gebhart/patrepeval huggingface dataset:
BovinePGLYRP1polymorphisms and their association with resistance toMycobacterium aviumssp.paratuberculosis (2011)

Mycobacterium avium ssp. paratuberculosis (MAP) causes a chronic, granulomatous inflammatory condition of the intestines in ruminants and wild-type species. It causes significant economic losses to the dairy and beef industries owing to reduced productivity, premature culling and mortality. Bovine peptidoglycan recognition protein 1 is an important pattern recognition molecule that is capable of directly killing microorganisms. The goal of this study was to identify single nucleotide polymorphisms (SNPs) in the gene encoding bovine peptidoglycan recognition protein 1 and to assess their association with susceptibility to MAP infection in dairy cattle. Blood and milk samples were collected from Holsteins in Southwestern and Eastern Ontario and tested for MAP infection using blood and milk ELISAs. A resource population consisting of 197 infected (S/P > 0.25) and 242 healthy (S/P < 0.10) cattle was constructed. Sequencing of pooled DNA was used to identify three SNPs (c.102G>C, c.480G>A and c.625C>A) that were genotyped in the resource population. Statistical analysis was performed using a logistic regression model fitting the additive and dominance effects of each SNP in the model. SNP c.480G>A (P = 0.054) was found to be associated with susceptibility to MAP infection. Cows with a copy of the major allele 'G' at this locus had an odds ratio of 1.51 (95% CI: 0.99-2.31) for being infected with MAP.
Association of lymphomatoid granulomatosis with Epstein-Barr viral infection of B lymphocytes and response to interferon-alpha 2b (1996)

Lymphomatoid granulomatosis (LyG) is an angiodestructive lymphoproliferative disorder (LPD) often involving the lungs. Its etiology is uncertain, but a number of previous studies had suggested it is a T-cell LPD associated with Epstein-Barr virus (EBV). Because of the similarity between LYG and nasal angiocentric lymphoma, the term angiocentric immunoproliferative lesion was proposed for both entities. Optimal therapy is unknown, but chemotherapy is often used. We studied four patients with LYG over a 5-year period. Biopsy samples were analyzed by immunohistochemistry, EBV in situ hybridization, and for Ig heavy-chain (IgH) gene rearrangements, Clinically, we assessed EBV serology, lymphocyte subsets, and the efficacy of interferon-alpha2b (IFN-alpha2b), All biopsy samples showed an exuberant T-cell infiltrate with scattered atypical large B cells. Double labeling showed EBV in the B cells but not T cells. Clonal IgH gene rearrangements were detected in 2 of 3 patients studied, 1 of whom had three distinct clones, and light-chain restriction showed two clones in an additional patient. All patients had positive EBV serologies. and markedly abnormal lymphocyte subsets. With IFN, 3 patients are alive and disease free at 36, 43, and 60 months; 1 patient achieved a partial response for 16 months but discontinued therapy and died with lymphoma. These results indicate that LYG is a T-cell-rich EBV-associated B-cell LPD in which the infiltrating T cells are numerous but reactive. IgH gene rearrangements may be polyclonal, monoclonal, or oligoclonal. Its association with immune defects suggests it is related to posttransplant LPD. However, LYG and nasal angiocentric lymphoma are distinct entities and should no longer be included together under the term angiocentric immunoproliferative lesion. IFN is effective therapy and should be studied further.
Approaches to Enhancing the Sensitivity of Carbohydrate Separations in Capillary Electrophoresis (2013)

Electrophoresis in both capillaries (CE) and microchips (ME) is an extremely powerful liquid phase-separation technique that is indispensable for the separation of carbohydrates. It is capable of separating both small mono- and disaccharides, through to more complex oligo- and polysaccharides, with high resolution, but as with all CE and ME separations, the detection limits are often inferior to those that can be achieved with liquid chromatographic methods. One avenue to address this is to use an on-line concentration strategy. Various approaches have been developed over the past 20 years, and this chapter will highlight their application to improve the sensitivity of carbohydrate separations in both CE and ME.
Thick YBa2Cu3O7−x+BaSnO3 films with enhanced critical current density at high magnetic fields (2008)

