gebhart/patrepeval huggingface dataset:
T cell knockout mice have diminished alveolar bone loss after oral infection withPorphyromonas gingivalis (2002)

Periodontal diseases are chronic inflammatory diseases that can result in resorption of the alveolar bone of the jaw. We have developed a murine model in which alveolar bone loss is induced by oral infection with Porphyromonas gingivalis, an oral anaerobic bacterium associated with periodontal disease in humans. Here we compared a strain of immunocompetent mice (C57BL/6J) to the same strain of mice made T cell deficient by genetic deletion of the alpha chain of their T cell receptors (C57BL/6J-Tcra). T cell deficiency did not affect the ability of P. gingivalis to implant in the oral cavity. The two strains of mice had equal percentages of P. gingivalis among their cultivable anaerobes 7 weeks after infection. The same bacterial load led to much less bone resorption in the T cell deficient mice than in the immune normal mice, measured as either the number of sites with significant loss, or as the total amount of bone resorbed. T cell deficient mice lost bone at only three out of 14 measurement sites, compared with eight out of 14 sites in the wild-type mice. The total amount of bone lost was 70% less in the T cell deficient mice. T cell deficient mice had lower titers of P. gingivalis-specific IgG than the wild-type mice after oral infection did, but the same titers of specific IgA. Lower titers did not correlate with greater bone loss. Antigen-activated T lymphocytes are known to induce osteoclastogenesis; here we demonstrate that T cell deletion decreases the amount of alveolar bone loss induced by infection of the murine oral cavity.
Evaluation of Several Minor Alkaloid Levels in Tobacco with Separation of R- and S-Nornicotine (2013)

Abstract The chiral separation of minor alkaloids from tobacco is of interest because R and S isomers of these compounds have differences in their physiological activity. This difference is also reflected in the physiological properties of tobaccospecific N ’-nitrosamines (TSNAs), in particular that of N ’-nitrosonornicotine. This compound results mainly from nornicotinenitrosation. The previously reported analytical techniques for the enantiomer separation of minor alkaloids have various shortcomings, such as the need for bidimensional chromatography or poor enantiomer separation. A new method for the analysis of nornicotine, anabasine and anatabine has been developed, based on an original derivatization and a simple gas chromatography/ mass spectrometry (GC/MS) analysis. The method allows separate quantitation of S-nornicotine and R-nornicotine, and the analysis of anabasine and anatabine (without isomer separation). It was found that the proportion of S-nornicotine in the total nornicotine present in tobacco varies, depending on the tobacco type, between 52.6% for a flue-cured tobacco to 91.4% for a Burley. Green tobaccos (freeze dried) showed lower levels of minor alkaloids and S-nornicotine accounted for between 31.6% to 43.8% of the total nornicotine (in the analyzed samples).
Max-margin latent feature relational models for entity-attribute networks (2014)

Link prediction is a fundamental task in statistical analysis of network data. Though much research has concentrated on predicting entity-entity relationships in homogeneous networks, it has attracted increasing attentions to predict relationships in heterogeneous networks, which consist of multiple types of nodes and relational links. Existing work on heterogeneous network link prediction mainly focuses on using input features that are explicitly extracted by humans. This paper presents an approach to automatically learn latent features from partially observed heterogeneous networks, with a particular focus on entity-attribute networks (EANs), and making predictions for unseen pairs. To make the latent features discriminative, we adopt the max-margin idea under the framework of maximum entropy discrimination (MED). Our maximum entropy discrimination joint relational model (MED-JRM) can jointly predict entity-entity relationships as well as the missing attributes of entities in EANs. Experimental results on several real networks demonstrate that our model has improved performance over state-of-the-art homogeneous and heterogeneous network link prediction algorithms.
Transparency in Human-Machine Mutual Action (2021)

