gebhart/patrepeval huggingface dataset:
MIM/BEG4, a Sonic hedgehog-responsive gene that potentiates Gli-dependent transcription (2004)

Sonic hedgehog (Shh) signaling plays a critical role during development and carcinogenesis. While Gli family members govern the transcriptional output of Shh signaling, little is known how Gli-mediated transcriptional activity is regulated. Here we identify the actin-binding protein Missing in Metastasis (MIM) as a new Shh-responsive gene. Together, Gli1 and MIM recapitulate Shh-mediated epidermal proliferation and invasion in regenerated human skin. MIM is part of a Gli/Suppressor of Fused complex and potentiates Gli-dependent transcription using domains distinct from those used for monomeric actin binding. These data define MIM as both a Shh-responsive gene and a new member of the pathway that modulates Gli responses during growth and tumorigenesis.
Biochemical and genetic analysis of variant mouse hepatoma cells defective in the induction of benzo(a)pyrene-metabolizing enzyme activity. (1983)

We have analyzed wild type mouse hepatoma (Hepa 1c1c7) cells and variant cells which are defective in the induction of benzo(a)pyrene-metabolizing enzyme activity. One type of variant has no detectable basal or inducible aryl hydrocarbon hydroxylase activity. This class contains apparently normal cytosolic receptors for 2,3,7,8-tetrachlorodibenzo-p-dioxin, but is unable to translocate the inducer-receptor complex to the nucleus. The second type of variant has low levels of basal and inducible aryl hydrocarbon hydroxylase activity. This class contains cytosolic receptors which are decreased either in their number or in their ability to bind 2,3,7,8-tetrachlorodibenzo-p-dioxin; translocation of the inducer-receptor complex to the nucleus is apparently normal. Cell fusions indicate that both variant phenotypes are recessive with respect to wild type. Complementation analyses indicate that the defects are located on different genes.
Learning Instruction Scheduling Heuristics from Optimal Data (2006)

I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii The development of modern pipelined and multiple functional unit processors has increased the available instruction level parallelism. In order to fully utilize these resources, compiler writers spend large amounts of time developing complex scheduling heuristics for each new architecture. In order to reduce the time spent on this process, automated machine learning techniques have been proposed to generate scheduling heuristics. We present two case studies using these techniques to generate instruction scheduling heuristics for basic blocks and super blocks. A basic block is a block of code with a single flow of control and a super block is a collection of basic blocks with a single entry point but multiple exit points. We improve previous techniques for automated generation of basic block scheduling
Piezoelectric Properties of Epitaxial NaNbO<sub>3</sub> Thin Films Deposited on (001)SrRuO<sub>3</sub>/Pt/MgO Substrates (2007)

Sodium niobate (NaNbO3, NN) thin films were deposited on (001)SrRuO3/Pt/MgO substrates by rf magnetron sputter deposition. The X-ray diffraction (XRD) pattern of the sputtered NN thin films showed epitaxial growth with a (001)-oriented perovskite structure. From the reciprocal space maps, the lattice parameters of the in-plane and out-of-plane directions were a=0.392 nm and c=0.395 nm, respectively. The relative dielectric constant εr and the range of the dielectric loss tan δ were about 270 and 0.05–0.13 at 1 kHz, respectively. The P–E hysteresis loop showed clear ferroelectricity with spontaneous polarization Ps of 20 µC/cm2 and coercive electric field Ec of 50 kV/cm. The transverse piezoelectric properties were evaluated from the tip displacement of NN/MgO unimorph cantilevers. The transverse piezoelectric coefficient e31* (=d31/s11E) was -0.9 C/m2, which is almost compatible with that of the bulk NN ceramics. The tip deflection showed typical butterfly curves owing to the polarization reversal, indicating that the sputtered NN thin films had a high piezoelectric performance.
Chromogranin‐ and Somatostatin‐containing Neuroendocrine Cells in the Porcine Uterus An Immunocytochemical Study (1989)