The thickness dependence was studied for the critical current density (Jc) of YBa2Cu3O7−x(YBCO)+BaSnO3 (BSO) nanocomposite films. These films showed a significantly reduced decline of the Jc with thickness, especially at high magnetic fields. For example, a 2 μm thick YBCO+BSO film had a Jc∼3×105 A/cm2 at 5 T as compared to a typical Jc of 2.4×103 A/cm2 at 5 T for a 300 nm thick YBCO film. The thick YBCO+BSO films maintained high Tc (&amp;gt;88 K) and had a high density (2.5×1011/cm2) of continuous BSO nanocolumns that likely contributed for the observed Jc enhancements.
Finite blocklength coding for multiple access channels (2012)

This paper studies the maximum achievable rate region of multiple access channels (MAC) for a given blocklength n and a desired error probability ϵ. The inner region for the discrete memoryless MAC is approximated by a single-lettered expression I - 1/√n Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">inv</sub> (V, ϵ) where I is associated with the capacity pentagon bounds by Ahlswede and Liao, V is the MAC dispersion matrix, and Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">inv</sub> is the complementary multivariate Gaussian cumulative distribution region. For outer regions, we provide general converse bounds for both average error probability and maximum error probability criteria, and a single-lettered approximation for the discrete memoryless MAC.
Diverse Pseudomonas aeruginosa gene products stimulate respiratory epithelial cells to produce interleukin-8. (1995)

Respiratory epithelial cells play a crucial role in the inflammatory response during Pseudomonas aeruginosa infection in the lungs of patients with cystic fibrosis. In this study, we determined whether the binding of specific Pseudomonas gene products (pilin, flagellin) to their receptors on respiratory epithelial cells would result in production of the neutrophil chemoattractant IL-8. Piliated wild-type organisms, purified pili, or antibody to the pilin receptor (asialoGM1) evoked significant production of IL-8 by immortalized airway epithelial cells, whereas nonpiliated organisms were less able to bind to respiratory epithelial cells and stimulated much less IL-8 secretion (P < 0.01). A piliated, nonflagellated strain was also associated with decreased binding and a diminished level of IL-8 production when compared to wild-type organisms. Isogenic, nonadherent rpoN mutants, lacking pilin and flagellin, did not bind or elicit an IL-8 response. In addition, the IL-8 response was four-fold higher in a cystic fibrosis cell line compared with its corrected cell line. The Pseudomonas autoinducer, an exoproduct secreted during chronic infection, was found to stimulate IL-8 in a dose-dependent manner. P. aeruginosa adhesins, which are necessary for initial infection, directly stimulate IL-8 production by respiratory epithelial cells and therefore play a major role in the pathogenesis of Pseudomonas infection in patients with cystic fibrosis. The inflammatory response is subsequently perpetuated by Pseudomonas autoinducer which is secreted during chronic infection.
Intranasal dexmedetomidine and intravenous ketamine for procedural sedation in a child with alpha-mannosidosis: a magic bullet? (2019)

intranasal dexmedetomidine and intravenous ketamine could be a feasible option for MRI and lumbar puncture in children with alpha-mannosidosis needing sedation.
The Tunable Functionality of α,β‐Unsaturated Carbonyl Compounds Enables Their Differential Application in Biological Systems (2010)

alpha,beta-Unsaturated carbonyl compounds as potential drug candidates is a controversial topic since their potential Michael acceptor activity can lead to cell damage and cytotoxicity. Nevertheless, the alpha,beta-unsaturated carbonyl functionality can be employed as a tool to fine tune biological activity by directly manipulating this entity. Depending on their electronic properties, alpha,beta-unsaturated carbonyl functionalities display different reactivities, namely Michael addition, radical scavenging, oxidation or double bond isomerization. Modifying the alpha-position of the alpha,beta-unsaturated carbonyl system, a concept that has not been widely explored, could produce new, very interesting derivatives. Currently in drug development, irreversible binding in active sites has proven to be one answer to drug resistance in cancer treatment. Overall, natural products containing the alpha,beta-unsaturated carbonyl unit possess multiple biological activities that could be transferred into novel pharmaceutical agents.
Certifiable quantum dice (2012)

We introduce a protocol through which a pair of quantum mechanical devices may be used to generate n random bits that are ε-close in statistical distance from n uniformly distributed bits, starting from a seed of uniform bits. The bits generated are certifiably random, based only on a simple statistical test that can be performed by the user, and on the assumption that the devices obey the no-signalling principle. No other assumptions are placed on the devices' inner workings: it is not necessary to even assume the validity of quantum mechanics.
Mass Spectrometry–Based Detection of Hemoglobin E Mutation by Allele-Specific Base Extension Reaction (2007)

