gebhart/patrepeval huggingface dataset:
Open-system geometric phase based on system-reservoir joint state evolution (2014)

The geometric phase is of fundamental interest and plays an important role in quantum information processing. However, the definition and calculation of this phase for open systems remain problematic due to the lack of agreement on generalizations of the parallel transport condition to mixed-state nonunity evolutions. Here we tackle this problem by associating the open-system geometric phase with the parallel transport of the joint system-reservoir state and find that the associated geometric phase can be calculated when the total Hamiltonian is time independent. Our approach not only provides a way around the nonunitary evolution obstacle, but also sheds light on the relation between the geometric phase and the system-reservoir entanglement. Based on this approach, we calculate the geometric phase of different quantum systems subject to energy decay, showing that it is robust against decoherence, which is in distinct contrast with previous results.
Antibody Cross-Linking of the Thymocyte-Specific Cell Surface Molecule CTX Causes Abnormal Mitosis and Multinucleation of Tumor Cells (1997)

The thymocyte-specific cell surface molecule CTX is a developmentally regulated type I transmembrane protein of the immunoglobulin superfamily which, in the amphibian Xenopus, is exclusively expressed by a large fraction of cortical thymocytes and by different cell lines derived from independent spontaneous thymic tumors. Antibody cross-linking of CTX in vitro inhibits the growth of tumor cells and causes morphological alterations. Cells divide abnormally, accumulate in the G2/M phase of the cell cycle, and become multinucleated. This demonstrates, for the first time, that multinucleation can be induced by specifically cross-linking a cell surface molecule.
Sources of intensity nonuniformity in spin echo images at 1.5 T (1994)

This manuscript describes a number of sources of nonuniformity for spin echo images at 1.5 T. Both coil tuning and crosstalk can have significant effects on image nonuniformity. For short repetition times, nonuniformity increases with decreasing TR, possibly due to gradient eddy currents. In sections of RF coils with poor RF uniformity, image nonuniformity varies with both echo time and the number of echoes in a multiecho sequence. For the particular imager used, there are small differences between transverse and sagittal/coronal nonuniformity. The temporal stability of image nonuniformity is very good. The use of uniform oil phantoms is shown to be superior to low pass filtered images for correction of image nonuniformity.
Oncogenes and tumor-suppressor genes. (1991)

The functional role of oncogenes in human lung carcinogenesis has been investigated by transfer of activated oncogenes into normal cells or an immortalized bronchial epithelial cell line, BEAS-2B. Transfection of v-Ha-ras, Ki-ras, or the combination of myc and raf into BEAS-2B cells produced tumorigenic cell lines, while transfection of raf or myc alone produced nontumorigenic cell lines. In addition to studying the pathogenic role of oncogenes, we are attempting to define negative growth-regulating genes that have tumor-suppressive effects for human lung carcinomas. Our strategy to identify tumor-suppressor genes involves loss of heterozygosity studies, monochromosome-cell fusion, and cell-cell fusion studies. Loss of heterozygosity studies have revealed consistent allelic DNA sequence deletions on chromosome 17p in squamous cell carcinomas, while large cell carcinomas and adenocarcinomas retained this locus. Mutations in p53, a tumor-suppressor gene located on chromosome 17p, have been observed. Cell-cell hybrid clones produced from fusion of nontumorigenic BEAS-2B cells with tumorigenic HuT292DM cells generally are nontumorigenic. The mechanistic role of the known tumor-suppressor genes Rb-1 and p53 in the development of human lung carcinomas is being investigated in this epithelial cell model of human bronchogenic carcinogenesis.
Systems for Identifying New Drugs Are Often Faulty (1997)