Endocrine cells scattered in organic mucosae were defined "Neuroendocrine" (NE) cells because they constitute a section of the Diffuse Neuroendocrine System (DNES). Such cells have never been evidentiated in the normal endometrium. By means of histochemical and immunohistochemical techniques, NE cells, some of which contain the hormone somatostatin, are described in the glandular epithelium of the uterine horn in non-pregnant, non-castrated, young and adult sows. As is known, the uterine horn is the organ of pregnancy in the pig. The localization, distribution and morphology of the uterine NE and somatostatin-containing cells are reported and the importance of their function, in the pregnant and non-pregnant porcine uterus, is discussed.
9-Silafluorene and 9-germafluorene: novel platforms for highly efficient red phosphorescent organic light-emitting diodes (2018)

<italic>De novo</italic> molecular platforms have been applied to build host materials for highly efficient PHOLEDs. A 9-silafluorene derivative was studied for the first time as a host and an external quantum efficiency of over 28% was achieved successfully in red PHOLEDs.
Recycling of Rubber (1995)

The recycle of rubber lags far behind that of thermoplastics. This lag results primarily from a great preponderance of rubber articles being fabricated from thermoset materials. As a result, the most facile means of disposing of many used rubber articles, including pneumatic tires, is through incineration to generate energy. This situation will continue until new technology is generated for the fabrication of recyclable rubber articles. Promising technology toward this end is now being offered by thermoplastic elastomers -- materials with properties of rubber but which can be processed as a conventional thermoplastic.
Differential Onset of Expression of α7 and β1D Integrins During Mouse Heart and Skeletal Muscle Development (1998)

beta 1D is a recently identified isoform of the beta 1 integrin subunit selectively expressed in skeletal and cardiac muscles. In the present study we determined the temporal expression of beta 1D and its association with alpha subunits during mouse development. By immunohistochemistry and western blot analysis we demonstrated that beta 1D begins to be expressed in skeletal muscles of 17 days embryo (stage E17). Its level progressively increases reaching maximal values few days after birth and remaining high in adult mice. At earlier stages of development (E11-E17) the beta 1A isoform is expressed in skeletal muscle cells. After E17 beta 1A is downregulated and disappears from muscle fibers few days after birth. In cardiac muscle the regulation of the beta 1D expression is different: beta 1D and beta 1A are coexpressed in the heart of E11 embryo. Subsequently expression of beta 1A declines, while beta 1D increases until it becomes the unique beta 1 isoform in cardiomyocytes few days after birth. Previous studies (Belkin et al J. Cell Biol. 132: 211-226, 1996) demonstrated that beta 1D in adult mouse cardiomyocytes is exclusively associated with alpha 7B. Western blot analysis shows that alpha 7B starts to be expressed in the heart only at stage E17, while beta 1D is expressed already at E11 embryo, indicating that alpha subunits other than alpha 7 should associate with beta 1D in early developmental stages. To investigate this aspect, beta 1 associated alpha subunits were identified by western blotting from cardiomyocytes integrin complexes immunoprecipitated with alpha subunit specific antibodies. We found that, during cardiomyocyte development, beta 1D associates with several alpha subunits namely with alpha 5, alpha 6A and alpha 7B. In conclusion these data show that the expression of the beta 1D muscle specific integrin during development occurs much earlier in heart than in skeletal muscle and it can dimerize with different alpha subunits.
Breakpoint-specific multiplex polymerase chain reaction allows the detection of IKZF1 intragenic deletions and minimal residual disease monitoring in B-cell precursor acute lymphoblastic leukemia (2012)

Deletion of the Ikaros (IKZF1) gene is an oncogenic lesion frequently associated with BCR-ABL1-positive acute lymphoblastic leukemias. It is also found in a fraction of BCR-ABL1-negative B-cell precursor acute lymphoblastic leukemias, and early studies showed it was associated with a higher risk of relapse. Therefore, screening tools are needed for evaluation in treatment protocols and possible inclusion in risk stratification. Besides monosomy 7 and large 7p abnormalities encompassing IKZF1, most IKZF1 alterations are short, intragenic deletions. Based on cohorts of patients, we mapped the microdeletion breakpoints and developed a breakpoint-specific fluorescent multiplex polymerase chain reaction that allows detection of recurrent intragenic deletions. This sensitive test could also detect IKZF1 subclonal deletions, whose prognostic significance should be evaluated. Moreover, we show that consensus breakpoint sequences can be used as clonal markers to monitor minimal residual disease. This paper could be useful for translational studies and in clinical management of BCP-ALL.
Trafficking of Glucose, Lactate, and Amyloid-β from the Inferior Colliculus through Perivascular Routes (2009)

