gebhart/patrepeval huggingface dataset:
Subclinical Manifestations of Vulvar Human Papillomavirus Infection (1991)

We studied the presence of human papillomavirus (HPV) DNA by in situ hybridization in 74 colposcopically defined subclinical vulvar lesions obtained from 51 patients (mean age 25 years, range 18-42 years) referred for atypical Papanicolaou smears to the Colposcopy Clinic. Serial sections of formalin-fixed, paraffin-embedded biopsy tissue were stained by routine hematoxylin and eosin stain or were separately hybridized with biotin-labeled probes of HPV types 6, 11, 16, and 18 at high stringency and with mixed HPV probes at low stringency. Histologic evidence of HPV infection (koilocytosis or dysplasia) was found in eight lesions. Overall, 10 lesions were positive by in situ hybridization with HPV DNA. Although certain colposcopic features were more strongly associated with HPV DNA than others were, we were unable to demonstrate any consistent correlation between HPV DNA positivity or specific HPV DNA types and colposcopic categories. There was little correlation between HPV DNA positivity and the histopathologic incidence of HPV infection and dysplasia. Three of the 10 hybridization-positive lesions were severely dysplastic as compared with 0 of 64 nonhybridizing lesions. In spite of this association between HPV DNA and dysplasia, HPV DNA hybridization added no additional clinically relevant information to the histopathologic findings. We emphasize the significance of careful colposcopic examination of the vulva with directed biopsies.
A Study of the Forces on an Oscillating Cylinder (2007)

Flow over a cylindrical structure is a problem of interest in different engineering fields, especially offshore structures like risers and spars, which are constantly subject to sea waves. In this study, numerical simulation of the flow over a fixed cylinder at a low Reynolds number was carried out using the Reynolds-averaged Navier-Stokes model. It is well known theoretically and experimentally that the lift is self excited and has a frequency equal to the vortex shedding frequency. Then the cylinder was forced to oscillate in the cross-stream direction with different frequencies and amplitudes. The flow structure, including the lift and drag, was examined within the so-called lock-in frequency range, where the lift frequency is entrained by the cylinder frequency. The frequency-response curves for the lift and drag and the phase between the hydrodynamic force and the cylinder were produced for different motion amplitudes. These curves change significantly as either the motion amplitude or frequency is varied. Two modes of response were identified associated with high lift and low lift; each one has different characteristics.
Assembling Magnetic Nanowires into Networks: A Layered CoIICarboxylate Coordination Polymer Exhibiting Single‐Chain‐Magnet Behavior (2006)

Parallel chains of CoII dimers are interlinked by trans-1,2-cyclohexanedicarboxylate ligands in a laminated coordination polymer (see picture; C gray, Co tourquise, O red), which exhibits single-chain-magnet behavior due to strong Ising-like intrachain ferromagnetic interaction that can not easily be reversed by the relatively weak interchain antiferromagnetic interaction. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z601349_s.pdf or from the author. 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.
Risk-Averse Model Predictive Control Design for Battery Energy Storage Systems (2019)

When batteries supply behind-the-meter services such as arbitrage or peak load management, an optimal controller can be designed to minimize the total electric bill. The limitations of the batteries, such as on voltage or state-of-charge, are represented in the model used to forecast the system's state dynamics. Control model inaccuracy can lead to an optimistic shortfall, where the achievable schedule will be costlier than the schedule derived using the model. To improve control performance and avoid optimistic shortfall, we develop a novel methodology for high performance, risk-averse battery energy storage controller design. Our method is based on two contributions. First, the application of a more accurate, but non-convex, battery system model is enabled by calculating upper and lower bounds on the globally optimal control solution. Second, the battery model is then modified to consistently underestimate capacity by a statistically selected margin, thereby hedging its control decisions against normal variations in battery system performance. The proposed model predictive controller, developed using this methodology, performs better and is more robust than the state-of-the-art approach, achieving lower bills for energy customers and being less susceptible to optimistic shortfall.
Principal Components Analysis (1989)

Introduction Basic Concepts of Principal Components Geometrical Properties of Principal Components Decomposition Properties of Principal Components Principal Components of Patterned Correlation Matrices Rotation of Principal Components Using Principal Components to Select a Subset of Variables Principal Components Versus Factor Analysis Uses of Principal Components in Regression Analysis Using Principal Components to Detect Outlying and Influential Observations Use of Principal Components in Cluster Analysis Use of Principal Components Analysis in Conjunction with Other Multivariate Analysis Procedures Other Techniques Related to Principal Components Summary and Conclusions
Femtomolar Ln(III) Affinity in Peptide-Based Ligands Containing Unnatural Chelating Amino Acids (2012)

