gebhart/patrepeval huggingface dataset:
Adaptation of Pandemic H1N1 Influenza Viruses in Mice (2010)

The molecular mechanism by which pandemic 2009 influenza A viruses were able to sufficiently adapt to humans is largely unknown. Subsequent human infections with novel H1N1 influenza viruses prompted an investigation of the molecular determinants of the host range and pathogenicity of pandemic influenza viruses in mammals. To address this problem, we assessed the genetic basis for increased virulence of A/CA/04/09 (H1N1) and A/TN/1-560/09 (H1N1) isolates, which are not lethal for mice, in a new mammalian host by promoting their mouse adaptation. The resulting mouse lung-adapted variants showed significantly enhanced growth characteristics in eggs, extended extrapulmonary tissue tropism, and pathogenicity in mice. All mouse-adapted viruses except A/TN/1-560/09-MA2 grew faster and to higher titers in cells than the original strains. We found that 10 amino acid changes in the ribonucleoprotein (RNP) complex (PB2 E158G/A, PA L295P, NP D101G, and NP H289Y) and hemagglutinin (HA) glycoprotein (K119N, G155E, S183P, R221K, and D222G) controlled enhanced mouse virulence of pandemic isolates. HA mutations acquired during adaptation affected viral receptor specificity by enhancing binding to alpha2,3 together with decreasing binding to alpha2,6 sialyl receptors. PB2 E158G/A and PA L295P amino acid substitutions were responsible for the significant enhancement of transcription and replication activity of the mouse-adapted H1N1 variants. Taken together, our findings suggest that changes optimizing receptor specificity and interaction of viral polymerase components with host cellular factors are the major mechanisms that contribute to the optimal competitive advantage of pandemic influenza viruses in mice. These modulators of virulence, therefore, may have been the driving components of early evolution, which paved the way for novel 2009 viruses in mammals.
Channel estimation and adaptive power allocation for performance and capacity improvement of multiple-antenna OFDM systems (2002)

We describe several techniques for the analysis and design of OFDM multiple-antenna systems, which include channel estimation and tracking, optimal training sequences for initial channel acquisition, and adaptive power allocation with closed-loop updating of channel state information for capacity improvement.
Association of ATP1A1 and Dear Single-Nucleotide Polymorphism Haplotypes With Essential Hypertension (2007)

Essential hypertension remains a major risk factor for cardiovascular and cerebrovascular diseases. As a complex multifactorial disease, elucidation of susceptibility loci remains elusive. ATP1A1 and Dear are candidate genes for 2 closely linked rat chromosome-2 blood pressure quantitative trait loci. Because corresponding human syntenic regions are on different chromosomes, investigation of ATP1A1 (chromosome [chr]-1p21) and Dear (chr-4q31.3) facilitates genetic analyses of each blood pressure quantitative trait locus in human hypertension. Here we report the association of human ATP1A1 (P<0.000005) and Dear (P<0.03) with hypertension in a relatively isolated, case/control hypertension cohort from northern Sardinia by single-nucleotide polymorphism haplotype analysis. Sex-specific haplotype analyses detected stronger association of both loci with hypertension in males than in females. Haplotype trend-regression analyses support ATP1A1 and Dear as independent susceptibility loci and reveal haplotype-specific association with hypertension and normotension, thus delineating haplotype-specific subsets of hypertension. Although investigation in other cohorts needs to be performed to determine genetic effects in other populations, haplotype subtyping already allows systematic stratification of susceptibility and, hence, clinical heterogeneity, a prerequisite for unraveling the polygenic etiology and polygene-environment interactions in essential hypertension. As hypertension susceptibility genes, coexpression of ATP1A1 and Dear in both renal tubular cells and vascular endothelium suggest a cellular pathogenic scaffold for polygenic mechanisms of hypertension, as well as the hypothesis that ATP1A1 and/or Dear could contribute to the known renal and vascular endothelial dysfunction associated with essential (polygenic) hypertension.
A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin (2007)

