gebhart/patrepeval huggingface dataset:
Biochemical Composition of Lymphocytic Choriomeningitis Virus Interfering Particles (1981)

Lymphocytic choriomeningitis (LCM) was interfering particles were enriched relative to infectious virions by ultracentrifugation in a shallow gradient made of Urografin. Electrophoretic analysis revealed that they lacked the small ('S') 23S RNA as well as GP-1 and GP-2 of the infectious virion and also lacked a newly characterized glycoprotein of apparent mol. wt. 85 x 10(3); instead, they contained a novel glycoprotein with mol. wt. 65 x 10(3).
Dynamics of the matrix metalloproteinases MMP‐1 and MMP‐8 in acute open human dermal wounds (1998)

Extracellular matrix degradation during dermal wound healing involves multiple levels of regulation by several enzymes of the matrix metalloproteinase family, their activators, and their inhibitors. This study tested the hypothesis that a temporal pattern of interstitial collagenase appearance occurs during normal dermal wound healing, with matrix metalloproteinase-8 originating from neutrophils appearing earlier than the fibroblast-derived matrix metalloproteinase-1. Open (6 mm) full-thickness dermal wounds, which were covered by transparent occlusive dressings, were made in healthy human volunteers (n = 20). Wound fluids from under the dressings were collected daily through day 8, and wound tissue biopsies were obtained on days 0, 2, 4, 14, and 28. Collagenases were extracted from homogenized tissue biopsies for analysis. Samples were analyzed for the presence of matrix metalloproteinase-1 and matrix metalloproteinase-8 by enzyme-linked immunosorbent assays and by collagenase activity assays using purified types I and III collagen as substrates. In addition, tissue inhibitor of metalloproteinases-1 and matrix metalloproteinase-1/tissue inhibitor of metalloproteinases-1 complexes in wound fluids were measured. Results showed a differential temporal pattern of matrix metalloproteinase-1 and matrix metalloproteinase-8 in wound exudates with peak levels of matrix metalloproteinase-8 occurring on day 4 and matrix metalloproteinase-1 peak levels on day 7. Maximal levels in tissue for both enzymes occurred on day 2. At all time points examined, levels of matrix metalloproteinase-8 were statistically higher than matrix metalloproteinase-1 (100-fold to 200-fold). Tissue inhibitor of metalloproteinases-1 levels declined over time, whereas levels of matrix metalloproteinase-1/tissue inhibitor of metalloproteinase-1 complexes increased to a plateau on day 7. This study provides new evidence implicating matrix metalloproteinase-8 as a major collagenase in healing human dermal wounds. It also shows a temporal pattern in the appearance of the matrix metalloproteinases, tissue inhibitor of metalloproteinase-1, and matrix metalloproteinase-1/tissue inhibitor of metalloproteinases-1 complexes, suggesting that a tightly regulated pattern of expression of matrix metalloproteinases and their inhibitors is essential for normal wound healing in humans.
Resistance to therapy in BRCA2 mutant cells due to loss of the nucleosome remodeling factor CHD4 (2015)

Hereditary cancers derive from gene defects that often compromise DNA repair. Thus, BRCA-associated cancers are sensitive to DNA-damaging agents such as cisplatin. The efficacy of cisplatin is limited, however, by the development of resistance. One cisplatin resistance mechanism is restoration of homologous recombination (HR), which can result from BRCA reversion mutations. However, in BRCA2 mutant cancers, cisplatin resistance can occur independently of restored HR by a mechanism that remains unknown. Here we performed a genome-wide shRNA screen and found that loss of the nucleosome remodeling factor CHD4 confers cisplatin resistance. Restoration of cisplatin resistance is independent of HR but correlates with restored cell cycle progression, reduced chromosomal aberrations, and enhanced DNA damage tolerance. Suggesting clinical relevance, cisplatin-resistant clones lacking genetic reversion of BRCA2 show de novo loss of CHD4 expression in vitro. Moreover, BRCA2 mutant ovarian cancers with reduced CHD4 expression significantly correlate with shorter progression-free survival and shorter overall survival. Collectively, our findings indicate that CHD4 modulates therapeutic response in BRCA2 mutant cancer cells.
Competitive Aryl−Iodide vs Aryl−Aryl Reductive Elimination Reactions in Pt(IV) Complexes:  Experimental and Theoretical Studies (2007)

