gebhart/patrepeval huggingface dataset:
Proinflammatory Effects of Staphylococcus Aureus Exotoxin B on Nasal Epithelial Cells (2006)

OBJECTIVE The aim of this study was to evaluate the effects of Staphylococcus aureus exotoxin B (SE‐B) on proinflammatory cytokine/chemokine releases in primary nasal epithelial cell cultures (NECC) of subjects with and without chronic rhinosinusitis (CRS). STUDY DESIGN AND SETTING NECC (CRS: n = 14; Controls: n = 11) were stimulated with SE‐B. Protein concentrations of interleukin‐(IL)‐1β, IL‐6, and IL‐8 levels were measured in NECC supernatants by ELISA before (T0) and after 24 hr stimulation with SE‐B (T1). RESULTS T0: supernatants of the NECC of CRS patients contained significant lower levels of IL‐8 (2.1 ng/ml) compared to Controls (IL‐8: 6.2 ng/ml; P &lt; 0.01). T1: SE‐B induced a significant increase of IL‐6 in NECC ( P &lt; 0.001). IL‐1β was not detectable. CONCLUSIONS This is the first study evaluating the effects of exotoxins on NECC. SE‐B showed proinflammatory effects on NECC. SIGNIFICANCE Our data suggest that resident NECC are involved in immunological responses to Staphylococcus aureus toxins, supplementing the so‐called “superantigen hypothesis” in CRS.
Biophysical Characterization of O-Glycosylated CD99 Recognition by Paired Ig-like Type 2 Receptors (2008)

Paired Ig-like type 2 receptors (PILRs) are one of the paired receptor families, which consist of two functionally opposite members, inhibitory (PILRalpha) and activating (PILRbeta) receptors. PILRs are widely expressed in immune cells and recognize the sialylated O-glycosylated ligand CD99, which is expressed on activated T cells, to regulate immune responses. To date, their biophysical properties have not yet been examined. Here we report the affinity, kinetic, and thermodynamic analyses of PILR-CD99 interactions using surface plasmon resonance (SPR) together with site-directed mutagenesis. The SPR analysis clearly demonstrated that inhibitory PILRalpha can bind to CD99 with low affinity (K(d) approximately 2.2 microm), but activating PILRbeta binds with approximately 40 times lower affinity (K(d) approximately 85 microm). In addition to our previous mutagenesis study (Wang, J., Shiratori, I., Saito, T., Lanier, L. L., and Arase, H. (2008) J. Immunol. 180, 1686-1693), the SPR analysis showed that PILRalpha can bind to each Ala mutant of the two CD99 O-glycosylated sites (Thr-45 and Thr-50) with similar binding affinity to wild-type CD99. This indicated that both residues act as independent and equivalent PILRalpha binding sites, consistent with the highly flexible structure of CD99. On the other hand, it is further confirmed that PILRbeta can bind the T50A mutant, but not the T45A mutant, indicating a recognition difference between PILRalpha and PILRbeta. Kinetic studies demonstrated that the PILR-CD99 interactions show fast dissociation rates, typical of cell-cell recognition receptors. Thermodynamic analyses revealed that the PILRalpha-CD99 interaction is enthalpically driven with a large entropy loss (-TDeltaS = 8.9 kcal.mol(-1)), suggesting the reduction of flexibility upon complex formation. This is in contrast to the entropically driven binding of selectins to sugar-modified ligands involved in leukocyte rolling and infiltration, which may reflect their functional differences.
Effect of hypoxia and reoxygenation on the formation and release of reactive oxygen species by porcine pulmonary artery endothelial cells (1995)