The molecular basis for Toll-like receptor (TLR) recognition of microbial ligands is unknown. We demonstrate that mouse and human TLR5 discriminate between different flagellins, and we use this difference to map the flagellin recognition site on TLR5 to 228 amino acids of the extracellular domain. Through molecular modeling of the TLR5 ectodomain, we identify two conserved surface-exposed regions. Mutagenesis studies demonstrate that naturally occurring amino acid variation in TLR5 residue 268 is responsible for human and mouse discrimination between flagellin molecules. Mutations within one conserved surface identify residues D295 and D367 as important for flagellin recognition. These studies localize flagellin recognition to a conserved surface on the modeled TLR5 structure, providing detailed analysis of the interaction of a TLR with its ligand. These findings suggest that ligand binding at the beta sheets results in TLR activation and provide a new framework for understanding TLR-agonist interactions.
Towards a privacy measurement criterion for voting systems (2005)

This paper provides a definition for perfect privacy in electronic and other voting systems, and an entropy-based criterion to measure the deviation from perfect privacy. Its use is illustrated with examples.
The Binding of 2-(4′-Methylaminophenyl)Benzothiazole to Postmortem Brain Homogenates Is Dominated by the Amyloid Component (2003)

2-(4'-methylaminophenyl)benzothiazole (BTA-1) is an uncharged derivative of thioflavin-T that has high affinity for Abeta fibrils and shows very good brain entry and clearance. In this study, we asked whether BTA-1, at concentrations typical of those achieved during positron emission tomography (PET) studies, could specifically bind to amyloid deposits in the complex milieu of human brain or whether amyloid binding was overshadowed by nonspecific binding, found even in brains that did not contain amyloid deposits. We quantitatively assessed [3H]BTA-1 binding to crude homogenates of postmortem brain obtained from nine Alzheimer's disease (AD) subjects, eight controls, and six subjects with non-AD dementia. BTA-1 binding was >10-fold higher in AD brain, and the majority (94%) of the binding was specific (displaceable). High-affinity [3H]BTA-1 was observed only in AD brain gray matter and was not present in control brain gray matter, AD brain white matter, or cerebellum. The K(d) of [3H]BTA-1 for binding to AD brain (5.8 +/- 0.90 nm) was very similar to the K(d) for binding to synthetic Abeta fibrils. In addition, the K(i) of various BTA analogs for inhibition of [3H]BTA-1 binding to AD brain homogenates was very similar to their K(i) for inhibition of [3H]BTA-1 binding to synthetic Abeta fibrils. Nanomolar concentrations of [3H]BTA-1 did not appear to bind to neurofibrillary tangles. Finally, BTA-1 did not appear to bind significantly to common neuroreceptors or transporter sites. These data suggest that the binding of BTA-1 to AD brain is dominated by a specific interaction with Abeta amyloid deposits.
Prospects for the Therapeutic Use of Antigene Oligonucleotides (1996)

An outgrowth of classic nucleic acid interaction studies, oligonucleotide-directed triple helix formation is a unique method for creating highly specific chemical ligands that recognize and bind to particular sequences of duplex DNA. Under permissive conditions, these oligonucleotide-based compounds can approach or exceed the binding affinity and sequence specificity of natural DNA-binding proteins. Triple helix recognition has been found to be useful in certain cell-free applications including precise chromosome fragmentation. It has been proposed that such oligonucleotides could also form the basis for gene-targeted (antigene) drugs that might repress transcription from undesired genes in living cells. However, current strategies for oligonucleotide-directed triple helix formation suffer from important constraints involving requirements for stabilizing binding conditions, restrictions on permitted target sequences, and inefficient nuclear delivery of oligonucleotides. Implementation of oligonucleotide-directed triple helix formation as a viable approach to cancer therapy must therefore await clever solutions to a series of fascinating problems.
<title>Scatter Measurements On LAK9 And SF1 Glasses At 0.915 µm</title> (1983)

Measurements of two refractive samples were made at 0.915 &mu;m of the BRDF to angles as close as 3° from specular. The data fit a one-dimensional power spectrum using vector electromagnetic theory. The autocorrelation length and its error were estimated and from these a most probable value and upper bound of the BRDF at 1° from specular were determined.
Interleukin-8 gene induction in the myocardium after ischemia and reperfusion in vivo. (1995)

