gebhart/patrepeval huggingface dataset:
A stable genomic source of P element transposase in Drosophila melanogaster. (1988)

A single P element insert in Drosophila melanogaster, called P[ry+ delta 2-3](99B), is described that caused mobilization of other elements at unusually high frequencies, yet is itself remarkably stable. Its transposase activity is higher than that of an entire P strain, but it rarely undergoes internal deletion, excision or transposition. This element was constructed by F. Laski, D. Rio and G. Rubin for other purposes, but we have found it to be useful for experiments involving P elements. We demonstrate that together with a chromosome bearing numerous nonautonomous elements it can be used for P element mutagenesis. It can also substitute efficiently for "helper" plasmids in P element mediated transformation, and can be used to move transformed elements around the genome.
Regulated interactions between partner and non-partner sensors and response regulators that control glycopeptide resistance gene expression in enterococci (1999)

Transcription of the vanA and vanB glycopeptide resistance gene clusters is regulated by the VanRS and VanRBSB two-component regulatory systems, respectively. Histidine to glutamine substitutions were introduced at positions 164 of VanS and 233 of VanSB to prevent autophosphorylation of the sensor kinases and transfer of the phosphate groups to the VanR and VanRB response regulators. VanSH164Q and VanSBH233Q abolished activation of VanR and VanRB by host kinases. The phosphatase activity of VanSBH233Q was negatively modulated by vancomycin whereas VanSH164Q prevented transcription of the resistance genes under all growth conditions. Cross-talk was detected between VanRB and VanS in a vanSB null mutant. VanR is required for activation of promoters PR and PH allowing transcription of the regulatory (vanRS) and resistance (vanHAXYZ) genes, respectively. Under non-inducing conditions, activation of VanR by cross-talk was blocked by the presence of a multicopy plasmid carrying PH. Presence of the high-affinity VanR-binding sites of the regulatory region of PH on the multicopy vector probably sequestered VanR, thereby preventing autoactivation of the PR promoter. Under such circumstances, stimulation of the host kinase by glycopeptides or moenomycin was required for expression of the resistance genes.
Distribution of Neuropeptides in Synovium of the Knee With Osteoarthritis (2000)

Synovial tissue was obtained from medial, lateral, and suprapatellar sites of 21 knees (15 patients) with medial compartmental osteoarthritis at surgery. All patients reported pain around the medial joint of their knees while walking and climbing stairs. For investigation of the synovial innervation, six samples were stained with modified gold chloride and the others with an immunohistochemical method using antisera against neuropeptides. The extent of synovitis in each part was scored using a new 10-point scale. The results showed that the synovium had an extensive neural network in the somatic and autonomic nervous systems. Neuropeptides were most abundant, with an especially large number of substance P and calcitonin gene related peptide immunoreactive free nerve endings. Some of the substance P positive nerve endings were surrounded by monocytes. Substance P and calcitonin gene related peptide were found more frequently in the medial than in the lateral or suprapatellar areas. Substance P positive free nerve endings showed more dendritic morphologic features in the medial region than did those in the lateral and suprapatellar regions, and small nerves were accompanied by newly developed vessels in synovial villi. In the medial region, the synovitis was more remarkable than in the lateral region. These findings suggest that free nerve endings containing substance P may modulate inflammation and the pain pathway in osteoarthritis.
[The treatment of atherosclerosis--drug therapy]. (1993)

Drug treatment against atherosclerosis has been evaluated recently in many epidemiological studies. Lipid Research Clinics Group convincingly reported in a large scale design that anion exchange resin effectively reduced blood cholesterol level and concomitantly decreased the events of coronary heart disease. Subsequently, anion exchange resin with or without combined administration of niacin or statin was found to inhibit the progression of coronary atherosclerotic lesions in FATS, SCOR, CLAS and STARS. Fenofibrate also successfully reduced the coronary artery narrowings. Based on these intervention studies, several hypocholesterolemic agents are definitely effective in the treatment of coronary atherosclerosis.
Signal transduction by epidermal growth factor and heregulin via the kinase-deficient ErbB3 protein (1998)