The platinum(IV) complex trans-(dmpe)Pt(IV)(Ar)2I2 (2, dmpe = 1,2-dimethylphosphinoethane, Ar = 4-FC6H4) rapidly reacts, upon moderate heating in solution under ambient light, via two distinct pathways: isomerization to the corresponding cis-isomer (3) and Ar-I reductive elimination to give (dmpe)Pt(II)(Ar)I (4). Complex 3 undergoes, upon prolonged heating at high temperatures, an exclusive Ar-Ar reductive elimination reaction to give (dmpe)Pt(II)I2. Experimental and DFT studies showed that the 2-to-3 isomerization proceeds via three pathways: photochemical or thermal phosphine chelate opening and a mechanism involving cleavage of the Pt-I bond. The isomerization reaction is significantly slowed down but not stopped in the absence of light or in the presence of an excess of tetra-n-butylammonium iodide. On the other hand, the Ar-I reductive elimination from 2 proceeds via the Pt(delta+)-I(delta-) ion pairlike transition state. Use of the rigid dmpe analogue 1,2-dimethylphosphinobenzene (dmpbz) as the ligand shuts down the chelate ring-opening isomerization pathway and enables faster Ar-I reductive elimination thus making the latter reaction the major reaction route for the dmpbz supported trans-diiodo Pt(IV) complex 8.
Specific killing of human T-leukemia cells by immunotoxins prepared with ricin A chain and monoclonal anti-human T-cell leukemia antibodies. (1984)

In this study, immunotoxins containing monoclonal anti-human T-cell leukemia antibodies are shown to be capable of specific killing of human T-leukemia cells in vitro. These immunotoxins were prepared by conjugating ricin A chain (RIA) with our recently generated murine monoclonal antibodies, SN1 and SN2, the latter of which was obtained from a hybridoma clone N6/D11 described previously by Negoro and Seon (Cancer Res., 42: 4259-4262, 1982), directed to two unique human T-cell leukemia antigens. We have shown previously that these monoclonal antibodies do not react with non-T-leukemia cells nor with various normal cells including normal T-cells, thymocytes, and bone marrow cells (Proc. Natl. Acad. Sci. U. S. A., 80: 845, 1983; Cancer Res., 42: 4259, 1982). Control conjugate was also prepared by conjugating RIA with a murine monoclonal immunoglobulin G (IgG), the isotype of which is the same as that of SN1 and SN2, i.e., IgG1-kappa. In initial experiments, the cytotoxic activity of an SN1 IgG:RIA conjugate preparation and the control IgG conjugate preparation against leukemic T-cell lines and normal B-cell lines was tested by two different test procedures, i.e., by measuring direct killing of the cells and by measuring inhibitory activity against protein synthesis in the cells. In each test, the SN1 conjugate showed specific cytotoxic activity against T-leukemia cells, whereas the control conjugate was not cytotoxic against either T-leukemia cells or normal B-cells. Nearly complete killing of T-leukemia cells and inhibition of protein synthesis in T-leukemia cells were observed at the concentrations of 10(-8) to 10(-7) M of the SN1 IgG:RIA conjugate. In subsequent experiments, another preparation of SN1 IgG:RIA conjugate and an SN2 IgG:RIA conjugate preparation were tested individually and together for their inhibitory activity against protein synthesis in T-leukemia cells and control cells. With T-leukemia cells, specific inhibition was observed for both SN1 IgG:RIA and SN2 IgG:RIA. The combined use of these conjugates did not display a synergistic effect. Nevertheless, the combined use of different immunotoxins directed to different antigen molecules will be important in clinical use, since uncultured tumor cells derived freshly from patients, in general, display heterogeneity with respect to the expression of tumor-associated antigens. These immunotoxins may be useful for the in vitro eradication of tumor cells in the bone marrow taken from patients with T-cell leukemia.(ABSTRACT TRUNCATED AT 400 WORDS)
Microneedle arrays as medical devices for enhanced transdermal drug delivery (2011)

