gebhart/patrepeval huggingface dataset:
Effect of oxygen pressure on properties of $NdBa_2Cu_3O_{7-$\delta$}$ films on $SrTiO_3 (100)$ substrates grown by pulsed laser deposition (2004)

We report a successful fabrication of $high-J_c NdBa_2Cu_3O_{7-}$(NdBCO) films on (100) SrTiO substrates by pulsed laser deposition (PLD) in high oxygen pressures ranging from 400 to 800 mTorr. Fabricated NdBCO films exhibited only c-axis orientation, good out-of-plane and in-plane textures, and also excellent superconducting properties, including critical temperature () and critical current density () of above 90 K and the highest of 3.1 at 77 K in self-field, implying that NdBCO is a perspective alternative to YBCO for coated conductor. In low oxygen pressures ranging from 100 to 200 mTorr, however, the films showed a-, c-mixed orientation and degraded values due to the formation of $Nd_{1+x}Ba_{2-x}Cu_3O_{7-}-type solid solutions with an excessive substitution of Nd^{3+} ions for the Ba^{2+}$ sites.
Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-p K a Polar Moiety (2015)

Signaling pathways intersecting with the p21-activated kinases (PAKs) play important roles in tumorigenesis and cancer progression. By recognizing that the limitations of FRAX1036 (1) were chiefly associated with the highly basic amine it contained, we devised a mitigation strategy to address several issues such as hERG activity. The 5-amino-1,3-dioxanyl moiety was identified as an effective means of reducing pK a and logP simultaneously. When positioned properly within the scaffold, this group conferred several benefits including potency, pharmacokinetics, and selectivity. Mouse xenograft PK/PD studies were carried out using an advanced compound, G-5555 (12), derived from this approach. These studies concluded that dose-dependent pathway modulation was achievable and paves the way for further in vivo investigations of PAK1 function in cancer and other diseases.
Reinvestigation of Thermoelectric Properties of n- and p-Type (2014)

be an intrinsic semiconductor. Our experimental results show that increase of the Au composition causes a transition from n-type to p-type conduction between x = 4.6 and 4.9. We have also calculated the band structures of the Ba8AuxSi46x clathrate including a vacancy by ab initio calculation based on density functional theory with structure optimization. It was found that the vacancy behaves like an electron acceptor and the numbers of vacancies at 24k sites for the synthesized Ba8AuxSi46xy clathrates can be estimated as 0.4 in a unit cell.
Generating Efficient Stack Code for Java (1999)

Optimizing Java byte code is complicated by the fact that it uses a stack-based execution model. Changing the intermediate representation from the stack-based to the register-based one brings the problem of Java byte code optimizations into well-studied domain of compiler optimizations for registerbased codes. In this paper we describe the technique to convert a register-based code into the Java byte code. The code generation techniques developed for the stack-based computers are not directly applicable to this problem as the comparative cost of the local memory and stack manipulation instructions in JVM is quite different from that in the stack-based computers. Naive verbose translation of the registerbased code into the Java byte code produces the code with many redundant store and load instructions. The tool that we have developed allows to remove 90-100 % of the stores to the local (i.e., non-global) variables. It produces the Java byte code that is slightly faster and shorter than...
Dissection of multi‐protein complexes using mass spectrometry: Subunit interactions in transthyretin and retinol‐binding protein complexes (1998)

Complexes formed between transthyretin and retinol-binding protein prevent loss of retinol from the body through glomerular filtration. The interactions between these proteins have been examined by electrospray ionization combined with time-of-flight mass analysis. Conditions were found whereby complexes of these proteins, containing from four to six protein molecules with up to two ligands, are preserved in the gas phase. Analysis of the mass spectra of these multimeric species gives the overall stoichiometry of the protein subunits and provides estimates for solution dissociation constants of 1.9 ± 1.0 × 10−7 M for the first and 3.5 ± 1.0 × 10−5 M for the second retinol-binding protein molecule bound to a transthyretin tetramer. Dissociation of these protein assemblies within the gas phase of the mass spectrometer shows that each retinol-binding protein molecule interacts with three transthyretin molecules. Mass spectral analysis illustrates not only a correlation with solution behavior and crystallographic data of a closely related protein complex but also exemplifies a general method for analysis of multi-protein assemblies. Proteins Suppl. 2:3–11, 1998. © 1998 Wiley-Liss, Inc.
Alterations in CPT‐1 mRNA and fatty acid profile in hepatic cell lines in response to treatment with t10,c12‐ or c9,t11‐conjugated linoleic acid (2008)