The role of protein tyrosine kinase activity in ErbB3-mediated signal transduction was investigated. ErbB3 was phosphorylated in vivo in response to either heregulin (HRG) in cells expressing both ErbB3 and ErbB2, or epidermal growth factor (EGF) in cells expressing both ErbB3 and EGF receptor. A recombinant receptor protein (ErbB3-K/M, in which K/M stands for Lys-->Met amino acid substitution) containing an inactivating mutation in the putative ATP-binding site was also phosphorylated in response to HRG and EGF. Both the wild-type ErbB3 and mutant ErbB3-K/M proteins transduced signals to phosphatidylinositol 3-kinase, Shc and mitogen-activated protein kinases. Separate kinase-inactivating mutations in the EGF receptor and ErbB2 proteins abolished ErbB3 phosphorylation and signal transduction activated by EGF and HRG respectively. Hence the protein tyrosine kinase activity necessary for growth factor signalling via the ErbB3 protein seems to be provided by coexpressed EGF and ErbB2 receptor proteins.
Fast numerical algorithms for total variation based image restoration (2008)

Image restoration models based on total variation (TV) have been popular and successful since their introduction by Rudin, Osher, and Fatemi (ROF) in 1992. The nonsmooth TV seminorm allows them to preserve sharp discontinuities (edges) in an image while removing noise and other unwanted fine scale detail. On the other hand, the TV term, which is the L1 norm of the gradient vector, poses computational challenge in solving those models efficiently. Furthermore, the global coupling of the gradient operator makes the problem extra harder than other L1 minimization problems where the variables under the L 1 norm are separable. In this paper we propose several new algorithms to tackle these difficulties from different perspectives. Numerical experiments show that they are competitive with the existing popular methods and some of them are significantly faster despite of their simplicity. The first algorithm we introduce is a primal-dual hybrid gradient descent method that alternates between the primal and the dual updates. It utilizes the information from both the primal and dual variables and therefore is able to converges faster than the pure primal or pure dual method in the same category. We then proposed gradient projection (GP) methods to solve the dual problem of the ROF model based on the special structure of the dual constraints. We also test variants of GP algorithms with different step selection strategies, including techniques based on the Barzilai-Borwein method. In this same line, a block co-ordinate descent method is proposed for solving the dual ROF problem. The subproblem at each single block can be solved exactly using different techniques. We also propose a basic multilevel optimization framework for the dual formulation, aiming to speedup our solution process for large scale problems. Finally, we study the connections between some existing methods and give an improvement to CGM method based on the primal-dual interior-point algorithms.
A rational approach in the search for potent inhibitors against HIV proteinase (1991)

Synthetic peptides described as dog renin inhibitors were found to effectively inhibit the aspartyl protease of human immunodeficiency virus (HIV). The selection of oligopeptides for the HIV protease inhibition study was based on 1) the current strategy of inhibiting aspartyl proteases with transition state analogs, and 2) our previous observations regarding optimal structural differentiation at the P2 position among human, dog, and rat renin inhibitors. In an in vitro assay system consisting of recombinant HIV protease and a synthetic decapeptide substrate (at pH 5.5), results show that HIV protease was unaffected by statine-containing analogs carrying histidine at the P2 position whereas analogs containing valine at the same position yielded anti-protease IC50 values ranging from 50 to 500 nM. As anticipated, some analogs were also shown to inhibit processing of recombinant polyprotein substrate by HIV protease in vitro. The anti-viral activity of three inhibitors was studied in HIV-infected CEM and MT-2 cells. Results showed that one compound, Ac-Naphthylalanyl-Pro-Phe-Val-Statine-Leu-Phe-NH2 (antiprotease IC50 value = 0.4 microM), protected the infected cells effectively with IC50 values (0.73 microM for CEM cells and 0.88 microM for MT-2 cells). This antiviral effect is comparable to those obtained with AZT and ddC in parallel studies of MT-2 cells.
Physical basis for high power semiconductor nanosecond opening switches (2003)

