gebhart/patrepeval huggingface dataset:
Streptococcus pneumoniaeinfection suppresses allergic airways disease by inducing regulatory T-cells (2010)

An inverse association exists between some bacterial infections and the prevalence of asthma. We investigated whether Streptococcus pneumoniae infection protects against asthma using mouse models of ovalbumin (OVA)-induced allergic airway disease (AAD). Mice were intratracheally infected or treated with killed S. pneumoniae before, during or after OVA sensitisation and subsequent challenge. The effects of S. pneumoniae on AAD were assessed. Infection or treatment with killed S. pneumoniae suppressed hallmark features of AAD, including antigen-specific T-helper cell (Th) type 2 cytokine and antibody responses, peripheral and pulmonary eosinophil accumulation, goblet cell hyperplasia, and airway hyperresponsiveness. The effect of infection on the development of specific features of AAD depended on the timing of infection relative to allergic sensitisation and challenge. Infection induced significant increases in regulatory T-cell (Treg) numbers in lymph nodes, which correlated with the degree of suppression of AAD. Tregs reduced T-cell proliferation and Th2 cytokine release. The suppressive effects of infection were reversed by anti-CD25 treatment. Respiratory infection or treatment with S. pneumoniae attenuates allergic immune responses and suppresses AAD. These effects may be mediated by S. pneumoniae-induced Tregs. This identifies the potential for the development of therapeutic agents for asthma from S. pneumoniae.
Biosynthesis of Isoprenoid Wax Ester inMarinobacter hydrocarbonoclasticusDSM 8798: Identification and Characterization of Isoprenoid Coenzyme A Synthetase and Wax Ester Synthases (2007)

Marinobacter hydrocarbonoclasticus DSM 8798 has been reported to synthesize isoprenoid wax ester storage compounds when grown on phytol as the sole carbon source under limiting nitrogen and/or phosphorous conditions. We hypothesized that isoprenoid wax ester synthesis involves (i) activation of an isoprenoid fatty acid by a coenzyme A (CoA) synthetase and (ii) ester bond formation between an isoprenoid alcohol and isoprenoyl-CoA catalyzed, most likely, by an isoprenoid wax ester synthase similar to an acyl wax ester synthase, wax ester synthase/diacylglycerol acyltransferase (WS/DGAT), recently described from Acinetobacter sp. strain ADP1. We used the recently released rough draft genome sequence of a closely related strain, M. aquaeolei VT8, to search for WS/DGAT and acyl-CoA synthetase candidate genes. The sequence information from putative WS/DGAT and acyl-CoA synthetase genes identified in this strain was used to clone homologues from the isoprenoid wax ester synthesizing Marinobacter strain. The activities of the recombinant enzymes were characterized, and two new isoprenoid wax ester synthases capable of synthesizing isoprenoid ester and acyl/isoprenoid hybrid ester in vitro were identified along with an isoprenoid-specific CoA synthetase. One of the Marinobacter wax ester synthases displays several orders of magnitude higher activity toward acyl substrates than any previously characterized acyl-WS and may reflect adaptations to available carbon sources in their environments.
Human Beta Interferon Scaffold Attachment Region Inhibits De Novo Methylation and Confers Long-Term, Copy Number-Dependent Expression to a Retroviral Vector (2000)

Moloney murine leukemia virus-based retroviral vector expression is gradually lost during prolonged in vitro culture of CEMSS T cells. However, when the human beta interferon scaffold attachment region (IFN-SAR) was inserted into the vector immediately upstream of the 3' long terminal repeat (LTR), expression was maintained for the length of the study (4 months). Clonal analysis of the retrovirus vector-infected CEMSS cells showed that SAR-containing retroviral vector expression levels were positively correlated with the proviral copy numbers (P < 0.0001), while there was no correlation between the proviral copy numbers and expression levels in control vector-infected clones. Thirty-three percent of the CEMSS cell clones infected with the control vector showed evidence of partial or complete methylation in the 5' LTR region. In sharp contrast, we detected no methylation in the clones infected with the SAR-containing vector. To demonstrate a direct inhibitory effect of methylation on retroviral vector expression, we have transfected 293 cells with in vitro-methylated proviral DNA. In transiently transfected cells, expression of methylated LTR was reduced but not completely inhibited, irrespective of the presence of the IFN-SAR sequence. In stably transfected cells, however, methylation completely abolished expression of the control vector but not of the SAR-containing vector. Furthermore, the expression of the SAR-containing vector was stable over time, indicating the ability of the SAR sequence to alleviate methylation-mediated transcriptional repression of a vector. This study extends our understanding of the mechanisms of retroviral vector inactivation by methylation and provides insight into a functional role for the SAR elements.
Enhancement of color images in poor visibility conditions (2000)