Metabolic brain imaging is widely used to evaluate brain function and disease, and quantitative assays require local retention of compounds used to register changes in cellular activity. As labeled metabolites of [1- and 6-(14)C]glucose are rapidly released in large quantities during brain activation, this study evaluated release of metabolites and proteins through perivascular fluid flow, a pathway that carries solutes from brain to peripheral lymphatic drainage sites. Assays with [3,4-(14)C]glucose ruled out local oxidation of glucose-derived lactate as a major contributor of label loss. Brief infusion of [1-(14)C]glucose and D-[(14)C]lactate into the inferior colliculus of conscious rats during acoustic stimulation labeled the meninges, consistent with perivascular clearance of [(14)C]metabolites from interstitial fluid. Microinfusion of Evans blue albumin and amyloid-beta(1-40) (Abeta) caused perivascular labeling in the inferior colliculus, labeled the surrounding meninges, and Abeta-labeled-specific blood vessels in the caudate and olfactory bulb and was deposited in cervical lymph nodes. Efflux of extracellular glucose, lactate, and Abeta into perivascular fluid pathways is a normal route for clearance of material from the inferior colliculus that contributes to underestimates of brain energetics. Convergence of 'watershed' drainage to common pathways may facilitate perivascular amyloid plaque formation and pathway obstruction in Alzheimer's disease.
The affinities, potencies and efficacies of some benzodiazepine‐receptor agonists, antagonists and inverse‐agonists at rat hippocampal GABA<sub>A</sub>‐receptors (1987)

The abilities of some benzodiazepine-receptor agonists, antagonists and inverse agonists to modulate the inhibitory potency of the gamma-aminobutyric acid (GABA)A-receptor agonist, isoguvacine, on the CA1 population spike recorded from slices of rat hippocampus, were determined. Concentration-response curves were constructed of the extent to which the benzodiazepine-receptor ligands shifted the isoguvacine concentration-response curve to the left or right. These were compared to their displacement curves of [3H]-Ro15-1788 binding to rat hippocampal membranes under near physiological assay conditions. The above comparisons suggest that the effect on the potency of isoguvacine produced by the benzodiazepine-receptor agonists, diazepam and flunitrazepam, and the partial agonists, Ro16-6028 and Ro17-1812, closely parallels their degree of benzodiazepine-receptor occupancy. Thus, the partial agonists, Ro16-6028 and Ro17-1812, were unable to produce as large a maximum response as the full agonists, diazepam and flunitrazepam. The maximum effects produced by diazepam, flunitrazepam, Ro16-6028, Ro17-1812, the antagonist, propyl-beta-carboline-3-carboxylate, and the inverse agonist, methyl-6, 7-dimethyl-4-ethyl-beta-carboline-3-carboxylate (DMCM), on the potency of isoguvacine in the hippocampal slice corresponded to the change in their affinities produced by the addition of GABA in the radioligand binding studies (GABA-shift). This suggests that the changes in affinity of benzodiazepine-receptor ligands produced by GABAA-receptor activation reflects their ability to modify GABAA-receptor function. The benzodiazepine-receptor antagonists, Ro15-1788 and CGS 8216, had apparent agonist and inverse agonist effects, respectively, on the potency of isoguvacine. These effects occurred at concentrations above those required for saturation of the benzodiazepine-receptor, as labelled by [3H]-Ro15-1788, and were not in agreement with the absence of any effect of GABAA-receptor stimulation in the GABA-shift experiments. This indicates that these events are not mediated by an action at the classical benzodiazepine-receptor site. 6 It is concluded that hippocampal GABAA-receptor function can be allosterically modulated in a manner consistent with the agonist/inverse-agonist model of benzodiazepine-receptor activation, and that compounds exist with varying efficacies throughout this range.
A Point Creation Strategy for Mesh Generation Using Crystal Lattices as Templates. (2000)