The authors describe how, as a result of long-time research and development, a very high power, repetitive mode, semiconductor-based nanosecond technique is now commercially available. Drift step recovery diodes and inverse recover diodes are preferable as a base for generators with pulse rise times of 0.5-3 ns and pulse powers less than 50-80 MW. Silicon opening switch diodes are preferable at pulse rise times higher than 5 ns with any power and at any pulse rise time if the pulse power is higher than 100 MW.
Principles of Optics (1999)

Principles of Optics is one of the classic science books of the twentieth century, and probably the most influential book in optics published in the past 40 years. The new edition is the first ever thoroughly revised and expanded edition of this standard text. Among the new material, much of which is not available in any other optics text, is a section on the CAT scan (computerized axial tomography), which has revolutionized medical diagnostics. The book also includes a new chapter on scattering from inhomogeneous media which provides a comprehensive treatment of the theory of scattering of scalar as well as of electromagnetic waves, including the Born series and the Rytov series. The chapter also presents an account of the principles of diffraction tomography - a refinement of the CAT scan - to which Emil Wolf, one of the authors, has made a basic contribution by formulating in 1969 what is generally regarded to be the basic theorem in this field. The chapter also includes an account of scattering from periodic potentials and its connection to the classic subject of determining the structure of crystals from X-ray diffraction experiments, including accounts of von Laue equations, Bragg's law, the Ewald sphere of reflection and the Ewald limiting sphere, both generalized to continuous media. These topics, although originally introduced in connection with the theory of X-ray diffraction by crystals, have since become of considerable relevance to optics, for example in connection with deep holograms. Other new topics covered in this new edition include interference with broad-band light, which introduces the reader to an important phenomenon discovered relatively recently by Emil Wolf, namely the generation of shifts of spectral lines and other modifications of spectra of radiated fields due to the state of coherence of a source. There is also a section on the so-called Rayleigh-Sommerfield diffraction theory which, in recent times, has been finding increasing popularity among optical scientists. There are also several new appendices, including one on energy conservation in scalar wavefields, which is seldom discussed in books on optics. The new edition of this standard reference will continue to be invaluable to advanced undergraduates, graduate students and researchers working in most areas of optics.
Análisis de la dimensión sonora en el cine de suspenso. (2002)

Los films de origen y periodos diferentes del cine de suspenso, conforman la unidad de analisis del proyecto, que tiene como objetivo realizar un estudio cualitativo de la dimension sonora en el cine. A traves de la ubicacion temporal de los eventos sonoros, del analisis musical de las composiciones, de la tipificacion de las fuentes sonoras y de los recursos tecnicos implementados, el proyecto tiene como objetivo registrar las tipologias de eventos sonoros y categorizar las modalidades de intervencion en las realizaciones cinematograficas.
Association of Higher Levels of High-Density Lipoprotein Cholesterol in Elderly Individuals and Lower Risk of Late-Onset Alzheimer Disease (2010)

High HDL-C levels in elderly individuals may be associated with a decreased risk of AD.
Effects of Different Ionizing Radiations on Human Cells in Tissue Culture: I. Irradiation Techniques and Dosimetry (1960)

G. W. Barendsen, T. L. J. Beusker, Effects of Different Ionizing Radiations on Human Cells in Tissue Culture: I. Irradiation Techniques and Dosimetry, Radiation Research, Vol. 13, No. 6 (Dec., 1960), pp. 832-840
Tissue repair by thrombin-derived peptides in the rat. (1993)