Endothelial cells are critical targets in both hypoxia- and reoxygenation-mediated lung injury. Reactive O2 species (ROS) have been implicated in the pathogenesis of hypoxic and reoxygenation lung injury, and xanthine dehydrogenase/oxidase (XDH/XO) is a major generator of the ROS. Porcine pulmonary artery endothelial cells (PAEC) have no detectable XDH/XO. This study was undertaken to examine 1) ROS production by hypoxic porcine PAEC and their mitochondria and 2) ROS production and injury in reoxygenated PAEC lacking XDH/XO activity. Intracellular H2O2 generation and extracellular H2O2 and O2 divided release were measured after exposure to normoxia (room air-5% CO2), hypoxia (0% O2-95% N-5% CO2), or hypoxia followed by normoxia or hyperoxia (95% O2-5% CO2). Exposure to hypoxia results in significant reductions in intracellular H2O2 formation and extracellular release of H2O2 and O2 by PAEC and mitochondria. The reductions occur with as little as a 2 h exposure and progress with continued exposure. During reoxygenation, cytotoxicity was not observed, and the production of ROS by PAEC and their mitochondria never exceeded levels observed in normoxic cells. The absence of XDH/XO may prevent porcine PAEC from developing injury and increased ROS production during reoxygenation.
Gene therapy may have future role in cancer treatment (1987)

WHEN GENE THERAPY becomes clinical reality, one of its first uses may be in treating cancer patients with drug-resistant tumors. John S. Lazo, PhD, associate professor of pharmacology, Yale University School of Medicine, New Haven, Conn, told the Bristol Myers Symposium on Cancer Research that he can foresee using gene therapy to restore sensitivity to chemotherapy in resistant cells; to produce toxic chemicals in resistant tumor cells; and to make normal host cells resistant to chemotherapy so that higher doses of cytotoxic compounds can be used. The trick, of course, is to isolate the genes that can produce proteins to do these things; to get those genes into the proper cells; and to see that the genes are expressed appropriately in vivo. Researchers at several institutions have been investigating gene therapy for genetic disease, and have found that it is indeed possible to transplant a gene into a stem cell
Inhaled Human Insulin Treatment in Patients with Type 2 Diabetes Mellitus (2001)

Pulmonary delivery of insulin in type 2 diabetic patients who require insulin improved glycemic control, was well tolerated, and demonstrated no adverse pulmonary effects. Larger-scale studies are ongoing to provide long-term efficacy and safety data.
Induced thermal stress fields for three-dimensional distortion control of Si wafer topography (2004)

Localized, controlled heating can induce a thermal stress field in silicon wafers and displace the surface topography in three dimensions, which is useful for nanoscale regulation of overlay in microcontact printing systems. Simulation and experimental results are presented to demonstrate the use of a thermal array consisting of a dense distribution of independent heating elements to locally displace silicon wafer alignment microstructures. An experimental apparatus comprised of a 7×7 array of thermal cycling sources is used to control the absolute three-dimensional position of surface microstructures. The system is used to demonstrate out-of-plane sensitivity of 1.4 μm/°C by thermomechanical displacement contributions from thermal expansion of the heating element. Rolloff in out-of-plane displacement of 200 nm/mm/°C in silicon at the boundary between heated and nonheated regions in this apparatus is exhibited. Dynamic real-time control of the substrate flatness is thus feasible and is demonstrated with the apparatus using feedback from three alignment microscopes, to sub-100 nm levels of regulation. Control of the in-plane microstructure position is achieved by stabilizing the vertical displacement with a mechanical nanopositioning stage, while establishing a thermal stress field to produce displacement sensitivity of 70 nm/°C. Real-time feedback control of the in-plane microstructure position is demonstrated, also within sub-100 nm of the target regulation level.
Thromboxane A2 Induces Differentiation of Human Mesenchymal Stem Cells to Smooth Muscle-Like Cells (2008)

