gebhart/patrepeval huggingface dataset:
MucR, a Novel Membrane-Associated Regulator of Alginate Biosynthesis inPseudomonas aeruginosa (2008)

Alginate biosynthesis by Pseudomonas aeruginosa was shown to be regulated by the intracellular second messenger bis-(3'-5')-cyclic-dimeric-GMP (c-di-GMP), and binding of c-di-GMP to the membrane protein Alg44 was required for alginate production. In this study, PA1727, a c-di-GMP-synthesizing enzyme was functionally analyzed and identified to be involved in regulation of alginate production. Deletion of the PA1727 gene in the mucoid alginate-overproducing P. aeruginosa strain PDO300 resulted in a nonmucoid phenotype and an about 38-fold decrease in alginate production; thus, this gene is designated mucR. The mucoid alginate-overproducing phenotype was restored by introducing the mucR gene into the isogenic DeltamucR mutant. Moreover, transfer of the MucR-encoding plasmid into strain PDO300 led to an about sevenfold increase in alginate production, wrinkly colony morphology, increased pellicle formation, auto-aggregation, and the formation of highly structured biofilms as well as the inhibition of swarming motility. Outer membrane protein profile analysis showed that overproduction of MucR mediates a strong reduction in the copy number of FliC (flagellin), required for flagellum-mediated motility. Translational reporter enzyme fusions with LacZ and PhoA suggested that MucR is located in the cytoplasmic membrane with a cytosolic C terminus. Deletion of the proposed C-terminal GGDEF domain abolished MucR function. MucR was purified and identified using tryptic peptide fingerprinting and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Overall, experimental evidence was provided suggesting that MucR specifically regulates alginate biosynthesis by activation of alginate production through generation of a localized c-di-GMP pool in the vicinity of Alg44.
Analysis of rodent platelet glycoprotein IIb: evidence for evolutionarily conserved domains and alternative proteolytic processing (1990)

Recently, the full-length primary amino acid sequence for human glycoproteins (GP) IIb and IIIa have been derived from their respective cDNAs. Potential functional domains within these proteins have been proposed based primarily on homology with similar domains in other proteins having known biologic function. To further understand the relationship between structure and function of the platelet fibrinogen receptor, we have begun comparative studies of the human GPIIb/IIIa receptor with the corresponding rodent receptor. The rodent rGPIIb/IIIa receptor differs from the human receptor, having low affinity for R.G.D- containing oligopeptides and not binding at all to the C-terminus of the gamma chain of human fibrinogen. We describe the structure of rodent platelet GPIIb derived from a combination of peptide sequencing, and cDNA and partial genomic DNA sequence analysis. The initial transcript is 1037 amino acid residues, having 78% amino acid identity with its 1039 residue human analog. Both heavy chains have the N- terminal sequence L.N.L.D, agreeing with the consensus derived from other integrin family alpha heavy chains. All 18 cysteine residues occur at positions conserved in human GPIIb and the vitronectin receptor alpha subunit VNR alpha. The putative calcium-binding domains of the GPIIbs have a high level of amino acid identity (92%), supporting the supposition that these regions have a critical biologic role. The final 48 C-terminal amino acid residues of the heavy chain of rodent GPIIb share only 56% identity with its human counterpart, and the proposed cleavage site of human GPIIb into its heavy and light chains is not present in the rodent sequence. Although we demonstrate that rodent GPIIb is split into two subunits during its maturation, this process either involves a different recognition sequence in the rodent or occurs at a different site. Finally, partial genomic DNA sequence analysis indicates that there are at least two rodent GPIIb genes: a normal gene, containing introns in positions similar to those in the human gene, and a processed pseudogene. The human haploid genome contains only a single GPIIb gene.
Synthesis of Large‐Area Graphene Layers on Poly‐Nickel Substrate by Chemical Vapor Deposition: Wrinkle Formation (2009)

Large-area, few-layer graphene is grown on a poly-nickel substrate using optimized CVD conditions. High temperature, short growth time, and an optimal gas mixing ratio (C2H2/H2 = 2/45) are found to be necessary to synthesize highly crystalline few-layer grapheme, which may find applications in electronic devices. The wrinkles that are observed under all growth conditions are proposed to be formed by two processes.
Preferential selection of deletion mutations of the outer membrane lipoprotein gene of Escherichia coli by globomycin. (1981)