An ordered sequence of events occurs following tissue damage to bring about healing. One molecule involved in this process is thrombin. Utilizing rat linear incision and full dermal excision models, we have investigated the ability of two thrombin-derived RGD-containing peptides, p517 and p508, to enhance tissue repair under normal and healing-impaired conditions. p508, at 0.5 micrograms peptide per wound, produced a significant .23% improvement in wound strength in a dose-dependent manner. Similarly, a single application of 0.5 micrograms p517 per 6-cm linear incision would significantly increased wound-breaking strength approximately 18% at nine days postsurgery (control: 3.95 +/- 0.13 Newtons, vs. p517: 4.68 +/- 0.13 Newtons; P < 0.001). However, in glucocorticoid-stressed rats, the application of 0.5 micrograms per wound p508 or 517 did not significantly influence steroid-impaired healing. In the full dermal skin excision wound model, a single application of 0.5 micrograms p508 per wound at the time of surgery significantly reduced average wound area at days 3 and 5, when healing was impaired by glucocorticoid administration. Wound area was also reduced by p508 treatment at day 3 in the normal animal, but this effect was not statistically significant. We suggest wound-healing benefits of p508 and p517 may activate wound fibroblast proliferation or stimulate other cell types in the wound site through an RGD-mediated interaction.
Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity (2010)

Copy-number variations (CNVs) are widespread in the human genome, but comprehensive assignments of integer locus copy-numbers (i.e., copy-number genotypes) that, for example, enable discrimination of homozygous from heterozygous CNVs, have remained challenging. Here we present CopySeq, a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can incorporate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. We benchmarked CopySeq by genotyping 500 chromosome 1 CNV regions in 150 personal genomes sequenced at low-coverage. The assessed copy-number genotypes were highly concordant with our performed qPCR experiments (Pearson correlation coefficient 0.94), and with the published results of two microarray platforms (95-99% concordance). We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched >800 olfactory receptor (OR) human gene and pseudogene loci. CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others. Among genetic variants affecting OR loci we identified deleterious variants including CNVs and SNPs affecting ~15% and ~20% of the human OR gene repertoire, respectively, implying that genetic variants with a possible impact on smell perception are widespread. Finally, we found that for several OR loci the reference genome appears to represent a minor-frequency variant, implying a necessary revision of the OR repertoire for future functional studies. CopySeq can ascertain genomic structural variation in specific gene families as well as at a genome-wide scale, where it may enable the quantitative evaluation of CNVs in genome-wide association studies involving high-throughput sequencing.
An inhibitory mutant of c-Raf-1 blocks v-Src-induced activation of the Egr-1 promoter. (1991)

The protein-tyrosine kinase activity of v-Src leads to the transcriptional activation of the mitogen-responsive transcription factor Egr-1. c-Raf-1 is a serine/threonine protein kinase that has been implicated in the transduction of signals induced by mitogens. The involvement of c-Raf-1 in v-Src-induced Egr-1 expression was investigated using an inhibitory mutant of c-Raf-1. We report here that expression of a kinase-defective mutant of c-Raf-1 inhibits v-Src-induced activation of the Egr-1 promoter. This inhibition is reversed by overexpression of wild type c-Raf-1. Consistent with an involvement of c-Raf-1 in a signaling pathway leading to Egr-1 expression, we find that v-Raf induces Egr-1 promoter activation. These data suggest that c-Raf-1 is a component in an intracellular signaling pathway initiated by v-Src leading to the induction of the mitogen-responsive transcription factor Egr-1.
Mapping of interacting domains between the nucleocapsid protein and the phosphoprotein of vesicular stomatitis virus by using a two-hybrid system. (1993)

