human breasts. Growth factors were found only in benign or malignant mammary epithelial cells and not in stromal cells. Normal and benign lesions were found to be negative for reactivity with each antibody. Carcinoma in situ and invasive breast carcinomas demonstrated a significantly higher percentage of stained cells than that observed in benign lesions; forty (49%) of 82 invasive carcinomas were positive for TGF-alpha, 31 (38%) for TGF-beta, 31 (38%) for IGF-I and 34 (41%) for neu product. No overall correlations were found between expression of each growth factor and the clinical stage or degree of histologic differentiation of the carcinomas. A significant positive correlation was observed between ER status and IGF-I expression and between PgR status and TGF-beta expression. In the majority of the carcinomas, co-expression between TGF-alpha, TGF-beta and IGF-I was observed; the percentage of cases with parallel positive or negative expression of two growth factors was as follows; TGF-alpha - TGF-beta (70%), TGF-alpha - IGF-I (57%), TGF-beta - IGF-I (71%). The concomitant expression of TGF-alpha and neu oncogene product in cell surface was also observed. The relapse-free intervals of the patients were studied in association with expression of each growth factor. TGF-beta-positive tumors showed a significantly better prognosis than TGF-beta - negative tumors (within the first 2 years of observation). However, TGF-alpha, IGF-I and neu overexpression showed no effect on the prognosis of the patients.