Globomycin is an antibiotic which inhibits the processing of the prolipoprotein. Eighty globomycin-resistant mutants were independently isolated from Escherichia coli K-12 which had a deletion mutation in chromosomal lipoprotein gene (lpp), but contained a plasmid carrying the wild-type lpp gene. Twenty-six of the mutants did not have the lipoprotein in the membrane fractions. From the analysis of the plasmids of these mutants, all of the lipoprotein-deficient mutations were found to be due to deletion mutations around the lpp gene.
Two-Photon Microscopy for Imaging of the (Atherosclerotic) Vascular Wall: A Proof of Concept Study (2004)

Thus, TPLSM potentially allows combined functional and structural studies and can therefore be eminently suitable for investigating structure-function relationships at the cellular level in atherogenesis in the mouse.
Vaccine- and antigen-dependent type 1 and type 2 cytokine induction after primary vaccination of infants with whole-cell or acellular pertussis vaccines (1997)

Cytokine profiles were examined 1 month after primary vaccination of infants with a whole-cell pertussis vaccine (wP) (Connaught) or either of two acellular pertussis vaccines, aP-Chiron Biocine (aP-CB) or aP-SmithKline Beecham (aP-SB), each combined with diphtheria-tetanus toxoids (DT), in Bordetella pertussis antigen-stimulated or unstimulated peripheral blood mononuclear cells (PBMC). Pertussis toxin (PT), filamentous hemagglutinin (FHA), and pertactin (PRN) were used as antigens, and the children were defined as responsive when their PBMC proliferated in response to these antigens. The controls were either children who received only DT or children who received pertussis vaccine but whose PBMC did not proliferate upon stimulation with B. pertussis antigens (unresponsive children). Antigen-stimulated PBMC of responsive wP recipients were characterized by an elevated production of T-helper-cell type 1 cytokines gamma interferon (IFN-gamma) and interleukin 2 (IL-2), low to minimal production of IL-5, and no production of IL-4. The PBMC of aP vaccine-responsive recipients showed, in addition to the elevated IFN-gamma production, a consistent, antigen-dependent production of type 2 cytokines (IL-4 and IL-5), with PRN being the most and PT being the least effective antigen. Type 2 cytokine induction was more pronounced in aP-SB than in aP-CB recipients, as shown by the presence of IL-4 mRNA transcripts and higher IL-5 production in the former (161.6 +/- 36 and 47.9 +/- 44 pg/ml [mean +/- standard error for five subjects each], respectively, after PRN stimulation). Appreciable, antigen-unstimulated (constitutive) IFN-gamma production was also detected in PBMC cultures of all vaccinees. However, this spontaneous IFN-gamma production was, in most vaccinees, significantly lower than the antigen-driven cytokine production. In contrast, no constitutive type 2 cytokine production was ever observed in any vaccine group. PBMC from the two control groups (either DT or pertussis vaccine recipients) did not show any type 2 cytokine production, while IFN-gamma production was comparable in both antigen-stimulated and unstimulated conditions. Absence of type 2 cytokines and low levels of constitutive IFN-gamma production were also seen in prevaccination children. Thus, pertussis vaccines induce in infants a basically type 1 cytokine profile, which is, however, accompanied by some production of type 2 cytokines. The latter are more expressed by aP-SB than by aP-CB recipients, and with PRN than with other antigens, and they are minimally expressed in wP recipients and with PT as antigen. Our data also highlight a constitutive IFN-gamma production in infancy, which might reflect natural immunization and/or the burden of concomitant vaccinations and which may have an impact on T-helper-cell cytokine pattern polarization consequent to pertussis vaccination.
The Bone Marrow Vascular Niche: Home of HSC Differentiation and Mobilization (2005)

The bone marrow vascular niche consists of a network of thin-walled and fenestrated sinusoidal vessels whose integrity is maintained and supported by surrounding hematopoietic cells. However, this dependence is highly reciprocal in that the bone marrow vasculature provides not only a conduit for mature hematopoietic cells to the peripheral circulation but also a site where hematopoietic progenitors, especially megakaryocytes, differentiate and set the stage for full reconstitution of hematopoiesis.
Genome Architecture of the Human β-Globin Locus Affects Developmental Regulation of Gene Expression (2005)