Recent advances in human-computer integration (HInt) have focused on the development of human-machine systems, where both human and machine autonomously act upon each other. However, a key challenge in designing such systems is augmenting the user’s physical abilities while maintaining their sense of self-attribution. This challenge is particularly prevalent when both human and machine are capable of acting upon each other, thereby creating a human-machine mutual action (HMMA) system. To address this challenge, we present a design framework that is based on the concept of transparency . We define transparency in HInt as the degree to which users can self-attribute an experience when machines intervene in the users’ action. Using this framework, we form a set of design guidelines and an approach for designing HMMA systems. By using transparency as our focus, we aim to provide a design approach for not only achieving human-machine fusion into a single agent, but also controlling the degrees of fusion at will. This study also highlights the effectiveness of our design approach through an analysis of existing studies that developed HMMA systems. Further development of our design approach is discussed, and future prospects for HInt and HMMA system designs are presented.
Influence of initial vaccination with 13-valent pneumococcal conjugate vaccine or 23-valent pneumococcal polysaccharide vaccine on anti-pneumococcal responses following subsequent pneumococcal vaccination in adults 50 years and older (2013)

In adults 50 to 64 years of age, initial vaccination with PCV13 establishes an immune state that results in recall anti-pneumococcal responses upon subsequent vaccination with either conjugated or free polysaccharide vaccine. In contrast, initial vaccination with PPSV23 results in an immune state in which subsequent PPSV23 administration yields generally lower responses compared with the initial responses.
Three-dimensional numerical simulations of synthetic jet actuator flows in a microchannel (2004)

The flow produced by a synthetic jet actuator located in one wall of a microchannel is investigated using computational l1uid dynamics (CFD) simulations.In the case of no cross-flow, the ejected vortices travel to the opposite wall and replenish the remains of the vortex left behind from the previous cycle.When cross-flow is added, the vortex penetration increases with both stroke length and frequency.The flow in the cavity appears to be nearly symmetrical.with the greatest effect seen near the orifice.In the orifice itself, three-dimensional effects are more noticeable with decreasing jet-to-cross-flow momentum ratio.The microchannel cross-flow causes the vortices to tumble about their transverse axis, the effect of which also increases with decreasing jet-to-cross-flow momentum ratio.
Hot Rolled High Strength Steels for Suspension and Chassis Parts NANOHITEN and BHT® Steel (2007)

Since hot rolled steel sheets for automobile suspension and chassis parts are frequently formed by burring, materials for these applications must possess hole expansionability as well as high strength. “NANOHITEN” is a type of precipitation hardened steel with a soft ferrite single phase matrix and ultra-fi ne carbides of single nanometer size which successfully satisfi es both strength and hole expansionability requirements. “BHT ® steel” achieves a very large increase in tensile strength in baking treatment utilizing the strain aging effect of N, which has a high solubility limit. As a result, strength after forming is on virtually the same level as when conventional materials with higher strength levels are used.
The chemical synthesis of the GstI protein by NCL on a X‐Met site (2006)

The small GstI protein (63 amino acids) of Rhizobium leguminosarum is the endogenous inhibitor of the glnII (glutamine synthetase II) gene expression. It has been suggested that GstI has a predominantly beta-structure and mediates the block of translation and stabilization of glnII mRNA through direct binding to its 5' untranslated region. Because of the unavailability of adequate amounts of purified recombinant protein, the mechanism as well as the protein tridimensional structure remain very poorly understood. To obtain the full-length protein, we have undertaken the chemical synthesis of the protein by different approaches. In a first attempt, the stepwise synthesis was unsuccessful, with strong aggregation experienced on the N-terminal side, after residue 44 from the C-terminus. In a second approach, we set up the conditions to carry out a native chemical ligation (NCL). Albeit the protein contains two Cysteine residues, located at positions 40 and 47, to minimize the size of the N-terminal segment to be synthesized, we have devised an alternative strategy of ligation on Met32, utilizing homoCys as the ligating moiety and then alkylating the resulting polypeptide with methyl iodide. New conditions to quantitatively methylate thiol groups in complex polypeptides have been conceived, obtaining the protein in very good yields and purity. A CD spectroscopy investigation has revealed that the protein does not adopt canonical secondary structures but is very rich in beta-structure (approximately 60%), in agreement with a previous study carried out on samples obtained by recombinant methods.
A low mode confinement integrated waveguide platform for high resolution displacement sensing (2013)

