gebhart/patrepeval huggingface dataset:
Resistance to DNA fragmentation and chromatin condensation in mice lacking the DNA fragmentation factor 45 (1998)

The DNA fragmentation factor 45 (DFF45) is a subunit of a heterodimeric nuclease complex critical for the induction of DNA fragmentation in vitro. To understand the in vivo role of DFF45 in programmed cell death, we generated DFF45 mutant mice. DNA fragmentation activity is completely abolished in cell extracts from DFF45 mutant tissues. In response to apoptotic stimuli, splenocytes, thymocytes, and granulocytes from DFF45 mutant mice are resistant to DNA fragmentation, and splenocytes and thymocytes are also resistant to chromatin condensation. Nevertheless, development of the immune system in the DFF45 mutant mice is normal. These results demonstrate that DFF45 is critical for the induction of DNA fragmentation and chromatin condensation in vivo, but is not required for normal immune system development.
Effect of Flexible Chain Length on the Photoorientation Behavior of Surface-Grafted Liquid Crystalline Azobenzene Block Copolymer Brush (2013)

A liquid crystalline (LC) azobenzene homopolymer brush film of poly[4-(10-methacryloxydecyloxy)-4′-pentylazobenzene] (P5Az10MA), and two diblock copolymer brushes consisting of the same LC azobenzene (Az) block connected with poly(hexyl methacrylate) block (PHMA-b-P5Az10MA) have been synthesized on initiator-immobilized quartz surfaces by atom transfer radical polymerization. In the diblock polymer brushes, the length of PHMA blocks tethering to the substrate surface were changed (26 nm and 51 nm). The orientation and structural features of the liquid crystalline block, containing an Az mesogenic group of the polymer brushes were evaluated by UV-vis spectroscopy and grazing incident X-ray diffraction measurements. Upon irradiation with 436 nm linearly polarized light (LPL), the levels of photoinduced in-plane anisotropy and reorienting behavior among the brushes showed significant differences as a result of degree of freedom of the flexible buffer chain spacers.
Molecular mechanisms in atopic eczema: insights gained from genetic studies (2016)

Atopic eczema (synonymous with atopic dermatitis) is a common heterogeneous phenotype with a wide spectrum of severity, from mild transient disease to a severe chronic disorder with atopic and non-atopic comorbidities. Eczema is a complex trait, resulting from the interaction of multiple genetic and environmental factors. The skin, as an organ that can be biopsied easily, provides opportunities for detailed molecular genetic analysis. Strategies applied to the investigation of atopic eczema include candidate gene and genome-wide studies, extreme phenotypes, and comparative analysis of inflammatory skin diseases. Genetic studies have identified a central role for skin barrier impairment in eczema predisposition and perpetuation; this has brought about a paradigm shift in understanding atopic disease, but specific molecular targets to improve skin barrier function remain elusive. The role of Th2-mediated immune dysfunction is also central to atopic inflammation, and has proved to be a powerful target for biological therapy in atopic eczema. Advances in understanding eczema pathogenesis have provided opportunities for patient stratification, primary prevention, and therapy development, but there remain considerable challenges in the application of this knowledge to optimize benefit for patients with atopic eczema in the era of personalized medicine. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cloning, sequencing, and disruption of the Bacillus subtilis sigma 28 gene (1988)

Bacillus subtilis contains multiple forms of RNA polymerase holoenzyme, distinguished by the presence of different specificity determinants known as sigma factors. The sigma 28 factor was initially purified as a unique transcriptional activity in vegetatively growing B. subtilis cells. Purification of the sigma 28 protein has allowed tryptic peptides to be prepared and sequenced. The sequence of one tryptic peptide fragment was used to prepare an oligonucleotide probe specific for the sigma 28 structural gene, and the gene was isolated from a B. subtilis subgenomic library. The complete nucleotide sequence of the sigma 28 gene was determined, and the cloned sigma 28 gene was used to construct a mutant strain which does not express the sigma 28 protein. This strain also failed to synthesize flagellin protein and grew as long filaments. The predicted sigma 28 gene product is a 254-amino-acid polypeptide with a calculated molecular weight of 29,500. The sigma 28 protein sequence was similar to that of other sequenced sigma factors and to the flbB gene product of Escherichia coli. Since the flbB gene product is a positive regulator of flagellar synthesis in E. coli, it is likely that sigma 28 functions to regulate flagellar synthesis in B. subtilis.
Adjuvant influenza vaccines. (1969)