Neutrophil adhesion and direct cytotoxicity for cardiac myocytes require chemotactic stimulation and are dependent upon CD18-ICAM-1 binding. To characterize the potential role of IL-8 in this interaction, canine IL-8 cDNA was cloned and the mature recombinant protein expressed in Escherichia coli BL21 cells. Recombinant canine IL-8 markedly increased adhesion of neutrophils to isolated canine cardiac myocytes. This adhesion resulted in direct cytotoxicity for cardiac myocytes. Both processes were specifically blocked by antibodies directed against CD18 and IL-8. In vivo, after 1 h of coronary occlusion, IL-8 mRNA was markedly and consistently induced in reperfused segments of myocardium. IL-8 mRNA was not induced in control (normally perfused) myocardial segments. Minimal amounts of IL-8 mRNA were detected after 3 or 4 h of ischemia without reperfusion. Highest levels of induction were evident in the most ischemic myocardial segments. IL-8 mRNA peaked in the first 3 h of reperfusion and persisted at high levels beyond 24 h. IL-8 staining was present in the inflammatory infiltrate near the border between necrotic and viable myocardium, as well as in small veins in the same area. These findings provide the first direct evidence for regulation of IL-8 in ischemic and reperfused canine myocardium and support the hypothesis that IL-8 participates in neutrophil-mediated myocardial injury.
Navier-Stokes methods to predict circulation control airfoil performance (1992)

Abstract : The predictive capability of the two-dimensional compressible mass- averaged Navier-Stokes equations was investigated for a typical circulation control air-foil. The governing equations were solved using the implicit approximate factorization algorithm of Beam-Warming with the turbulence model of Baldwin-Lomax. To account for the unique characteristics of circulation control airfoils, an empirical turbulence model correction due to Bradshaw was used. This thesis is unique in that the predictive capability of the computational method is explored by examining the importance of the empirical Bradshaw curvature correction constant on the computed results. Using a generic value of the curvature constant at various blowing coefficient levels, the computational method was able to accurately predict airfoil pitching moment and lift curve slope due to blowing. Predicted levels of airfoil lift coefficient, although reasonable, were found to be consistently low compared with experiment due to the generic curvature constant providing premature jet detachment from the Coanda surface. Computed and measured airfoil drag results followed the same trends, but lack of overall drag coefficient agreement was disappointing. Lift coefficient was found to be quite sensitive, pitching moment not sensitive, and drag coefficient moderately sensitive to the value of the curvature constant used. For the highest blowing coefficient case considered, the value of curvature constant required for the computational lift coefficient to match the experimental lift coefficient was also determined.
FAIRY: a randomized controlled patient-blind phase III study to compare the efficacy and safety of intravenous ferric carboxymaltose (Ferinject®) to placebo in patients with acute isovolemic anemia after gastrectomy - study protocol for a randomized controlled trial (2014)

NCT01725789 (international: http://www.clinicaltrials.gov) and NCCCTS-12-644 (NCC, Korea).
Purines. LXXV. Dimroth Rearrangement, Hydrolytic Deamination, and Pyrimidine-Ring Breakdown of 7-Alkylated 1-Alkoxyadenines: N(1)-C(2) versus N(1)-C(6) Bond Fission. (1997)

On treatment with boiling H2O for 5-6h, 1-alkoxy-7-alkyladenines (13) underwent hydrolytic cleavage at the N(1)-C(2) and the N(1)-C(6) bonds to produce the imidazole-5-carboxamidines (14) in 53-60% yields and the imidazole-5-carboxamides (18) in 5-7% yields, respectively. The Dimroth rearrangement of 13 to N6-alkoxy-7-alkyladenine (15) was found to proceed through 14 more slowly than that of the 9-alkyl analogues 1 at pH 7 and above, being accompanied by hydrolysis to give the deformylated product (16) and by deamination through 18 leading to 7-alkylhypoxanthine (12), 1-alkoxy-7-alkylhypoxanthine (19), and 1-alkyl-4-aminoimidazole-5-carboxamide (20). Interestingly, the N(1)-C(6) bond fission product 17a was obtained from 13a by treatment with 0.01N aqueous NaOH at 4°C for 35d, but in only 2% yield, or more efficiently (in 56% yield) by pyrolysis at 150°C for 1h. On the other hand, 13 underwent acid hydrolysis faster than 1, providing the deformylated product 16 in 85-96% yields on treatment with 1-2N aqueous HCl at room temperature for 2-5h. 4-amino-N'-methoxy-1-methyl-5-carboxamidine (16a) was alternatively obtained in 59% yield by treatment of 1-methoxy-7-methyladenine (13a) with boiling 2N aqueous NaOH for 10min. Efficient preparations of the rearranged products 15 (80-86%) were accomplished by treating 13 with boiling 0.1N aqueous NaOH for 20-30min.
Inhibition of hereditary hepatitis and liver tumor development in Long-Evans cinnamon rats by the copper-chelating agent trientine dihydrochloride (1996)