We demonstrate an integrated waveguide technology and apply it to displacement sensing. The waveguide consists of a 175 nm thick Si3N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> core layer with a 3,000 nm SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> bottom cladding and exhibits a large evanescent field. Although the nanophotonic waveguides feature sub-X/4 vertical confinement, they are fabrication tolerant with micron-scale lateral features. The technology enables complex photonic circuits without electron-beam lithography, which is commonly required for silicon nanophotonics. An unbalanced Mach-Zehnder interferometer is demonstrated in which the presence of an optical fiber near the waveguide surface induces a phase shift, which correlates with the fiber's position. We discuss future work and prospects for high-resolution displacement sensing.
Blood-based monitoring identifies acquired and targetable driver HER2 mutations in endocrine-resistant metastatic breast cancer (2019)

Plasma genotyping identifies potentially actionable mutations at variable mutant allele frequencies, often admixed with multiple subclonal variants, highlighting the need for their clinical and functional validation. We prospectively monitored plasma genotypes in 143 women with endocrine-resistant metastatic breast cancer (MBC), identifying multiple novel mutations including <i>HER2</i> mutations (8.4%), albeit at different frequencies highlighting clinical heterogeneity. To evaluate functional significance, we established ex vivo culture from circulating tumor cells (CTCs) from a patient with <i>HER2</i>-mutant MBC, which revealed resistance to multiple targeted therapies including endocrine and CDK 4/6 inhibitors, but high sensitivity to neratinib (IC50: 0.018 μM). Immunoblotting analysis of the <i>HER2</i>-mutant CTC culture line revealed high levels of HER2 expression at baseline were suppressed by neratinib, which also abrogated downstream signaling, highlighting oncogenic dependency with HER2 mutation. Furthermore, treatment of an index patient with <i>HER2</i>-mutant MBC with the irreversible HER2 inhibitor neratinib resulted in significant clinical response, with complete molecular resolution of two distinct clonal <i>HER2</i> mutations, with persistence of other passenger subclones, confirming HER2 alteration as a driver mutation. Thus, driver <i>HER2</i> mutant alleles that emerge during blood-based monitoring of endocrine-resistant MBC confer novel therapeutic vulnerability, and ex vivo expansion of viable CTCs from the blood circulation may broadly complement plasma-based mutational analysis in MBC.
Time-dependent depolarization of aligned HD molecules (2008)

An aligned sample of HD(v = 1, J = 2, M(J) = 0) molecules is prepared under collision-free conditions using the S(0) stimulated Raman pumping transition. Subsequent coupling to the spins of the deuteron I(D) and the proton I(H) causes the initial degree of alignment to oscillate and decrease as monitored over the time range from 0-13 mus via the O2 line of the [2 + 1] REMPI E,F(1)Sigma-X(1)Sigma (0,1) band. The time dependence of the rotational alignment is also calculated using both a hierarchical coupling scheme in which the rotational angular momentum J is regarded first to couple to I(D), and then the resultant F(i) to couple to I(H), to form the total angular momentum F and a non-hierarchical coupling scheme in which the HD energy level structure is not assumed to be diagonal in the |I(H)(JI(D))F(i)FM(F)> basis set. The experimental data is in good agreement with the non-hierarchical calculation but not with the hierarchical calculation, as expected for this system. Additionally, we calculate the time dependence of the H and D nuclear spin polarizations.
RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application (2019)

There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here, we introduce an open source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying retrosynthetic transformations encoded as SMARTS strings. RDChiral is designed to enforce the introduction, destruction, retention, and inversion of tetrahedral centers as well as the cis/trans chirality of double bonds. We also introduce an open source implementation of a retrosynthetic template extraction algorithm to generate SMARTS patterns from atom-mapped reaction SMILES strings. In this manuscript, we describe the implementation of these two pieces of code and illustrate their use through many examples.The two .json.gz files can be generated from the open source USPTO data available at https://figshare.com/articles/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873 using the code contained in the rdchiral GitHub repository. They are placed here for convenience if you would prefer to copy them into the templates/data subfolder instead of creating them from the source .rsmi file.
Characteristics of CO<sub>2</sub> Laser Welded 800MPa Grade TRIP Steel (2004)