Thromboxane A(2) (TxA(2)) is involved in smooth muscle contraction and atherosclerotic vascular diseases. Accumulating evidence suggests a pivotal role for mesenchymal stem cells (MSCs) in vascular remodeling. In the present study, we demonstrate for the first time that the TxA(2) mimetic U46619 induces differentiation of human adipose tissue-derived MSCs (hADSCs) to smooth muscle-like cells, as demonstrated by increased expression of smooth muscle-specific contractile proteins such as alpha-smooth muscle actin (alpha-SMA), calponin, smoothelin, and smooth muscle-myosin heavy chain. Using an in vitro collagen gel lattice contraction assay, we showed that U46619-induced expression of the contractile proteins was associated with increased contractility of the cells. U46619 increased the intracellular Ca(2+) concentration in hADSCs and pretreatment of the cells with the thromboxane receptor antagonist SQ29548 or the calmodulin (CaM) inhibitor W13 abrogated the U46619-induced alpha-SMA expression and contractility, suggesting a pivotal role of Ca(2+)/CaM in the U46619-stimulated smooth muscle differentiation of hADSCs. In addition, U46619 elicited activation of RhoA in hADSCs, and pretreatment of the cells with the Rho kinase-specific inhibitor Y27632 or overexpression of the dominant-negative mutants of RhoA and Rho kinase blocked U46619-stimulated alpha-SMA expression and contractility. Furthermore, U46619 induced phosphorylation of myosin light chain (MLC) through CaM/MLC kinase- and Rho kinase-dependent pathways, and the MLC kinase inhibitor ML-7 abrogated U46619-induced alpha-SMA expression and contractility. These results suggest that U46619 induces differentiation of hADSCs to contractile smooth muscle-like cells through CaM/MLCK- and RhoA-Rho kinase-dependent actin polymerization.
Split-peak phenomenon in nonlinear chromatography. 2. Characterization of the adsorption kinetics of proteins on reversed-phase supports (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSplit-peak phenomenon in nonlinear chromatography. 2. Characterization of the adsorption kinetics of proteins on reversed-phase supportsHelene. Place, Bernard. Sebille, and Claire. Vidal-MadjarCite this: Anal. Chem. 1991, 63, 13, 1222–1227Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/ac00013a008https://doi.org/10.1021/ac00013a008research-articleACS PublicationsRequest reuse permissionsArticle Views100Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Growth and development of the axr1 mutants of Arabidopsis. (1990)

We have recovered eight new auxin-resistant lines of Arabidopsis that carry mutations in the AXR1 gene. These eight lines, together with the 12 lines described in a previous report, define at least five different axr1 alleles. All of the mutant lines have a similar phenotype. Defects include decreases in plant height, root gravitropism, hypocotyl elongation, and fertility. Mutant line axr1-3 is less resistant to auxin than the other mutant lines and has less severe morphological abnormalities. This correlation suggests that the morphological defects are a consequence of a defect in auxin action. To determine whether the altered morphology of mutant plants is associated with changes in cell size or tissue organization, tissue sections were examined using scanning electron microscopy. No clear differences in cell size were observed between wild-type and mutant tissues. However, the vascular bundles of mutant stems were found to be less well differentiated than those in wild-type stems. The auxin sensitivity of rosette-stage plants was determined by spraying plants with auxin solutions. Mutant rosettes were found to be significantly less sensitive to exogenously applied auxin than wild-type rosettes, indicating that the AXR1 gene functions in aerial portions of the plant. Our studies suggest that the AXR1 gene is required for auxin action in most, if not all, tissues of the plant and plays an important role in plant development. Linkage studies indicate that the gene is located on chromosome 1 approximately 2 centiMorgans from the closest restriction fragment length polymorphism.
Cheyne-Stokes Breathing During Sleep in Patients With Left Ventricular Heart Failure (1985)

Fifteen patients with left ventricular heart failure (LVF) without known breathing disorders during sleep had full-night recordings of sleep and breathing to study the incidence and impact of the apnea of Cheyne-Stokes breathing. This group showed a marked degree of sleep-related breathing abnormalities, 40% demonstrating Cheyne-Stokes breathing with five or more central apneas per hour of sleep. Cheyne-Stokes breathing during sleep in patients with LVF predicted an increased short-term mortality rate. All six patients with LVF and Cheyne-Stokes breathing with more than five apneas per hour of sleep were dead within six months, while only three of nine patients without recurrent apnea died within six months, a significant difference (P less than .05) even in this small group. Among seven patients with LVF studied with the polysomnogram, there were statistically significant differences between the Cheyne-Stokes and non-apnea groups in total sleep time, awakening per hour, and the number of arterial desaturations. Although sleep disturbances have been anecdotally described in patients with LVF, no previous investigation has determined the incidence and impact of Cheyne-Stokes breathing during sleep in LVF. Our findings that Cheyne-Stokes breathing predicts an adverse short-term mortality rate confirm the clinical impression that Cheyne-Stokes breathing is a poor prognostic sign in LVF.
The Dynamic Response of Vascular Endothelial Cells to Fluid Shear Stress (1981)