Degradation of images by the atmosphere often restricts imaging applications to good visibility conditions. For example, when imaging the terrain from a forward-looking airborne camera, the atmospheric degradation causes both a loss in contrast and color information. Enhancement of such images is a difficult task due to the complexity in restoring both the luminance and chrominance while maintaining good color fidelity. One particular problem is the fact that the level of contrast loss depends strongly on the wavelength; shorter wavelengths i.e., blue are more effected. In this paper, a novel method is presented for the enhancement of color images. This method is based on the underlying physics of the degradation and the parameters required for enhancement are estimated from the image itself. The proposed method is tested using synthetic images to explore the limitations and reliability of the method under different visibility conditions. Enhancement is performed on real images taken using an airborne camera at a height of approximately 1000 meters in hazy conditions for which the visibility is approximately 10 kilometers. Significant improvements in terms of contrast, visible range and color fidelity are evident when compared to existing methods.
Integrated optics ring-resonator sensors for protein detection (2005)

Using an integrated optics ring-resonator biosensor, we have demonstrated the detection of protein in low concentrations. We detected 0.3 nM of avidin in a buffered saline solution; the calculated detection limit is 0.1 nM (6.8 ng/ml) for avidin, which compares favorably with those of other optical protein detection techniques. Further improvement is possible. Our ring resonator utilizes Si(x)N(y)/SiO2 waveguides, which, owing to evanescent field interaction, change the effective refractive index when target molecules are immobilized on their surfaces. The selectivity of the sensor depends on the biotin surface coating, which causes the specific binding and immobilization of avidin.
The Behavior Measurement of Simulated Ground by Digital Close-Range Photogrammetry (2008)

Digital close-range photogrammetric technique can measure and describe 3D geometric farm from 2D image. This technique is increasingly applied in the field of sciences. In the fields of civil and mechanical engineering, which need precise measurements for design, expensive measuring equipments are widely used. In occasions where visual inspection is required in addition to other forms of measurements, appropriate measuring equipments have not been yet available. This study utilizes digital close-range photogrammetric technique to quantitatively analyze behavior patterns before and after destruction from test model of reinforced-soil wall. Then the results are compared with the measurements obtained using digital theodolite to verify the reliability of the proposed method.
Use of Epoxides in the Sol−Gel Synthesis of Porous Iron(III) Oxide Monoliths from Fe(III) Salts (2001)

Iron oxide-based porous solids were prepared by a sol−gel process using Fe(III) salts in various solvents. It was observed that the addition of propylene oxide to Fe(III) solutions resulted in the formation of transparent red-brown monolithic gels. The resulting gels were converted to either xerogels by atmospheric drying or aerogels by supercritical extraction with CO2(l). Some of the dried materials were characterized by nitrogen adsorption and desorption analysis and transmission electron microscopy (TEM). The results of those analyses indicate that the materials have high surface areas (∼300−400 m2/g), pore sizes with mesoporic dimensions (2−23 nm), and a microstructure made up of 5−10 nm diameter clusters of iron(III) oxide. The dependence of both gel formation and its rate was studied by varying the epoxide/Fe(III) ratio, the Fe(III) precursor salt, amount of water (H2O/Fe(III)) present, and the solvent employed. All of these variables were shown to affect the rate of gel formation and provide a convenient control of this parameter. Finally, an investigation of the mechanism of Fe2O3 gel formation was performed. Both pH and nuclear magnetic resonance (NMR) studies suggest that the added epoxide acts as an irreversible proton scavenger that induces the Fe(III) species to undergo hydrolysis and condensation to form an inorganic iron oxide framework. This method can be extended to prepare other transition- and main-group metal oxide materials.
The complete nucleotide sequence of tobacco necrosis virus strain D (1991)

