gebhart/patrepeval huggingface dataset:
Synthesis, fabrication, and characterization of self-exciting, self-sensing PZT/silicon dioxide piezoelectric micro-cantilever sensors (2006)

A piezoelectric cantilever (PEC) consists of a piezoelectric layer, e.g., leadzirconate titanate (PZT) bonded to a non-piezoelectric layer, e.g., silica. Compared to other current biosensing technologies, PEC‘s ability to withstand damping in water and its all-electric, self-exciting, self-sensing features make it stand out for in-liquid biosensing applications that is in-situ, real-time, multiplexed, and high throughput.The scaling analysis of PECs shows that reducing a PEC’s dimension can increase its mass sensitivity dramatically. The goal of the thesis study is to fabricate miniaturized piezoelectric micro-cantilever sensors (PEMS) with femtogram mass detection sensitivity (10-15 gram/Hz) for biological and chemical sensing applications. To achieve the goal, the thesis study encompasses three major components: (1) fundamental studies on the sensor physics to allow an optimal sensor design, (2) lead zirconate titanate (PZT) sol-gel thin film development, (3) microfabrication of the PZT PEMS.For the fundamental study, the effects of the sensor’s geometry on its detection sensitivity were examined both theoretically and experimentally to show that a proper nonpiezoelectric extension enhances a PEMS detection sensitivity. Using a unique sol-gel method using ethylene glycol as the solvent, dense, smooth, and defect-free PZT thin films were obtained with superb dielectric and ferroelectric properties, an intrinsic dielectric constant eint=2100 and a saturation polarization Ps=55 μC/cm2. Integrating with silicon based micro-fabrication technologies, PZT/SiO2 PEMS 300 to 40 　m long were successfully fabricated exhibiting resonance peaks with high quality factors ranging from 120 to 320. Mass detection sensitivities of 6.7 ×10-16 g/Hz and 9.1 ×10-16 g/Hz (mass of a single virus or a fraction of a single cell) were obtained with 40 　m and 60 　m PZT/SiO2 PEMS, respectively, in humidity detection – the smallest and most sensitive PZT based PEMS ever reported.%%%%Ph.D., Materials Science and Engineering  – Drexel University, 2006
A Phase 2 Clinical Trial of Deforolimus (AP23573, MK-8669), a Novel Mammalian Target of Rapamycin Inhibitor, in Patients with Relapsed or Refractory Hematologic Malignancies (2008)

Deforolimus was well-tolerated in patients with heavily pretreated hematologic malignancies, and antitumor activity was observed. Further investigation of deforolimus alone and in combination with other therapeutic agents is warranted in patients with selected hematologic malignancies.
Constitutive expression of human cytomegalovirus glycoprotein B (gpUL55) with mutagenized carboxy-terminal hydrophobic domains (1995)

Stable transfectants were selected from human astrocytoma cells (U373) after transfection with recombinant expression vectors carrying the human cytomegalovirus (HCMV) glycoprotein B (gB; gpUL55) gene with alternative deletions of hydrophobic domain segment 1 (hd1) or segment 2 (hd2) of the carboxy-terminal potential bipartite membrane anchor domain. Comparative analysis of HCMV gB forms from cell lines gB(Mhd1) and gB(Mhd2), expressing mutagenized gB, and those from cells expressing authentic gB showed that deletion of hd1, but not that of hd2, interfered with efficient proteolytic cleavage of the gB precursor. Both mutagenized gB forms exhibited correct transport to the cell surface. Deletion of hd2, but not that of hd1, caused loss of membrane anchoring of the gB molecule, resulting in secretion of the respective gB form into the culture medium. The carboxy-terminal cleavage product of the soluble gB molecule, which migrated more slowly than its authentic counterpart, was modified by complex carbohydrate side chains and formed disulphide-linked complexes. Our observations indicate that hd2 is essential as well as sufficient for membrane anchoring of the HCMV gB molecule. For hd1, a potential fusogenic role is suggested by the conserved positional pattern of glycine residues, which is comparable to that of known fusion peptides of other viruses.
miRNA analysis in B‐cell chronic lymphocytic leukaemia: proliferation centres characterized by low miR‐150 and high BIC /miR‐155 expression (2008)