We have developed an in-vitro system for studying the dynamic response of vascular endothelial cells to controlled levels of fluid shear stress. Cultured monolayers of bovine aortic endothelial cells are placed in a cone-plate apparatus that produces a uniform fluid shear stress on replicate samples. Subconfluent endothelial cultures continuously exposed to 1-5 dynes/cm2 shear proliferate at a rate comparable to that of static cultures and reach the same saturation density (congruent to 1.0-1.5 X 10(5) cells/cm2). When exposed to a laminar shear stress of 5-10 dynes/cm2, confluent monolayers undergo a time-dependent change in cell shape from polygonal to ellipsoidal and become uniformly oriented with flow. Regeneration of linear "wounds" in confluent monolayer appears to be influenced by the direction of the applied force. Preliminary studies indicate that certain endothelial cell functions, including fluid endocytosis, cytoskeletal assembly and nonthrombogenic surface properties, also are sensitive to shear stress. These observations suggest that fluid mechanical forces can directly influence endothelial cell structure and function. Modulation of endothelial behavior by fluid shear stresses may be relevant to normal vessel wall physiology, as well as the pathogenesis of vascular diseases, such as atherosclerosis.
Avoiding the high Bonferroni penalty in genome‐wide association studies (2009)

A major challenge in genome-wide association studies (GWASs) is to derive the multiple testing threshold when hypothesis tests are conducted using a large number of single nucleotide polymorphisms. Permutation tests are considered the gold standard in multiple testing adjustment in genetic association studies. However, it is computationally intensive, especially for GWASs, and can be impractical if a large number of random shuffles are used to ensure accuracy. Many researchers have developed approximation algorithms to relieve the computing burden imposed by permutation. One particularly attractive alternative to permutation is to calculate the effective number of independent tests, M(eff), which has been shown to be promising in genetic association studies. In this study, we compare recently developed M(eff) methods and validate them by the permutation test with 10,000 random shuffles using two real GWAS data sets: an Illumina 1M BeadChip and an Affymetrix GeneChip Human Mapping 500K Array Set. Our results show that the simpleM method produces the best approximation of the permutation threshold, and it does so in the shortest amount of time. We also show that M(eff) is indeed valid on a genome-wide scale in these data sets based on statistical theory and significance tests. The significance thresholds derived can provide practical guidelines for other studies using similar population samples and genotyping platforms.
Light-scattering properties of undiluted human blood subjected to simple shear (1999)

An experimental investigation was performed into the effect of simple shear on the light-scattering properties of undiluted human blood. Undiluted human blood was enclosed between two glass plates with an adjustable separation between 30 and 120 microns and with one plate moving parallel to the other. For various shear rates and layer thicknesses, the angular light distribution and the collimated transmission were measured for 633-nm light. For shear rates above 150 s-1, the transmission results directly yielded a total attenuation coefficient of 120 mm-1. At lower shear rates the total attenuation followed an irregular pattern. From the angular intensity distributions, the anisotropy for single scattering was deduced by inverse Monte Carlo simulations. A continuous increase of the average cosine g with the shear rate was observed, with g in the range 0.95-0.975.
Linguistic features for automatic evaluation of heterogenous MT systems (2007)

Evaluation results recently reported by Callison-Burch et al. (2006) and Koehn and Monz (2006), revealed that, in certain cases, the BLEU metric may not be a reliable MT quality indicator. This happens, for instance, when the systems under evaluation are based on different paradigms, and therefore, do not share the same lexicon. The reason is that, while MT quality aspects are diverse, BLEU limits its scope to the lexical dimension. In this work, we suggest using metrics which take into account linguistic features at more abstract levels. We provide experimental results showing that metrics based on deeper linguistic information (syntactic/shallow-semantic) are able to produce more reliable system rankings than metrics based on lexical matching alone, specially when the systems under evaluation are of a different nature.
Metabolic Perturbance in Autism Spectrum Disorders: A Metabolomics Study (2012)

