gebhart/patrepeval huggingface dataset:
Patients with unstable angina pectoris show an increased frequency of the Fc gamma RIIa R131 allele (2012)

Patients with Systemic Lupus Erythematosus (SLE) carry an increased risk for the development of coronary artery disease (CAD). The R131 allele of the Fc gamma receptor IIa (FcγRIIa) is associated with SLE incidence and disease severity but also with CAD. Compared to stable angina pectoris (SAP) the unstable angina (UAP), as a manifestation of destabilizing CAD, is associated with increased risk of persistent instability, myocardial infarction, and death. Identification of clinically relevant determinants for unstable angina promises reduction of UAP-associated mortality in patients with SLE. We conducted a clinical study among 553 consecutive patients with stable angina pectoris (n = 330) and unstable angina pectoris (n = 223). All patients were genotyped for a frequent functional variant at position 131 of the mature FcγRIIa. UAP, but not SAP was significantly associated with the R/R131 genotype (P < 0.001). In troponin-negative patients with angina carrying the R/R131 genotype the odds ratio for suffering from UAP was 4.02 (95% confidence interval, 2.52-6.41) compared to those with non-R/R131 genotypes. In a multivariable analysis, the R/R131 genotype independently predicted the risk for development of UAP in a model adjusted for classical atherogenic risk factors. Our data imply that risk stratification of SLE- and other high risk patients with troponin-negative angina could be significantly improved by FcγRIIa genotyping.
Reciprocity of exposure time and irradiance on energy density during photoradiation on wound healing in a murine pressure ulcer model (2007)

Varying irradiance and exposure time to achieve a specified energy density affects phototherapy outcomes in this model. Variation of exposure time and irradiance may account for conflicting results in the literature. Further studies of these effects are warranted.
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease (2016)

Abstract Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share patterns of transcriptional regulation. Accordingly, shared transcriptional regulation (coexpression) may help prioritise loci associated with a given trait, and help to identify the biological processes underlying it. Using cap analysis of gene expression (CAGE) profiles of promoter and enhancer-derived RNAs across 1824 human samples, we have quantified coexpression of RNAs originating from trait-associated regulatory regions using a novel analytical method (network density analysis; NDA). For most traits studied, sequence variants in regulatory regions were linked to tightly coexpressed networks that are likely to share important functional characteristics. These networks implicate particular cell types and tissues in disease pathogenesis; for example, variants associated with ulcerative colitis are linked to expression in gut tissue, whereas Crohn’s disease variants are restricted to immune cells. We show that this coexpression signal provides additional independent information for fine mapping likely causative variants. This approach identifies additional genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. This approach enables a deeper biological understanding of the causal basis of complex traits. ONE SENTENCE SUMMARY We discover that variants associated with a specific disease share expression profiles across tissues and cell types, enabling fine mapping and identification of new disease-associated variants, illuminating key cell types involved in disease pathogenesis.
Supplementary Figure 3 from Autotaxin and LPA<sub>1</sub> and LPA<sub>5</sub> Receptors Exert Disparate Functions in Tumor Cells versus the Host Tissue Microenvironment in Melanoma Invasion and Metastasis (2023)

&lt;p&gt;Supplementary Figure 3. (A) ATX and LPA receptor profiling in B16F10 cells transduced with GFP lentivirus using quantitative real-time PCR. Data are expressed as mean {plus minus} SD of an experiment performed twice in quadruplicates. (B) Representative images of lungs harvested at day 21 from mice that were injected with PBS (left panel, control) and mice that were injected with 1 x 105 GFP-expressing B16F10 cells (right panel). Arrow denotes a single fluorescent tumor nodule on lung surface. Scale bar = 200 microns.&lt;/p&gt;
Easy Way to Fabricate Nanostructures on a Reactive Polymer Surface (2009)