To test the role of gene order in globin gene expression, mutant human beta-globin locus yeast artificial chromosome constructs were used, each having one additional globin gene encoding a "marked" transcript (epsilon(m), gamma(m), or beta(m)) integrated at different locations within the locus. When a beta(m)-globin gene was placed between the locus control region (LCR) and the epsilon-globin gene, beta(m)-globin expression dominated primitive and definitive erythropoiesis; only beta(m)-globin mRNA was detected during the fetal and adult definitive stages of erythropoiesis. When an (A)gamma(m)-globin gene was placed at the same location, (A)gamma(m)-globin was expressed during embryonic erythropoiesis and the fetal liver stage of definitive erythropoiesis but was silenced during the adult stage. The downstream wild-type gamma-globin genes were not expressed. When an epsilon(m)-globin gene was placed between the delta- and beta-globin genes, it remained silent during embryonic erythropoiesis; only the LCR-proximal wild-type epsilon-globin gene was expressed. Placement of a beta(m)-globin gene upstream of the (G)gamma-globin gene resulted in expression of beta(m)-globin in embryonic cells and in a significant decrease in expression of the downstream wild-type beta-globin gene. These results indicate that distance from the LCR, an inherent property of spatial gene order, is a major determinant of temporal gene expression during development.
ChemInform Abstract: Non‐Polymerase‐Cycling‐Assembly‐Based Chemical Gene Synthesis: Strategies, Methods, and Progress (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Spectral information divergence for hyperspectral image analysis (2003)

The authors propose an information theoretic criterion, called spectral information divergence (SID) for spectral similarity and discriminability. It is derived from the concept of divergence arising in information theory and can be used to describe the statistics of a spectrum. Unlike spectral angle mapper (SAM) which extracts geometric features between two spectra, SID views each pixel spectrum as a random variable and then measures the discrepancy of probabilistic behaviors between two spectra. In order to evaluate SID, SAM is used for comparison via hyperspectral data. Experimental results show that SID can characterise spectral similarity and variability more effectively than SAM.
Inside Macintosh : 日本語版 (1988)

システムソフトウェアバージョン７．０環境の紹介 ユーザインタフェースガイドライン 互換性ガイドライン Ｅｄｉｔｉｏｎ Ｍａｎａｇｅｒ Ｅｖｅｎｔ Ｍａｎａｇｅｒ Ａｐｐｌｅ Ｅｖｅｎｔ Ｍａｎａｇｅｒ Ｐｒｏｇｒａｍ‐ｔｏ‐Ｐｒｏｇｒａｍ Ｃｏｍｍｕｎｉｃａｔｉｏｎｓ Ｔｏｏｌｂｏｘ Ｆｉｎｄｅｒ Ｉｎｔｅｒｆａｃｅ〔ほか〕
Microwave Thermal Keratoplasty for Myopia: Keratoscopic Evaluation in Porcine Eyes (2001)

Microwave thermal keratoplasty applied in the paracentral cornea may flatten the central cornea.
Studies of reagents for spectrophotometric measurement of ionic magnesium (1977)

Four mono-azo aryl dyes having the o-carboxy-o′-hydroxy functionality were investigated as reagents for the measurement of ionic Mg 2+ in solutions containing complexing ligands. 2-(2′-Carboxyl-1′-benzeneazo)-1,8-dihydroxynaphthalene-3,6-disulfonic acid came closest to the ideal of having absorbance unaffected by pH over the pH range of interest and of differentiating between Ca 2+ and Mg 2+ complex formation. Ligand acid dissociation constants and formation constants for the metal–ligand complexes were measured.
Mutated BCR-ABL Generates Immunogenic T-cell Epitopes in CML Patients (2012)

Our in vitro studies support the hypothesis that leukemia-driven genetic alterations are targeted by the immune system in association with a clinical response, and suggest the possibility of immunizing relapsed patients with CML against newly acquired tumor neoantigens.
Adaptive beamforming for an OFDM system (2003)

This paper presents an adaptive beamforming algorithm for an OFDM system with an adaptive array antenna. The proposed algorithm for adaptive beamforming in the OFDM system is derived by (1) calculating the pilot error signals in the frequency-domain, (2) transforming the frequency-domain error signals into time-domain error signals, (3) updating the filter coefficients of the adaptive beamformer in the direction of minimizing the MSE. Convergence behavior and performance improvement of the proposed approach are investigated through computer simulation by applying it to the conventional OFDM system.
Program/erase dynamics and channel conduction in nanocrystal memories (2004)