Emulsified inactivated influenza vaccines have been in use for some 18 years and the goal of enhanced serological response lasting 2 years or more has been attained. The safety of the method in relation to immediate pyrogenic reactions has been demonstrated and no carcinogenic effects are known to have occurred in man. However, the problem of delayed local reactions after the injection of mineral-oil vaccines has not been solved. British experience of adverse reactions to commercial adjuvant influenza vaccine is quoted.New methods for obtaining adjuvant action without the risk of local abscess formation are needed both for inactivated whole virus and for split haemagglutinin vaccines. Reversal of water-in-mineral-oil emulsion to oil-in-water emulsion reduces viscosity and permits diffusion of the depot injection. A trial in Britain has shown equally good adjuvant properties of the reversed emulsion incorporating influenza virus vaccine so far as serological response is concerned, although it has not yet been conducted on a scale that would allow of adequate evaluation of the likelihood of delayed local reactions.
<sup>1</sup>H chemical shifts in NMR: Part 23, the effect of dimethyl sulphoxide <i>versus</i> chloroform solvent on <sup>1</sup>H chemical shifts (2006)

The 1H chemical shifts of 124 compounds containing a variety of functional groups have been recorded in CDCl3 and DMSO-d6 (henceforth DMSO) solvents. The 1H solvent shift Delta delta = delta(DMSO) - delta(CDCl3) varies from -0.3 to +4.6 ppm. This solvent shift can be accurately predicted (rms error 0.05 ppm) using the charge model of alpha, beta, gamma and long-range contributions. The labile protons of alcohols, acids, amines and amides give both, the largest solvent shifts and the largest errors. The contributions for the various groups are tabulated and it is shown that for H.C.C.X gamma-effects (X = OH, NH, =O, NH.CO) there is a dihedral angle dependence of the gamma-effect. The group contributions are discussed in terms of the possible solvent-solute interactions. For protic hydrogens, hydrogen bonding is the dominant interaction, but for the remaining protons solvent anisotropy and electric field effects appear to be the major factors.
Preparation of Pellets of Different Shape and Their Characterization (2001)

Pellets of different shapes were produced by modifying the processing parameters of a standardized pellet formulation. The target size of these pellets was 1-1.4 mm. Initially the shape of the pellets was assessed by visual observation. In total, eight batches of pellets were produced of which four were considered to be round, whereas the other four deviated from the spherical shape by various degrees. The different pellet fractions were then characterized for their size, shape, surface, and density properties employing a series of established techniques in order to identify the most appropriate method of characterization and the interrelationships between these properties. The results showed that attempting a task of preparing pellets of graded differences in shape from the same powder blend can result in changes of other important pellet properties such as surface roughness, surface area, and pellet dimensions. Some of these changes could be anticipated by considering the process variables involved, whereas others changed in a manner for which there is no immediate explanation.
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart (2011)

Catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic) is a publicly available resource providing information on somatic mutations implicated in human cancer. Release v51 (January 2011) includes data from just over 19,000 genes, 161,787 coding mutations and 5573 gene fusions, described in more than 577,000 tumour samples. COSMICMart (COSMIC BioMart) provides a flexible way to mine these data and combine somatic mutations with other biological relevant data sets. This article describes the data available in COSMIC along with examples of how to successfully mine and integrate data sets using COSMICMart. DATABASE URL: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/.
Identification of New Dicaffeoylquinic Acids from<i>Chrysanthemum morifolium</i>and their Antioxidant Activities (2005)