The fabrication of advanced architectures in poly(glycidylmethacrylate-co-styrene) (PGMA-S) copolymers using direct laser interference patterning (DLIP) and its selective functionalization is reported. The structure features depend mainly on the laser energy used and on the styrene content in the copolymer. The topography, measured by electronic scanning microscopy, show regular and ordered arrays for the polystyrene (PS) and for the copolymers PGMA-S. The surface PS homopolymer is ablated at the position of maximum light fluence (constructive interference), while in the copolymers the surfaces swell up at the regions with maximal fluence. The styrene units are shown to absorb the laser energy giving photothermally ablated regions or promoting the chemical decomposition of acrylate units or polymer segments. In that way, DLIP provides a unique way to produce regularly ordered structures protruding or depressing from the polymer surface without altering to a large extent the chemical nature of the material. In addition, it is shown, using fluorescence microscopy, that amine-polyethylenglycol-CdSe quantum dots (NH(2)-PEG-QDs) could be spatially localized by reaction with patterned surfaces of PGMA-S. In that way, it is proven that a patterned and chemically reactive surface can be created using DLIP of PGMA-S.
Referrals from general practice to hospital outpatient departments: a strategy for improvement. (1989)

This approach to determining the appropriateness of referrals benefits the general practitioners, the consultant, and the patient.
Inside information on xenon adsorption in porous organic cages by NMR (2017)

A solid porous molecular crystal formed from an organic cage, CC3, has unprecedented performance for the separation of rare gases. Here, xenon was used as an internal reporter providing extraordinarily versatile information about the gas adsorption phenomena in the cage and window cavities of the material. <sup>129</sup>Xe NMR measurements combined with state-of-the-art quantum chemical calculations allowed the determination of the occupancies of the cavities, binding constants, thermodynamic parameters as well as the exchange rates of Xe between the cavities. Chemical exchange saturation transfer (CEST) experiments revealed a minor window cavity site with a significantly lower exchange rate than other sites. Diffusion measurements showed significantly reduced mobility of xenon with loading. <sup>129</sup>Xe spectra also revealed that the cage cavity sites are preferred at lower loading levels, due to more favourable binding, whereas window sites come to dominate closer to saturation because of their greater prevalence.
The Chemokine-Based Peptide, CXCL9(74-103), Inhibits Angiogenesis by Blocking Heparan Sulfate Proteoglycan-Mediated Signaling of Multiple Endothelial Growth Factors (2021)

Growth factors such as vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF) and epidermal growth factor (EGF) are important angiogenesis-mediating factors. They exert their effects not only through their respective receptor tyrosine kinases (RTKs), but they also require molecular pairing with heparan sulfate proteoglycans (HSPGs). Angiogenic growth factors and their signaling pathways are commonly targeted in current anti-angiogenic cancer therapies but have unfortunately insufficient impact on patient survival. Considering their obvious role in pathological angiogenesis, HS-targeting drugs have become an appealing new strategy. Therefore, we aimed to reduce angiogenesis through interference with growth factor-HS binding and downstream signaling using a CXCL9-derived peptide with a high affinity for glycosaminoglycans (GAGs), CXCL9(74-103). We showed that CXCL9(74-103) reduced EGF-, VEGF165- and FGF-2-mediated angiogenic processes in vitro, such as endothelial cell proliferation, chemotaxis, adhesion and sprouting, without exerting cell toxicity. CXCL9(74-103) interfered with growth factor signaling in diverse ways, e.g., by diminishing VEGF165 binding to HS and by direct association with FGF-2. The dependency of CXCL9(74-103) on HS for binding to HMVECs and for exerting its anti-angiogenic activity was also demonstrated. In vivo, CXCL9(74-103) attenuated neovascularization in the Matrigel plug assay, the corneal cauterization assay and in MDA-MB-231 breast cancer xenografts. Additionally, CXCL9(74-103) reduced vascular leakage in the retina of diabetic rats. In contrast, CXCL9(86-103), a peptide with low GAG affinity, showed no overall anti-angiogenic activity. Altogether, our results indicate that CXCL9(74-103) reduces angiogenesis by interfering with multiple HS-dependent growth factor signaling pathways.
High-energy picosecond laser pulse recirculation for compton scattering (2007)