The incorporation of unnatural chelating amino acids in short peptide sequences leads to lanthanide-binding peptides with a higher stability than sequences built exclusively from natural residues. In particular, the hexadentate peptide P(22), which incorporates two unnatural amino acids Ada(2) with aminodiacetate chelating arms, showed picomolar affinity for Tb(3+). To design peptides with higher denticity, expected to show higher affinity for Ln(3+), we synthesized the novel unnatural amino acid Ed3a(2) which carries an ethylenediamine triacetate side-chain and affords a pentadentate coordination site. The synthesis of the derivative Fmoc-Ed3a(2)(tBu)(3)-OH, with appropriate protecting groups for direct use in the solid phase peptide synthesis (Fmoc strategy), is described. The two high denticity peptides P(HD2) (Ac-Trp-Ed3a(2)-Pro-Gly-Ada(2)-Gly-NH(2)) and P(HD5) (Ac-Trp-Ada(2)-Pro-Gly-Ed3a(2)-Gly-NH(2)) led to octadentate Tb(3+) complexes with femtomolar stability in water. The position of the high denticity amino acid Ed3a(2) in the hexapeptide sequence appears to be critical for the control of the metal complex speciation. Whereas P(HD5) promotes the formation of polymetallic species in excess of Ln(3+), P(HD2) forms exclusively the mononuclear complex. The octadentate coordination of Tb(3+) by both P(HD) leads to total dehydration of the metal ion in the mononuclear complexes with long luminescence lifetimes (>2 ms). Hence, we demonstrated that unnatural amino acids carrying polyaminocarboxylate side-chains are interesting building blocks to design high affinity Ln-binding peptides. In particular the novel peptide P(HD2) forms a unique octadentate Tb(3+) complex with femtomolar stability in water and an improvement of the luminescence properties with respect to the trisaquo TbP(22) complex by a factor of 4.
Horizontal and Vertical Water Particle Velocities Induced by Waves (1972)

Measurements of horizontal and vertical water particle velocities induced by regular waves, wind waves generated by a wind wave tank and ocean waves in shallow water were made using a Doppler-type sonic current meter. For regular waves, the validity of wave theories such as Stokes and cnoidal waves is investigated by comparison between theoretical curves and the experimental results. For wind waves and ocean waves, power spectra of water particle velocities and cross-correlations between surface displacement and water particle velocity are considered, especially in the latter case, directional spectra calculated from both the records are compared each other.
CD8 T cell responses to ECTV-WT and ECTV-IFN-γbp<sup>Δ</sup>. (2015)

&lt;p&gt;Mice (n = 5–10/group) were infected with ECTV-WT or ECTV-IFN-γbp and sacrificed 7 days later to measure splenic CTL activity. Shown is % specific lysis of &lt;sup&gt;51&lt;/sup&gt;Cr-labelled, ECTV-infected P815 target cells by splenocytes from (A) ECTV-WT- or (B) ECTV-IFN-γbp&lt;sup&gt;Δ&lt;/sup&gt;-infected WT and GKO mice. (C) Percent specific lysis of targets by splenocytes at 75:1 effector-to-target ratio. Two-way ANOVA followed by Fisher’s LSD test for significance was used for statistical analysis: (i) CTL response to ECTV-WT vs. ECTV-IFN-γbp&lt;sup&gt;Δ&lt;/sup&gt; in IL-13&lt;sup&gt;−/−&lt;/sup&gt; (p &lt; 0.0001) and STAT-6&lt;sup&gt;−/−&lt;/sup&gt; (p &lt; 0.0001) (ii) CTL response to ECTV-WT in WT vs IL-4&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0083), vs STAT-6&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0003), vs IL-13&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0001), vs IL-13&lt;sup&gt;−/−&lt;/sup&gt;/IL-4Rα&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0037) mice; (iii) CTL response to ECTV-IFN-γbp in WT vs STAT-6&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0002); vs IL-13&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0478); vs IL-4Rα&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.0174) and IL-13&lt;sup&gt;−/−&lt;/sup&gt;/IL-4Rα&lt;sup&gt;−/−&lt;/sup&gt; (p = 0.000046) mice. ****, p&lt;0.0001. (D—F) Spleen cells from mice infected mice were re-stimulated for 5 h with ECTV-infected P815 cells or H-2&lt;sup&gt;d&lt;/sup&gt; 8 T cell peptide determinants prior to intracellular IFN-γ staining followed by flow cytometry. Data shown are means of absolute numbers of ECTV-specific IFN-γ&lt;sup&gt;+&lt;/sup&gt; 8 T cells in spleens of ECTV-WT- vs. ECTV-IFN-γbp&lt;sup&gt;&lt;b&gt;Δ&lt;/b&gt;&lt;/sup&gt;-infected mice (D) and determinant-specific IFN-γ&lt;sup&gt;+&lt;/sup&gt; 8 T cells following infection with ECTV-WT (E) or ECTV-IFN-γbp (F) viruses. Two-way ANOVA followed by Fisher’s LSD test for significance was used for statistical analysis. For panels D, E and F, IFN-γ&lt;sup&gt;+&lt;/sup&gt; 8 T cell numbers in WT mice were significantly higher (p&lt;0.0001) than numbers in all GKO strains. Data shown for D-F are representative of one of three independent experiments with similar results. *, &lt;i&gt;p&lt;/i&gt;&lt; 0.05; **, &lt;i&gt;p&lt;/i&gt; &lt; 0.01; ***, &lt;i&gt;p&lt;/i&gt; &lt; 0.0001.&lt;/p&gt;
Interband magnetoabsorption of In_{0.53}Ga_{0.47}As (1980)