A strategy is presented to define background meshes based on crystal lattices. Crystal-based background meshes have much better initial distribution of minimum dihedral angles than regular background meshes, facilitating the optimization procedures that rely on previously defined tetrahedral meshes. In addition, these background meshes can reduce significantly, or even eliminate, the number of slivers generated during a Delaunay triangulation. Keywords: FE mesh generation, background mesh, crystal lattices, triangulation, tetrahedralization, computational geometry. 1 INTRODUCTION Discretization of geometric models representing domains of interest is an essential part of numerical solution of Partial Differential Equations. Delaunay triangulation algorithms are frequently used to generate unstructured meshes for Finite Element Analysis. Although Delaunay triangulation has a well-defined method to create the connectivity of a set of points, it does not provide a method for genera...
Comments on ’’On the mechanism of transduction in optical fiber hydrophones’’ [J. Acoust. Soc. Am. 66, 976–979 (1979)] (1980)

In a recent paper [H. L. Price, ’’On the mechanism of transduction in optical fiber hydrophones,’’ J. Acoust. Soc. Am. 66, 976–979 (1979)] it is concluded from static arguments that an optical fiber subjected to hydrostatic pressure undergoes an increase in length because the fiber is ’’squeezed out’’ toward the ends by the transverse pressure on its sides. We show that this conclusion is not correct. Static equilibrium demands that the stress in the fiber be hydrostatic just as in the surrounding fluid and that an increase in pressure be accompanied by a decrease in fiber length. We further point out that reference to appropriate original optical data taken under hydrostatic pressure renders the calculation of physical length changes unnecessary in the calculation of optical hydrophone sensitivity.
Polymorphic dextromethorphan metabolism: Co-segregation of oxidative O-demethylation with debrisoquin hydroxylation (1985)

Dextromethorphan hydrobromide, 25 mg po, was given to 268 unrelated Swiss subjects to study urinary drug and metabolite profiles. Rates of O-demethylation yielding the main metabolite dextrorphan were expressed by the urinary dextromethorphan/dextrorphan metabolic ratio. We found a bimodal distribution of this parameter in our population study, which indicates that there are two phenotypes for dextromethorphan O-demethylation. The antimode at a metabolic ratio of 0.3 separated the poor metabolizer (PM; n = 23; prevalence of 9%) from extensive metabolizer (EM) phenotypes. Urinary output of dextrorphan was less than 6% of the dose in all PMs and was 50% in the 245 EMs. Pedigree analysis of 14 family studies revealed an autosomal-recessive transmission of deficient dextromethorphan O-demethylation. In these families, 37 heterozygous genotypes could be identified; however, through use of the urinary drug and metabolite analysis it was not possible to identify the heterozygous genotypes within the EM phenotype group. Co-segregation of dextromethorphan O-demethylation with debrisoquin 4-hydroxylation was also studied. Complete concordance of the two phenotypic assignments was obtained, with a Spearman rank correlation coefficient of rs = 0.78 (n = 62; P less than 0.0001) for dextromethorphan and debrisoquin metabolic ratios. Presumably the two drug oxidation polymorphisms are under the same genetic control. Thus the innocuousness and ubiquitous availability of dextromethorphan render it attractive for worldwide pharmacogenetic investigations in man.
Biological basis of suicide and suicidal behavior (2013)

Some encouraging information emerged from the present review, primarily related to some of the neurobiological mechanisms mentioned above. It is hoped that neurobiological studies may eventually result in the identification of appropriate biomarkers for suicidal behavior as well as appropriate therapeutic targets for its treatment.
An Evaluation of Technology to Remove Problematic Organic Compounds from the International Space Station Potable Water (2014)