The complete sequence of the RNA genome of tobacco necrosis virus strain D (TNV-D) consisting of 3759 nucleotides has been determined. The positive strand contains five open reading frames (ORFs). The 5'-proximal ORF encodes a 22K protein terminating with an amber codon which may be read through to produce a 82K protein (p82). Two small centrally located ORFs each encode two out-of-frame 7K proteins (p7a and p7b). The 3'-proximal ORF encodes the 29K coat protein (CP), the N terminus of which has been sequenced directly. The genomic organization of TNV-D is very similar to that of TNV-A but differs in the placement of the p7a ORF, which does not overlap the p82 ORF in TNV-D, and in the absence of an ORF downstream of the CP gene in TNV-D. The p82 ORF shows extensive sequence similarity with the putative polymerases of the carmovirus group. This ORF is also as closely related to the corresponding ORF of TNV-A as it is to the corresponding ORF of the tombusvirus cucumber necrosis virus. The amino acid sequence of the TNV-D CP gene is similar to both the TNV-A and southern bean mosaic virus CP genes. Of the two p7 ORFs, p7a exhibits amino acid sequence similarity with corresponding proteins from TNV-A, melon necrotic spot virus, carnation mottle virus, turnip crinkle virus and maize chlorotic mottle virus, whereas the p7b ORF appears to be unique to TNV-A and TNV-D. Only the 3'-terminal three nucleotides of TNV-D genomic RNA are identical to the 3'-terminal nucleotides of the TNV satellite virus.
A CD16/CD30 bispecific monoclonal antibody induces lysis of hodgkin's cells by unstimulated natural killer cells In AND In vivo (1993)

In order to target NK cells against the Hodgkin's-derived cell line L540, we developed bispecific monoclonal antibodies (Bi-MAbs) by somatic hybridization of the 2 mouse hybridoma cell line HRS-3 and A9 which produce monoclonal antibodies (MAbs) with reactivity against the Hodgkin and Reed-Sternberg cell-associated CD30 antigen and the CD16 antigen (Fc gamma III receptor), respectively. The CD16 MAb-producing cell line A9 was selected as a partner for HRS-3 because of its efficiency in inducing lysis of the A9 hybridoma cells by resting NK cells. The hybrid hybridoma cell line HRS-3/A9 produced the supernatant with the strongest bispecific reactivity and was repeatedly subcloned and used for ascites production. Crude supernatant and purified HRS-3/A9 Bi-MAb triggered specific lysis of the CD30+ Hodgkin's-derived cell line L540, but not of the CD30- cell line HPB-ALL by unstimulated peripheral-blood lymphocytes and NK-cell-enriched populations. Moreover, treatment of SCID mice bearing heterotransplanted human Hodgkin's tumors with HRS-3/A9 and human peripheral blood lymphocytes induced specific complete tumor regression in 10/10 animals. We thus report successful tumor treatment in an in vivo model using NK-cell-associated Bi-MAbs and show that the Bi-MAb HRS-3/A9 is an efficient promoter of the anti-tumor effects of NK cells in vitro and in vivo.
Wafer-Scale Growth and Transfer of Aligned Single-Walled Carbon Nanotubes (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Experimental demonstration of wafer-scale growth of well-aligned, dense, single-walled carbon nanotubes on <formula formulatype="inline"><tex Notation="TeX">$4^{\prime\prime}$</tex></formula> ST-cut quartz wafers is presented. We developed a new carbon nanotube (CNT) wafer-scale growth process. This process allows quartz wafers to be heated to the CNT growth temperature of <formula formulatype="inline"><tex Notation="TeX">$865\, ^\circ$</tex></formula>C through the alpha–beta phase transformation temperature of quartz (<formula formulatype="inline"><tex Notation="TeX">$573\, ^\circ$</tex> </formula>C) without wafer fracture. We also demonstrate wafer-scale CNT transfer to transfer these aligned CNTs from quartz wafers to silicon wafers. The CNT transfer process preserves CNT density and alignment. Carbon nanotube FETs fabricated using these transferred CNTs exhibit high yield. Wafer-scale growth and wafer-scale transfer of aligned CNTs enable carbon nanotube very large-scale integration circuits and their large-scale integration with silicon CMOS. </para>
The Voice Handicap Index (VHI) (1997)