Interband magneto-optical absorption in the Faraday and the Voigt configurations has been studied near liquid-He temperature in ${\mathrm{In}}_{0.53}$${\mathrm{Ga}}_{0.47}$As grown by liquid-phase epitaxy on InP. Using a quasi-Ge model analysis with exciton corrections, the interband data has yielded ${E}_{g}=0.813\ifmmode\pm\else\textpm\fi{}0.001$ eV, ${m}_{0}(\frac{1}{{m}_{c}}+\frac{1}{{m}_{\mathrm{hh}}})=26.5\ifmmode\pm\else\textpm\fi{}0.5$, ${m}_{0}(\frac{1}{{m}_{c}}+\frac{1}{{m}_{\mathrm{lh}}})=44.0\ifmmode\pm\else\textpm\fi{}1.0$, and ${\ensuremath{\gamma}}_{3}\ensuremath{-}{\ensuremath{\gamma}}_{2}=0.7\ifmmode\pm\else\textpm\fi{}0.2$. Using ${E}_{p}=25.3$ eV and $\ensuremath{\Delta}=0.36$ eV (from linear interpolation between InAs and GaAs) and $\frac{{m}_{c}}{{m}_{0}}=0.041$ (from earlier intraband measurements), the present interband data has yielded a set of parameters for the quasi-Ge model; in particular, ${m}_{\mathrm{hh}}\ensuremath{\simeq}0.47{m}_{0}$ and ${m}_{\mathrm{lh}}\ensuremath{\simeq}0.050{m}_{0}$. A precise determination of ${E}_{p}$ requires a direct measurement of $\ensuremath{\Delta}$ and ${g}_{c}$.
Functional Reconstitution of a Highly Purified μ‐Opioid Receptor Protein with Purified G Proteins in Liposomes (1995)

A mu-opioid receptor protein (mu-ORP) purified to homogeneity from bovine striatal membranes has been functionally reconstituted in liposomes with highly purified heterotrimeric guanine nucleotide regulatory proteins (G proteins). A mixture of bovine brain G proteins, predominantly GoA, was used for most of the experiments, but some experiments were performed with individual pure G proteins, GoA, GoB, Gi1, and Gi2. Low Km GTPase was stimulated up to 150% by mu-opioid receptor agonists when both mu-ORP and a G protein (either the brain G protein mixture or a single heterotrimeric G protein) were present in the liposomes. Stimulation by a selective mu-agonist was concentration dependent and was reversed by the antagonist (-)-naloxone, but not by its inactive enantiomer, (+)-naloxone. The mu selectivity of mu-ORP was demonstrated by the inability of delta and kappa agonists to stimulate GTPase in this system. High-affinity mu-agonist binding was also restored by reconstitution with the brain G protein mixture and with each of the four pure Gi and G(o) proteins studied. The binding of mu agonists is sensitive to inhibition by GTP gamma S and by sodium.
Strong hydrogen bonds as a design element for developing new non‐linear optical crystals: Co‐crystals of merocyanine dyes and phenol derivatives (1996)

