gebhart/patrepeval huggingface dataset:
Surface participation and dielectric loss in superconducting qubits (2015)

We study the energy relaxation times (T1) of superconducting transmon qubits in 3D cavities as a function of dielectric participation ratios of material surfaces. This surface participation ratio, representing the fraction of electric field energy stored in a dissipative surface layer, is computed by a two-step finite-element simulation and experimentally varied by qubit geometry. With a clean electromagnetic environment and suppressed non-equilibrium quasiparticle density, we find an approximately proportional relation between the transmon relaxation rates and surface participation ratios. These results suggest dielectric dissipation arising from material interfaces is the major limiting factor for the T1 of transmons in 3D circuit quantum electrodynamics architecture. Our analysis also supports the notion of spatial discreteness of surface dielectric dissipation.
Chemical Nucleases: New Reagents In Molecular Biology (1990)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Mechanism of action and selectivity of a novel fungicide, pyribencarb (2010)

Pyribencarb is a novel benzylcarbamate-type fungicide, which is active against a wide range of plant pathogenic fungi. In this paper, the inhibitory effects of this fungicide on the electron transport system of fungi, plants, rat and carp were examined to elucidate its mode of action and selectivity. Pyribencarb potently inhibited succinate-cytochrome c reductase (SCR) activities of Botrytis cinerea (cucumber gray mold), Corynespora cassiicola (leaf spot) and decylubiquinol-cytochrome c reductase (UCR) activity of B. cinerea. Pyribencarb inhibited the UCR of B. cinerea in an uncompetitive manner with respect to decylubiquinol, which was the same as strobilurin fungicides, and the substrate-dependent inhibition constant was found from calculation to be 13 nM. These results suggested that the target site of pyribencarb is cytochrome b of complex III in the electron transport system of the respiratory chain. On the other hand, the inhibitory potency of pyribencarb on SCR activities of plants, rats and carp was relatively weak compared with that of strobilurin fungicides, indicating that pyribencarb is a Qo inhibitor of cytochrome b, whose properties are superior to well-known Qo inhibitor fungicides in terms of target. The binding site of pyribencarb on cytochrome b was assumed to be a little different from that of strobilurin fungicides, because pyribencarb inhibited SCRs of strobilurin fungicide-resistant strains of B. cinerea and C. cassiicola with relatively low concentrations. The binding site was also discussed through comparison of amino acid sequences of plants, rats, carp, yeast and fungi, including B. cinerea, which was elucidated in this paper.
An Overview of Epithelio-Mesenchymal Transformation (1995)

Epithelium is the tissue phenotype of early embryos and primitive adults of the chordate phylum. A second tissue type, however, is produced by epithelial-mesenchymal transformation (EMT) in higher chordates, such as vertebrata. Mesenchymal cells have the ability, which true epithelia do not, to invade and migrate through the extracellular matrix (ECM) to create dramatic cell transpositions. The first-formed or primary mesenchymal cells in amniote vertebrates migrate from the primitive streak to differentiate into the mesodermal and endodermal epithelia. Definitive mesenchyme with connective tissue and muscle potentials arises from the epithelial mesoderm at about the same time as the neural crest mesenchyme forms from the ectoderm. Later on in embryogenesis. EMT is used to remodel unwanted epithelia, such as that of the palate medial edges. We discuss the mechanisms by which epithelial cells transform into mesenchyme and vice versa. On the one hand, cells activate putative mesenchymal master genes, turn off epithelial genes, and acquire motility machinery that allows them to interact in 3 dimensions (3D) with ECM via actin cortex while sliding their endoplasm into their new front ends. On the other hand, primary mesenchymal cells can reactivate epithelial regulatory genes, such as E-cadherin, turn off the motility machinery for invading ECM, and reexpress apical-basal polarity. We review the genes, such as FSP1, src, ras, and fos, that are activated in cells transforming to mesenchyme and the genes their neighbors activate to induce EMT, such as those for TGF beta, NT-3, and sonic hedgehog. Suspension in 3D collagen gels can induce adult epithelium to undergo EMT; alpha 5 beta 1 integrin is activated on surfaces in contact with collagen, including apical surfaces that do not normally express integrins. In vivo, it is possible that pathological manipulations of a cell's environment likewise induce EMT. Of the examples we give, the creation of invasive metastatic carcinoma cells by EMT is the most fearful. Interestingly, transfection of either metastatic cells or normal embryonic fibroblasts with the E-cadherin gene converts them to the epithelial phenotype. It may be possible in the future to manipulate the tissue phenotype of diseased cells to the advantage of the animal.
Distributed functions of detection and discrimination of vibrotactile stimuli in the hierarchical human somatosensory system (2015)