We present new models for nanocrystal (NC) memories, addressing program/erase (P/E) transients and carrier conduction in the channel controlled by discrete nodes. The model allows for the calculation of the achievable threshold-voltage (V/sub T/) window and P/E times under uniform tunneling-injection conditions. Comparisons with experimental data are shown, demonstrating that our physically-based model correctly captures the VT dependence on critical cell and bias parameters. The model can be used to draw technological guidelines for window optimization in NC cells.
Magnetic resonance imaging of the knee: evaluation of meniscal disease. (1992)

The advent of MR imaging in musculoskeletal radiology, coupled with advances in the past decade in the treatment of knee disorders, has fueled an explosion of interest in MR imaging of the knee. Evaluation of meniscal pathology has been central to this development. The accuracy of MR imaging in the diagnosis of meniscal tears is now well established; attention has more recently been focused on the prevalence, natural history, and clinical significance of other intrameniscal signal abnormalities, as well as on the postoperative meniscus. Nonmeniscal knee disorders that may clinically mimic meniscal lesions are also reliably diagnosed with MR imaging. Technical advances in pulse sequences allow knee imaging with enhanced accuracy and efficiency.
A time-efficient and accurate strain estimation concept for ultrasonic elastography using iterative phase zero estimation (1999)

In ultrasonic elastography, the exact estimation of temporal displacements between two signals is the key to estimating strain. An algorithm was previously proposed that estimates these displacements using phase differences of the corresponding base-band signals. A major advantage of these algorithms compared with correlation techniques is the computational efficiency. In this paper, an extension of the algorithm is presented that iteratively takes into account the time shifts of the signals to overcome the problems of aliasing and accuracy in the estimation of the phase shift. Thus, it can be proven that the algorithm is equivalent to the search of the maximum of the correlation function. Furthermore, a robust logarithmic compression is proposed that only compresses the envelope of the signal. This compression does not introduce systematic errors and significantly reduces decorrelation noise. The resulting algorithm is a computationally simple and very fast alternative to conventional correlation techniques, and the accuracy of strain images is improved.
DOSE RANGING STUDY OF LUTEIN SUPPLEMENTATION IN ELDERLY WITH AND WITHOUT AGE RELATED MACULAR DEGENERATION (2004)

Age-related macular degeneration (AMD) is the leading cause of blindness among people over the age of 65. Epidemiological studies have indicated that people with a high intake of two dietary carotenoids, lutein and zeaxanthin that accumulate in the human macula, are at a reduced risk of AMD. Possible role of lutein and zeaxanthin in the prevention of AMD has been attributed to their antioxidant function and their ability to act as optical filters. The objectives of this study were to investigate the association between three doses of orally ingested lutein supplements and serum levels of this carotenoid in elderly with and without AMD; to evaluate the possible interaction between supplemental lutein and other dietary carotenoids, retinol, and tocopherol; to correlate the serum levels of lutein with the total macular pigment optical density (MPOD). Forty-five subjects over the age of 60 were divided into 3 groups: subjects without AMD and subjects with middle and end stage of AMD. Subjects in each group were randomized to receive one of the three doses of 2.5, 5, and 10 mg/day of lutein (containing 5% zeaxanthin) for 6 months. Subjects were followed up for 6 months. Carotenoids and their metabolites in the serum of subjects were analyzed by HPLC at weeks 0, 1, 4, 12, 26, 38, and 52. The MPOD of subjects was measured by Heterochromatic Flicker Photometry (HCFP). The data were analyzed using analysis of variance and covariance with repeated measurements (SAS, version 8.2). The mean serum concentrations of lutein in all subjects increased with supplementation. Subjects receiving 10 mg/day of lutein had a 3-4 fold increase in their serum levels of lutein, while those receiving 2.5 and 5 mg/day dose had approximately 2 fold increase. In conclusion, the serum concentration of lutein appears to be dose dependent and the presence or the absence of AMD does not interfere with the serum levels of this carotenoid. Supplemental lutein does not interact with other dietary carotenoids, retinol, and tocopherol. The results from MPOD measurements by HCFP were inconsistent and could not be used to reach any conclusion with regard to MPOD changes.
No effect of a type I collagen gel coating in uncemented implant fixation (2005)