To date, no instruments exist to quantify the psychosocial consequences of voice disorders. The aim of the present investigation was the development of a statistically robust Voice Handicap Index (VHI). An 85-item version of this instrument was administered to 65 consecutive patients seen in the Voice Clinic at Henry Ford Hospital. The data were subjected to measures of internal consistency reliability and the initial 85-item version was reduced to a 30-item final version. This final version was administered to 63 consecutive patients on two occasions in an attempt to assess test-retest stability, which proved to be strong. The findings of the latter analysis demonstrated that a change between two administrations of 18 points represents a significant shift in psychosocial function.
Surface wave measurements using a single continuously scanning laser Doppler vibrometer: Application to elastography (2013)

A continuous scanning laser Doppler vibrometry (CSLDV) obtained sweeping a single laser beam along a periodic scan pattern allows measuring surface vibrations at many points simultaneously by demultiplexing the CSLDV signal. This known method fundamentally differs from conventional scanning laser vibrometry techniques in which the laser beam is kept at a fixed point during each measurement and then moved to a new position prior to the next measurement. This article demonstrates the use of a CSLDV for measuring in a non-contact fashion the velocity of low-frequency surface waves (f < 100 Hz) propagating over soft materials, namely here gel surfaces-mimicking human body soft tissues-and skeletal muscles, to develop an affordable and noninvasive elastography modality. The CSLDV vibration measurements obtained with a single laser beam, linearly scanned over the test surface at 200 Hz over lengths up to 6 cm, were validated using an array of three fixed laser Doppler vibrometers distributed along the same scan line. Furthermore, this CSLDV setup was used to measure the increase in surface wave velocity over the biceps brachii muscle which was directly correlated to the actual stiffening of the biceps occurring while a subject was performing voluntary contractions at an increasing level.
Ultrasound Improves Tissue Perfusion in Ischemic Tissue through a Nitric Oxide Dependent Mechanism (2002)

Ultrasound accelerates enzymatic fibrinolysis in vitro and in animal models and may be used as an adjunct to thrombolytic therapy. Ultrasound can also affect vascular tone directly, and we have now investigated the effect of ultrasound on tissue perfusion in a rabbit model of acute muscle ischemia to characterize the magnitude and temporal course of vasodilation and determine its mechanism. After ligation of the femoral artery of rabbits, tissue perfusion in the gracilis muscle as determined using a laser Doppler probe declined by 53% from 13.7 +/- 0.3 U to 6.4 +/- 0.2 U. The tissue became acidotic as pH declined from normal to 7.05 +/- 0.2. Application of 40 kHz ultrasound at intensities from 0.25 to 0.75 W/cm(2) progressively improved perfusion over 60 min and reversed acidosis, but these effects were both completely blocked by pre-treatment with the nitric oxide synthase inhibitor L-NAME. Nitric oxide synthase activity in muscle was measured using an assay based on the conversion of radiolabeled L-arginine to L-citrulline and demonstrated an increase of 3.6-fold following ultrasound exposure. This effect was greatest at locations close to the transducer and declined progressively away from it. Histologic examination showed greater capillary circumference in ultrasound exposed muscle compared to unexposed tissue with no other histologic changes. We conclude that the application of 40 kHz at low intensity improves perfusion and reverses acidosis in acutely ischemic muscle through a nitric oxide dependent mechanism.
Transcriptional Control of the Sulfur-Regulated cysH Operon, Containing Genes Involved in l -Cysteine Biosynthesis in Bacillus subtilis (2000)