In this work we show that with strong hydrogen bonds, including a ‘very strong’ hydrogen bond and/or strong hydrogen-bonding networks, highly non-linear optically active chromophores, merocyanine dyes and phenol derivatives, are assembled as salt or semi-salt crystals, leading to improvement in crystallinity and interesting non-linear optical properties. Our approach is discussed in connection with four co-crystal structures.
Development of Fibrotic Penile Lesions Secondary to the Intracorporeal Injection of Vasoactive Agents (1988)

Fibrotic penile lesions developed in 4 patients who had undergone intracorporeal injection of vasoactive agents. These lesions persisted for at least 3 months, and in some instances they caused pain and curvature of the penis during erection.
Radiofrequency Treatment for Obstructive Tonsillar Hypertrophy (2000)

Temperature-controlled radiofrequency submucosal tissue volume reduction is a safe and effective method of treating symptomatic obstructive tonsillar hypertrophy. It is well tolerated by the patient under local anesthesia in the physician's office and has minimal postprocedure pain and dysphagia, with rapid return to normal activity. The procedure reduces tonsil size and increases airway size, leading to a reduction in symptoms.
Conformational Transition Associated with E1-E2 Interaction in Small Ubiquitin-like Modifications (2009)

Ubiquitin-like modifications regulate nearly every aspect of cellular functions. A key step in these modifications is the recognition of the carrier enzyme (E2) by the activating enzyme (E1). In this study, we have found that a critical E2-binding surface on the E1 of the small ubiquitin-like modifier has unusually high populations in both ordered and disordered states. Upon binding the E2, the disordered state is converted to the ordered state, which resembles the structure of the bound conformation, providing a mechanism to resolve the "Levinthal Paradox" search problem in a folding-upon-binding process. The significance of the folding-unfolding equilibrium is shown by the loss of functions of the mutations that shift the equilibrium to the folded state. This study highlights the importance of conformational flexibility in the molecular recognition event.
Beneficial Use of Ash and Char From Biomass Gasification (2011)

Biomass is likely to be a significant energy resource in the future. A common way to recover energy from biomass is through gasification where synthesis gas is produced; by-products of this process are tar and ash/char. This research investigates the potential to use the ash/char as a catalyst by understanding the properties of char generated under different gasification conditions. Specifically, it is desired to produce a porous char which could be used as a catalyst or as a support for more catalytically active metals. In this work, poplar wood was gasified under CO2, steam, and air at different reaction temperatures. Experiments were done in a fluidized bed reactor at temperatures of 500°C, 750°C and 920°C and char was recovered. BET-surface area measurements showed that gasification under CO2 has the potential to produce char with a higher surface area than char produced from steam gasification. Higher temperature or longer gasification times resulted in the production of a more porous char. TGA experiments showed that gasification under CO2 resulted in a higher mass loss compared to gasification with steam. Gasification with steam/CO2 mixtures yielded a mass loss similar to that of steam only which could be indicative of competitive reactions between steam and CO2. Experiments done in an ESEM allowed for visual observation of the changes in physical properties of the biomass during gasification. With CO2, physical changes were observed at temperatures as low as 400°C whereas physical changes were not observed under steam at this temperature.
Quasicrystalline tilings with nematic colloidal platelets (2014)

Complex nematic fluids have the remarkable capability for self-assembling regular colloidal structures of various symmetries and dimensionality according to their micromolecular orientational order. Colloidal chains, clusters, and crystals were demonstrated recently, exhibiting soft-matter functionalities of robust binding, spontaneous chiral symmetry breaking, entanglement, shape-driven and topological driven assembly, and even memory imprinting. However, no quasicrystalline structures were found. Here, we show with numerical modeling that quasicrystalline colloidal lattices can be achieved in the form of original Penrose P1 tiling by using pentagonal colloidal platelets in layers of nematic liquid crystals. The tilings are energetically stabilized with binding energies up to 2500 kBT for micrometer-sized platelets and further allow for hierarchical substitution tiling, i.e., hierarchical pentagulation. Quasicrystalline structures are constructed bottom-up by assembling the boat, rhombus, and star maximum density clusters, thus avoiding other (nonquasicrystalline) stable or metastable configurations of platelets. Central to our design of the quasicrystalline tilings is the symmetry breaking imposed by the platelet shape and the surface anchoring conditions at the colloidal platelets, which are misaligning and asymmetric over two perpendicular mirror planes. Finally, the design of the quasicrystalline tilings as platelets in nematic liquid crystals is inherently capable of a continuous variety of length scales of the tiling, ranging over three orders of magnitude in the typical length (from ~ 10 nm to ~ 10 μm), which could allow for the design of quasicrystalline photonics at multiple frequency ranges.
Inhibitory Effect of Lipopolysaccharide on Immune Response After DNA Immunization Is Route Dependent (1998)