In order to exploit the transdermal route for systemic delivery of a wide range of drug molecules, including peptide/protein molecules and genetic material, a means of disrupting the excellent barrier properties of the uppermost layer of the skin, the stratum corneum, must be sought. The use of microneedle (MN) arrays has been proposed as a method to temporarily disrupt the barrier function of the skin and thus enable enhanced transdermal drug delivery. MN arrays consist of a plurality of micron-sized needles, generally ranging from 25 to 2000 µm in height, of a variety of different shapes and composition (e.g., silicon, metal, sugars and biodegradable polymers). The application of such MN arrays to the skin results in the creation of aqueous channels that are orders of magnitude larger than molecular dimensions and, therefore, should readily permit the transport of macromolecules. This article will focus on recent and future developments for MN technology, focusing on the materials used for MN fabrication, the forces required for MN insertion and potential safety aspects that may be involved with the use of MN devices.
Gratings photowritten in ion-exchanged glass channelwaveguides (1999)

Gratings are photowritten in ion-exchanged glass channel waveguides. The transmission of these waveguides shows a rejection dip of almost 20 dB. The polarisation dependence of these waveguide gratings is measured and discussed.
Spread spectrum data leap through AC power wiring (1996)

There have been two serious impediments to the growth of the power-line carrier (PLC) communications industry in particular, and the home and building automation market in general: line noise, which plays havoc with communications' reliability, and the lack of a standard communication network protocol. Both stumbling blocks have been removed-the first, by the development of spread-spectrum PLC technology, which all but eliminates the noise impediment, and the second, by the industry-wide adoption of the Electronic Industries Association's Consumer Electronics Bus (CEBus) standard. The author discusses the use of spread spectrum for distributed control systems. The techniques of spread spectrum and carrier-detect narrowband communication are compared. Impulse noise is also discussed as are frequency hopping and the CEBus approach.
Effect of alteration of left ventricular activation sequence on the left ventricular end-systolic pressure-volume relation in closed-chest dogs. (1985)

We investigated the effect of pacing from the atrium and various ventricular sites on the left ventricular end-systolic pressure-volume relation following autonomic blockade in a total of 10 dogs chronically instrumented to measure left ventricular pressure and determine left ventricular volume from three ultrasonic endocardial dimensions. During ventricular pacing, left ventricular end-diastolic volume, stroke volume, and end-systolic pressure were decreased, while the end-systolic volume was relatively unchanged. Left ventricular end-systolic pressure-volume relations were generated by vena caval occlusions during pacing at a constant rate from the left atria, and the epicardium of the right ventricular free wall, right ventricular apex, and left ventricular free wall. The left ventricular end-systolic pressure-volume relations were described by straight lines for each site (r greater than 0.96 and SEE less than 2.9 mm Hg in all but one instance). Compared to atrial pacing, the left ventricular end-systolic pressure-volume relations were shifted (P less than 0.001) to the right during pacing from ventricular sites. During atrial pacing, the volume intercept of the left ventricular end-systolic pressure-volume relation was 16.0 +/- 7.2 ml (mean +/- SD), and increased to 18.7 +/- 7.8 ml (P less than 0.05) during pacing from the right ventricular free wall, to 19.6 +/- 7.7 ml (P less than 0.05) during pacing from the right ventricular apex, and to 20.0 +/- 7.5 ml (P less than 0.05) during pacing from the left ventricular free wall. These volume intercepts correlated roughly with the extent of dyssynchronous activation as estimated by the QRS duration (r = 0.59 to 0.93) and the time for left ventricular endocardial activation (r = 0.92 and 0.95). During ventricular pacing, the slope of the left ventricular end-systolic pressure-volume relation changed only slightly. Similar results were obtained during pacing from right ventricular endocardial sites. We conclude that alterations of the normal activation sequence produced by ventricular pacing depress left ventricular pumping function independent of loading conditions, as indicated by a rightward shift of the left ventricular end-systolic pressure-volume relation. The extent of this shift appears to be in proportion to the degree of dyssynchronous activation. The decreased stroke volume during ventricular pacing is due both to a decreased end-diastolic volume (decreased preload) and the rightward shift of the end-systolic pressure-volume relation (decreased pump function).
Shuttling of the herpes simplex virus type 1 regulatory protein ICP27 between the nucleus and cytoplasm mediates the expression of late proteins (1997)