Several miRNAs have been reported to be associated with immunoglobulin heavy chain (IgH) mutation and ZAP-70 expression status in blood samples of B-cell chronic lymphocytic leukaemia/small lymphocytic lymphoma (B-CLL/SLL). In the bone marrow and lymphoid tissues, proliferation centres (PCs) represent an important site of activation and proliferation of the neoplastic cells, suggesting that these tissues better reflect the biology of CLL than circulating blood cells. We collected 33 lymph nodes and 37 blood CLL samples and analysed IgH mutation status and ZAP-70 expression status. Expression of 15 miRNAs was analysed by qRT-PCR and RNA-ISH. Sixty-three per cent of the lymph node cases contained mutated IgH genes and 49% of the lymph node cases were ZAP-70-positive, and a significant correlation was observed between ZAP-70 expression and IgH mutation status. Of the blood CLL samples, 49% contained mutated IgH sequences. The miRNA expression pattern in CLL lymph node and blood samples was very similar. Three of 15 miRNAs (miR-16, miR-21, and miR-150) showed a high expression level in both blood and lymph node samples. No difference was observed between ZAP-70-positive or -negative and between IgH-mutated or unmutated cases. No correlation was found between miR-15a and miR-16 expression levels and 13q14 deletion in the blood CLL samples. RNA in situ hybridization (ISH) revealed strong homogeneous staining of miR-150 in the tumour cells outside the PCs. In reverse BIC/pri-miR-155 expression was observed mainly in individual cells including prolymphocytes of the PCs. This reciprocal pattern likely reflects the different functions and targets of miR-150 and miR-155.
The Anti-inflammatory Cytokine, Interleukin (IL)-10, Blocks the Inhibitory Effect of IL-1β on Long Term Potentiation (2001)

Several effects of the proinflammatory cytokine, interleukin-1 beta (IL-1 beta), have been described in the central nervous system, and one area of the brain where marked changes have been reported is the hippocampus. Among these changes are an IL-1 beta-induced inhibition of long term potentiation (LTP) in perforant path-granule cell synapses and an attenuation of glutamate release in synaptosomes prepared from the hippocampus. Evidence suggests that, at least in circulating cells, the anti-inflammatory cytokine, IL-10, antagonizes certain effects of IL-1. We investigated the effect of IL-10 on IL-1 beta-induced inhibition of LTP and glutamate release. The evidence presented indicates that IL-1 beta stimulates the stress-activated protein kinase, c-Jun-activated protein kinase (JNK), and IL-1 receptor-associated kinase, which may explain its inhibitory effect on release and LTP, and that IL-10 reversed the IL-1 beta-induced stimulation of JNK activity and inhibition of release and LTP. We observed that IL-10 abrogated the stimulatory effect of IL-1 beta on superoxide dismutase activity and reactive oxygen species production, whereas the H(2)O(2)-induced inhibition of LTP was also blocked by IL-10. We present evidence that suggests that the action of IL-10 may be mediated by its ability to induce shedding of the IL-1 type I receptor.
Gene expression profiling gets to the root of human hair follicle stem cells (2005)

Hair follicle stem cells sustain growth and cycling of the hair follicle and are located in the permanent portion of the follicle known as the bulge. In this issue of the JCI, Ohyama et al. report the characterization of global gene expression patterns of human hair follicle stem cells after their isolation using sophisticated laser capture techniques to microdissect out bulge cells. They discovered a panel of cell surface markers useful for isolating living hair follicle stem cells, a finding with potential therapeutic implications since isolated stem cells in mice can generate new hair follicles when transplanted to other mice. The findings of Ohyama et al. validate the use of the mouse for studying hair follicle biology but also underscore critical differences between mouse and human stem cell markers. In particular, CD34, which delineates hair follicle stem cells in the mouse, is not expressed by human hair follicle stem cells, while CD200 is expressed by stem cells in both species. Ultimately, this information will assist efforts to develop cell-based and cell-targeted treatments for skin disease.
Fatty acids composition of 10 microalgal species (2005)