Abstract Trans 10, cis 12‐conjugated linoleic acid ( t 10, c 12‐CLA) increases liver weights and hepatic lipids in mice. The purpose of this study was to determine the effects of CLA isomers ( t 10, c 12‐CLA or c 9, t 11‐CLA) and carnitine palmitoyl transferase‐1 (CPT‐1) inhibitors (etomoxir or hemipalmitoylcarnitinium) on CPT‐1 mRNA, fatty acid profile, and cholesterol synthesis in AML‐12 and HepG2 cells. t 10, c 12‐CLA was incorporated to a greater extent in both cell lines than c 9, t 11‐CLA. In addition, t 10, c 12‐CLA increased the free cholesterol content of AML‐12 and HepG2 cells four‐ and fivefold, respectively. Cells incubated with medium containing CPT‐1 inhibitors or t 10, c 12‐CLA had higher levels of mRNA for CPT‐1 in both cell lines, indicating an increased fatty acid oxidation in hepatic cell lines due to t 10, c 12‐CLA. Following treatment withdrawal, percentages of c 9, t 11‐CLA or t 10, c 12‐CLA remained elevated in cells initially treated with c 9, t 11‐CLA or t 10, c 12‐CLA, suggesting a potential for carryover effects of the CLA isomers. The results presented here demonstrate a potential role for t 10, c 12‐CLA in the modulation of hepatic fatty acid oxidation and cholesterol synthesis.
Little Evidence of a Role for theα1GABAASubunit‐Containing Receptor in a Rhesus Monkey Model of Alcohol Drinking (2013)

Alcohol-drinking animals appeared more sensitive to the effects of GABAergic compounds on drinking behavior. However, these results do not support a strong contribution of α1GABAA receptors to the reinforcing effects of alcohol in primates.
Anti-Idiotypic Monobodies Derived from a Fibronectin Scaffold (2013)

Mimetics of conformational protein epitopes have broad applications but have been difficult to identify using conventional peptide phage display. The 10th type III domain of human fibronectin (FNfn10) has two extended, randomizable surface-exposed loops and might be more amenable to the identification of such mimetics. We therefore selected a library of FNfn10 clones, randomized in both loops (15 residues in all), for binding to monoclonal antibodies (mAbs) that recognize the HIV-1 envelope glycoprotein. Anti-idiotypic monobodies (αIMs) mimicking both "linear" epitopes (2F5 and 4E10 mAbs) and conformational epitopes (b12 and VRC01 mAbs) were generated. αIMs selected against 2F5 and 4E10 frequently displayed sequence homology to the corresponding linear native epitopes. In the case of b12 and VRC01, we expected that the two constrained loop domains of FNfn10 would both contribute to complex conformational interactions with target antibodies. However, mutagenesis studies revealed differences from this simple model. An αIM selected against b12 was found to bind its cognate antibody via only a few residues within the BC loop of FNfn10, with minimal contribution from the FG loop. Unexpectedly, this was sufficient to generate a protein that engaged its cognate antibody in a manner very similar to that of HIV-1 Env, and with a strong KD (43 nM). In contrast, an αIM selected against VRC01 engaged its cognate antibody in a manner that was dependent on both BC and FG loop sequences. Overall, these data suggest that the FNfn10 scaffold can be used to identify complex structures that mimic conformational protein epitopes.
Duration control methods for HMM phoneme recognition (1988)

Two kinds of duration control for HMM (hidden Markov model) phoneme recognition are proposed: phoneme duration control for an HMM phone model and an event duration control for an HMM state. The phoneme duration control is carried out by combining an HMM output probability with a phoneme duration probability. The phoneme duration probability is calculated using a phoneme duration histogram obtained from training samples. Phoneme duration control is effective in discriminating phonemes with different durations such as /n/ and /N/. Event duration control is realized as a state duration penalty calculated from an HMM state duration probability of training samples. Event duration control is effective in discriminating phonemes with different event structures such as /s/ and /ts/. Recognition experiments are carried out using Japanese phonemes extracted from an isolated word database uttered by one male speaker. The phoneme recognition rate is improved from 84.8%–90.0% using these duration control techniques.
Ray tracing a three-dimensional scene using a hierarchical data structure (2023)

Ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. One example embodiment is a method for ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. In this example embodiment, the hierarchical data structure includes at least a parent node and a corresponding plurality of child nodes. The method includes a first act of determining that a first active ray in the packet hits the parent node and a second act of descending to each of the plurality of child nodes.
A Correlation Between Electric Fields That Target the Cell Membrane Potential and Dividing HeLa Cancer Cell Growth Inhibition (2020)

These findings have value for the understanding of the mechanisms of cancer cells growth inhibition with electric fields and suggest an interesting area of research on the interaction between electromagnetic fields and cancer cells.
Dynamic Fluorescence Measurements of Two-State Systems: Applications to Calcium-Chelating Probes (1993)

A fluorescence technique for characterizing ligand binding is evaluated. This technique uses the combination of steady-state and time-resolved methods to recover molar concentrations and overcomes errors inherent in the use of either method alone. The technique is applicable to time-resolved measurements made either with time-domain or frequency-domain instrumentation. A straightforward single-frequency phase/modulation approach is presented to determine whether an experimental system can be described by a two-state system. The approach is based on a nonlinear transformation of the phase/modulation data that results in a linear model function. Here, the theory is applied to the fluorescent calcium-binding probes Quin-2 and Calcium Green, but is relevant to studies involving other interacting systems. The technique described is used to assess the fraction of bound ligand (Ca2+) and binding constants for these probes.
Experimental Constraints on the Axion Dark Matter Halo Density (2002)

Most of the mass of the Milky Way galaxy is contributed by its halo, presumably in the form of non-interacting cold dark matter. The axion is a compelling cold dark matter candidate. We report results from a search which probes the local galactic halo axion density using the Sikivie RF cavity technique. Candidates over the frequency range 550$$ $\le$ f $\le$$$ 810 MHz (2.3$$ $\mu$eV $\le$$$ m$_{a}$ $\le$ 3.4 $\mu$eV) were investigated. The absence of a signal suggests that KSVZ axions contribute no more than 0.45 GeV/cm$^3$ of mass density to the local dark matter halo over this mass range.
Neutron Reflectivity from the Monolayer of SAN Random Copolymer (2001)

Abstract The detailed structural aspects of the monolayer of SAN random copolymer with 22.6 wt% AN content at the air/water interface were investigated using neutron reflectivity(NR) technique. NR data at various surface pressures were analyzed to obtain the thickness, the density, and the concentration distribution. Well defined double-layered structure could fit the data.
Molecular and Cellular Aspects of Chemical Carcinogenesis (1995)

Different DNA-adducts produced by one given genotoxic agent can lead to different mutational preferences, as exemplified in this mini-review, by the cis-diamminedichloroplatinum(II)-induced d(GpG)-N7(1)-N7(2) adduct, giving rise predominantly to G→T transversions targeted to the 5′-modified G, the d(ApG)-N7(l)-N7(2) adduct to A→T transversions, while for the d(GpTpA)-N7(l)-N7(3) adduct no crosslink-specific mutations were observed. Expression of mutated Hras put under the control of cell-compartment specific promoters in different layers of the mouse skin showed that the consequent expression of the malignant phenotype depended on the degree of differentiation of the cell, progression to carcinomas occurring in the basal cells of the hair follicles, but not in the suprabasal layer of the epidermis. The novel Ca2+-independent protein kinase C η is expressed in differentiating and differentiated epithelial cells of the skin and was activated by cholesterol sulfate whereby tumor promotion was inhibited. Finally, the hypothesis was tested whether hypomethylation of DNA is a nongenotoxic mechanism underlying the aberrant expression of protooncogenes involved in carcinogenesis. The 5-methyleytosine content of the mouse liver tumorigenesis-relevant Hras and raf oncogenes was lower in the liver of the liver tumor-prone B6C3F1 and C3H/He mice than in the relatively resistant C57BL/6 mice, indicating that differences in DNA methylation, at least in part, account for the different susceptibilities to nongenotoxic liver carcinogens.
Optimization of the JUNO liquid scintillator composition using a Daya Bay antineutrino detector (2020)