The herpes simplex virus type 1 (HSV-1) immediate-early protein ICP27 is required posttranscriptionally for the expression of HSV-1 late genes during a productive infection. ICP27 also inhibits host cell pre-mRNA splicing, effectively shutting off host cell protein synthesis. Here we describe intragenic suppressors of LG4, a virus with a conditional lethal mutation in the gene encoding ICP27. At the restrictive temperature, tsICP27 from LG4 fails to inhibit host cell pre-mRNA splicing and to activate the expression of HSV-1 late-gene products. Although the suppressors of LG4 restore virus growth, they still fail to inhibit host cell pre-mRNA splicing. Thus, the role of ICP27 in the synthesis of late proteins is independent of host shutoff. In HSV-1-infected cells, ICP27 shuttles between the nucleus and the cytoplasm. Shuttling of ICP27 occurs only at late times during infection. In transfected cells, ICP27 shuttling was dependent on coexpression of RNA from a late HSV-1 gene. While shuttling does not occur in cells infected with LG4 at 39.5 degrees C, the suppressors of LG4 restore shuttling. Temperature shift experiments correlate the defect in shuttling with the temperature-sensitive phenotype of LG4. These data provide a correlation between shuttling of ICP27 and the expression of HSV-1 late-gene products. We propose that ICP27 regulates late-gene protein synthesis by facilitating the export of late RNAs.
Fusion of the Mycobacterium tuberculosis Antigen 85A to an Oligomerization Domain Enhances Its Immunogenicity in Both Mice and Non-Human Primates (2012)

To prevent important infectious diseases such as tuberculosis, malaria and HIV, vaccines inducing greater T cell responses are required. In this study, we investigated whether fusion of the M. tuberculosis antigen 85A to recently described adjuvant IMX313, a hybrid avian C4bp oligomerization domain, could increase T cell responses in pre-clinical vaccine model species. In mice, the fused antigen 85A showed consistent increases in CD4(+) and CD8(+) T cell responses after DNA and MVA vaccination. In rhesus macaques, higher IFN-γ responses were observed in animals vaccinated with MVA-Ag85A IMX313 after both primary and secondary immunizations. In both animal models, fusion to IMX313 induced a quantitative enhancement in the response without altering its quality: multifunctional cytokines were uniformly increased and differentiation into effector and memory T cell subsets was augmented rather than skewed. An extensive in vivo characterization suggests that IMX313 improves the initiation of immune responses as an increase in antigen 85A specific cells was observed as early as day 3 after vaccination. This report demonstrates that antigen multimerization using IMX313 is a simple and effective cross-species method to improve vaccine immunogenicity with potentially broad applicability.
High speed, wide velocity dynamic range Doppler optical coherence tomography (Part I): System design, signal processing, and performance (2003)

Improvements in real-time Doppler optical coherence tomography (DOCT), acquiring up to 32 frames per second at 250 x 512 pixels per image, are reported using signal processing techniques commonly employed in Doppler ultrasound imaging. The ability to measure a wide range of flow velocities, ranging from less than 20 microm/s to more than 10 cm/s, is demonstrated using an 1.3 microm DOCT system with flow phantoms in steady and pulsatile flow conditions. Based on full implementation of a coherent demodulator, four different modes of flow visualization are demonstrated: color Doppler, velocity variance, Doppler spectrum, and power Doppler. The performance of the former two, which are computationally suitable for real-time imaging, are analyzed in detail under various signal-to-noise and frame-rate conditions. The results serve as a guideline for choosing appropriate imaging parameters for detecting in vivo blood flow.
Variations in the Percent Ethanol (v/v) per °Brix Conversions of Wines from Different Climatic Regions (1985)