Specific interaction between the nucleocapsid protein (N) and the phosphoprotein (P) of vesicular stomatitis virus (VSV), an important step in the life-cycle of the virus, was studied by using a two-hybrid system. Plasmids encoding P fused with the yeast GAL4 DNA-binding domain (pGALP) and N fused with the herpes simplex virus VP16 transactivating region (pVPN) were transfected into CHO cells along with a reporter plasmid encoding chloramphenicol acetyltransferase (CAT). The ability of N and P to associate in vivo was measured by activation of the CAT gene by the VP16 transactivating region. Transfection of plasmids pGALP and pVPN resulted in a high level of CAT activity, indicating that the N and P portions of the fusion proteins associated very strongly with each other. Progressive C-terminal deletions of the P protein revealed two regions that are important for association with the N protein: the N-terminal acidic domain and the C-terminal basic domain. Phosphorylation of P protein was not required for N-P association. Various deletions and mutations of the N protein revealed the C-terminal 5 amino acids (Val-Glu-Phe-Asp-Lys), in particular the amino acids Val-Glu-Phe, to be critical for N association with P. This two-hybrid system can be used in other viral systems to study the interaction between proteins involved in transcription and replication.
Polymer Layered Silicate Nanocomposites (1996)

Abstract Polymer nanocomposites with layered silicates as the inorganic phase (reinforcement) are discussed. The materials design and synthesis rely on the ability of layered silicates to intercalate in the galleries between their layers a wide range of monomers and polymers. Special emphasis is placed on a new, versatile and environmentally benign synthesis approach by polymer melt intercalation. In contrast to in‐situ polymerization and solution intercalation, melt intercalation involves mixing the layered silicate with the polymer and heating the mixture above the softening point of the polymer. Compatibility with various polymers is accomplished by derivatizing the silicates with alkyl ammonium cations via an ion exchange reaction. By fine‐tuning the surface characteristics nanodispersion (i. e. intercalation or delamination) can be accomplished. The resulting polymer layered silicate (PLS) nanocomposites exhibit properties dramatically different from their more conventional counterparts. For example, PLS nanocomposites can attain a particular degree of stiffness, strength and barrier properties with far less inorganic content than comparable glass‐ or mineral reinforced polymers and, therefore, they are far lighter in weight. In addition, PLS nanocomposites exhibit significant increase in thermal stability as well as self‐extinguishing characteristics. The combination of improved properties, convenient processing and low cost has already led to a few commercial applications with more currently under development.
Synergy of Ethanol and Putative Neurotransmitters: Glycine and Serine (1972)

The putative neurotransmitters, glycine and serine, significantly enhanced the sleeping time (loss of the righting reflex) that was induced by ethanol in mice. The observed synergistic effect between ethanol and the amino acids is probably not related to an alteration of ethanol metabolism, but rather to an interaction of these compounds in the central nervous system.
The role of IL-6 and IL-23 in colitis associated cancer (88.30) (2009)

Abstract Colitis associated cancer (CAC) is the most serious complication of inflammatory bowel diseases (IBD). Pro-inflammatory cytokines regulated by NF-B were suggested to regulate pre-neoplastic growth during CAC tumorigenesis. We tried to dissect the roles of individual cytokines in CAC tumorigenesis. Using genetic tools and a mouse model of azoxymethane/dextrane sodium sulfate induced CAC we demonstrate that IL-6 and IL-23 are critical tumor promoters during early CAC tumorigenesis. IL-6 and IL-23 act on cells of innate and adaptive immunity, particularly on T cells. Additionally, these cytokines have direct and indirect effects on intestinal epithelial (IEC) and neoplastic cells. These effects are mediated by transcription factor STAT3, whose IEC-specific ablation reduces CAC tumorigenicity. We conclude that IL-6 and IL-23 regulate multiple stages of colonic tumorigenesis, particularly tumor initiation and tumor growth. Selective inhibition of these cytokines may be beneficial for treatment and prevention of CAC. Supported by RFA from Crohn`s and Colitis Foundation of America (CCFA #1762) to S.G. and by grants from the NIH and a Jeannik M. Littlefield-AACR grant in metastatic colon cancer to M.K.