Frequency upconversion of laser-generated photons by inverse Compton scattering for applications such as nuclear spectroscopy and gamma-gamma collider concepts on the future ILC would benefit from an increase of average source brightness. The primary obstacle to higher average brightness is the relatively small Thomson scattering cross section. It has been proposed that this limitation can be partially overcome by use of laser pulse recirculation. The traditional approach to laser recirculation entails resonant coupling of low-energy pulse train to a cavity through a partially reflective mirror [ 1]. Here we present an alternative, passive approach that is akin to "burst-mode" operation and does not require interferometeric alignment accuracy. Injection of a short and energetic laser pulse is achieved by placing a thin frequency converter, such as a nonlinear optical crystal, into the cavity in the path of the incident laser pulse. This method leads to the increase of x-ray/gamma-ray energy proportional to the increase in photon energy in frequency conversion. Furthermore, frequency tunability can be achieved by utilizing parametric amplifier in place of the frequency converter.
Mast cells and hypoxia drive tissue metaplasia and heterotopic ossification in idiopathic arthrofibrosis after total knee arthroplasty (2010)

Taken together, we suggest that hypoxia-associated oxidative stress initiates mast cell proliferation and FGF secretion, spurring fibroblast proliferation and tissue fibrosis. Fibroblasts within this hypoxic environment undergo metaplastic transformation to fibrocartilage, followed by heterotopic ossification, resulting in increased joint stiffness. Thus, hypoxia and associated oxidative stress are potential therapeutic targets for fibrosis and metaplastic progression of idiopathic arthrofibrosis after TKA.
On the effect of N-GaN/P-GaN/N-GaN/P-GaN/N-GaN built-in junctions in the n-GaN layer for InGaN/GaN light-emitting diodes (2014)

N-GaN/P-GaN/N-GaN/P-GaN/N-GaN (NPNPN-GaN) junctions embedded between the n-GaN region and multiple quantum wells (MQWs) are systematically studied both experimentally and theoretically to increase the performance of InGaN/GaN light emitting diodes (LEDs) in this work. In the proposed architecture, each thin P-GaN layer sandwiched in the NPNPN-GaN structure is completely depleted due to the built-in electric field in the NPNPN-GaN junctions, and the ionized acceptors in these P-GaN layers serve as the energy barriers for electrons from the n-GaN region, resulting in a reduced electron over flow and enhanced the current spreading horizontally in the n- GaN region. These lead to increased optical output power and external quantum efficiency (EQE) from the proposed device.
Growth and characterization of hafnium silicate films prepared by UV/ozone oxidation (2004)

Physical and electrical properties of hafnium silicate (HfSixOy) dielectric films prepared by room-temperature UV/ozone (O3) oxidation of hafnium silicide (HfSi2) are reported. Angle-resolved x-ray photoelectron spectroscopy was used to determine chemical bonding at the film interface and within the bulk film. These films, with 12 at. % Hf composition, have a dielectric constant (κ) of ∼8–9 and exhibit a flat-band voltage shift of 60 mV. The leakage current density at VFB+1 V is 4.7×10−5 A/cm2 for a 4.7-nm-thick film (capacitance equivalent thickness=2.6 nm) and breakdown strength was &amp;gt;8 MV/cm.
Optical assays based on colloidal inorganic nanoparticles (2018)

Colloidal inorganic nanoparticles have wide applications in the detection of analytes and in biological assays. A large number of these assays rely on the ability of gold nanoparticles (AuNPs, in the 20 nm diameter size range) to undergo a color change from red to blue upon aggregation. AuNP assays can be based on cross-linking, non-cross linking or unmodified charge-based aggregation. Nucleic acid-based probes, monoclonal antibodies, and molecular-affinity agents can be attached by covalent or non-covalent means. Surface plasmon resonance and SERS techniques can be utilized. Silver NPs also have attractive optical properties (higher extinction coefficient). Combinations of AuNPs and AgNPs in nanocomposites can have additional advantages. Magnetic NPs and ZnO, TiO<sub>2</sub> and ZnS as well as insulator NPs including SiO<sub>2</sub> can be employed in colorimetric assays, and some can act as peroxidase mimics in catalytic applications. This review covers the synthesis and stabilization of inorganic NPs and their diverse applications in colorimetric and optical assays for analytes related to environmental contamination (metal ions and pesticides), and for early diagnosis and monitoring of diseases, using medically important biomarkers.
HaloTag Protein‐Mediated Site‐Specific Conjugation of Bioluminescent Proteins to Quantum Dots (2006)