Ethanol yield per degree Brix has been shown to vary from area to area, and somewhat from year to year (4,5,9). These differences were verified statistically in 1981 and 1982. Two explanations were evident for the variations in the ethanol per °Brix. Grapes that are non-irrigated and slightly shriveled tend not to crush easily. These higher sugared grapes then release sugar during the holding period prior to pressing or, with red grapes, during fermentation. The original must sample will indicate a lower °Brix than the real °Brix of the must later. The other explanation is fruit low in nitrogen grows fewer yeast; hence, less sugar is converted into cellular material, and a higher efficiency of ethanol production results. Dry land vineyards generally have fruit of a lower yeast nutrient content. These observations were verified by analytical data and calculations.
Asymptotically good codes correcting insertions, deletions, and transpositions (1999)

We present simple, polynomial time encodable and decodable codes which are asymptotically good for channels allowing insertions, deletions, and transpositions. As a corollary, they achieve exponential error probability in a stochastic model of insertion-deletion.
Evidence that a region(s) of the Clostridium perfringens enterotoxin molecule remains exposed on the external surface of the mammalian plasma membrane when the toxin is sequestered in small or large complexes (1996)

In studies performed to investigate the topology of Clostridium perfringens enterotoxin (CPE) when this toxin is associated with intestinal brush border membrane (BBMs), it was shown that radiolabeled CPE antibodies react more strongly against intact CPE-treated BBMs than against control BBMs. Immunoprecipitation studies then demonstrated that CPE antibodies are able to react with both small and large CPE-containing complexes while these complexes are still present in intact BBMs. Therefore, at least a portion of the CPE molecule appears to remain surface exposed in BBMs throughout the action of this toxin.
Plant colonization by pink-pigmented facultative methylotrophic bacteria (PPFMs) (2004)

Bacteria belonging to the genus Methylobacterium are characterized by being able to rely on methanol as a sole carbon and energy source and by presenting a more or less intense pink reddish pigmentation. These bacteria, also referred to as pink-pigmented methylotrophic bacteria (PPFMs), are common inhabitants of the phyllosphere and are found in many other environmental samples. Since they grow slowly they are often overlooked and their impact on phyllosphere microbial communities and on the plants harboring them is not well studied nor has their ecology been elucidated. In a survey of PPFM colonization in three different agricultural sites, PPFM populations were identified on both red clover and winter wheat, but red clover was more consistently colonized. Isolations from collected leaves showed PPFM populations to decrease from spring towards summer, but they increased again towards the end of the cropping season. Isolates from red clover readily colonized winter wheat leaves and vice versa in greenhouse experiments, but population sizes were dependent on the application procedure. Tested isolates had also good potential to colonize the rhizosphere, especially after seed inoculations. Confocal scanning laser microscopy showed gfp-tagged isolates to colonize the surface of clover leaves by forming large aggregates.
Advancing the Quorum in Pseudomonas aeruginosa : MvaT and the Regulation of N -Acylhomoserine Lactone Production and Virulence Gene Expression (2002)

Pseudomonas aeruginosa regulates the production of many exoproteins and secondary metabolites via a hierarchical quorum-sensing cascade through LasR and RhlR and their cognate signal molecules N-(3-oxododecanoyl)-L-homoserine lactone (3O-C12-HSL) and N-(butanoyl)-L-homoserine lactone (C4-HSL). In this study, we found that transcription of the quorum sensing-regulated genes lecA (coding for PA-IL lectin), lasB (coding for elastase), and rpoS appeared to be growth phase dependent and their expression could not be advanced to the logarithmic phase in cells growing in batch culture by the addition of exogenous C4-HSL and 3O-C12-HSL. To identify novel regulators responsible for this growth phase dependency, a P. aeruginosa lecA::lux reporter strain was subjected to random transposon mutagenesis. A number of mutants affected in lecA expression were found that exhibited altered production of multiple quorum sensing-dependent phenotypes. While some mutations were mapped to new loci such as clpA and mvaT and a putative efflux system, a number of mutations were also mapped to known regulators such as lasR, rhlR, and rpoS. MvaT was identified as a novel global regulator of virulence gene expression, as a mutation in mvaT resulted in enhanced lecA expression and pyocyanin production. This mutant also showed altered swarming ability and production of the LasB and LasA proteases, 3O-C12-HSL, and C4-HSL. Furthermore, addition of exogenous 3O-C12-HSL and C4-HSL to the mvaT mutant significantly advanced lecA expression, suggesting that MvaT is involved in the growth phase-dependent regulation of the lecA gene.