An alternative mass spectrometry-based protocol for noninvasive prenatal diagnosis, ASBER, has been successfully developed to allow the detection of a minor DNA population with a point mutation.
The application of advanced operator genetic algorithms to electromagnetic optimization problems (1999)

This dissertation discusses the application of genetic algorithms to problems of interest in electromagnetic engineering. Rather than simply apply a simple genetic algorithm to a given problem or overhaul genetic algorithms to make them more efficient for all problems, the approach taken in this thesis is to construct genetic algorithms that work well for certain classes of problems. Specifically, Pareto genetic algorithms are applied to the simultaneous optimization of several measures of merit of antenna arrays. Domain-decomposition genetic algorithms are introduced and applied to the optimization of E-plane microwave filters and frequency selective surfaces. Domain decomposition, the technique of breaking a given problem into parts and optimizing each part separately, is shown to accelerate both the analysis of the devices and the convergence of the genetic algorithm. To further accelerate the procedure, three novel model-order reduction techniques are introduced that enable efficient modeling of frequency selective surfaces and thus vastly enlarge the types of devices that can be designed in practice. Finally, dominance and diploidy structures are introduced into the genetic algorithm for application to the control of adaptive antenna arrays. All of the above-described design techniques are illustrated with practical examples, and the adaptive array control is demonstrated with simulations. Genetic algorithms are shown to be an efficient and effective technique for both off-line and on-line optimization of electromagnetic devices.
Evidence for increased plasma levels of calcitonin gene-related peptide in migraine outside of attacks (2000)

Although calcitonin gene-related peptide (CGRP) has been shown to be elevated in jugular venous blood of adult migraineurs during acute migraine attacks, it remains unknown whether CGRP is increased outside of attacks in jugular or cubital venous blood. The aim of the present study was to compare interictal plasma levels of CGRP in adult migraine patients and in healthy controls. Twenty patients with a diagnosis of migraine with or without aura and 20 healthy controls were included. In blood from the cubital vein, CGRP levels were significantly higher in patients (75+/-8 pmol/l (mean+/-SEM)) than in controls (49+/-3 pmol/l) (P=0.005). The subgroup of patients suffering exclusively from migraine without aura (n=14) also had significantly higher levels of CGRP (82+/-10 pmol/l) than controls (n=20; 49+/-3 pmol/l) (P=0.001). The findings could not be explained by confounding factors such as age, sex or use of contraceptive pills. We therefore conclude that CGRP is increased in cubital venous blood of migraineurs outside of attack. It is hypothesized that this finding may reflect a long-lasting or permanent abnormal neurogenic vascular control in patients with migraine.
Correlation of Glioma Cell Regression with Inhibition of Insulin-Like Growth Factor 1 and Insulin-Like Growth Factor-Binding Protein-2 Expression (1997)

To explore the antitumor effect of insulin-like growth factor 1 (IGF-I) antisense RNA and the interaction of IGF-I with insulin-like growth factor-binding proteins (IGFBPs) in glioma cells, a recombinant retrovirus expressing IGF-I antisense RNA was constructed and introduced into C6 glioma cells. IGF-I antisense RNA reverses the transformed phenotype in glioma cells and inhibits glioma cell growth by blocking overexpression of endogenous IGF-I. Expression of IGFBP-2 is increased in glioma cells as compared with normal adult glial cells. IGF-I antisense RNA also inhibits expression of IGFBP-2 in glioma cells, but does not influence expression of the other IGFBPs. Although IGFBP-2 in conditioned medium from wild-type C6 cell cultures itself does not directly influence glioma cell growth, it synergistically enhances exogenous IGF-I-mediated DNA synthesis in IGF-I-negative C6 cells. These findings indicate the inhibitory effect of IGF-I antisense RNA on growth and development of glioma cells. IGF-I-dependent glioma cell growth may, in some circumstances, require IGFBP-2 as a cofactor. The antitumor effect of IGF-I antisense RNA is also associated with inhibition of IGFBP-2 expression.
Site‐specific integration of the Streptomyces plasmid pSAM2 in Mycobacterium smegmatis (1991)