According to the hierarchical view of human somatosensory network, somatic sensory information is relayed from the thalamus to primary somatosensory cortex (S1), and then distributed to adjacent cortical regions to perform further perceptual and cognitive functions. Although a number of neuroimaging studies have examined neuronal activity correlated with tactile stimuli, comparatively less attention has been devoted toward understanding how vibrotactile stimulus information is processed in the hierarchical somatosensory cortical network. To explore the hierarchical perspective of tactile information processing, we studied two cases: (a) discrimination between the locations of finger stimulation; and (b) detection of stimulation against no stimulation on individual fingers, using both standard general linear model (GLM) and searchlight multi-voxel pattern analysis (MVPA) techniques. These two cases were studied on the same data set resulting from a passive vibrotactile stimulation experiment. Our results showed that vibrotactile stimulus locations on fingers could be discriminated from measurements of human functional magnetic resonance imaging (fMRI). In particular, it was in case (a) we observed activity in contralateral posterior parietal cortex (PPC) and supramarginal gyrus (SMG) but not in S1, while in case; (b) we found significant cortical activations in S1 but not in PPC and SMG. These discrepant observations suggest the functional specialization with regard to vibrotactile stimulus locations, especially, the hierarchical information processing in the human somatosensory cortical areas. Our findings moreover support the general understanding that S1 is the main sensory receptive area for the sense of touch, and adjacent cortical regions (i.e., PPC and SMG) are in charge of a higher level of processing and may thus contribute most for the successful classification between stimulated finger locations.
Thermal conductivity of opals and related composites (2001)

The thermal current flow through periodic composites and the corresponding effective thermal conductivities are studied within a continuum approach. We formulate a boundary-integral method for calculating the thermal conductivity of structures with two- and three-dimensional periodic lattices. Explicit results are given for lattices involving overlapping features and contact is made with the Maxwell approximation for simple porous media. As a particular example detailed calculations are made for the thermal conductivities of media in the synthetic opal class of composites. We consider opals that are comprised of overlapping spheres arrayed in face-centered-cubic lattices and inverse opals that are formed by filling the interconnected pores of opal lattices.
Volatile Organic Compounds of Lung Cancer and Possible Biochemical Pathways (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTVolatile Organic Compounds of Lung Cancer and Possible Biochemical PathwaysMeggie Hakim†, Yoav Y. Broza†, Orna Barash†, Nir Peled‡, Michael Phillips§, Anton Amann∥⊥, and Hossam Haick*†View Author Information† The Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel‡ The Thoracic Cancer Research and Detection Center, Sheba Medical Center, Tel-Aviv University, Tel-Aviv 52621, Israel§ Menssana Research, Inc., Fort Lee, New Jersey 07024, United States∥ Breath Research Institute, Austrian Academy of Sciences, 6850 Dornbirn, Austria⊥ University-Clinic for Anesthesia, Innsbruck Medical University, 6020 Innsbruck, Austria*E-mail: [email protected]Cite this: Chem. Rev. 2012, 112, 11, 5949–5966Publication Date (Web):September 19, 2012Publication History Received26 April 2012Published online19 September 2012Published inissue 14 November 2012https://pubs.acs.org/doi/10.1021/cr300174ahttps://doi.org/10.1021/cr300174areview-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views15447Altmetric-Citations665LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aldehydes,Anatomy,Cells,Chromatography,Volatile organic compounds Get e-Alerts
SOCIAL CAPITAL AND VALUE CREATION: THE ROLE OF INTRAFIRM NETWORKS. (1998)

