gebhart/patrepeval huggingface dataset:
GIVING MEANINGFUL INTERPRETATION TO ORDINATION AXES: ASSESSING LOADING SIGNIFICANCE IN PRINCIPAL COMPONENT ANALYSIS (2003)

Principal component analysis (PCA) is one of the most commonly used tools in the analysis of ecological data. This method reduces the effective dimensionality of a multivariate data set by producing linear combinations of the original variables (i.e., components) that summarize the predominant patterns in the data. In order to provide meaningful interpretations for principal components, it is important to determine which variables are associated with particular components. Some data analysts incorrectly test the statistical significance of the correlation between original variables and multivariate scores using standard statistical tables. Others interpret eigenvector coefficients larger than an arbitrary absolute value (e.g., 0.50). Resampling, randomization techniques, and parallel analysis have been applied in a few cases. In this study, we compared the performance of a variety of approaches for assessing the significance of eigenvector coefficients in terms of type I error rates and power. Two novel approaches based on the broken-stick model were also evaluated. We used a variety of simulated scenarios to examine the influence of the number of real dimensions in the data; unique versus complex variables; the magnitude of eigenvector coefficients; and the number of variables associated with a particular dimension. Our results revealed that bootstrap confidence intervals and a modified bootstrap confidence interval for the broken-stick model proved to be the most reliable techniques.
Development of Autoantibody Signatures as Novel Diagnostic Biomarkers of Non–Small Cell Lung Cancer (2010)

Abstract Purpose: To select autoantibody signatures as noninvasive biomarkers of non–small cell lung cancer (NSCLC). Experimental Design: A phage cDNA expression library was constructed with fresh samples from 30 lung cancer patients and biopanned using serum pools of 10 NSCLC patients and 10 healthy controls. A six–phage peptide detector was discovered by two-step immunoscreenings and was validated in an independent set of 90 NSCLC patients and 90 matched healthy controls, 30 NSCLC patients with chemotherapy, and 12 chronic obstructive pulmonary disease (COPD) patients. The expression of a peptide target was validated by using immunohistochemistry. Factors affecting NSCLC-related death were evaluated by Cox regression analysis. Results: Six phage peptide clones showing higher seroreactivity than others in 30 NSCLC patients were selected for diagnostic validation. The six–phage peptide detector was able to discriminate between NSCLC patients and healthy controls with a sensitivity and specificity of &amp;gt;92%, and had similar validity for indicating NSCLC at early stage. The seroreactivity of the six phage peptides was significantly higher in the NSCLC patients than in those with chemotherapy and the COPD patients, respectively. Of the six phage peptides, one encoded a peptide showing 100% homology to olfactomedin 1. Expression of olfactomedin 1 protein was significantly higher in lung adenocarcinoma than in lung cancer of other histologic types and normal lung tissues. The autoantibody signature was not associated with the prognosis of the NSCLC patients. Conclusions: The six–phage peptide detector stands out as promising diagnostic biomarkers for NSCLC, unlikely for NSCLC relapse after chemotherapy. Olfactomedin 1 may be a novel target of lung adenocarcinoma. Clin Cancer Res; 16(14); 3760–8. ©2010 AACR.
Map-based lane identification and prediction for autonomous vehicles (2014)

A novel map-based lane identification and prediction algorithm is developed to characterize areas around an autonomous robot as it travels in an obstacle strewn and rugged roadway environment. The implementation of this algorithm employs probabilistic and heuristic methods to improve the placement of lane features, whose location is uncertain due do to vehicle motion and sensor data ambiguity. The resulting map can be effectively used for local and regional path planning and navigation. The algorithm uses data acquired from a LIDAR, compass, GPS, wheel encoders, and camera images.
Focal Atrial Fibrillation: Experimental Evidence for a Pathophysiologic Role of the Autonomic Nervous System (2001)

High-frequency electrical stimulation evokes rapid ectopic beats from the PV/SVC, which show variable degrees of conduction block to the atria and induce AF, resembling findings in patients with focal idiopathic paroxysmal AF. The occurrence of the arrhythmia in this animal model was likely due to alterations in local autonomic tone by high-frequency electrical stimulation. Further research is needed to prove absolutely that the observed effects of high-frequency electrical stimulation were caused by autonomic nerve stimulation.
A 90-Kilodalton Endothelial Cell Molecule Mediating Lymphocyte Binding in Humans (1992)