A method which allowed the stable integration of DNA fragments at a single site (attB) in the chromosome of Mycobacterium smegmatis was developed using an integrative element from Streptomyces ambofaciens, pSAM2. Vectors containing an Escherichia coli replicon (pBR322), the kanamycin resistance gene from Tn903 for selection in mycobacteria, and a fragment of pSAM2 containing the int gene as well as the attachment site (attP) were constructed and introduced to M. smegmatis by electroporation. Transformants showed stable integration of the plasmid into a single site (attB) of the mycobacterial genome. This approach should be valuable for analyses of gene expression in various mycobacterial species and permit the development of stable recombinant mycobacterial vaccine strains expressing bacterial or viral genes inserted in pSAM2.
Molecular Tectonic Model of Virus Structural Transitions: the Putative Cell Entry States of Poliovirus (2000)

Upon interacting with its receptor, poliovirus undergoes conformational changes that are implicated in cell entry, including the externalization of the viral protein VP4 and the N terminus of VP1. We have determined the structures of native virions and of two putative cell entry intermediates, the 135S and 80S particles, at approximately 22-A resolution by cryo-electron microscopy. The 135S and 80S particles are both approximately 4% larger than the virion. Pseudoatomic models were constructed by adjusting the beta-barrel domains of the three capsid proteins VP1, VP2, and VP3 from their known positions in the virion to fit the 135S and 80S reconstructions. Domain movements of up to 9 A were detected, analogous to the shifting of tectonic plates. These movements create gaps between adjacent subunits. The gaps at the sites where VP1, VP2, and VP3 subunits meet are plausible candidates for the emergence of VP4 and the N terminus of VP1. The implications of these observations are discussed for models in which the externalized components form a transmembrane pore through which viral RNA enters the infected cell.
Distinct Gene Expression Profiling after Infection of Immature Human Monocyte-Derived Dendritic Cells by the Attenuated Poxvirus Vectors MVA and NYVAC (2007)

Although recombinants based on the attenuated poxvirus vectors MVA and NYVAC are currently in clinical trials, the nature of the genes triggered by these vectors in antigen-presenting cells is poorly characterized. Using microarray technology and various analysis conditions, we compared specific changes in gene expression profiling following MVA and NYVAC infection of immature human monocyte-derived dendritic cells (MDDC). Microarray analysis was performed at 6 h postinfection, since these viruses induced extensive cytopathic effects, rRNA breakdown, and apoptosis at late times postinfection. MVA- and NYVAC-infected MDDC shared upregulation of 195 genes compared to uninfected cells: MVA specifically upregulated 359 genes, and NYVAC upregulated 165 genes. Microarray comparison of NYVAC and MVA infection revealed 544 genes with distinct expression patterns after poxvirus infection and 283 genes specifically upregulated after MVA infection. Both vectors upregulated genes for cytokines, cytokine receptors, chemokines, chemokine receptors, and molecules involved in antigen uptake and processing, including major histocompatibility complex genes. mRNA levels for interleukin 12beta (IL-12beta), beta interferon, and tumor necrosis factor alpha were higher after MVA infection than after NYVAC infection. The expression profiles of transcription factors such as NF-kappaB/Rel and STAT were regulated similarly by both viruses; in contrast, OASL, MDA5, and IRIG-I expression increased only during MVA infection. Type I interferon, IL-6, and Toll-like receptor pathways were specifically induced after MVA infection. Following MVA or NYVAC infection in MDDC, we found similarities as well as differences between these virus strains in the expression of cellular genes with immunological function, which should have an impact when these vectors are used as recombinant vaccines.
Endothelial Dysfunction and Elevated Blood Pressure in Mas Gene-Deleted Mice (2008)

Mas codes for a G protein–coupled receptor that is implicated in angiotensin-(1-7) signaling. We studied the cardiovascular phenotype of Mas -deficient mice backcrossed onto the FVB/N genetic background using telemetry and found that they exhibit higher blood pressures compared with controls. These Mas −/− mice also had impaired endothelial function, decreased NO production, and lower endothelial NO synthase expression. Reduced nicotinamide-adenine dinucleotide phosphate oxidase catalytic subunit gp91 phox protein content determined by Western blotting was higher in Mas −/− mice than in controls, whereas superoxide dismutase and catalase activities were reduced. The superoxide dismutase mimetic, Tempol, decreased blood pressure in Mas −/− mice but had a minimal effect in control mice. Our results show a major cardiovascular phenotype in Mas −/− mice. Mas -deletion results in increased blood pressure, endothelial dysfunction, and an imbalance between NO and reactive oxygen species. Our animals represent a promising model to study angiotensin-(1-7)–mediated cardiovascular effects and to evaluate Mas agonistic compounds as novel cardioprotective and antihypertensive agents based on their beneficial effects on endothelial function.
Genetic analysis of the antifungal activity of a soilborne Pseudomonas aureofaciens strain (1991)