On the dot: A genetically engineered haloalkane dehalogenase was used to conjugate Renilla luciferase to quantum dots (see picture). The quantum dots can emit light through bioluminescence resonance energy transfer (BRET). This specific conjugation occurs upon simple mixing under mild conditions, and may be applied for specific in vivo labeling of proteins with quantum dots for imaging.
Block Copolymer Photonic Gel for Mechanochromic Sensing (2011)

A mechanochromic sensor based on a block copolymer photonic gel is presented. This material provides a simple yet quantitative means to measure the local stress of an interface via a color change by making advantageous use of the photonic band gap properties and mechanical compliance of a one-dimensional periodic microstructure of a hydrophobic block-hydrophilic polyelectrolyte block copolymer gel. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Current-driven magnetization switching in ferromagnetic bulk Rashba semiconductor (Ge,Mn)Te (2018)

Multiferroic materials with both ferroelectric and ferromagnetic orders provide a promising arena for the electrical manipulation of magnetization through the mutual correlation between those ferroic orders. Such a concept of multiferroics may expand to semiconductor with both broken symmetries of spatial inversion and time reversal, that is, polar ferromagnetic semiconductors. Here, we report the observation of current-driven magnetization switching in one such example, (Ge,Mn)Te thin films. The ferromagnetism caused by Mn doping opens an exchange gap in original massless Dirac band of the polar semiconductor GeTe with Rashba-type spin-split bands. The anomalous Hall conductivity is enhanced with increasing hole carrier density, indicating that the contribution of the Berry phase is maximized as the Fermi level approaches the exchange gap. By means of pulse-current injection, the electrical switching of the magnetization is observed in the (Ge,Mn)Te thin films as thick as 200 nm, pointing to the Rashba-Edelstein effect of bulk origin. The efficiency of this effect strongly depends on the Fermi-level position owing to the efficient spin accumulation at around the gap. The magnetic bulk Rashba system will be a promising platform for exploring the functional correlations among electric polarization, magnetization, and current.
ChemInform Abstract: 195Pt NMR Study of Pt/TiO2 and Pt/SiO2 Catalysts: Strong Metal‐Support Interaction (SMSI). (1990)

Abstract It is shown that 195 Pt NMR can be used to study the interaction of metal surface atoms with adsorbates or species that have migrated from the support to the Pt surface during thermal treatment.
Nanosecond laser induced energetic ion formation from a nanoparticle: The origin of ion detection loss in a single particle mass spectrometry (2014)

Here we study the interaction of a nanosecond laser pulse with a nanoparticle to explore the mechanism of energetic ion formation and in particular the particle size dependence. Multiphoton ionization and the subsequent electron impact ionization accompanied by inverse Bremsstrahlung process are determined appropriate for generation of multiple charged ions. The Coulomb expansion of a positive ion cloud is then calculated with molecular dynamics simulations, resulting in temporal evolution of ions, a radial distribution of kinetic energy of ions, and size-dependency of the ion kinetic energy. A mass spectrum peak of ion simulated by the present model is found comparable to the experimental data. Alternatively, a direct measurement of kinetic energy is also explained by the model.
Vaccine Generation of Protective Ebola Antibodies and Identification of Conserved B-Cell Signatures (2018)