Screening potential anticancer agents to find ones promising enough to make human clinical trials worthwhile has not been as straightforward as researchers would like. Not only have very few of the drugs that showed anticancer activity in animals carrying transplanted human tumors--known as xenografts--made it into the clinic, but a recent study conducted at the National Cancer Institute suggests that the tests are also missing drugs that do work in humans, possibly because animals and humans do not handle the drugs exactly the same way. And attempts to use human cells in culture don9t seem to be faring any better, partly because cell culture provides no information about whether a drug will make it to the tumor site. To create better models of cancer development in humans, investigators are now drawing on knowledge of human cancer-related gene mutations to genetically alter mice so that they carry the same kinds of changes that lead to cancer in humans. The hope is that the mice will develop tumors that behave the same way the human tumors do.
Digging Deeper: Applied Ecological Economics (2015)

This booklet was designed as part of an honors contract for macroeconomics at Johnson County Community College (JCCC) in the spring of 2015. Inspiration for this project came from the author's personal desire to learn more about how one could apply economics to environmental issues.
Multiplexed dispersive readout of superconducting phase qubits (2012)

We introduce a frequency-multiplexed readout scheme for superconducting phase qubits. Using a quantum circuit with four phase qubits, we couple each qubit to a separate lumped-element superconducting readout resonator, with the readout resonators connected in parallel to a single measurement line. The readout resonators and control electronics are designed so that all four qubits can be read out simultaneously using frequency multiplexing on the one measurement line. This technology provides a highly efficient and compact means for reading out multiple qubits, a significant advantage for scaling up to larger numbers of qubits.
Controlling doping and carrier injection in carbon nanotube transistors (2002)

Carbon nanotube field-effect transistors (CNTFETs) fabricated out of as-grown nanotubes are unipolar p-type devices. Two methods for their conversion from p- to n-type devices are presented. The first method involves conventional doping with an electron donor, while the second consists of annealing the contacts in vacuum to remove adsorbed oxygen. A comparison of these methods shows fundamental differences in the mechanism of the transformation. The key finding is that the main effect of oxygen adsorption is not to dope the bulk of the tube, but to modify the barriers at the metal–semiconductor contacts. The oxygen concentration and the level of doping of the nanotube are therefore complementary in controlling the CNTFET characteristics. Finally, a method of controlling individually the contact barriers by local heating is demonstrated.
Semisynthetic Organisms with Expanded Genetic Codes (2018)

[Image: see text]
Hybrid Microgels Photoresponsive in the Near-Infrared Spectral Range (2004)

We report for the first time a photothermally responsive composite material based on polymer microgel particles doped with gold nanorods. We used the dependence of the longitudinal surface plasmon of the gold nanorods on their aspect ratio to synthesize nanoparticles with strong absorption in the near-IR spectral range (in the "water window"). The nanoparticles were incorporated in the interior of temperature-responsive poly(N-isopropylacrylamide-acrylic acid) microgels. Upon irradiation at lambda = 810 nm, hybrid microgel particles doped with Au nanorods underwent a strong deswelling phase transition. These photothermally responsive microgels can be used to carry and release small molecules (e.g., small protein molecules and drugs).
Crystal Structure ofEscherichia coliPenicillin-Binding Protein 5 Bound to a Tripeptide Boronic Acid Inhibitor:  A Role for Ser-110 in Deacylation (2005)

Penicillin-binding protein 5 (PBP 5) from Escherichia coli is a well-characterized d-alanine carboxypeptidase that serves as a prototypical enzyme to elucidate the structure, function, and catalytic mechanism of PBPs. A comprehensive understanding of the catalytic mechanism underlying d-alanine carboxypeptidation and antibiotic binding has proven elusive. In this study, we report the crystal structure at 1.6 A resolution of PBP 5 in complex with a substrate-like peptide boronic acid, which was designed to resemble the transition-state intermediate during the deacylation step of the enzyme-catalyzed reaction with peptide substrates. In the structure of the complex, the boron atom is covalently attached to Ser-44, which in turn is within hydrogen-bonding distance to Lys-47. This arrangement further supports the assignment of Lys-47 as the general base that activates Ser-44 during acylation. One of the two hydroxyls in the boronyl center (O2) is held by the oxyanion hole comprising the amides of Ser-44 and His-216, while the other hydroxyl (O3), which is analogous to the nucleophilic water for hydrolysis of the acyl-enzyme intermediate, is solvated by a water molecule that bridges to Ser-110. Lys-47 is not well-positioned to act as the catalytic base in the deacylation reaction. Instead, these data suggest a mechanism of catalysis for deacylation that uses a hydrogen-bonding network, involving Lys-213, Ser-110, and a bridging water molecule, to polarize the hydrolytic water molecule.
Cloning of the cDNA for a hematopoietic cell-specific protein related to CD20 and the beta subunit of the high-affinity IgE receptor: evidence for a family of proteins with four membrane-spanning regions. (1994)