Trientine dihydrochloride (trientine) is an alternative medicinal copper chelating agent for patients with Wilson's disease of penicillamine intolerance. We examined the effects of trientine on the spontaneous development of hepatitis and hepatic tumors, by its short-term and long-term administration to Long-Evans cinnamon (LEC) rats with an accumulation of copper in the liver, as animal models of Wilson's disease. Male rats were given trientine in their drinking water at 1500 ppm for 18 weeks, from 6 weeks to 24 weeks of age in short-term experiment, and 1500 ppm for 27 weeks then 750 ppm for 52 weeks, from 8 to 87 weeks of age in the long-term experiment. Development of hepatitis was observed in the control LEC rats at 18 weeks of age. They had high levels of plasma transaminases (glutamic oxaloacetic transaminase [GOT], glutamic pyruvic transaminase [GPT]), and on pathological examination, hepatocyte destruction was observed. Histological findings revealed that short-term administration of trientine inhibited the development of hepatitis remarkably. The plasma GOT and GPT levels of treated animals were only slightly higher than those of normal LEA (Long-Evans with agouti coat color) rats, a sibling line of LEC rats. Copper levels in the liver were decreased by a maximum of 50 percent. In the long-term administration of trientine, the incidence of hepatic cell carcinoma (HCC) in the treated rats was 67 percent that of the untreated LEC rats, and the number of HCCs per rat in the treated group was 0.7 +/- 0.5, being significantly lower as compared with 4.7 +/- 3.5 in the untreated rats. Additionally, the development of cholangiofibrosis in LEC rats was completely prevented by long-term administration of the agent. The copper level in the liver of treated rats was reduced by 33 percent at 87 weeks of age. Development of HCC in LEC rats might be partly, but not totally, because of copper accumulation. No effects on the levels of copper, iron, or zinc in the liver of LEA rats was detected, and no adverse effects were detected in either LEC or LEA rats after both short- and long-term administration of trientine in drinking water.
Outer membrane vesicle-mediated release of cytolethal distending toxin (CDT) from Campylobacter jejuni (2009)

Our results strongly suggest that the release of outer membrane vesicles is functioning as a route of C. jejuni to deliver all the subunits of CDT toxin (CdtA, CdtB, and CdtC) to the surrounding environment, including infected host tissue.
C-Reactive Protein Concentrations and Subsequent Ovarian Cancer Risk (2007)

II.
Enhanced thermal stability of silica-encapsulated metal nanoshells (2001)

A silica-encapsulating layer of a 60–70 nm thickness is fabricated around composite nanoparticles consisting of a silica core and a gold shell (metal nanoshells). The outer silica layer provides greatly enhanced thermal stability to the nanoparticle, effectively raising its melting temperature by 300° relative to uncoated nanoshells. Both spectroscopic and microscopic structural evaluations are used to assess changes in the nanostructure when subjected to potentially destructive heating cycles. This encapsulation method may prove valuable in enhancing the thermal stability of other types of assembled nanostructures and nanoscale photonic materials.
The influence of 5′ and 3′ end structures on pre-mRNA metabolism (1995)

The 5' cap structure of RNA polymerase II transcripts and the poly(A) tail found at the 3' end of most mRNAs have been demonstrated to play multiple roles in gene expression and its regulation. In the first part of this review we will concentrate on the role played by the cap in pre-mRNA splicing and how it may contribute to efficient and specific substrate recognition. In the second half, we will discuss the roles that polyadenylation has been demonstrated to play in RNA metabolism and will concentrate in particular on an elegant mechanism where regulation of polyadenylation is used to control gene expression.
Crystal Structure of a Complement Factor D Mutant Expressing Enhanced Catalytic Activity (1995)

Complement factor D is a serine protease regulated by a novel mechanism that depends on conformational changes rather than cleavage of a zymogen for expression of proteolytic activity. The conformational changes are presumed to be induced by the single natural substrate, C3bB, and to result in reversible reorientation of the catalytic center and of the substrate binding site of factor D, both of which have atypical conformations. Here we report that replacement of Ser94, Thr214, and Ser215 of factor D (chymotrypsinogen numbering has been used for comparison purposes) with the corresponding residues of trypsin, Tyr, Ser, and Trp, is sufficient to induce substantially higher catalytic activity associated with a typical serine protease alignment of the catalytic triad residues His57, Asp102, and Ser195. These results provide a partial structural explanation for the low reactivity of "resting-state" factor D toward synthetic substrates.
The role of carbohydrate in sperm-ZP3 adhesion (1996)