Using data collected from multiple respondents in all the business units of a large multinational electronics company, we examined the relationships both among the structural, relational, and cogni...
Coplanar-waveguide-based terahertz hot-electron-bolometer mixers mproved embedding circuit description (2002)

Series-fed coplanar-waveguide embedding circuits have been recently developed for terahertz mixers using, in particular, superconducting devices as sensors. Although these mixers show promising performance, they usually also show a considerable downward shift in the resonating frequency when compared with calculations using simplified models. This effect is basically caused by parasitics due to the extremely small details (in terms of wavelength) of the device and to the connection of the remaining circuitry (i.e., RF filter). In this paper, we present an improved equivalent-network model of such devices that agrees with measured results. We first propose a method to calculate the characteristic impedance and propagation constant of the coplanar waveguide, etched between two semi-infinite media, which connect the receiving slot antennas to the superconducting device. In the formulation, we take into account, for the first time, the radiation power leakage. We then describe the procedure to calculate the reactances due to the detailed geometry of the mixer device and circuit and we correct the input impedance, calculated with a commonly used simplified network. Finally, by comparing our results with a complete set of measured data, for seven mixers in the range between 500 GHz-3 THz, we analyze the features of our model and propose further improvements. Useful guidelines for designing terahertz mixer circuits are also given.
Mechanism of d -Cycloserine Action: Alanine Racemase from Escherichia coli W (1972)

The antibiotic d-cycloserine is an effective inhibitor of alanine racemase. The lack of inhibition by l-cycloserine of alanine racemase from Staphylococcus aureus led Roze and Strominger to formulate the cycloserine hypothesis. This hypothesis states that d-cycloserine has the conformation required of the substrates on the enzyme surface and that l-cycloserine cannot have this conformation. Alanine racemase from Escherichia coli W has been examined to establish whether these observations are a general feature of all alanine racemases. The enzyme (molecular weight = 95,000) has Michaelis-Menten constants of 4.6 x 10(-4)m and 9.7 x 10(-4)m for d- and l-alanine, respectively. The ratio of V(max) in the d- to l-direction is 2.3. The equilibrium constant calculated from the Haldane relationship is 1.11 +/- 0.15. Both d- and l-cycloserine are competitive inhibitors with constants (K(i)) of 6.5 x 10(-4)m and 2.1 x 10(-3)m, respectively. The ratio of K(m)d-alanine to K(i)d-cycloserine is 0.71, and the ratio of K(m)l-alanine to K(i)l-cycloserine is 0.46. Since l-cycloserine is an effective inhibitor, it is concluded that the cycloserine hypothesis does not apply to the enzyme from E. coli W.
Adaptive resolution in physics based virtual environments (2008)

We propose a systematic approach to adaptive resolution in physics based virtual environments (VEs) that combines the conventional requirements of realtime performance, visual appearance with impor ...
The Evolution of Automation in Drilling (2007)

Abstract This paper has been written for the keynote speech to be given in the "Drilling Automation – Where Are The Game Changers?" plenary session for the 2007 SPE Annual Technical Conference and Exhibition in Anaheim, California. The paper covers the evolution of drilling mechanization and automation from the mid-nineteenth century to today. In the history of drilling, there have many aspects of drilling mechanization and automation that have been investigated, machines designed and built, and operations implemented with varying levels of success and many failures. These aspects include drilling fluid systems, cementing operations, downhole automation, and the rig floor. Because drilling mechanization and automation history has been centered on the rig floor and related surface operations, the focus of this paper is on the rig floor for drilling operations such as rate of penetration, rotary systems, rig floor mechanization and automation, and entire drilling rig automation.
An On‐Line Approach To Monitor Ethanol Fermentation Using FTIR Spectroscopy (2007)