Fatty acids composition of 10 species of microalgae was determined at the exponential phase and the stationary phase. The microalgae consist of two species of diatoms, Bacillariophyceae, (Nitzschia cf. ovalis, Thalassiosira sp.) five species of green microalgae, Prasinophyceae (Tetraselmis sp.) and Chlorophyceae, (Dictyosphaerium pulchellum, Stichococcus sp., Chlorella sp., Scenedesmus falcatus) and three species of blue green microalgae, Cyanophyceae (Anacystis sp., Synechococcus sp., Synechocystis sp.).Medium for culture diatoms and green microalgae was F/2, and BG-11 media was used for Cyanophyceae. The microalgae were cultured beneath light intensity 143 μEm-2s-1, light: dark illustration 12:12 hrs., temperature 28ºC, and salinities 8-30 psu. The microalgae were harvested for analyzing fatty acid by centrivugal machine at 3500 rpm. for 5 min. at temperature 20ºC and stored at -80ºC prior to analysis.Fatty acids composition of microalgae differed from species to species. The majority fatty acids composition of diatoms at the exponential phase and the stationary phase were C16:1n-7 (17.12-31.47% and 28.22-42.02%), C16:0 (13.25-19.61% and 18.83-20.67%), C20:5 n-3 (16.65-26.67% and 11.32-23.68%) respectively. The principle fatty acids composition of green microalgae, Prasinophyceae, Tetraselmis sp. were C18:3n-3 (16.17-16.67%), C16:0 (15.33-17.45%), C18:1n-9 (12.25-15.43%), C18:2n-6 (9.66-19.97%). The fatty acids composition of green microalgae, Chlorophyceae, were C18:3 n-3 (20.02-26.49% and 15.35- 30.63%), C16:0 (5.76-17.61% and 11.41-20.03%), C18:2n-6 (4.67-17.54% and 7.48-20.61%) respectively. The major amounts of fatty acids content of blue green microalgae were C16:1n-7 (9.28-34.91% and 34.48- 35.04%), C14:0 (13.34-25.96% and 26.69-28.24%), C16:0 (5.89-29.15% and 5.70-16.81%) except for Anacystis sp.which had a high amount of C18:3 n-3 (23.18-27.98%) but low amount of C14:0 (3.66-4.98%).Bacillariophyceae contained the highest amount of highly unsaturated fatty acids (HUFAs) at both growth phases. Prasinophyceae had a small amount while in Chlorophyceae and Cyanophyceae they were not detected. Nitzschia cf. ovalis and Thalassiosira sp. had amount of C20:4n-6 (0.08-4.40%),C20:5 n-3 (11.32- 26.67%) and C22:6 n-3 (0.80-4.20%) respectively. Tetraselmis sp. had amounts of C20:4n-6 and C20:5 n-3 ranging from 0.99-1.13% and 4.18-4.70% respectively. In conclusion, Nitzschia cf. ovalis and Thalassiosira sp. would serve as good nutritional sources of HUFAs for aquaculture animals.
Fusion of Lidar and Imagery for Reliable Building Extraction (2008)

We propose a new building detection and description algorithm for lidar data and photogrammetric imagery using directional histograms, splitting and merging segments, and line segments matching. Our algorithm consists of three steps. In the first step, we extract initial building regions from lidar data. Here, we apply a modified local maxima technique coupled with directional histograms and the entropies of these histograms. In the second step, given the color segmentation results from the photogrammetric imagery, we extract coarse building boundaries based on the lidar results with region segmentation and merging from aerial imagery. In the third step, we extract precise building boundaries based on the coarse building boundaries using line segments matching and perceptual grouping. Experimental results on multisensor data demonstrate that the proposed algorithm produces accurate and reliable results.
Database extensions for complex domains (2002)

Future versions of the Oracle Server will provide an open and extensible framework for supporting complex data domains including, but not limited to, text, image, spatial, video, and OLAP. This framework encompasses features for defining, storing, updating, indexing, and retrieving complex forms of data with full transaction semantics. The underpinning for these features is an extended Oracle Server that is an object-relational database management system (ORDBMS).
Quinolines (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
TLR agonists induce the differentiation of human bone marrow CD34+ progenitors into CD11c+ CD80/86+ DC capable of inducing a Th1‐type response (2007)

We recently reported that human bone marrow hematopoietic CD34(+) progenitors express functional Toll-like receptors (TLR) and can differentiate into myeloid cells just by stimulation with resiquimod (R848), a specific agonist for TLR7/8. However, the mechanisms by which R848 induces cell differentiation, the effects of other TLR agonists and the functionality of the differentiated cells are not known. Comparable to R848, loxoribine (a TLR7 agonist) and Pam(3)CSK(4) (a TLR2 agonist) induced cytokine production and cell differentiation along the myeloid lineage. R848 and loxoribine were more effective than Pam(3)CSK(4) at inducing the lineage-negative (CD11c(+) CD14(-)) dendritic cells (DC), whereas Pam(3)CSK(4) was more effective at inducing CD11c(+) CD14(+) monocytes. Both cell subsets expressed CD80/CD86 and HLA-DR molecules; however, they showed differential expression of CD1a, CD1b, CD1c, CD11b, CD206 and CD207 markers when compared with each other. Cell differentiation into DC was significantly inhibited by an anti-TNF-alpha nonoclonal antibody. The CD11c(+) CD14(-) subset was isolated and shown to be more potent in stimulating an alloreaction than the CD11c(+) CD14(+) subset. Collectively, these data highlight the differential effects of TLR agonists on human bone marow CD34(+) progenitor cells and provide a new opportunity for generating functional DC that would be useful in cancer vaccination.
Ex vivo expansion and maturation of peripheral blood CD34+ cells into the myeloid lineage (1992)