The effect of welding conditions on defects, microstructure, mechanical properties and formability of CO 2 welded 800MPa grade TRIP steel was investigated. Bead-on-plate welding was carried out under the various welding speed in 6kW with a shield gas of Helium. Extensive porosity was observed in the joints produced at a 4m/min of welding speed but was not observed in the joints when a welding speed greater than 6m/min was used. The maximum hardness was obtained at the weld metal and the HAZ near the weld metal and was the same regardless of the welding speed. The HAZ hardness near the base metal was reduced due to retained ferrite but was higher than that of the base metal. In a parallel tensile test to weld axis, the strength of the joints was higher than that of the base metal. Elongation was found to be lower than that of the raw material because a crack was initiated in the bead at the strength levels corresponding to the tensile strength of the base metal and was propagated perpendicular to tensile direction. The formability of joints was found to be 63% that of the raw material.
Non-linear registration improves statistical power to detect hippocampal atrophy in aging and dementia (2019)

Non-linear registration methods were most consistent in determining hippocampal atrophy and because of their better reproducibility, methods, such as ANTs, Elastix and NiftyReg, are preferred for determining hippocampal atrophy rates on longitudinal MRI. Since performances of non-linear registration methods are well comparable, the preferred method would mostly depend on computational efficiency.
Oxidation of Sulphides by Molecular Oxygen - Aldehyde System in the Absence of Metal Catalyst (1998)

Abstract Molecular Oxygen/2-methylpropanal system provides a simple, efficient, and environmentally acceptable synthetic tool to convert sulphides to sulphones in near quantitative yields and to sulphoxides in high selectivity and good yields under ambient conditions.
<title>A Monolithic Piezo-Electric Elasto-Optic Image Modulator</title> (1983)

A novel approach to electro-optical image manipulation was presented previously. The main advantage of this approach being the mapping of the two dimensional spatial Fourier transform into the temporal domain. This transformation is achieved in real time by using the image modulator whose dynamic optical transmittance at each pixel is given by:
Graph cuts is a max-product algorithm (2011)

The maximum a posteriori (MAP) configuration of binary variable models with submodular graph-structured energy functions can be found efficiently and exactly by graph cuts. Max-product belief propagation (MP) has been shown to be suboptimal on this class of energy functions by a canonical counterexample where MP converges to a suboptimal fixed point (Kulesza &amp;amp; Pereira, 2008). In this work, we show that under a particular scheduling and damping scheme, MP is equivalent to graph cuts, and thus optimal. We explain the apparent contradiction by showing that with proper scheduling and damping, MP always converges to an optimal fixed point. Thus, the canonical counterexample only shows the suboptimality of MP with a particular suboptimal choice of schedule and damping. With proper choices, MP is optimal. 1
CT diagnosis of adrenal abnormalities in patients with primary non-adrenal malignancies. (1986)

Fifty-seven patients with primary non-adrenal malignancy were found to have unsuspected adrenal abnormality on CT. In 33, comparison of histopathologic findings and/or the patients' hospital course or follow-up lead to the diagnosis of adrenal metastases (23), benign non-functioning adenomas (7), metastasis with hyperplasia (1), benign hyperplasia (1), and fatty infiltration (1). The analysis of CT findings indicated that: I) A heterogeneous adrenal mass showing contrast enhancement was always metastatic, II) Nonfunctioning adenomas were always 3 cm or smaller in diameter, III) Bilateral adrenal masses and growth of adrenal mass on follow-up CT or regression on treatment indicated metastases, and IV) metastatic disease could not be excluded purely on the basis of the size of the adrenal mass.
Approximate scalar finite-element beam-propagation method with perfectly matched layers for anisotropic optical waveguides (2001)