Two new dicaffeoylquinic acids, 3,5-dicaffeoyl- epi-quinic acid (1) and 1,3-dicaffeoyl- epi-quinic acid (2), were isolated from Chrysanthemum morifolium Ramar together with six known dicaffeoylquinic acid derivatives and three flavonoids. The structures of the new compounds were elucidated using of spectroscopic methods. These compounds were assessed for antioxidant activities in the DPPH radical and superoxide anion radical scavenging systems. Most of the isolates showed strong antioxidant activities in these assay systems. Two new compounds showed potent superoxide anion radical scavenging activity (IC50 = 2.9 +/- 0.1 for 1 and 2.6 +/- 0.4 microg/mL for 2, respectively) in the xanthine/xanthine oxidase system as compared to quercetin and also showed potent DPPH radical scavenging activity (IC50 = 5.6 +/- 0.1 for 1 and 5.8 +/- 0.2 microg/mL for 2, respectively).
Detection of partially phosphorylated forms of ERK by monoclonal antibodies reveals spatial regulation of ERK activity by phosphatases (2000)

When cells are stimulated by mitogens, extracellular signal-regulated kinase (ERK) is activated by phosphorylation of its regulatory threonine (Thr) and tyrosine (Tyr) residues. The inactivation of ERK may occur by phosphatase-mediated removal of the phosphates from these Tyr, Thr or both residues together. In this study, antibodies that selectively recognize all combinations of phosphorylation of the regulatory Thr and Tyr residues of ERK were developed, and used to study the inactivation of ERK upon mitogenic stimulation. We found that inactivation of ERK in the early stages of mitogenic stimulation involves separate Thr and Tyr phosphatases which operate differently in the nucleus and in the cytoplasm. Thus, ERK is differentially regulated in various subcellular compartments to secure proper length and strength of activation, which eventually determine the physiological outcome of many external signals.
Pigmentation and skin reaction to sun as risk factors for cutaneous melanoma: Western Canada Melanoma Study. (1984)

Between 1 April 1979 and 31 March 1981, 904 residents of the four western provinces of Canada (population 6.5 million), were diagnosed as suffering from primary cutaneous malignant melanoma. Of 801 patients aged 20-79 years, 665 (83%) were interviewed along with control subjects chosen at random from the general population and matched for age, sex, and province. After exclusion of 70 subjects with lentigo maligna or acral lentiginous melanoma, comparisons of the 595 case-control pairs showed that light hair, skin, and eye colour, a history of heavy freckling in adolescence, and a tendency to burn readily and tan poorly in the sun were significant risk factors for melanoma. The strongest primary associations were with blond hair (relative risk 7.1 compared with black hair), light colour of unexposed skin (relative risk 2.4), and severe freckling (relative risk 2.1). These associations were independent of ethnic origin and of recorded amount of exposure to the sun and were somewhat stronger for superficial spreading than for nodular melanoma. This study is the largest and most detailed of an incident series of melanomas to be published to date. The results were consistent with other studies reporting associations between melanoma and poor tanning ability, a tendency to burn easily, and a history of sunburn and showed that light hair colour was the strongest risk factor for the disease.
Complete nucleotide sequence of a gene conferring polymyxin B resistance on yeast: similarity of the predicted polypeptide to protein kinases. (1987)

Polymyxin B is an antibiotic that kills sensitive cells by disrupting their membranes. We have cloned a wild-type yeast gene that, when present on a high-copy-number plasmid, renders the cells resistant to the drug. The nucleotide sequence of this gene is presented. A single open reading frame within the sequence has the potential to encode a polypeptide (molecular mass of 77.5 kDa) that shows strong homologies to polypeptides of the protein kinase family. The gene, PBS2, located on chromosome X, is not allelic to the previously described PBS1 gene (where PBS signifies polymyxin B sensitivity). Although pbs1 mutations confer resistance to high levels of polymyxin B, double mutants, pbs1 pbs2, are not resistant to the drug, indicating that PBS2 is essential for pbs1 activity. Models based on the proposed protein kinase activity of the PBS2 gene product are presented to explain the interaction between PBS1 and PBS2 gene products involved in conferring polymyxin B resistance on yeast cells.
Photodynamic killing of retinoblastoma cells with hematoporphyrin and light. (1979)