We report the cloning of the cDNA for a human gene whose mRNA is expressed specifically in hematopoietic cells. A long open reading frame in the 1.7-kb mRNA encodes a 214-aa protein of 25 kDa with four hydrophobic regions consistent with a protein that traverses the membrane four times. To reflect the structure and expression of this gene in diverse hematopoietic lineages of lymphoid and myeloid origin, we named the gene HTm4. The protein is about 20% homologous to two other "four-transmembrane" proteins; the B-cell-specific antigen CD20 and the beta subunit of the high-affinity receptor for IgE, Fc epsilon RI beta. The highest homologies among the three proteins are found in the transmembrane domains, but conserved residues are also recognized in the inter-transmembrane domains and in the N and C termini. Using fluorescence in situ hybridization, we localized HTm4 to human chromosome 11q12-13.1, where the CD20 and Fc epsilon RI beta genes are also located. Both the murine homologue for CD20, Ly-44, and the murine Fc epsilon RI beta gene map to the same region in murine chromosome 19. We propose that the HTm4, CD20, and Fc epsilon RI beta genes evolved from the same ancestral gene to form a family of four-transmembrane proteins. It is possible that other related members exist. Similar to CD20 and Fc epsilon RI beta, it is likely that HTm4 has a role in signal transduction and, like Fc epsilon RI beta, might be a subunit associated with receptor complexes.
Standardization of Prothrombin Time for Laboratory Control of Oral Anticoagulant Therapy (1999)

Laboratory monitoring of oral anticoagulants is mandatory to ensure efficacy and safety of therapy. The test of choice is the prothrombin time (PT), using thromboplastins, which vary markedly in respect of the defect induced by oral anticoagulants. Standardization is improved by the use of the WHO calibration model for thromboplastins. This system defines the International Sensitivity Index (ISI) of a reagent in relation to a reference material. This is then used together with a locally determined mean normal PT to derive the International Normalized Ratio (INR). There is an inverse relationship between sensitivity and ISI, the lower the ISI the greater is the sensitivity of the reagent. There are important practical advantages to using a sensitive reagent with ISI of 1.2 or less. The ISI system was originally designed for manual tests and in some cases the ISI is influenced by the use of coagulometers, which generally have the effect of lowering the ISI. For this reason the ISI should be assigned for the combination of reagent and endpoint detection system. A thromboplastin should not be used with techniques for which the ISI is unknown. In some instances there is variation between instruments of the same type, in which case a local calibration using plasma calibrants with assigned values can be considered. The precise requirements for such local calibrations are presently the subject of research in a number of centers. The INR/ISI system is increasingly being adopted in many countries for anticoagulant therapy. Some past difficulties leading to discrepancies between results with different reagents have now been resolved and the view that this is the best available system for standardization of the PT for monitoring oral anticoagulants is widely held.
An Experimental Investigation of the Diversion Characteristics of Foam in Berea Sandstone Cores of Contrasting Permeabilities (1997)