Interactions between leukocyte surface receptors and their ligands on vascular endothelial cells control lymphocyte traffic between the blood and various lymphoid organs, as well as extravasation of leukocytes into sites of inflammation. A heretofore undescribed 90-kilodalton human endothelial cell adhesion molecule (VAP-1) defined by a monoclonal antibody 1B2 is described. The expression pattern, molecular mass, functional properties, and an amino-terminal amino acid sequence define VAP-1 as an endothelial ligand for lymphocytes. VAP-1 helps to elucidate the complex heterotypic cell interactions that direct tissue-selective lymphocyte migration in man.
Nanofibers Support Oligodendrocyte Precursor Cell Growth and Function as a Neuron-Free Model for Myelination Study (2013)

Nanofiber-based scaffolds may simultaneously provide immediate contact guidance for neural regeneration and act as a vehicle for therapeutic cell delivery to enhance axonal myelination. Additionally, nanofibers can serve as a neuron-free model to study myelination of oligodendrocytes. In this study, we fabricated nanofibers using a polycaprolactone and gelatin copolymer. The ratio of the gelatin component in the fibers was confirmed by energy dispersive X-ray spectroscopy. The addition of gelatin to the polycaprolactone (PCL) for nanofiber fabrication decreased the contact angle of the electrospun fibers. We showed that both polycaprolactone nanofibers as well as polycaprolactone and gelatin copolymer nanofibers can support oligodendrocyte precursor cell (OPC) growth and differentiation. OPCs maintained their phenotype and viability on nanofibers and were induced to differentiate into oligodendrocytes. The differentiated oligodendrocytes extend their processes along the nanofibers and ensheathed the nanofibers. Oligodendrocytes formed significantly more myelinated segments on the PCL and gelatin copolymer nanofibers than those on PCL nanofibers alone.
Serum and nasal wash antibodies associated with resistance to experimental challenge with influenza A wild-type virus (1986)

To identify immunological predictors of resistance to influenza A infection and illness, the immunological status of live and inactivated virus vaccines subsequently challenged with H1N1 or H3N2 wild-type virus was examined. We refer to prechallenge antibodies of vaccinees receiving live attenuated virus as infection induced and those receiving inactivated virus as inactivated vaccine induced. Inactivated vaccine-induced protection against wild-type virus infection or illness correlated with the level of neuraminidase-inhibiting antibody in serum, local hemagglutinin immunoglobulin G (IgG) (but not IgA) enzyme-linked immunosorbent assay antibody, and hemagglutination-inhibiting antibody in serum. In contrast, infection-induced resistance to wild-type virus infection correlated with local hemagglutinin IgA antibody and neuraminidase-inhibiting antibody in serum, but not with hemagglutination-inhibiting antibody in serum. These observations suggest that live vaccine virus infection-induced and inactivated vaccine-induced immunity may involve different compartments of the immune system; sufficient antibody in either serum or nasal secretions is capable of conferring resistance.
Localization of the 92 kd gelatinase mRNA in squamous cell and adenocarcinomas of the lung using in situ hybridization. (1994)

We have used in situ hybridization for RNA to localize cells containing mRNA for the 92 kd gelatinase in carcinomas of the lung. We used archival material to analyze sections from 12 cases of squamous cell carcinomas of the lung including six stage I and three stage II and from three cases of adenocarcinoma of the lung. Presence of mRNA in the tissue was verified by in situ hybridization for gamma actin. The 92 kd gelatinase mRNA was found in all 12 squamous cell carcinomas tumors and was highly expressed in the tumor cells themselves. In addition, it was found in host stromal cells surrounding the tumor, but not in normal lung fibroblasts. In contrast it was not found in the adenocarcinomas of the lung or in the stroma surrounding these tumors. The mRNA for the 92 kd gelatinase was present in normal pulmonary tissue, bronchial epithelium, basal cell hyperplasia of bronchial epithelium, alveolar macrophages, and focally in bronchial mucous glands. It was not present in normal alveoli, vascular cells, cartilage, or most lymphocytes. We corroborated the presence of the mRNA for the 92 kd gelatinase by ribonuclease protection assay. The levels of mRNA for the 92 kd gelatinase in two specimens of squamous cell carcinoma were 6- to 10-fold greater than in the nonneoplastic tissue and two adenocarcinoma specimens.
Discovery and Structure−Activity Relationship of the First Non-Peptide Competitive Human Glucagon Receptor Antagonists (1998)

