gebhart/patrepeval huggingface dataset:
Nuclear Heat Shock Response and Novel Nuclear Domain 10 Reorganization in Respiratory Syncytial Virus-Infected A549 Cells Identified by High-Resolution Two-Dimensional Gel Electrophoresis (2004)

The pneumovirus respiratory syncytial virus (RSV) is a leading cause of epidemic respiratory tract infection. Upon entry, RSV replicates in the epithelial cytoplasm, initiating compensatory changes in cellular gene expression. In this study, we have investigated RSV-induced changes in the nuclear proteome of A549 alveolar type II-like epithelial cells by high-resolution two-dimensional gel electrophoresis (2DE). Replicate 2D gels from uninfected and RSV-infected nuclei were compared for changes in protein expression. We identified 24 different proteins by peptide mass fingerprinting after matrix-assisted laser desorption ionization-time of flight mass spectrometry (MS), whose average normalized spot intensity was statistically significant and differed by +/-2-fold. Notable among the proteins identified were the cytoskeletal cytokeratins, RNA helicases, oxidant-antioxidant enzymes, the TAR DNA binding protein (a protein that associates with nuclear domain 10 [ND10] structures), and heat shock protein 70- and 60-kDa isoforms (Hsp70 and Hsp60, respectively). The identification of Hsp70 was also validated by liquid chromatography quadropole-TOF tandem MS (LC-MS/MS). Separate experiments using immunofluorescence microscopy revealed that RSV induced cytoplasmic Hsp70 aggregation and nuclear accumulation. Data mining of a genomic database showed that RSV replication induced coordinate changes in Hsp family proteins, including the 70, 70-2, 90, 40, and 40-3 isoforms. Because the TAR DNA binding protein associates with ND10s, we examined the effect of RSV infection on ND10 organization. RSV induced a striking dissolution of ND10 structures with redistribution of the component promyelocytic leukemia (PML) and speckled 100-kDa (Sp100) proteins into the cytoplasm, as well as inducing their synthesis. Our findings suggest that cytoplasmic RSV replication induces a nuclear heat shock response, causes ND10 disruption, and redistributes PML and Sp100 to the cytoplasm. Thus, a high-resolution proteomics approach, combined with immunofluorescence localization and coupled with genomic response data, yielded unexpected novel insights into compensatory nuclear responses to RSV infection.
Expression and clinical significance of erb-B receptor family in hepatocellular carcinoma (2001)

In order to elucidate the clinical significance of the erbB family, epidermal growth factor receptor (EGF-R), c-erbB-2, c-erbB-3 and c-erbB-4 in hepatocellular carcinoma (HCC), we investigated the expression of these proteins by means of immunohistochemistry for HCC as well as adjacent noncancerous lesions. EGF-R was expressed in 68% of the HCC examined and showed correlation with the proliferating activity, stage, intrahepatic metastasis and carcinoma differentiation. c-erbB-2 was expressed in only 21% of the cases and showed no relationships with the clinicopathological parameters. c-erbB-3 protein was observed in 84% of the HCC and 38.1% of the noncancerous lesions. Its expression in HCC was equal to or greater than noncancerous lesions in 90.5% of the cases, and was related to the stage, portal invasion, cell proliferating activity, tumour size, intrahepatic metastasis and carcinoma differentiation. c-erbB-4 protein was expressed in 61.0% of HCC and in as much as 86.1% of the noncancerous lesions. Unlike the expression of c-erbB-3, that of c-erbB-4 in HCC was less than that of the adjacent noncancerous lesions in 51.2% of the cases. No statistical significance could be established between this protein expression in HCC and clinicopathological features. EGF-R and c-erbB-3 affected disease-free survival, but were not recognized as independent prognostic factors by multivariate analysis. The present study suggests that, of the four receptors, EGF-R and c-erbB-3 play important roles in the progression of HCC.
3D CITY MODELS: AN OPERATIONAL APPROACH USING AERIAL IMAGES AND CADASTRAL MAPS (2003)