Abstract Foam has been used successfully in the field as a diverting agent for matrix acidizing when layers of contrasting permeabilities are present. However, the mechanisms governing the diversion performance of foam are still not properly understood and only a limited number of foam diversion papers can be found in the literature. This paper discusses the results from several dual-core experiments using 11- and 22-inch long and 1.5-inch diameter fired Berea sandstone cores (permeability range: 10 to 1000 md) in which parameters such as foam quality, total injection rate, foam slug size, etc. are varied systematically for different permeability contrasts. Each experiment consists of a gas-free surfactant injection phase, followed by a foam injection phase, which is then followed by a brine injection phase simulating the post-foam acid injection stage. The pressure data along each core at four locations and the weight of the liquid effluents for each core are recorded continuously. An attempt is made to quantify the diversion performance by the introduction of various diversion factors. The effect of each of the variables such as foam quality, injection rate, slug size etc. on the diversion factors are then compared for different permeability contrasts. Results show strong dependence of the diversion performance on permeability contrast, foam quality and total flow rate. This study provides important guidelines for designing acid jobs for different permeability contrasts and ranges when foam is used as a diverting agent.
Functional Interactions of Phospholemman (PLM) (FXYD1) with Na+,K+-ATPase (2006)

Human FXYD1 (phospholemman, PLM) has been expressed in Pichia pastoris with porcine alpha1/His10-beta1 subunits of Na+,K+-ATPase or alone. Dodecyl-beta-maltoside-soluble complexes of alpha1/beta1/PLM have been purified by metal chelate chromatography, either from membranes co-expressing alpha1,His10-beta1, and PLM or by in vitro reconstitution of PLM with alpha1/His10-beta1 subunits. Comparison of functional properties of purified alpha1/His10-beta1 and alpha1/His10-beta1/PLM complexes show that PLM lowered K0.5 for Na+ ions moderately (approximately 30%) but did not affect the turnover rate or Km of ATP for activating Na+,K+-ATPase activity. PLM also stabilized the alpha1/His10-beta1 complex. In addition, PLM markedly (>3-fold) reduced the K0.5 of Na+ ions for activating Na+-ATPase activity. In membranes co-expressing alpha1/His10-beta1 with PLM the K0.5 of Na+ ions was also reduced, compared with the control, excluding the possibility that detergent or lipid in purified complexes compromise functional interactions. When expressed in HeLa cells with rat alpha1, rat PLM significantly raised the K0.5 of Na+ ions, whereas for a chimeric molecule consisting of transmembranes segments of PLM and extramembrane segments of FXYD4, the K0.5 of Na+ ions was significantly reduced, compared with the control. The opposite functional effects in P. pastoris and HeLa cells are correlated with endogenous phosphorylation of PLM at Ser68 or unphosphorylated PLM, respectively, as detected with antibodies, which recognize PLM phosphorylated at Ser68 (protein kinase A site) or unphosphorylated PLM. We hypothesize that PLM interacts with alpha1/His10-beta1 subunits at multiple locations, the different functional effects depending on the degree of phosphorylation at Ser68. We discuss the role of PLM in regulation of Na+,K+-ATPase in cardiac or skeletal muscle cells.
111. Carbazoles, carbolines, and related compounds. Part I. Quindoline derivatives (1947)

S. J. Holt and V. Petrow, J. Chem. Soc., 1947, 607 DOI: 10.1039/JR9470000607
Magnetization reversal in exchange biased nanocap arrays (2007)

Arrays of self-assembled polystyrene spheres with various particle sizes have been used as a substrate to study the exchange bias effect along the out-of-plane direction of Pt/Co multilayers capped with IrMn layers. The evolution of the reversal process of the resulting magnetic nanocaps was investigated by magnetic force microscopy (MFM) and magnetic transmission x-ray microscopy (M-TXM). Tip–sample interaction-induced irreversible and reversible switching events have been observed during multiple scanning cycles in MFM imaging which are ascribed to the so-called training effect. During M-TXM imaging a drastic change in morphology has been found due to the x-ray exposure, leading to the formation of much larger spherical particles. Interestingly, these merged particles reveal again an exchange coupled single-domain magnetic cap with magnetic behaviour similar to magnetic films deposited directly on spheres of similar size.
Alternative Start Sites in the Saccharomyces cerevisiae GLR1 Gene Are Responsible for Mitochondrial and Cytosolic Isoforms of Glutathione Reductase (2004)