We recently identified a single potently neutralizing monoclonal antibody (mAb), mAb114, isolated from a human survivor of natural Zaire ebolavirus (EBOV) infection, which fully protects nonhuman primates (NHPs) against lethal EBOV challenge. To evaluate the ability of vaccination to generate mAbs such as mAb114, we cloned antibodies from NHPs vaccinated with vectors encoding the EBOV glycoprotein (GP). We identified 14 unique mAbs with potent binding to GP, 4 of which were neutralized and had the functional characteristics of mAb114. These vaccine-induced macaque mAbs share many sequence similarities with mAb114 and use the same mAb114 VH gene (ie, IGHV3-13) when classified using the macaque IMGT database. The antigen-specific VH-gene repertoire present after each immunization indicated that IGHV3-13 mAbs populate an EBOV-specific B-cell repertoire that appears to become more prominent with subsequent boosting. These findings will support structure-based vaccine design aimed at enhanced induction of antibodies such as mAb114.
Effect of Low-Dose Propantheline on Food-Stimulated Gastric Acid Secretion (1977)

We evaluated the widely held notion that anticholinergic drugs must be used in near toxic doses to inhibit gastric acid secretion effectively. Nine patients with duodenal ulcer were studied after a low dose (15 mg) and after a near toxic dose (averaging 48 mg) of the anticholinergic, propantheline. Mean (+/- S.E.) inhibition of food-stimulated acid secretion was identical with the two doses of propantheline: 29 +/- 10 and 29 +/- 11 per cent, respectively. In addition, when 15 mg of propantheline was combined with the histamine H2-receptor antagonist, cimetidine, acid secretion was suppressed to a greater degree than with either drug alone. A low dose of propantheline is as effective as a near toxic dose in suppressing food-stimulated acid secretion and augments the inhibitory effect of cimetidine.
Identifying in vivo DCE MRI parameters correlated with ex vivo quantitative microvessel architecture: A radiohistomorphometric approach (2013)

We introduce a novel radiohistomorphometric method for quantitative correlation and subsequent discovery of imaging markers for aggressive prostate cancer (CaP). While this approach can be employed in the context any imaging modality and disease domain, we seek to identify quantitative dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) attributes that are highly correlated with density and architecture of tumor microvessels, surrogate markers of CaP aggressiveness. This retrospective study consisted of five Gleason score matched patients who underwent 3 Tesla multiparametric MRI prior to radical prostatectomy (RP). The excised gland was sectioned and quartered with a rotary knife. For each serial section, digitized images of individual quadrants were reconstructed into pseudo whole mount sections via previously developed stitching program. The individual quadrants were stained with vascular marker CD31 and annotated for CaP by an expert pathologist. The stained microvessel regions were quantitatively characterized in terms of density and architectural arrangement via graph algorithms, yielding a series of quantitative histomorphometric features. The reconstructed pseudo whole mount histologic sections were non-linearly co-registered with DCE MRI to identify tumor extent on MRI on a voxel-by-voxel basis. Pairwise correlations between kinetic and microvessel features within CaP annotated regions on the two modalities were computed to identify highly correlated attributes. Preliminary results of the radiohistomorphometric correlation identified 8 DCE MRI kinetic features that were highly and significantly (p&lt;0.05) correlated with a number of microvessel parameters. Most of the identified imaging features were related to rate of washout (Rwo) and initial area under the curve (IAUC). Association of those attributes with Gleason patterns showed that the identified imaging features clustered most of the tumors with primary Gleason pattern of 3 together. These results suggest that Rwo and IAUC may be promising candidate imaging markers for identification of aggressive CaP <i>in vivo</i>.
Synthetic Methodology Utilized to Prepare Substituted Imidazole P38 MAP Kinase Inhibitors (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Engineering absorption and blackbody radiation in the far-infrared with surface phonon polaritons on gallium phosphide (2014)

We demonstrate excitation of surface phonon polaritons on patterned gallium phosphide surfaces. Control over the light-polariton coupling frequencies is demonstrated by changing the pattern periodicity and used to experimentally determine the gallium phosphide surface phonon polariton dispersion curve. Selective emission via out-coupling of thermally excited surface phonon polaritons is experimentally demonstrated. Samples are characterized experimentally by Fourier transform infrared reflection and emission spectroscopy, and modeled using finite element techniques and rigorous coupled wave analysis. The use of phonon resonances for control of emissivity and excitation of bound surface waves offers a potential tool for the exploration of long-wavelength Reststrahlen band frequencies.