Hematoporphyrin and white light exerted a lethal effect on two cell lines of retinoblastoma cells. The lowest values of dye concentration and light exposure capable of killing an entire cell population were, respectively, 2 X 10(-5) M and 6 min exposure to an irradiance of 6.0 microwatts/sq mm. Cells exposed to light in the presence of the dye did not require lengthy incubation periods but were rapidly killed with increasing periods of light exposure. Cells washed free of the dye, however, required a minimum sensitizing period of 3.5 hr to achieve a value close to 100% cell death. An inhibitor of this photodynamic process was demonstrated in normal serum. When the concentration of either fetal calf serum, rabbit serum, or rabbit plasma was increased to 25% from a standard 10%, there was as much as a 100-fold greater requirement of hematoporphyrin concentration to produce the same lethal response. The suggested explanation for this phenomenon is a porphyrin-binding plasma factor, hemopexin, which is a natural beta-glycoprotein believed to be responsible for the transport of circulating porphyrins to the liver for their elimination. Retinoblastoma cells grow in suspension and thereby provide an excellent tool for study of photosensitive dyes, especially in the case of the rapidly growing Y79 cell line.
Glucocorticoid‐inducible expression of a bacterial avirulence gene in transgenic <i>Arabidopsis</i> induces hypersensitive cell death (1998)

Pathogenic strains of Pseudomonas syringae pv. tomato carrying the avrRpt2 avirulence gene specifically induce a hypersensitive cell death response in Arabidopsis plants that contain the complementary RPS2 disease resistance gene. Transient expression of avrRpt2 in Arabidopsis plants having the RPS2 gene has been shown to induce hypersensitive cell death. In order to analyze the effects of conditional expression of avrRpt2 in Arabidopsis plants, transgenic lines were constructed that contained the avrRpt2 gene under the control of a tightly regulated, glucocorticoid-inducible promoter. Dexamethasone-induced expression of avrRpt2 in transgenic lines having the RPS2 gene resulted in a specific hypersensitive cell death response that resembled a Pseudomonas syringae-induced hypersensitive response and also induced the expression of a pathogenesis-related gene (PR1). Interestingly, high level expression of avrRpt2 in a mutant rps2-101C background resulted in plant stress and ultimately cell death, suggesting a possible role for avrRpt2 in Pseudomonas syringae virulence. Transgenic RPS2 and rps2 plants that contain the glucocorticoid-inducible avrRpt2 gene will provide a powerful new tool for the genetic, physiological, biochemical, and molecular dissection of an avirulence gene-specified cell death response in both resistant and susceptible plants.
CMOS compatible fabrication methodsfor submicron Josephson junction qubits (2001)

The authors have developed two distinct processes for the fabrication of mesoscopic Josephson junction qubits that are compatible with conventional CMOS processing. These devices, based on superconducting Al/Al2O3/Al tunnel junctions, are fabricated by electron beam lithography using single-layer and multi-layer resists. The new single-layer resist process is found to have significant advantages over conventional fabrication methods using suspended tri-layer shadow masks. It is simpler and more accurate to implement, and avoids the significant areas of redundant metallisation that are an unavoidable by-product of the tri-layer shadow mask method.
Preparation of novel heterogeneous cation‐permeable membranes from blends of sulfonated poly(phenylene sulfide) and poly(ether sulfone) (2003)

Abstract Novel heterogeneous cation‐exchange membranes using poly (ether sulfone)(PES) as binder and sulfonated poly(phenylene sulfide) (SPPS) powder as polyelectrolyte were prepared by the solution casting‐immersion method. Compared with a conventional route for heterogeneous membrane, the steps of milling resin into fine powders and the pressing at high temperature are avoided, and thus permits a simple technique for the preparation of such membrane. The effect of the particle size and loading of SPPS resin on the properties of the membranes such as ion‐exchange capacity, water content, electrical resistance, transport number, diffusion coefficient of electrolytes, etc., have been studied. It is shown that the membrane fundamental properties are largely dependent on both the resin loading and the particle size of SPPS resin. By adjusting these two important parameters, one can obtain heterogeneous membrane with both good conductivity, selectivity, and proper water content for different industrial purposes such as electrodialysis, diffusional dialysis, etc. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 91: 167–174, 2004
Comparative proteomics analysis reveals roles for <scp>FADD</scp> in the regulation of energy metabolism and proteolysis pathway in mouse embryonic fibroblast (2013)