Even though many efficient building reconstruction methods have been published so far, automatic processes are still missing for the production of 3D city models. This gap between research results and effective production tools seems mainly due to a lack of cooperation between all these methods. Building reconstruction in dense urban areas is such a complex problem that it is hopeless to look for an universal solution that could efficiently reconstruct every building, from a simple gabled roof to a whole cathedral. In this paper we first present a general strategy to combine several automatic and user-assisted processes to produce three-dimensional city models in a real production context using aerial images and 2D ground maps. The strategy aims at taking advantage of each algorithm to be sure they complement each other. Then we illustrate this strategy by describing our operational implementation and its results. In this implementation, the first step is a combination of two automatic algorithms: a model driven and a data driven process. In a second step, user-assisted tools supplement the reconstruction: some are adapted to precise landscape features while others are more generic. 1
Fixation of Maximal Shift Scarf Osteotomy with Inside-Out Plating: Technique Tip (2011)

Level of Evidence: V, Expert Opinion
Optimized and robust experimental design: a non-linear application to EM sounding (1998)

Pragmatic experimental design requires objective consideration of several classes of information including the survey goals, the range of expected Earth responses, acquisition costs, instrumental capabilities, experimental conditions and logistics. In this study we consider the ramifications of maximizing model parameter resolution through non-linear experimental design. Global optimization theory is employed to examine and rank different EM sounding survey designs in terms of model resolution as defined by linearized inverse theory. By studying both theoretically optimal and heuristic experimental survey configurations for various quantities of data, it is shown that design optimization is critical for minimizing model variance estimates, and is particularly important when the inverse problem becomes nearly underdetermined. We introduce the concept of robustness so that survey designs are relatively immune to the presence of potential bias errors in important data. Bias may arise during practical measurement, or from designing a survey using an appropriate model.
Burkitt Lymphoma: Revisiting the Pathogenesis of a Virus-Associated Malignancy (2007)

Burkitt lymphoma (BL), a tumor occurring in endemic, sporadic and AIDS-associated forms, is the classic example of a human malignancy whose pathogenesis involves a specific cellular genetic change, namely, a chromosomal translocation deregulating expression of the c-myc oncogene, complemented in many cases by the action of an oncogenic virus, the Epstein-Barr virus (EBV). Here we review recent work in two complementary areas of research: (1) on cellular genetic changes that occur in addition to the c-myc translocation in BL, in particular the capacity of p53/ ARF pathway breakage or of c-myc mutation to decouple the pro-proliferative effects of c-myc deregulation from its pro-apoptotic effects; and (2) on a postulated role for EBV in BL pathogenesis, through adopting restricted forms of virus latent gene expression that remain compatible with the c-myc-driven growth program but offer the tumor additional protection from apoptosis. We stress the many fundamental questions that remain to be resolved and, in that regard, highlight the general lessons that might be learned through understanding how two other infectious agents, malaria and HIV, dramatically enhance BL incidence.
Chemical Conversion of Natural Polymyxin B and Colistin to Their N-Terminal Derivatives (2007)

Abstract The chemical conversions of natural polymyxin B and colistin, which are fatty-acylated cyclic decapeptides, to polymyxin (2–10) and colistin (2–10) derivatives were examined. The Nα-free and side chain Nγ-protected nonapeptides, i.e., tetrakis(Nγ-trifluoroacetyl)–polymyxin B (2–10) and tetrakis(Nγ-trifluoroacetyl)–colistin (2–10), were prepared by trifluoroacetylation of polymyxin B and colistin, followed by chemical cleavage with 50% methanesulfonic acid to remove Nα-alkanoyl–Nγ-trifluoroacetyl–Dab–OH. The Nγ-protected nonapeptides were useful starting materials for the semi-synthesis of N-terminal derivatives by selective Nα-acylation at Thr2, followed by the removal of the Nγ-trifluoroacetyl protecting group with aqueous piperidine. Further, myristoyl–polymyxin B (2–10) and myristoyl–colistin (2–10) retained their antimicrobial activity with an MIC of 2–4 nmol mL−1 against Escherichia coli, Salmonella Typhimurium, and Pseudomonas aeruginosa. They also retained their high lipopolysaccahride (LPS) binding activity. Acetyl–polymyxin B (2–10) and acetyl–colistin (2–10) exhibited very low biological activities, except for a high bactericidal activity specifically against Pseudomonas aeruginosa with an MIC of 2 nmol mL−1. The distinct sensitivity of three Gram-negative bacteria tested toward acetyl-nonapeptides suggested that the N-terminal hydrophobic character of the fatty-acylated polymyxin peptides was necessary for the bactericidal activity against Escherichia coli and Salmonella Typhimurium, but not against Pseudomonas aeruginosa.
Energy-effective issue logic (2001)