To maximize the light yield of the liquid scintillator (LS) for the Jiangmen Underground Neutrino Observatory (JUNO), a 20 t LS sample was produced in a pilot plant at Daya Bay. The optical properties of the new LS in various compositions were studied by replacing the gadolinium-loaded LS in one antineutrino detector. The concentrations of the fluor, PPO, and the wavelength shifter, bis-MSB, were increased in 12 steps from 0.5 g/L and &lt;0.01 mg/L to 4 g/L and 13 mg/L, respectively. The numbers of total detected photoelectrons suggest that, with the optically purified solvent, the bis-MSB concentration does not need to be more than 4 mg/L. To bridge the one order of magnitude in the detector size difference between Daya Bay and JUNO, the Daya Bay data were used to tune the parameters of a newly developed optical model. Then, the model and tuned parameters were used in the JUNO simulation. This enabled to determine the optimal composition for the JUNO LS: purified solvent LAB with 2.5 g/L PPO, and 1 to 4 mg/L bis-MSB.
Temperature and Thermal Stress Distributions in a Tubular Solid Oxide Fuel Cell (1993)

Abstract The temperature and thermal stress distributions in two model cells for a tubular solid oxide fuel cell, which have a different thickness of the electrolyte, were calculated by the finite element method to demonstrate the effects of electrolyte thickness on the mechanical stability of fuel cells. When the cells were operated at a constant voltage, their energy conversion efficiency increased with decreasing thickness of the electrolyte. A larger amount of heat was generated in the cell having a thinner electrolyte, thus producing a larger thermal stress. These results indicates that an excellent preparation method for the highly ionic conductive electrolyte is essential to produce a fuel cell with high mechanical stability.
Succinate dehydrogenase gene mutations are strongly associated with paraganglioma of the organ of Zuckerkandl (2010)

Organ of Zuckerkandl paragangliomas (PGLs) are rare neuroendocrine tumors that are derived from chromaffin cells located around the origin of the inferior mesenteric artery extending to the level of the aortic bifurcation. Mutations in the genes encoding succinate dehydrogenase subunits (SDH) B, C, and D (SDHx) have been associated with PGLs, but their contribution to PGLs of the organ of Zuckerkandl PGLs is not known. We aimed to describe the clinical presentation of patients with PGLs of the organ of Zuckerkandl and investigate the prevalence of SDHx mutations and other genetic defects among them. The clinical characteristics of 14 patients with PGL of the organ of Zuckerkandl were analyzed retrospectively; their DNA was tested for SDHx mutations and deletions. Eleven out of 14 (79%) patients with PGLs of the organ of Zuckerkandl were found to have mutations in the SDHB (9) or SDHD (2) genes; one patient was found to have the Carney-Stratakis syndrome (CSS), and his PGL was discovered during surgery for gastrointestinal stromal tumor. Our results show that SDHx mutations are prevalent in pediatric and adult PGLs of the organ of Zuckerkandl. Patients with PGLs of the organ of Zuckerkandl should be screened for SDHx mutations and the CSS; in addition, asymptomatic carriers of an SDHx mutation among the relatives of affected patients may benefit from tumor screening for early PGL detection.
Parent-of-origin effects on voluntary exercise levels and body composition in mice (2009)

Despite the health-related benefits of exercise, many people do not engage in enough activity to realize the rewards, and little is known regarding the genetic or environmental components that account for this individual variation. We created and phenotyped a large G(4) advanced intercross line originating from reciprocal crosses between mice with genetic propensity for increased voluntary exercise (HR line) and the inbred strain C57BL/6J. G(4) females (compared to males) ran significantly more when provided access to a running wheel and were smaller with a greater percentage of body fat pre- and postwheel access. Change in body composition resulting from a 6-day exposure to wheels varied between the sexes with females generally regulating energy balance more precisely in the presence of exercise. We observed parent-of-origin effects on most voluntary wheel running and body composition traits, which accounted for 3-13% of the total phenotypic variance pooled across sexes. G(4) individuals descended from progenitor (F(0)) crosses of HRfemale symbol and C57BL/6Jmale symbol ran greater distances, spent more time running, ran at higher maximum speeds/day, and had lower percent body fat and higher percent lean mass than mice descended from reciprocal progenitor crosses (C57BL/6Jfemale symbol x HRmale symbol). For some traits, significant interactions between parent of origin and sex were observed. We discuss these results in the context of sex dependent activity and weight loss patterns, the contribution of parent-of-origin effects to predisposition for voluntary exercise, and the genetic (i.e., X-linked or mtDNA variations), epigenetic (i.e., genomic imprinting), and environmental (i.e., in utero environment or maternal care) phenomena potentially modulating these effects.
Annexin A1 on the Surface of Early Apoptotic Cells Suppresses CD8+ T Cell Immunity (2013)