The first non-peptide competitive human glucagon receptor antagonist, 2-(benzimidazol-2-ylthio)-1-(3,4-dihydroxyphenyl)-1-ethan one, NNC 92-1687 (2), is described. This antagonist has a binding affinity of 20 microM (IC50) and a functional Ki = 9.1 microM at the human glucagon receptor. A structure-activity relationship (SAR) was obtained on this compound, and the results show that only the benzimidazole part can be changed without complete loss of affinity. Analogues with tert-butyl or benzyloxy groups in the 5-position of the benzimidazole moiety were found to be equipotent or slightly more potent, all displaying binding affinities around 5-20 microM. Most of the changes to the catechol and the linker gave compounds without any affinity toward the human glucagon receptor. The 3-hydroxy group could, however, in the presence of a 4-hydroxy group be changed to a methoxy or a chloro group while retaining affinity.
Invasiveness of human endometrial stromal cells is promoted by decidualization and by trophoblast-derived signals (2010)

Enhanced motility and invasive capacity of decidualized ESCs in the presence of trophoblastic cells lead us to hypothesize a major contribution of the decidua in encapsulating the early conceptus and supporting subsequent trophoblast invasion. Our findings thus suggest a far more active role of the decidua in the implantation process than hitherto recognized.
The synthesis of perloline, 6-(3,4-Dimethoxyphenyl)-5-hydroxy-5,6-dihydrobenzo[c]-[2,7]naphthyridin-4(3H)-one (1983)

Dehydroperloline is obtained in high overall yield by an intramolecular cyclization of the benzyne generated from 4-(2-bromophenyl)- N -(3,4-dimethoxyphenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide (21), by use of lithium hexamethyldisilazide. A benzyne intermediate has not been established. The pyridinone (21) was prepared in three steps from 2-[1-(2-bromophenyl)ethylidene]malononitrile.&amp;nbsp;Dehydroperloline was smoothly reduced by sodium bis(methoxyethoxy)aluminium hydride to perloline, isolated as its hydrochloride.
A CCD color signal separation IC for single-chip color imagers (1984)

A CCD color signal separation IC for solid-state imagers with color filter arrays is described. The device simplifies peripheral circuitry and enhances picture qualities such as resolution, color fidelity, and stability for single-chip color imaging systems by incorporating CCD delay lines, sample-and-hold circuits, and dual clamp circuit. Also described is a color filter array utilizing Bayer geometry, which is used in the separation IC. Color images corresponding to a horizontal resolution of 340 TV lines with no erroneous color have been obtained from the device when used with a 580/spl times/475 element CCD imager.
Fast adiabatic qubit gates using onlyσzcontrol (2014)

A controlled-phase gate was demonstrated in superconducting Xmon transmon qubits with fidelity reaching 99.4%, relying on the adiabatic interaction between the $|11\ensuremath{\rangle}$ and $|02\ensuremath{\rangle}$ states. Here we explain the theoretical concepts behind this protocol, which achieves fast gate times with only ${\ensuremath{\sigma}}_{z}$ control of the Hamiltonian, based on a theory of nonlinear mapping of state errors to a power spectral density and use of optimal window functions. With a solution given in the Fourier basis, optimization is shown to be straightforward for practical cases of an arbitrary state change and finite bandwidth of control signals. We find that errors below ${10}^{\ensuremath{-}4}$ are readily achievable for realistic control wave forms.
Cross-reactivity of anti-DNA antibodies with proteoglycans. (1984)

Ten sera of patients with systemic lupus erythematosus (SLE) were tested in an enzyme linked immunosorbent assay for their ability to react with glycosaminoglycans, constituents of proteoglycans, in relation to their anti-DNA reactivity. The SLE sera reacted with hyaluronic acid and chondroitin sulphate and this reactivity correlated with the anti-DNA activity of these sera. By contrast, sera obtained from patients with other autoimmune diseases or normal sera lacked any of these reactivities. Anti-DNA antibodies purified by affinity chromatography with either oligo dT cellulose or Cibracon blue F3Ga Sepharose reacted with DNA as well as with hyaluronic acid. The cross-reactivity of anti-DNA antibodies could be confirmed by the reaction of a mouse monoclonal anti-DNA antibody with DNA, hyaluronic acid, and chondroitin sulphate. This pattern of cross-reactivities of anti-DNA antibodies suggests that several compounds can function as antigenic targets for these antibodies provided that their structures contain repeating negatively charged groups.
IgG autoantibodies to complement C1q in pediatric-onset systemic lupus erythematosus. (1997)