The issue logic of a dynamically-scheduled superscalar processor is a complex mechanism devoted to start the execution of multiple instructions every cycle. Due to its complexity, it is responsible for a significant percentage of the energy consumed by a microprocessor. The energy consumption of the issue logic depends on several architectural parameters, the instruction issue queue size being one of the most important. In this paper we present a technique to reduce the energy consumption of the issue logic of a high-performance superscalar processor. The proposed technique is based on the observation that the conventional issue logic wastes a significant amount of energy for useless activity. In particular, the wake-up of empty entries and operands that are ready represents an important source of energy waste. Besides, we propose a mechanism to dynamically reduce the effective size of the instruction queue. We show that on average the effective instruction queue size can be reduced by a factor of 26% with minimal impact on performance. This reduction together with the energy saved for empty and ready entries result in about 90.7% reduction in the energy consumed by the wake-up logic, which represents 14.9% of the total energy of the assumed processor.
Comparative evaluation of plastic, hydrophobic and hydrophilic polymers as matrices for controlled-release drug delivery. (2003)

The results generated in this study showed that the profile and kinetics of drug release were functions of polymer type, polymer level and physico-chemical nature of drug. A controlled plasma level profile of drug can be obtained by judicious combination of polymers and modulation of polymer content in the matrix system.
Quantitative formation of core cross-linked star polymers via a one-pot two-step single electron transfer-living radical polymerization (2013)

A novel and highly efficient one-pot two-step strategy towards core cross-linked star polymers based on single electron transfer-living radical polymerization (SET-LRP) is described. Macroinitiators with high end-group fidelity were generated at high monomer conversions prior to the addition of cross-linkable monomers in the same pot to induce the formation of star polymers. Quantitative (>99%) star formation is achieved without the purification of unreacted monomers or macroinitiators.
Osteoporosis-pseudoglioma syndrome, a disorder affecting skeletal strength and vision, is assigned to chromosome region 11q12-13. (1996)

Osteoporosis-pseudoglioma syndrome (OPS) is an autosomal recessive disorder characterized by severe juvenile-onset osteoporosis and congenital or juvenile-onset blindness. The pathogenic mechanism is not known. Clinical, biochemical, and microscopic analyses suggest that OPS may be a disorder of matrix homeostasis rather than a disorder of matrix structure. Consequently, identification of the OPS gene and its protein product could provide insights regarding common osteoporotic conditions, such as postmenopausal and senile osteoporosis. As a first step toward determining the cause of OPS, we utilized a combination of traditional linkage analysis and homozygosity mapping to assign the OPS locus to chromosome region 11q12-13. Mapping was accomplished by analyzing 16 DNA samples (seven affected individuals) from three different consanguineous kindreds. Studies in 10 additional families narrowed the candidate region, supported locus homogeneity, and did not detect founder effects. The OPS locus maps to a 13-cM interval between D11S1298 and D11S971 and most likely lies in a 3-cM region between GSTP1 and D11S1296. At present, no strong candidate genes colocalize with OPS.
Fusigenic viral liposome for gene therapy in cardiovascular diseases. (1996)