Fermentation process control is currently limited by its inability to measure parameters such as substrate, product, and biomass concentrations rapidly for consistent on-line feedback. Physical and chemical parameters, such as temperature and pH, currently can be obtained on-line using appropriate sensors. However, to obtain information on the concentration of the substrate, product, and biomass, samples must be taken off-line for measurement. With the use of spectroscopic techniques, real-time monitoring of process constituents such as product and substrate is possible. Spectroscopic techniques are rapid and nondestructive, require minimal or no sample preparation, and can be used to simultaneously assess several constituents in complex matrices. The production of ethanol is the largest fermentation process in terms of production volume and economic value as a result of its prominence in the food, agricultural, and fuel industries. This study attempts to develop an on-line ethanol fermentation monitoring technique using Fourier transform infrared (FTIR) spectroscopy with a flow-through ATR capability. Models developed using multivariate statistics, employed to obtain on-line FTIR measurements, were successfully validated by off-line HPLC analysis and spectrophotometry data. Standard errors of prediction (SEP) values of 0.985 g/L (R2 = 0.996), 1.386 g/L (R2 = 0.998), and 0.546 (R2 = 0.972) were obtained for ethanol, glucose, and OD, respectively. This work demonstrates that FTIR spectroscopy could be used for rapid on-line monitoring of fermentation.
Depletion of FOXP3+ regulatory T cells promotes hypercholesterolemia and atherosclerosis (2013)

Atherosclerosis is a chronic inflammatory disease promoted by hyperlipidemia. Several studies support FOXP3-positive regulatory T cells (Tregs) as inhibitors of atherosclerosis; however, the mechanism underlying this protection remains elusive. To define the role of FOXP3-expressing Tregs in atherosclerosis, we used the DEREG mouse, which expresses the diphtheria toxin (DT) receptor under control of the Treg-specific Foxp3 promoter, allowing for specific ablation of FOXP3+ Tregs. Lethally irradiated, atherosclerosis-prone, low-density lipoprotein receptor-deficient (Ldlr(-/-)) mice received DEREG bone marrow and were injected with DT to eliminate FOXP3(+) Tregs. Depletion of Tregs caused a 2.1-fold increase in atherosclerosis without a concomitant increase in vascular inflammation. These mice also exhibited a 1.7-fold increase in plasma cholesterol and an atherogenic lipoprotein profile with increased levels of VLDL. Clearance of VLDL and chylomicron remnants was hampered, leading to accumulation of cholesterol-rich particles in the circulation. Functional and protein analyses complemented by gene expression array identified reduced protein expression of sortilin-1 in liver and increased plasma enzyme activity of lipoprotein lipase, hepatic lipase, and phospholipid transfer protein as mediators of the altered lipid phenotype. These results demonstrate that FOXP3(+) Tregs inhibit atherosclerosis by modulating lipoprotein metabolism.
New developments in the treatment of acute myeloid leukemia. (2000)

Curative therapy for acute myeloid leukemia (AML) remains unsatisfactory. However, three recent advances may play an important role in determining how AML is treated in the near future. First, the development of targeted antibody therapy using the anti-CD33-calicheamicin conjugate (gemtuzumab ozogamicin, Mylotarg) represents a novel targeted approach to the killing of leukemia cells. Second, modern molecular methods have improved our ability to identify minimal residual disease (MRD) in patients who appear to be in remission. These methods will allow physicians to tailor therapy, offering, for example, more intensive therapy to patients who harbor MRD. Lastly, the development of microarray gene expression technology allows for the simultaneous study of thousands of genes. With this technology, we may determine the genes responsible for the biological properties of treatment response and relapse in leukemia patients.
Increased expression of monocyte chemotactic protein-1 during active hepatic fibrogenesis: correlation with monocyte infiltration. (1998)