Antibodies to C1q were frequently positive in our patients with pediatric SLE and were correlated with laboratory variables of disease activity. However, unlike in adults with SLE, a high correlation between aC1q and glomerulonephritis was not found in these pediatric patients.
Comprehensive Genomic Profiling Facilitates Implementation of the National Comprehensive Cancer Network Guidelines for Lung Cancer Biomarker Testing and Identifies Patients Who May Benefit From Enrollment in Mechanism-Driven Clinical Trials (2016)

National Comprehensive Cancer Network guidelines for patients with metastatic non-small cell lung cancer (NSCLC) recommend testing for several genomic alterations (GAs). The feasibility and utility of comprehensive genomic profiling were studied in NSCLC and in lung adenocarcinoma (AD) without GAs. Of patients with NSCLC, 71% harbored at least one GA to a gene listed in the guidelines or KRAS; 273 cancer-related genes were altered in at least 0.1% of the AD cases. Although logistical and administrative hurdles limit the widespread use of next-generation sequencing, the data confirm the feasibility and potential utility of comprehensive genomic profiling in clinical practice.
Differential expression of muscular dystrophy in diaphragm versus hindlimb muscles of mdx mice (1992)

Contractile properties of diaphragm (DIA) from mdx and control mice were compared with those of hindlimb muscles [soleus (SOL) and extensor digitorum longus (EDL)] in vitro. Mice ranged in age from 2 weeks to 1.5 years. Muscles were directly stimulated and properties measured were: contraction time, half-relaxation time, active tension per unit area, fatigue index, and maximal velocity of shortening (Vmax). Active tension decreased significantly with age in mdx DIA but not in control DIA. SOL and EDL active tensions were less in mdx than control over the whole age range and did not decrease with age. Vmax was decreased in mdx DIA, but not in mdx SOL or EDL. These results demonstrate that DIA is more affected by muscular dystrophy than hindlimb muscles. Since many Duchenne patients exhibit respiratory distress, this differential expression of dystrophy in diaphragm, as compared to limb muscles, may have important clinical implications.
Identification of a human cDNA encoding a functional high affinity lipoxin A4 receptor. (1994)

Lipoxin A4 (LXA4) triggers selective responses with human neutrophils that are pertussis toxin sensitive and binds to high affinity receptors (Kd = 0.5 +/- 0.3 nM) that are modulated by stable analogues of guanosine 5'-triphosphate (GTP). Here, we characterized [11,12-(3)]LXA4 specific binding with neutrophil granule and plasma membranes, which each display high affinity binding sites (Kd = 0.7 +/- 0.1 nM) that were regulated by GTP gamma S. Since functional LXA4 receptors are inducible in HL-60 cells, we tested orphan cDNAs encoding 7-transmembrane region receptors cloned from these cells for their ability to bind and signal with LXA4. Chinese hamster ovary (CHO) cells transfected with the orphan receptor cDNA (pINF114) displayed specific 3H-LXA4 high affinity binding (1.7 nM). When displacement of LXA4 binding with pINF114-transfected CHO cells was tested with other eicosanoids, including LXB4, leukotriene D4 (LTD4), LTB4, or prostaglandin E2, only LTD4 competed with LXA4, giving a Ki of 80 nM. In transfected CHO cells, LXA4 also stimulated GTPase activity and provoked the release of esterified arachidonate, which proved to be pertussis toxin sensitive. These results indicate that pINF114 cDNA encodes a 7-transmembrane region-containing protein that displays high affinity for 3H-LXA4 and transmits LXA4-induced signals. Together, they suggest that the encoded protein is a candidate for a LXA4 receptor in myeloid cells.
Antioxidant Activity of the Aqueous Extracts of Spicy Food Additives—Evaluation and Comparison with Ascorbic Acid in In Vitro Systems (2004)