Prevention of an immune response against self-antigens derived from apoptotic cells is essential to preclude autoimmune and chronic inflammatory diseases. Here, we describe apoptosis induced externalization of endogenous cytosolic annexin 1 initiating an anti-inflammatory effector mechanism that suppresses the immune response against antigens of apoptotic cells. Cytosolic annexin 1 rapidly translocated to the apoptotic cell surface and inhibited dendritic cell (DC) activation induced by Toll like receptors (TLR). Annexin 1-inhibited DC showed strongly reduced secretion of pro-inflammatory cytokines (e.g. TNF and IL-12) and costimulatory surface molecules (e.g. CD40 and CD86), while anti-inflammatory mediators like PD-L1 remained unchanged. T cells stimulated by such DC lacked secretion of interferon-γ (IFN-γ) and TNF but retained IL-10 secretion. In mice, annexin 1 prevented the development of inflammatory DC and suppressed the cellular immune response against the model antigen ovalbumin (OVA) expressed in apoptotic cells. Furthermore, annexin 1 on apoptotic cells compromised OVA-specific tumor vaccination and impaired rejection of an OVA-expressing tumor. Thus, our results provide a molecular mechanism for the suppressive activity of apoptotic cells on the immune response towards apoptotic cell-derived self-antigens. This process may play an important role in prevention of autoimmune diseases and of the immune response against cancer.
Growth and characterization of AlInGaN quaternary alloys (1996)

We report on the deposition of AlyInxGa1−x−yN in the (0&amp;lt;y&amp;lt;0.15) and (0&amp;lt;x&amp;lt;0.14) composition range by metalorganic chemical vapor deposition. AlInGaN quaternary alloys offer a lattice-matched platform for InGaN-based light emitting heterostructure devices. Epitaxial growth of AlInGaN on (0001) sapphire substrates has been achieved at 750 °C. Alloy composition, lattice constants, and band gaps were obtained by energy dispersive spectroscopy, x-ray diffraction, and room temperature PL. Band edge emissions dominate the PL spectra of these quaternary films. Preliminary data suggest that the lattice constant of AlInGaN can be deduced from chemical composition using Vegard’s law, indicating solid solution in the grown quaternary films.
Supplementary Figure 1 from Rb Loss Is Characteristic of Prostatic Small Cell Neuroendocrine Carcinoma (2023)

&lt;p&gt;PDF file - 284K, Supplementary Figure S1: (A) High grade prostatic adenocarcinoma with neuroendocrine differentiation by diffuse expression of immunohistochemical markers. This case shows lack of small cell differentiation by hematoxylin and eosin staining (left panel, 200x and inset) based on presence of prominent nucleoli and abundant cytoplasms, without nuclear molding. However, neuroendocrine immunohistochemical markers are diffusely positive (middle panel). Rb protein is present in this case (right panel). (B) Large cell neuroendocrine prostate carcinoma (LCNEC) shows cords and trabeculae of cells, but with abundant pink cytoplasm, which is inconsistent with a diagnosis of small cell carcinoma (left panel and inset). Neuroendocrine markers are diffusely positive (middle panel), however Rb protein is preserved (right panel). (C) Castrate resistant prostate cancer metastasis from autopsy study that has been previously reported (reference 30). This liver metastasis from case 30 (Supplementary Table 1) is heterogeneously positive for Rb protein, with one nodule staining positive (lower left) and nearby nodules staining negative, despite Rb protein in endothelial cells (arrowhead) as an internal positive control. Additional liver and bone tumors from this patient were found to have homozygous deletion of RB1, suggesting inter-metastatic heterogeneity in RB1 status.&lt;/p&gt;