Uncemented joint replacement with a variety of substrate materials, structures, and coatings are commonplace in arthroplasty. Even with specialized surgical preparation of bone, intimate contact between the implant and host bone may not always be achieved. This study evaluated the in vivo effect of fibrillar atelopeptide and PEG crosslinked collagens coatings placed directly into porous sintered bead structures on bone ingrowth using a skeletally mature bicortical, bilateral ovine tibia model. Bone ingrowth into the implants increased with time, although differences were not significant. At 4 weeks woven bone was present within the pores that remodeled with time. Significantly lower levels of ingrowth were observed in the intramedullary region of the implants when compared with the cortical region. Implant metal type did not affect ingrowth in both regions analyzed. Both fibrillar and crosslinked forms of dermal type I collagen did not significantly alter bone ingrowth.
Intracellular Calcium Parallels Motoneuron Degeneration in SOD-1 Mutant Mice (1998)

Transgenic mice with Cu,Zn superoxide dismutase (SOD-1) mutations provide a unique model to examine altered Ca homeostasis in selectively vulnerable and resistant motoneurons. In degenerating spinal motoneurons of G93 A SOD-1 mice, developing vacuoles were filled with calcium, while calcium was gradually depleted from the cytoplasm and intact mitochondria. In oculomotor neurons, no degenerative changes, vacuolization, or increased calcium were noted. Motor axon terminals of interosseus muscle gradually degenerated and intracellular calcium was depleted. Oculomotor terminals of mutant SOD-1 mice were smaller and exhibited no degenerative changes, but did exhibit unique membrane-enclosed organelles containing calcium. Spinal motoneurons of SOD-1 mice were shown to have fewer calcium binding proteins, such as parvalbumin, compared with oculomotor neurons. These data suggest that the SOD-1 mutation is associated with impaired calcium homeostasis in motoneurons in vivo, with increased likelihood of degeneration associated with higher levels of intracellular calcium and lower to absent levels of calbindin-D28K and/or parvalbumin, and decreased likelihood of degeneration associated with minimally changed calcium and ample calbindin-D28K and/or parvalbumin.
Stress-inducible gene of Salmonella typhimurium identified by arbitrarily primed PCR of RNA. (1994)

Fingerprinting of RNA by arbitrarily primed PCR (RAP) can be used to identify conditionally expressed genes in prokaryotes. Differential gene expression in Salmonella typhimurium LT2 in response to peroxide treatment was examined as a system in which to demonstrate this strategy. This treatment models the induction of bacterial protective proteins that may occur when mammalian phagocytes use peroxide to fight S. typhimurium infection. To identify genes inducible by hydrogen peroxide stress, total RNA from peroxide-treated and untreated bacterial cultures were RAP fingerprinted with six different arbitrarily selected primers. A 435-base RAP product that was differentially amplified by RAP using the reverse sequencing primer was cloned and sequenced. Northern blot analysis confirmed that the RNA corresponding to this clone, RSP435, was induced when bacteria were treated with hydrogen peroxide. The RNA was not induced in an oxyR1 mutant that constitutively expressed a subset of hydrogen peroxide-inducible genes. Using pulsed-field gel electrophoresis and dot blot hybridization to an array of induced Mud-P22 integrations, the gene corresponding to RSP435 was mapped to two places, one between 19 and 21.5 min and one between 56 and 57 min. Thus, two similar or identical stress-inducible genes were found in different parts of the genome. Identification, cloning, and mapping of the conditionally expressed RSP435 cDNA were performed entirely by physical means, demonstrating that the strategy should complement genetic methods for many prokaryotic or archaebacterial systems and should be applicable to organisms in which genetic methods are difficult to perform or have not yet been developed.
Evaluation of HER2 and p53 expression in predicting response to docetaxel-based first-line chemotherapy in advanced breast cancer (2011)

Our data seem to indicate that FISH-determined HER2 status but not p53 is associated with docetaxel sensitivity in metastatic breast cancer.
Salicylic Acid: A Likely Endogenous Signal in the Resistance Response of Tobacco to Viral Infection (1990)

Some cultivars of tobacco are resistant to tobacco mosaic virus (TMV) and synthesize pathogenesis-related (PR) proteins upon infection. In a search for the signal or signals that induce resistance or PR genes, it was found that the endogenous salicylic acid levels in resistant, but not susceptible, cultivars increased at least 20-fold in infected leaves and 5-fold in uninfected leaves after TMV inoculation. Induction of PRl genes paralleled the rise in salicylic acid levels. Since earlier work has demonstrated that treatment with exogenous salicylic acid induces PR genes and resistance, these findings suggest that salicylic acid functions as the natural transduction signal.