Hematopoietic reconstitution (HR) after peripheral blood stem cell transplantation is characterized by a delay of 8 and 12 days for recovery to safe levels of neutrophils and platelets even in patients with the most rapid engraftment. We postulate that a further enhancement in the rate of HR may be achieved by transplanting with an expanded postprogenitor cell population that can provide mature functional cells within days of infusion. In this study we investigated the ability of combinations of hematopoietic growth factors (HGF) to generate nascent granulocyte-macrophage colony-forming units (CFU-GM) in a 7-day suspension culture of peripheral blood CD34+ cells. A combination of 6 HGF, ie, interleukin-1 beta (IL-1), IL-3, IL-6, granulocyte colony-stimulating factor (G-CSF), granulocyte-macrophage- CSF (GM-CSF), and stem cell factor (SCF), was identified as the most potent combination of those tested. Subsequently, large volume suspension cultures of CD34+ cells from the same patients using the same 6-factor combination were established and monitored for 21 days. An exponential rate of nucleated cell production (mean 1,324-fold increase) occurred during culture. CFU-GM production paralleled nucleated cell production until day 10, peaked at day 14 (mean 66-fold increase), and was then maintained until day 21. Cells produced in culture were predominantly neutrophil precursors and developed normally as assessed by morphology, immunophenotype, and superoxide generation. This stroma-free, cytokine-driven culture system can achieve a degree of amplification, which suggests the feasibility of ex vivo culture of hematopoietic progenitor cells as an adjunct to hematopoietic stem cell transplantation.
A Plasmid Selection System in Lactococcus lactis and Its Use for Gene Expression in L. lactis and Human Kidney Fibroblasts (2002)

We report the development of a nonantibiotic and nonpathogenic host-plasmid selection system based on lactococcal genes and threonine complementation. We constructed an auxotrophic Lactococcus lactis MG1363Deltathr strain which carries deletions in two genes encoding threonine biosynthetic enzymes. To achieve plasmid-borne complementation, we then constructed the minimal cloning vector, pJAG5, based on the genes encoding homoserine dehydrogenase-homoserine kinase (the hom-thrB operon) as a selective marker. Using strain MG1363Deltathr, selection and maintenance of cells carrying pJAG5 were obtained in threonine-free defined media. Compared to the commonly used selection system based on erythromycin resistance, the designed complementation system offers a competitive and stable plasmid selection system for the production of heterologous proteins in L. lactis. The potential of pJAG5 to deliver genes for expression in eukaryotes was evaluated by insertion of a mammalian expression unit encoding a modified green fluorescent protein. The successful delivery and expression of genes in human kidney fibroblasts indicated the potential of the designed nonantibiotic host-plasmid system for use in genetic immunization.
Efficacy and ocular penetration of sparfloxacin in experimental streptococcal endophthalmitis (1993)

Gram-positive cocci are the most common pathogens in severe human eye infections. Streptococcal endophthalmitis is a devastating infection, and intravitreal antibiotic therapy is limited by retinal toxicity. Because few systemic antistreptococcal antibiotics penetrate into the vitreous, sparfloxacin, a newer quinolone with improved antistreptococcal activity, might be of interest. We therefore assessed its efficacy by the intravitreal route in a rabbit model of streptococcal endophthalmitis. The vitreal bacterial count (mean +/- standard deviation log10 CFU per milliliter) was significantly reduced after an intravitreal injection of 800 micrograms of sprafloxacin (4.9 +/- 0.7) relative to the counts in untreated control (7.1 +/- 0.7) and pefloxacin-treated (7.8 +/- 1.2) eyes. After systemic administration to rabbits, the maximum concentration of sparfloxacin in serum was 5.6 micrograms.ml-1 and the half-life was 7.5 h. Sparfloxacin exhibited very good penetration ratios in the vitreous (54%), cornea (76%), and lens (36%). In the vitreous, the levels of sparfloxacin remained greater than the MICs for most gram-positive cocci for up to 18 h. Further experimental studies are warranted to determine the efficacy of systemic sparfloxacin as adjuvant therapy in the treatment of human endophthalmitis.
High-Throughput Screens Based on NAD(P)H Depletion (2003)