The antioxidant activity of the aqueous extracts of five umbelliferous fruits-caraway (Carum carvi), coriander (Coriandrum sativum), cumin (Cuminum cyminum), dill (Anethum graveolens) and fennel (Foeniculum vulgare)-were investigated in comparison with the known antioxidant ascorbic acid in in vitro studies. The amount of aqueous extract of these five umbelliferous fruits and ascorbic acid needed for 50% scavenging of superoxide radicals was found to be 105 μg (cara way), 370 μg (coriander), 220 μg (cumin), 190 μg (dill), 205 μg (fennel) and 260 μg (ascorbic acid). The amount needed for 50% inhibition of lipid peroxide was 2100 μg (caraway), 4500 μg (coriander), 4300 μg (cumin), 3100 μg (dill), 4600 μg (fennel) and 5000 μg (ascorbic acid). The quantity needed for 50% inhibition of hydroxyl radicals was 1150 μg (caraway), 1250 μg (coriander), 470 μg (cumin), 575 μg (dill), 700 μg (fennel) and 4500 μg (ascorbic acid). The daily use of the above fruits in various forms is very common in India and the present study revealed strong antioxidant activity of their extracts that was superior to known antioxidant ascorbic acid and indicate their intake may be beneficial as food additives.
Immune system and peripheral nerves in propagation of prions to CNS (2003)

Prions are not only unique in the way they replicate. Also the sequence of events triggered by peripheral prion infection, generically termed 'peripheral pathogenesis', sets prions aside from all other known pathogens. Whereas most bacteria, parasites, and viruses trigger innate and adaptive immune responses, the mammalian immune system appears to be remarkably oblivious to prions. Transmissible spongiform encephalopathies (TSEs) do not go along with inflammatory infiltrates, and antibodies to the prion protein are not typically raised during the course of the disease. On the other hand, there is conspicuous involvement of lymphoid organs, which accumulate sizeable concentrations of the infectious agent early during disease. Moreover, various states of immune deficiency can abolish peripheral pathogenesis and prevent 'take' of infection when prions are administered to peripheral sites. Here, we critically re-visit the current evidence for an involvement of the immune system in prion diseases, and will attempt to trace the elaborate mechanisms by which prions, upon entry into the body from peripheral sites, reach the brain.
Establishment of a simple assayin vitrofor hepatitis C virus NS3 serine protease based on recombinant substrate and single-chain protease (2002)

A simple and convenient assay in vitro for hepatitis C virus NS3 serine protease is based on recombinant substrate NS5ab and single-chain serine protease. This assay can be used in screening of enzyme inhibitors.
Effect of glycosylphosphatidylinositol (GPI)-phospholipase D overexpression on GPI metabolism (2004)

GPI-PLD [glycosylphosphatidylinositol (GPI)-specific phospholipase D (PLD)] is a secreted mammalian enzyme that specifically cleaves GPI-anchored proteins. In addition, the enzyme has been shown to cleave GPI anchor intermediates in cell lysates. The biosynthesis of the GPI anchor is well characterized; however, the mechanisms by which the levels of GPI anchor intermediates are regulated are still unknown. To investigate whether GPI-PLD plays a role in this regulation, we isolated stable HeLa cells overexpressing the enzyme. GPI-PLD-HeLa (GPI-PLD-transfected HeLa) cells showed a 3-fold increase in intracellular GPI-PLD activity and drastically decreased the levels of GPI-anchored proteins when compared with untransfected HeLa controls. Intracellular cleavage of GPI-anchored proteins has been suggested to occur early in the secretory pathway and, in agreement with this proposal, GPI-PLD activity in GPI-PLD-HeLa cells was detected not only in the endoplasmic reticulum and Golgi apparatus, but also in the plasma membrane. The enzyme was also active in lipid rafts, membrane microdomains in which GPI-anchored proteins and GPI anchor intermediates are concentrated, indicating that intracellular GPI-PLD cleavage may also occur in this compartment. Pulse-chase paradigms revealed the turnover rate of the last intermediate of the GPI anchor pathway in GPI-PLD-HeLa cells to be accelerated compared with the controls. Furthermore, 1,10-phenanthroline, a GPI-PLD inhibitor, reversed this effect. Our studies demonstrated that GPI-PLD can cleave not only GPI-anchored proteins, but also GPI anchor intermediates intracellularly. This observation opens the possibility that GPI-PLD can influence the steady-state levels of GPI-anchored proteins by hydrolysing the anchor before and after its attachment to proteins.