Fertilization is the most important cell adhesion event in the life time of any organism. In a number of organisms ranging from echinoderms to mammals, the recognition of carbohydrate epitopes by complimentary protein receptors has been proposed to be a critical factor in gamete interaction (Glabe et al, 1982; Florman and Wassarman, 1985; DeAngelis and Glabe, 1987). The following article briefly describes both how glycoproteins arise in vivo and lists some potential biological roles of the carbohydrate moieties of the given examples. The majority of the article will be concerned with the involvement of proteincarbohydrate interactions in mammalian sperm—zona binding.
Discovery and application of protein biomarkers for ovarian cancer (2008)

The present review summarizes the main advances in the past year, with the lists of biomarkers/panels, their potential applications, and new strategies/lessons we learned based on the most important work published during this period.
In Vitro Mineralization by Preosteoblasts in Poly(dl-lactide-co-glycolide) Inverse Opal Scaffolds Reinforced with Hydroxyapatite Nanoparticles (2010)

Inverse opal scaffolds made of poly(DL-lactide-co-glycolide) (PLGA) and hydroxyapatite (HAp) were fabricated using cubic-closed-packed (ccp) lattices of uniform gelatin microspheres as templates and evaluated for bone tissue engineering. The scaffolds exhibited a uniform pore size (213 +/- 4.4 microm), a porosity of approximately 75%, and an excellent connectivity in three dimensions. Three different formulations were examined: pure PLGA, HAp-impregnated PLGA (PLGA/HAp), and apatite (Ap)-coated PLGA/HAp. After seeding with preosteoblasts (MC3T3-E1), the samples were cultured for different periods of time and then characterized by X-ray microcomputed tomography (micro-CT) and scanning electron microscopy to evaluate osteoinductivity in terms of the amount and spatial distribution of mineral secreted from the differentiated preosteoblasts. Our results indicate that preosteoblasts cultured in the Ap-coated PLGA/HAp scaffolds secreted the largest amount of mineral, which was also homogeneously distributed throughout the scaffolds. In contrast, the cells in the pure PLGA scaffolds secreted very little mineral, which was mainly deposited around the perimeter of the scaffolds. These results suggest that the uniform pore structure and favorable surface properties could facilitate the uniform secretion of extracellular matrix from cells throughout the scaffold. The Ap-coated PLGA/HAp scaffold with uniform pore structure could be a promising material for bone tissue engineering.
An Improved Method for the Purification of Human Erythropoietin with High in Vivo Activity from the Urine of Anemic Patients. (1994)

An improved method for the purification of human erythropoietin with high in vivo activity from urine was developed. This method involved ion-exchange, gel permeation, affinity chromatography, and reverse-phase chromatography but did not involve any stabilizing procedures. The purified human urinary erythropoietin showed a single broad band with a molecular weight between 37000 and 39000 Da on sodium dodecyl sulfate polyacrylamide gel electrophoresis, and had an in vivo specific activity of 160000 IU/mg comparable to that of human erythropoietin produced in recombinant Chinese hamster ovary cells. We found that omission of the phenol treatment and ethanol precipitation which are usually used in the purification of human urinary erythropoietin greatly improved the biological activity of the final product. Phenol treatment followed by ethanol precipitation did not affect the amino acid composition but decreased the apparent molecular weight and N-acetylglucosamine content of human urinary erythropoietin. These findings suggest that phenol treatment followed by ethanol precipitation does not restore erythropoietin with high branched sugar chains which would have high in vivo specific activity as reported previously (M. Takeuchi, et al. (1989) Proc. Natl. Acad. Sci. U.S.A., 86, 7819-7822).
The paradox of discriminatory nondiscriminators resolved (1979)

In the Triangular Method, often used in sensory analysis, the subject has to select a stimulus from each tri-stimulus set presented. Results obtained under the instruction to select the odd stimulus are not inconsistent with those obtained under the instruction to select either the strongest or the weakest stimulus, as has been contended since a few decades.
Erythropoietin: A Potent Inducer of Peripheral Immuno/Inflammatory Modulation in Autoimmune EAE (2008)

Taken together, our findings reveal an important new locus whereby EPO induces substantial long-term tissue protection in the host through signaling to several critical subsets of immune cells that reside in the peripheral lymphatic system.