The DNA prepared from E. coli contained high levels of lipopolysaccharide (LPS). When antigen-encoding DNA was injected into mice, toxicity and increased IgM responses were observed. A method for purifying high yields of DNA (up to 12 mg/L of broth culture) with very low levels of LPS (0.05 ng/mg) was developed. When this purified DNA was used for immunization studies, the toxicity and increased IgM responses were abrogated. Thus, LPS was added to DNA in order to examine its influence on the IgG and cytotoxic T lymphocyte (CTL) response after intramuscular (i.m.) or intradermal (i.d.) DNA immunization. The IgG response to DNA-encoded antigen was inhibited in a dose-dependent manner by the i.d., but not the i.m., route of immunization. Surprisingly, no effect on the CTL response was observed. Therefore, the ability to produce high yields of plasmid DNA with very low levels of endotoxin contamination is advantageous for DNA immunization studies, not only for toxicologic but also for immunologic considerations. Furthermore, these results provide further evidence that immune induction occurs via different mechanisms after i.m. and i.d. DNA immunization.
Signaling through Mutants of the IgA Receptor CD89 and Consequences for Fc Receptor γ-Chain Interaction (2006)

Abstract The prototypic receptor for IgA (FcαRI, CD89) is expressed on myeloid cells and can trigger phagocytosis, tumor cell lysis, and release of inflammatory mediators. The functions of FcαRI and activating receptors for IgG (FcγRI and FcγRIII) are dependent on the FcR γ-chain dimer. This study increases our understanding of the molecular basis of the FcαRI-FcR γ-chain transmembrane interaction, which is distinct from that of other activatory FcRs. FcαRI is unique in its interaction with the common FcR γ-chain, because it is based on a positively charged residue at position 209, which associates with a negatively charged amino acid of FcR γ-chain. We explored the importance of the position of this positive charge within human FcαRI for FcR γ-chain association and FcαRI functioning with the use of site-directed mutagenesis. In an FcαRI R209L/A213H mutant, which represents a vertical relocation of the positive charge, proximal and distal FcR γ-chain-dependent functions, such as calcium flux, MAPK phosphorylation, and IL-2 release, were similar to those of wild-type FcαRI. A lateral transfer of the positive charge, however, completely abrogated FcR γ-chain-dependent functions in an FcαRI R209L/M210R mutant. By coimmunoprecipitation, we have demonstrated the loss of a physical interaction between FcR γ-chain and FcαRI M210R mutant, thus explaining the loss of FcR γ-chain-dependent functions. In conclusion, not only the presence of a basic residue in the transmembrane region of FcαRI, but also the orientation of FcαRI toward the FcR γ-chain dimer is essential for FcR γ-chain association. This suggests the involvement of additional amino acids in the FcαRI-FcR γ-chain interaction.
Transcriptome analysis reveals wingless regulates neural development and signaling genes in the region of wing pigmentation of a polka‐dotted fruit fly (2020)

How evolutionary novelties have arisen is one of the central questions in evolutionary biology. Preexisting gene regulatory networks or signaling pathways have been shown to be co-opted for building novel traits in several organisms. However, the structure of entire gene regulatory networks and evolutionary events of gene co-option for emergence of a novel trait are poorly understood. In this study, to explore the genetic and molecular bases of the novel wing pigmentation pattern of a polka-dotted fruit fly (Drosophila guttifera), we performed de novo genome sequencing and transcriptome analyses. As a result, we comprehensively identified the genes associated with the pigmentation pattern. Furthermore, we revealed that 151 of these associated genes were positively or negatively regulated by wingless, a master regulator of wing pigmentation. Genes for neural development, Wnt signaling, Dpp signaling, and effectors (such as enzymes) for melanin pigmentation were included among these 151 genes. None of the known regulatory genes that regulate pigmentation pattern formation in other fruit fly species were included. Our results suggest that the novel pigmentation pattern of a polka-dotted fruit fly might have emerged through multistep co-options of multiple gene regulatory networks, signaling pathways, and effector genes, rather than recruitment of one large gene circuit.