To improve the efficiency of liposome-mediated DNA transfer as a tool for gene therapy, we have developed a fusigenic liposome vector based on principles of viral cell fusion. The fusion proteins of hemagglutinating virus of Japan (HVJ; also Sendai virus) are complexed with liposomes that encapsulate oligodeoxynucleotide or plasmid DNA. Subsequent fusion of HVJ-liposomes with plasma membranes introduces the DNA directly into the cytoplasm. In addition, a DNA-binding nuclear protein is incorporated into the HVJ-liposome particle to enhance plasmid transgene expression. The fusigenic viral liposome vector has proven to be efficient for the intracellular introduction of oligodeoxynucleotide, as well as intact genes up to 100 kbp, both in vitro and in vivo. Many animal tissues have been found to be suitable targets for fusigenic viral liposome DNA transfer. In the cardiovascular system, we have documented successful cytostatic gene therapy in models of vascular proliferative disease using antisense oligodeoxynucleotides against cell cycle genes, double-stranded oligodeoxynucleotides as "decoys" to trap the transcription factor E2F, and expression of a transgene encoding the constitutive endothelial cell form of nitric oxide synthase. Similar strategies are also effective for the genetic engineering of vein grafts and for the treatment of a mouse model of immune-mediated glomerular disease.
Characterization of spatial heterogeneity of groundwater-stream water interactions using multiple depth streambed temperature measurements at the reach scale (2006)

Abstract. Streambed temperatures can be easily, accurately and inexpensively measured at many locations. To characterize patterns of groundwater-stream water interaction with a high spatial resolution, we measured 140 vertical streambed temperature profiles along a 220 m section of a small man-made stream. Groundwater temperature at a sufficient depth remains nearly constant while stream water temperatures vary seasonally and diurnally. In summer, streambed temperatures of groundwater discharge zones are relatively colder than downwelling zones of stream water. Assuming vertical flow in the streambed, the observed temperatures are correlated to the magnitude of water fluxes. The water fluxes are then estimated by applying a simple analytical solution of the heat conduction-advection equation to the observed vertical temperature profiles. The calculated water fluxes through the streambed ranged between 455 Lm−2 d−1 of groundwater discharging to the stream and approximately 10 Lm−2 d−1 of stream water entering the streambed. The investigated reach was dominated by groundwater discharge with two distinct high discharge locations accounting for 50% of the total flux on 20% of the reach length.
Chloroplast transport of a ribulose bisphosphate carboxylase small subunit-5-enolpyruvyl 3-phosphoshikimate synthase chimeric protein requires part of the mature small subunit in addition to the transit peptide. (1988)

Ribulose bisphosphate carboxylase small subunit protein is synthesized in the cytoplasm as a precursor and transported into the chloroplast where the amino-terminal portion, the transit peptide, is removed proteolytically. To obtain chloroplast delivery of the 43-kDa 5-enolpyruvyl 3-phosphoshikimate (EPSP) synthase of Salmonella typhimurium, we constructed fusion proteins between the bacterial EPSP synthase and the ribulose bisphosphate carboxylase small subunit. A fusion protein consisting of the transit peptide fused to the EPSP synthase was not transported in vitro or in vivo into chloroplasts. A second fusion protein consisting of the transit peptide and 24 amino acids of the mature small subunit fused to the EPSP synthase was transported both in vitro and in vivo into chloroplasts. It was processed into two polypeptides of 46 and 47 kDa, respectively. This heterogeneity in processing was not caused by the presence of the aroA start codon, since its removal resulted in the same pattern. Substituting 24 different amino acids for the 24 amino acids of the mature small subunit resulted in a fusion protein that was not transported into the chloroplast. It was concluded that a portion of the mature small subunit was needed for efficient chloroplast delivery.
THEORETICAL AND EXPERIMENTAL INVESTIGATION OF A MICROSTRIP RADIATOR WITH MULTIPLE LUMPED LINEAR LOADS (1983)