Fas-associated death domain-containing protein (FADD) is a classical apoptotic pathway adaptor. Further studies revealed that it also plays essential roles in nonapoptotic processes, which is assumed to be regulated by its phosphorylation. However, the exact mechanisms are still poorly understood. To study the nonapoptotic effects of FADD, a comprehensive strategy of proteomics identification combined with bioinformatic analysis was undertaken to identify proteins differentially expressed in three cell lines containing FADD and its mutant, FADD-A and FADD-D. The cell lines were thought to bear wild-type FADD, unphosphorylated FADD mimic and constitutive phosphorylated FADD mimic, respectively. A total of 47 proteins were identified to be significantly changed due to FADD phosphorylation. Network analysis using MetaCore™ identified a number of changed proteins that were involved in cellular metabolic process, including lipid metabolism, fatty acid metabolism, glycolysis, and oxidative phosphorylation. The finding that FADD-D cell line showed an increase in fatty acid oxidation argues that it could contribute to the leaner phenotype of FADD-D mice as reported previously. In addition, six proteins related to the ubiquitin-proteasome pathway were also specifically overexpressed in FADD-D cell line. Finally, the c-Myc gene represents a convergent hub lying at the center of dysregulated pathways, and was upregulated in FADD-D cells. Taken together, these studies allowed us to conclude that impaired mitochondrial function and proteolysis might play pivotal roles in the dysfunction associated with FADD phosphorylation-induced disorders.
"REAL TIME" ANALYSIS OF THE DRIVING SITUATION IN ORDER TO MANAGE ON-BOARD INFORMATION (2002)

This paper presents an overview of the European project CEMVOCAS (Centralized Management of VOCal interfaces aiming a better Automotive Safety). The aim of this project was to develop a system to diagnose (in real time) the driver's availability to receive vocal information. After a brief introduction focused on the research context, the methodology used to design & develop this technology is described, and the main results from the prototype evaluation that have been carried out in real driving conditions are provided. Good performances are registered in terms of (a) effectiveness (more than 80 % of the driving situations are correctly identified by CEMVOCAS), (b) efficiency (the managed messages disturbed the drivers less often than the not managed ones), and (c) satisfaction (good user opinion concerning the benefits of the automatic message management in terms of comfort and safety). For the covering abstract see ITRD E122427.
Microbial Conversion of Tall Oil Sterols to C <sub>19</sub> Steroids (1976)

Mycobacterium sp. NRRL B-3683 converted tall oil sterols to C 19 steroids as efficiently as it converted soybean sterols.
Quantum limited heterodyne detection in superconducting non-linear transmission lines at sub-millimeter wavelengths (1995)

A non-linear superconducting transmission line has been successfully employed in heterodyne detection of sub-millimeter waves. In our experiments an Nb/Al/AlOx/Nb tunnel junction, measuring 0.15×40 μm, with a critical current density of about 2500 A/cm2 is used as a distributed mixer element. We have demonstrated that quantum limited sensitivity can be achieved with this type of device. At 460 GHz, a Y-factor of 2.5 has been recorded, corresponding to a double-side-band receiver noise temperature of 80 K. The double-side-band conversion loss is about 1 dB and the mixer noise temperature is estimated to be 18(±10) K.
Localization of Human Rhinovirus Replication in the Upper Respiratory Tract by In Situ Hybridization (1995)

To localize the sites and determine the extent of human rhinovirus (HRV) replication in the upper respiratory tract, biopsies of nasal and nasopharyngeal epithelia were collected from 26 HRV- or 7 sham-inoculated volunteers on days 1, 3, and 5 and on days 12, 20, or 33 after inoculation and analyzed by in situ hybridization. HRV-infected cells were detected on at least 1 day in 22 of the 23 HRV-infected subjects and in 1 of the 7 sham-inoculated subjects who developed a cold and had nasal secretions positive for a picornavirus by polymerase chain reaction. Low numbers of in situ hybridization-positive ciliated cells were present in nasal biopsies. In the nasopharynx, most HRV-infected cells were ciliated, but infected nonciliated epithelial cells were also detected. Our results indicate that HRV replicates in a very small proportion of cells in the nasal epithelium and in both ciliated and nonciliated cells in the nasopharynx of experimentally infected humans.