The perfectly matched layer boundary condition for arbitrary anisotropic media is incorporated into the approximate scalar beam propagation method. The procedure is based on a finite-element method for three-dimensional anisotropic optical waveguides with off-diagonal elements in a permittivity tensor. In order to treat a wide-angle beam propagation, the Pade approximant operator is employed. To show the validity and usefulness of this approach, numerical results are presented for Gaussian beam propagation in free space and Gaussian beam excitation on a three-dimensional anisotropic optical waveguide.
Respiration and germination rates of tomato seeds at suboptimal temperatures and reduced water potentials (1996)

Suboptimal temperature (T) affects germination rates (reciprocal of time to radicle emergence) on a thermal time basis; that is, the T in excess of a base or minimum temperature multiplied by the time to a given per cent germination [tg) is a constant. Respiration rates are also sensitive to T, and proportional relationships are often found between respiration rates and germination rates. Reduced water potential (ψ) delays seed germination on a hydrotime basis (i.e. the ψ in excess of a base water potential multiplied by tg is a constant). It was tested whether respiration rates prior to radicle emergence vary in proportion to T and ψ as expected from the thermal and hydrotime models. Respiration rates (C02 evolution) of cold-tolerant, rapidly germinating (PI 341988) and cold-sensitive, more slowly germinating (T5) tomato [Lycopersicon esculentum Mill.) seeds were evaluated over a range of T and ψ conditions. For both genotypes, respiration rates until the beginning of radicle emergence were related to T on a thermal time basis and increased approximately linearly with ψ above -2.0 MPa, consistent with the hydrotime model. Respiration rates were uniquely related to germination rates, regardless of whether germination timing was affected by T, ψ, or genotype. However, germination timing was unaffected when respiration rates were manipulated by varying 02 partial pressure. Thus, while both germination and respiration rates vary with T and ψ consistent with thermal and hydrotime models of biological time, respiration rates per se were not the limiting factor in germination timing of tomato seeds.
Proteolytic activation of a bioactive cardiac peptide by in vitro trypsin cleavage. (1984)

Mammalian cardiac atria possess several unidentified biologically active peptides. Fractionation of rat atrial extracts by gel filtration chromatography revealed two major fractions [apparent molecular weights of 20,000-30,000 (peak I) and less than 10,000 (peak II)], both of which were potent natriuretic agents (eliciting a 25-fold increase in sodium excretion) and smooth muscle relaxants. Vigorous treatment with trypsin (100 units/ml at 37 degrees C for 15 min) of both fractions abolished all biological activity. Further purification of the lower molecular weight fraction (peak II) by ion-exchange chromatography indicated two subfractions that possessed potent natriuretic activity and that preferentially relaxed either intestinal (designated peak IIA) or vascular (peak IIB) smooth muscle assay tissues. The similarity of the biological effect of the high (peak I) and low (peak II) molecular weight peptides led us to test the possibility of precursor-product relationship. Mild proteolytic treatment of the high molecular weight peptide with trypsin (1 unit/ml at room temperature) markedly enhanced the smooth muscle relaxant activity. Subsequent analysis of the trypsin (1 unit/ml)-treated high molecular weight peptide (peak I) by gel filtration and ion-exchange chromatography revealed that the peptide now resembled the low molecular weight peptides (peaks IIA and IIB) present in the original atrial extract. These data suggest that the cardiac atria contain a relatively inactive (smooth muscle relaxant) high molecular weight peptide and suggest that biologically active low molecular weight peptides can subsequently be generated by proteolytic cleavage.
Quantitative proton magnetic resonance spectroscopic imaging: Regional variations in the corpus callosum and cortical gray matter (2005)

Metabolite concentrations, particularly Cho, showed strong regional variations both within cortical gray matter regions and between the genu and splenium of the corpus callosum. Mesial frontal regions showed the highest Cho signals. Differences in spectra presumably reflect underlying changes in structure and cellular composition. Normal spectral variations should always be considered when evaluating pathology within those brain regions.