The molecular mechanisms of regulation of the genes involved in the biosynthesis of cysteine are poorly characterized in Bacillus subtilis and other gram-positive bacteria. In this study we describe the expression pattern of the B. subtilis cysH operon in response to sulfur starvation. A 6.1-kb polycistronic transcript which includes the cysH, cysP, ylnB, ylnC, ylnD, ylnE, and ylnF genes was identified. Its synthesis was induced by sulfur limitation and strongly repressed by cysteine. The cysH operon contains a 5' leader portion homologous to that of the S box family of genes involved in sulfur metabolism, which are regulated by a transcription termination control system. Here we show that induction of B. subtilis cysH operon expression is dependent on the promoter and independent of the leader region terminator, indicating that the operon is regulated at the level of transcription initiation rather than controlled at the level of premature termination of transcription. Deletion of a 46-bp region adjacent to the -35 region of the cysH promoter led to high-level expression of the operon, even in the presence of cysteine. We also found that O-acetyl-L-serine (OAS), a direct precursor of cysteine, renders cysH transcription independent of sulfur starvation and insensitive to cysteine repression. We propose that transcription of the cysH operon is negatively regulated by a transcriptional repressor whose activity is controlled by the intracellular levels of OAS. Cysteine is predicted to repress transcription by inhibiting the synthesis of OAS, which would act as an inducer of cysH expression. These novel results provide the first direct evidence that cysteine biosynthesis is controlled at a transcriptional level by both negative and positive effectors in a gram-positive organism.
Cyclodextrin-Modified Polyethylenimine Polymers for Gene Delivery (2004)

Linear and branched poly(ethylenimines), lPEI and bPEI, respectively, grafted with beta-cyclodextrin are prepared to give CD-lPEI and CD-bPEI, respectively, and are investigated as in vitro and in vivo nonviral gene delivery agents. The in vitro toxicity and transfection efficiency are sensitive to the level of cyclodextrin grafting. The cyclodextrin-containing polycations, when combined with adamantane-poly(ethylene glycol) (AD-PEG) conjugates, form particles that are stable at physiological salt concentrations. PEGylated CD-lPEI-based particles give in vitro gene expression equal to or greater than lPEI as measured by the percentage of EGFP expressing cells. Tail vein injections into mice of 120 microg of plasmid DNA formulated with CD-lPEI and AD-PEG do not reveal observable toxicities, and both nucleic acid accumulation and expression are observed in liver.
Layer Two Tunneling Protocol (L2TP) Differentiated Services Extension (2002)

This document describes mechanisms which enable the Layer Two Tunneling Protocol (L2TP) to negotiate desired Per Hop Behavior (PHB) code for the L2TP control connection, as well as individual sessions within an L2TP tunnel.
Animal Models of Spinal Cord Injury (2000)

Animal models of spinal cord injury may be used both to investigate the biological responses of the tissue to injury and to test potential therapies. The most widely used models involve contusion or compression injury delivered to the surgically exposed spinal cord. Transection injuries are often more suitable for detailed studies of regeneration. At times, in vitro models can be used to answer more specific questions of cell biology or therapy. Locomotory behavior and lesion site histology are commonly used to measure the outcome from injury and the success of experimental therapy. Both of these measures present significant problems of interpretation.
AACR Special Conference in cancer research: ubiquitination in normal and cancer cells (2003)

The AACR Special Conference 2002 for Ubiquitination in Normal and Cancer Cells took place in Vancouver, BC, Canada. It was, indeed, special: a “special” location, a “special” audience and excellent talks that gave a detailed insight into the ubiquitination/proteasome-field. The following meeting highlights try to give a summary of some topics covered at the meeting, from basic research to successful applications of therapeutic agents, starting with cellular regulation, describing recently discovered structural features of enzymes involved in de-/ubiquitination, and, finally, presenting proteasome inhibition as a new approach in cancer chemotherapy.
Zr doped GSO:Ce single crystals and their scintillation performance (2005)

Cerium doped Gd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> (GSO:Ce) single crystal is used as a scintillator for Positron Emission Tomography (PET). GSO:Ce has a good balance of every scintillation properties, but the only disadvantage is the decreasing light output by coloring caused by a small amount of Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4+</sup> in the crystal especially at higher concentration of Ce. In order to improve the scintillation performance, we have tried to grow co-doped GSO single crystal using conventional starting materials with additional impurities, and evaluate the scintillation performance. Zr doping is found to be effective in preventing coloring and in improving light output. Around 200 ppm Zr doped GSO:Ce have shown maximum light output which is about 20% larger than that of conventional GSO:Ce. This improvement can be explained by the fact that the amount of Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4+</sup> in the crystal might be changed to Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> due to charge compensation caused by dopant Zr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4+</sup> in a Gd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> site thereby decreasing the light absorption in the crystal