Monocyte chemotactic protein (MCP)-1 is a chemoattractant and activator for circulating monocytes and T lymphocytes. We investigated MCP-1 protein and gene expression during chronic liver disease at different stages, using immunohistochemistry and in situ hybridization, respectively. In normal liver, a modest expression of MCP-1 was confined to few peri-sinusoidal cells and to bile duct epithelial cells. During chronic hepatitis, MCP-1 immunostaining and gene expression were evident in the inflammatory infiltrate of the portal tract. In tissue from patients with active cirrhosis, MCP-1 expression was clearly up-regulated and was present in the portal tract, in the epithelial cells of regenerating bile ducts, and in the active septa surrounding regenerating nodules. A combination of in situ hybridization for MCP-1 and immunohistochemistry showed that activated stellate cells and monocyte/macrophages contribute to MCP-1 expression in vivo together with bile duct epithelial cells. Comparison of serial sections of liver biopsies from patients with various degrees of necro-inflammatory activity showed that infiltration of the portal tracts with monocytes/macrophages is directly correlated with the expression of MCP-1. These data expand previous in vitro studies showing that secretion of MCP-1 may contribute to the formation and maintenance of the inflammatory infiltrate observed during chronic liver disease.
Emergence of Anaplasma marginale Antigenic Variants during Persistent Rickettsemia (1999)

Anaplasma marginale is an ehrlichial pathogen of cattle, in the order Rickettsiales, that establishes persistent cyclic rickettsemia in the infected host. Within each rickettsemic cycle, A. marginale expressing antigenically variant major surface protein 2 (MSP2) emerge. By cloning 17 full-length msp2 transcripts expressed during cyclic rickettsemia, we determined that emergent variants have a single, central hypervariable region encoding variant B-cell epitopes. The N- and C-terminal regions are highly conserved among the expressed A. marginale variants, and similar sequences define the MSP2 homologues in the agent of human granulocytic ehrlichiosis (HGE). This is in contrast to the MSP2 homologues in ehrlichial genogroup I pathogens, Ehrlichia chaffeensis, Ehrlichia canis, and Cowdria ruminantium, that have multiple hypervariable regions. By defining the variable and conserved regions, we were able to show that the single hypervariable region of A. marginale MSP2 encodes epitopes that are immunogenic and induce variant-specific antibody responses during persistent infection. These findings demonstrate that the MSP2 structural variants that emerge during each cycle of persistent rickettsemia are true antigenic variants, consistent with MSP2 antigenic variation as a mechanism of A. marginale persistence.
[The expression of cytokeratin No. 17 in squamous cell cancer of the cervix uteri: an immunohistochemical study of 19 cases]. (1992)

Monoclonal antibodies E3 against cytokeratin No. 17 were used for immunohistochemical examination of samples from 19 squamous-cell carcinomas of the uterine cervix and 10 cases of squamous-cell metaplasia of the endocervix. The above antibodies selectively labelled reserve cells of the cervical canal mucosa, basal layer of mature metaplastic epithelium and parabasal and basal cells of immature metaplastic squamous epithelium. In large-cell keratinizing, non-keratinizing and small-cell carcinomas, the expression of cytokeratin No. 17 revealed tendency to basal orientation and was in many respects similar to that in metaplastic squamous epithelium. It was suggested that all the squamous-cell carcinomas studied originated from reserve (metaplastic) cells.
Choice of peptide and peptide length for the generation of antibodies reactive with the intact protein (1985)

N-terminal peptides of bovine ribonuclease (RNase) of 20, 13 and 7 amino acid residues were isolated by reversed-phase high-performance liquid chromatography (HPLC). Antibodies were raised in mice against these peptides coupled to bovine serum albumin (BSA). It was shown that antibodies against the peptides reacted with the intact protein and that the immune response decreased with decreasing size of peptide. In order to obtain a satisfactory reaction with the intact protein, the peptide immunogen should be longer than 7 amino acids.