Tucson, Arizona
Large-area, free-standing gratings for atom interferometry produced using holographic lithography (1992)

Interferometers based on matter waves promise orders-of-magnitude improvements in metrology over laser-based systems by virtue of the fact that the de Broglie wavelengths of atoms are about 104 times shorter. To date, the required matched set of four aligned gratings for such atom interferometers has been made using electron beam lithography and, as a result, such gratings suffer from a lack of spatial-phase coherence. We report on processes we have developed for fabricating free-standing gratings over large areas using conventional holographic lithography and achromatic holographic lithography to achieve spatial periods of 200 and 100 nm, respectively (i.e., nominal linewidths of 100 and 50 nm, respectively).
Effect of Radical Nitriding on Fatigue Strength of Ni-Base Superalloy (2009)

In order to investigate the effect of nitriding on the crack initiation and propagation behavior of Ni-base super alloy, Alloy 718, rotating bending fatigue tests were carried out until 108 cycles at room temperature. By nitriding at 500°C for 12h, compound layer of about 5μm in thickness was formed and the initiation of a fatigue crack was strongly suppressed causing the increase in fatigue strength. A crack initiated in brittle manner at the compound layer in all of fractures. However the crack propagated in ductile manner controlled by the property of the base alloy. That is, there is no or little influence of nitriding on the crack growth rate of the alloy.
Tolerance and adaptation of ethanologenic yeasts to lignocellulosic inhibitory compounds (2006)

Synthetic mixtures of predominant lignocellulosic hexose sugars were supplemented with separate aliquots of three inhibitory compounds (furfural, hydroxymethylfurfural (HMF), and acetic acid) in a series of concentrations and fermented by the spent sulfite liquor (SSL)-adapted yeast strain Tembec T1 and the natural isolate Saccharomyces cerevisiae (S. cerevisiae) Y-1528 to compare tolerance and assess fermentative efficacy. The performance of Y-1528 exceeded that of Tembec T1 by a significant margin, with faster hexose sugar consumption, higher ethanol productivity, and in the case of furfural and HMF, faster inhibitor consumption. Nevertheless, furfural had a dose-proportionate effect on sugar consumption rate and ethanol productivity in both strains, but did not substantially affect ethanol yield. HMF had a similar effect on sugar consumption rate and ethanol productivity, and also lowered ethanol yield. Surprisingly, acetic acid had the least impact on sugar consumption rate and ethanol productivity, and stimulated ethanol yield at moderate concentrations. Sequential iterations of softwood (SW) and hardwood (HW) SSL were subsequently inoculated with the two yeast strains in order to compare adaptation to, and performance in lignocellulosic substrates in a cell recycle batch fermentation (CRBF) regime. Both strains were severely affected by the HW SSL, which was attributed to specific syringyl lignin-derived degradation products and synergistic interactions between inhibitors. Though ethanologenic capacity was preserved, a net loss of performance was evident from both strains, indicating the absence of adaptation to the substrates, regardless of the sequence in which the SSL types were employed.
A Mission Planning Expert System with Three-Dimensional Path Optimization for the NPS Model 2 Autonomous Underwater Vehicle (1990)

Unmanned vehicle technology has matured significantly over the last two decades. This is evidenced by its widespread use in industrial and military applications ranging from deep-ocean exploration to anti-submarine warefare. Indeed, the feasiblity of short-range, special-purpose vehicles (whether aunonomous or remotely operated) is no longer in question. The research efforts have now begun to shift their focus on development of reliable, longer-range, high-endurance and fully autonomous systems. One of the major underlying technologies required to realize this goal is Artificial Intelligence (AI). The latter offers great potential to endow vehicles with the intelligence needed for full autonomy and extended range capability; this involves the increased application of AI technologies to support mission planning and execution, navigation and contingency planning. This thesis addresses two issues associated with the above goal for Autonomous Underwater Vehicles (AUV's). Firstly, a new approach is proposed for path planning in underwater environments that is capable of dealing with uncharted obstacles and which requires significantly less planning time and computer memory. Secondly, it explores the use of expert system technology in the planning of AUV missions.