ABSTRACT A simple theory is developed for the analysis of microstrip patch elements which are loaded at one or more points with lumped linear load impedances. The analysis is based on a cavity model in which the shape of the field distribution between the patch and ground plane is assumed to be well approximated by that of the resonant modes of a corresponding magnetic- and electric-walled cavity. The resonant mode of the loaded cavity is represented as an appropriate superposition of the modes of the corresponding unloaded cavity. The characteristic equation for the resonant frequencies of the loaded cavity is obtained in terms of the load impedances and the unloaded cavity multiport open-circuit parameters. An analysis of the input impedance of a rectangular microstrip element shorted at an arbitrary point has been implemented and the results show good agreement with experiment. An ancilliary result showing the equivalence between a thin strip and a circular cylinder model of a feed current distribution is also obtained.
Co-delivery of nitric oxide and antibiotic using polymeric nanoparticles (2015)

The rise of hospital-acquired infections, also known as nosocomial infections, is a growing concern in intensive healthcare, causing the death of hundreds of thousands of patients and costing billions of dollars worldwide every year. In addition, a decrease in the effectiveness of antibiotics caused by the emergence of drug resistance in pathogens living in biofilm communities poses a significant threat to our health system. The development of new therapeutic agents is urgently needed to overcome this challenge. We have developed new dual action polymeric nanoparticles capable of storing nitric oxide, which can provoke dispersal of biofilms into an antibiotic susceptible planktonic form, together with the aminoglycoside gentamicin, capable of killing the bacteria. The novelty of this work lies in the attachment of NO-releasing moiety to an existing clinically used drug, gentamicin. The nanoparticles were found to release both agents simultaneously and demonstrated synergistic effects, reducing the viability of <i>Pseudomonas aeruginosa</i> biofilm and planktonic cultures by more than 90% and 95%, respectively, while treatments with antibiotic or nitric oxide alone resulted in less than 20% decrease in biofilm viability.
Polymeric organosilicon systems. 10. Synthesis and conducting properties of poly[2,5-(disilanylene)thienylenes] (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymeric organosilicon systems. 10. Synthesis and conducting properties of poly[2,5-(disilanylene)thienylenes]Joji Ohshita, Daisuke Kanaya, Mitsuo Ishikawa, Tsuneaki Koike, and Toru YamanakaCite this: Macromolecules 1991, 24, 8, 2106–2107Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/ma00008a062https://doi.org/10.1021/ma00008a062research-articleACS PublicationsRequest reuse permissionsArticle Views122Altmetric-Citations85LEARN 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
Buffer and load balancing in locally distributed database systems (2002)

The authors investigated the effectiveness of load balancing when the buffer space requirement and the availability of buffers at different database sites are considered. New load-balancing algorithms are proposed and a simulation study was conducted. The results indicate that, by considering buffer space as a major system resource, load balancing is still an effective approach to improving system performance in locally distributed database systems. The results also indicate that no complicated information about buffer space requirement and availability is necessary to achieve satisfactory performance improvements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cloning and Expression of a Novel Variant of Human Interferon-γ cDNA (1985)

A cDNA library was prepared from the poly(A) mRNA isolated from human peripheral blood lymphocytes which were induced by combined treatment with phytohemagglutinin and a phorbol ester. Recombinant plasmids containing human interferon-gamma (HuIFN-gamma) cDNAs were identified by the oligonucleotide-hybridization method. Nucleotide sequence analysis showed that the nucleotide and amino-acid sequences of HuIFN-gamma cDNA in plasmid pIFN gamma-G4 differed from the published data at amino acid position 9 (CAA for glutamine versus AAA for lysine). The cDNA in plasmid pIFN gamma-G4 was expressed under control of the simian virus 40 early promoter in monkey COS cells and a biologically active HuIFN-gamma was secreted from the cells. The cDNA was also inserted into an expression vector carrying an E. coli tryptophan promoter and was expressed in E. coli. The results suggest that the conversion from lysine to glutamine at amino acid position 9 might not affect the specific activity of HuIFN-gamma.