Screening conditions should simulate the final application as closely as possible. This is especially a challenge when chromophore-free (e.g., aliphatic) substrates are used and no simple and reliable high-throughput method for quantitative analysis of the respective reaction product is available. The screening procedure should also be generally applicable for a certain class of enzymes. Generation of “surrogate substrates” by derivatization with chromogenic groups can have a negative effect on enzyme development by directed evolution, e.g., by causing a change in substrate specificity.
Propagation of tau pathology in Alzheimer’s disease: identification of novel therapeutic targets (2013)

Accumulation and aggregation of the microtubule-associated protein tau are a pathological hallmark of neurodegenerative disorders such as Alzheimer's disease (AD). In AD, tau becomes abnormally phosphorylated and forms inclusions throughout the brain, starting in the entorhinal cortex and progressively affecting additional brain regions as the disease progresses. Formation of these inclusions is thought to lead to synapse loss and cell death. Tau is also found in the cerebrospinal fluid (CSF), and elevated levels are a biomarker for AD. Until recently, it was thought that the presence of tau in the CSF was due to the passive release of aggregated tau from dead or dying tangle-bearing neurons. However, accumulating evidence from different AD model systems suggests that tau is actively secreted and transferred between synaptically connected neurons. Transgenic mouse lines with localized expression of aggregating human tau in the entorhinal cortex have demonstrated that, as these animals age, tau becomes mislocalized from axons to cell bodies and dendrites and that human tau-positive aggregates form first in the entorhinal cortex and later in downstream projection targets. Numerous in vitro and in vivo studies have provided insight into the mechanisms by which tau may be released and internalized by neurons and have started to provide insight into how tau pathology may spread in AD. In this review, we discuss the evidence for regulated tau release and its specific uptake by neurons. Furthermore, we identify possible therapeutic targets for preventing the propagation of tau pathology, as inhibition of tau transfer may restrict development of tau tangles in a small subset of neurons affected in early stages of AD and therefore prevent widespread neuron loss and cognitive dysfunction associated with later stages of the disease.
The non-haem chloroperoxidase from Pseudomonas fluorescens and its relationship to pyrrolnitrin biosynthesis (1996)

The non-haem chloroperoxidase gene (cpoF) from the pyrrolnitrin producer Pseudomonas fluorescens BL914 was cloned using an oligonucleotide derived from part of the N-terminal amino acid sequence of chloroperoxidase (CPO-P) from Pseudomonas pyrrocina as a probe. Based on the overexpression of cpoF in Escherichia coli and the stabilty of CPO-F against higher temperatures and proteases, the enzyme was purified to homogeneity. Partial characterization of the enzyme showed that it belongs to the class of bacterial non-haem CPOs. To investigate the role of CPO-F in pyrrolnitrin biosynthesis, the cpoF gene was inactivated by insertion of a kanamycin cassette. Exchange of the chromosomal cpoF gene against the disrupted copy had no influence on pyrrolnitrin production demonstrating that CPO-F was not involved in pyrrolnitrin biosynthesis.
Interleukin 2- and polyomavirus middle T antigen-induced modification of phosphatidylinositol 3-kinase activity in activated T lymphocytes. (1991)

Stimulation of activated T lymphocytes with interleukin 2 (IL-2) results in rapid increases in intracellular protein tyrosine phosphorylation. Both the identity of the protein tyrosine kinase (PTK) activated by IL-2 receptor ligation and the identities of the critical target proteins for this PTK remain largely undefined. In this article, we demonstrate that stimulation of activated murine or human T cells with IL-2 for 10 to 30 min induces two- to threefold increases in the level of phosphatidylinositol (PtdIns) 3-kinase activity present in antiphosphotyrosine (p-Tyr) antibody immunoprecipitates from these cells. Furthermore, substantial levels of PtdIns 3-kinase activity were coprecipitated from IL-2-deprived T cells by antibodies to the src-related PTK p59fyn. Cellular stimulation with IL-2 induced a two- to threefold increase in the level of p59fyn-associated PtdIns 3-kinase activity. To examine the effect of a constitutive increase in PtdIns 3-kinase activity on the growth factor responsiveness of activated T cells, murine CTLL-2 cells were transfected with a polyomavirus middle T antigen (MTAg) expression vector. Anti-p-Tyr and anti-p59fyn immunoprecipitates from MTAg-transfected CTLL-2 cells contained three- to sixfold higher levels of PtdIns 3-kinase activity than wild-type cells. Immune complex kinase assays revealed that MTAg expression concomitantly induced a constitutive threefold increase in the PTK activity of p59fyn in these cells. However, stable MTAg expression did not abrogate the dependence of CTLL-2 cells on exogenous IL-2 for continued growth and proliferation.