Pseudomonas aureofaciens Q2-87 produces the antibiotic 2,4-diacetophloroglucinol (Phl), which inhibits Gaeumannomyces graminis var. tritici and other fungi in vitro. Strain Q2-87 also provides biological control of take-all, a root disease of wheat caused by this fungus. To assess the role of Phl in the antifungal activity of strain Q2-87, a genetic analysis of antibiotic production was conducted. Two mutants of Q2-87 with altered antifungal activity were isolated by site-directed mutagenesis with Tn5. One mutant, Q2-87::Tn5-1, did not inhibit G. graminis var. tritici in vitro and did not produce Phl. Two cosmids were isolated from a genomic library of the wild-type strain by probing with the mutant genomic fragment. Antifungal activity and Phl production were coordinately restored in Q2-87::Tn5-1 by complementation with either cosmid. Mobilization of one of these cosmids into two heterologous Pseudomonas strains conferred the ability to synthesize Phl and increased their activity against G. graminis var. tritici, Pythium ultimum, and Rhizoctonia solani in vitro. Subcloning and deletion analysis of these cosmids identified a 4.8-kb region which was necessary for Phl synthesis and antifungal activity.
Dexamethasone reduces the interstitial fluid pressure in a human colon adenocarcinoma xenograft. (1993)

The effect of dexamethasone on interstitial hypertension was evaluated in a human colonic adenocarcinoma. Two weeks after transplantation of the tumor line LS174T into SCID mice, recipients with tumors > 8.5 mm in diameter received one daily injection i.p. on days 1-4, at five different doses in the range of 0.3-30 mg/kg. Controls received saline. The interstitial fluid pressure (IFP) was determined in all tumors pretherapeutically on days 1, 4, and 7. A total of 68 tumors were examined, and in an additional group of 22 mice, the effect of 4-day dexamethasone therapy on blood pressure was evaluated. In the 3-, 10-, and 30-mg/kg dose groups a significant reduction in IFP was found, comparing treated versus controls and individual measurements from day 1 versus day 4. No effects were observed on day 7. A marginal effect was observed after 1.0 mg/kg, whereas 0.3 mg/kg did not affect the IFP. The systemic blood pressure was slightly increased by the dexamethasone therapy, and no treatment related changes in tumor sizes were observed. Our findings indicate that the reversible decrease in tumor IFP by dexamethasone is an effect of a reduced microvascular permeability and vascular hydraulic conductivity in the tumors.
Vaccine preventable diseases and vaccination coverage in Australia, 1999 to 2000 (2002)

Volume 26, Supplement, May 2002 The second comprehensive report on the epidemiology of vaccine preventable diseases (VPDs) and vaccination coverage in Australia is now available.The report reviews the most recently available data about notifications (1999 to 2000), hospitalisations (1998/1999 to 1999/2000) and deaths (1998 to 2000) for diseases targeted by the Australian Standard Vaccination Schedule in 2000 (measles, mumps, pertussis, diphtheria, tetanus, rubella, Hib disease, hepatitis B, influenza and polio) as well as 4 other vaccine preventable diseases that were not on the schedule in 2000 (varicella, hepatitis A, pneumococcal and meningococcal disease). Recent trends in vaccination coverage using data from the Australian Childhood Immunisation Registry (ACIR) are also reported. It provides an update of, and comparison with, the data presented in the first report (1993 to 1998).There were continued declines in notification rates for Hib disease, measles and rubella while pertussis remained the most commonly notified disease preventable by childhood vaccination. Influenza accounted for the highest number of hospitalisations and deaths of any vaccine preventable disease. In the review period, vaccination coverage targets reached those set by the 'Immunise Australia' program.This report is a valuable resource for health professionals, providing evidence of the impact of recent and ongoing initiatives in disease control and a baseline against which further changes can be measured.