Autism spectrum disorders (ASD) are a group of biological disorders with associated metabolic derangement. This study aimed to identify a pattern of metabolic perturbance in ASD using metabolomics in urinary specimens from 48 children with ASD and 53 age matched controls. Using a combination of liquid- and gas-chromatography-based mass spectrometry, we detected the levels of 82 metabolites (53 of which were increased) that were significantly altered between the ASD and the control groups using osmolality normalized data. Pattern analysis showed that the levels of several amino acids such as glycine, serine, threonine, alanine, histidine, glutamyl amino acids and the organic acid, taurine were significantly (p≤0.05) lower in ASD children. The levels of antioxidants such as carnosine were also reduced in ASD (p=0.054). Furthermore, several gut bacterial metabolites were significantly altered in ASD children who had gastrointestinal dysfunction. Overall, this study detected abnormal amino acid metabolism, increased oxidative stress, and altered gut microbiomes in ASD. The relationship of altered gut microbial co-metabolism and the disrupted metabolisms requires further investigation.
Engineered Recombinant Single-Chain Fragment Variable Antibody for Immunosensors (2005)

A recombinant single-chain fragment variable (scFv) antibody (designated A10B) was engineered to contain two histidines within the linker peptide used to join the scFv heavy and light chains. A piezoimmunosensor using the scFv was successfully developed. A10B scFv bound to the gold piezoimmunosensor surface were correctly oriented, retained antigen-binding activity, and coupled at high surface concentration. These results, and results obtained from an earlier study using an scFv containing a linker cysteine, suggest that the location on the linker sequence in which the amino acids were incorporated was well tolerated by the scFv and did not interfere with scFv antigen-binding activity. The scFv-modified QCM sensor was thoroughly characterized and used to specifically detect antigen in crude serum sample and had a sensitivity of 2.3 +/- 0.15 nM (n = 4) with a linear range over 2.3 x 10(-9) - 3.3 x 10(-(8) M. The piezoimmunosensor was also used to study the kinetics and thermodynamics of antigen/scFv antibody binding.
Diagnostic role of microRNA expression profile in the serum of pregnant women with fetuses with neural tube defects (2012)

The discovery of placental microRNAs (miRNAs) in maternal serum has opened up new possibilities for non-invasive prenatal diagnosis. However, the expression of miRNAs in the serum of pregnant women with fetuses with neural tube defects (NTDs) has not been characterized. In this article, we explored serum miRNAs as potential biomarkers in the serum of pregnant women with NTD fetuses. By using a miRNA microarray that covers 887 human miRNAs, we revealed 17 miRNAs with significant change in expression in serum of pregnant women with NTD fetuses and women with normal pregnancies. Quantitative reverse-transcription PCR (qRT-PCR) analysis validated that the expression for six miRNAs (miR-142-3p, miR-144, miR-720, miR-575, miR-765, and miR-1182) was up-regulated and that for miR-1275 was down-regulated. To determine whether these miRNAs were related to pregnancy, we compared the miRNA levels in pre- and post-delivery maternal serum samples. Six of these miRNAs were rapidly reduced in post-delivery serum (p < 0.05). Moreover, by receiver operating characteristic (ROC) curve analysis, the area under the ROC curve (AUC) of combining these six miRNAs was 0.803 (p < 0.001). Thus, we reveal six pregnancy-associated miRNAs that are deregulated in the serum of pregnant women with NTD fetuses and highlight the clinical potential of serum miRNAs as biomarkers for diagnosis and prognostication of fetal NTDs.
Usage Meets Link Analysis: Towards Improving Site Specific and Intranet Search via Usage Statistics (2004)

In this paper, we explore the possibility of incorporating usage statistics to improve ranking quality in site specific and intranet search engines. We introduce a number of usage based ranking approaches including a PageRank extension, Usage aware PageRank (UPR), an extension to HITS (UHITS), and a naïve approach that uses number of visits to pages as a quality measure. We compare these methods against each other and against two major link analysis approaches (PageRank and HITS). We investigate weighting schemes that take into account the probability of visiting a page directly (by typing or via bookmarks), as well as the relative probability of following a particular link from a given page. Both of these probabilities can be approximated from usage logs. We developed a site specific search engine