To combat oxidative damage, eukaryotic cells have evolved with numerous anti-oxidant factors that are often distributed between cytosolic and mitochondrial pools. Glutathione reductase, which regenerates the reduced form of glutathione, represents one such anti-oxidant factor, yet nothing is known regarding the partitioning of this enzyme within the cell. Using the bakers' yeast Saccharomyces cerevisiae as a model, we provide evidence that a single gene, namely GLR1, encodes both the mitochondrial and cytosolic forms of glutathione reductase. A deletion in GLR1 drastically increases levels of oxidized glutathione in these two subcellular compartments. The GLR1 gene has two inframe start codons that are both used as translation initiation sites. Translation from the first codon generates the mitochondrial form that includes a mitochondrial targeting signal, whereas translation from the second codon produces the cytosolic form that lacks this sequence. Our results indicate that the sequence context of the two AUG codons influences the efficiency of translation initiation at each site, which in turn affects the relative levels of cytosolic and mitochondrial Glr1p. This method of subcellular distribution of glutathione reductase may be conserved in mammalian cells as well.
Stroke as a complication of cardiac catheterization: Risk factors and clinical features (2001)

The authors aimed to delineate the risk factors and radiologic pattern of stroke complicating cardiac catheterization. Twenty-two cases were matched with three control subjects. Stroke was significantly associated with severity of coronary artery disease and length of fluoroscopy time (OR 1.96 and 1.65). The use of MRI with diffusion weighting allowed the identification of multiple asymptomatic lesions and a subset of lacunar-type infarcts (23%), which most likely occurred on an atheroembolic basis.
Haystack: a platform for creating, organizing and visualizing information using RDF (2002)

The Resource Definition Framework (RDF) is designed to support agent communication on the Web, but it is also suitable as a framework for modeling and storing personal information. Haystack is a personalized information repository that employs RDF in this manner. This flexible semistructured data model is appealing for several reasons. First, RDF supports ontologies created by the user and tailored to the user&amp;apos;s needs. At the same time, system ontologies can be specified and evolved to support a variety of high-level functionalities such as flexible organization schemes, semantic querying, and collaboration. In addition, we show that RDF can be used to engineer a component architecture that gives rise to a semantically rich and uniform user interface. We demonstrate that by aggregating various types of users&amp;apos; data together in a homogeneous representation, we create opportunities for agents to make more informed deductions in automating tasks for users. Finally, we discuss the implementation of an RDF information store and a programming language specifically suited for manipulating RDF.
Late-onset hypogonadism (LOH) : an emerging pathophysiological entity requiring the physician's attention (2006)

Late-onset hypogonadism (LOH) is an emerging pathophysiological entity. Not everybody is familiar with LOH or even recognizes its existence. Since the 19th century women's life expectancy has become progressively greater than that of men and therefore their ailments associated with aging from the climacteric onwards attracted medical attention much earlier than male aging health problems. In addition, male aging problems start at a later age than the climacteric occurs in women. However, men's life expectancy is also continuously increasing: in Europe a newborn male now has a life expectancy of about 75 years, and a 60-year-old man has a statistical possibility of reaching 80 years of age. The increasing number of aging men forces physicians to focus on their health problems.
Propostas de indicadores ambientais na gestão de recursos hídricos na comunidade de Ponta Grossa dos Fidalgos, Lagoa Feia – RJ: utilização do Modelo Força Motriz/Pressão-Situação-Impacto-Resposta (2011)

Selecting alternatives that work as a potential aid to the decision-making process between government and civil society, as well as the effective dialogue between these stakeholders is one of the most important tasks for a rational and conscious use of natural resources. The importance of this work is, to structure a methodology that aims to provide the understanding of the Lagoa Feia flood perimeter, aiming at the demarcation of Protected Areas along it and solution for the conflicts generated by the use of its margins, as well as the preservation of environmental quality and landscape. Thus the data and parameters obtained with this study can be used for the decisionmaking process.