gebhart/patrepeval huggingface dataset:
Raman spectroscopy of epitaxial graphene on a SiC substrate (2008)

The fabrication of epitaxial graphene (EG) on SiC substrate by annealing has attracted a lot of interest as it may speed up the application of graphene for future electronic devices. The interaction of EG and the SiC substrate is critical to its electronic and physical properties. In this work, the Raman spectroscopy was used to study the structure of EG and its interaction with SiC substrate. All the Raman bands of EG blueshift from that of bulk graphite and graphene made by micromechanical cleavage, which was attributed to the compressive strain induced by the substrate. A model containing $13\ifmmode\times\else\texttimes\fi{}13$ honeycomb lattice cells of graphene on carbon nanomesh was constructed to explain the origin of strain. The lattice mismatch between graphene layer and substrate causes the compressive stress of $2.27\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$ on graphene. We also demonstrate that the electronic structures of EG grown on Si- and C-terminated SiC substrates are quite different. Our experimental results shed light on the interaction between graphene and SiC substrate, which are critical to the future applications of EG.
Lens and Optics for Optical Disk System (1987)

Various types of pick-up lenses and optical systems for pick-ups are discussed. We evaluated optical performances of objective lenses. Aspherical lenses for CD player pick-ups have wider field angle compared to the conventional triplet objective lens. We also evaluated reliability of both plastic and glass molded lenses which are designed in the same way. Plastic lens caused spherical aberration due to temperature change. Optical pick-ups for CD players are remarkably simplified by means of aspherical lens or holographic element. On the other hand, pick-ups for write once or erasable optical disk system consist of many optical components. For these pick-ups, we developed a single bi-aspheric molded glass lens which has high NA (0.55) and remarkable light weight (85mg).
Structures and Gas Separation Properties of Silicone-Containing Polyimides (1997)

In order to obtain polymer materials suitable for thermally stable gas separation membranes, silicone-containing polyimides (SPIs) with various chemical structures and silicone contents were prepared, and the relationship between the chemical structures and the gas separation properties was studied. The permeability of gases such as oxygen, nitrogen, carbon dioxide and methane increased with the silicone content, while the permselectivity decreased. Therefore the permeability and the permselectivity were found to be controlled by the silicone content as well as the chemical structure of the SPIs.
Design and Construction of Functional Supramolecular Metalloprotein Assemblies (2019)

Nature puts to use only a small fraction of metal ions in the periodic table. Yet, when incorporated into protein scaffolds, this limited set of metal ions carry out innumerable cellular functions and execute essential biochemical transformations such as photochemical H<sub>2</sub>O oxidation, O<sub>2</sub> or CO<sub>2</sub> reduction, and N<sub>2</sub> fixation, highlighting the outsized importance of metalloproteins in biology. Not surprisingly, elucidating the intricate interplay between metal ions and protein structures has been the focus of extensive structural and mechanistic scrutiny over the last several decades. As a result of such top-down efforts, we have gained a reasonably detailed understanding of how metal ions shape protein structures and how protein structures in turn influence metal reactivity. It is fair to say that we now have some idea-and in some cases, a good idea-about how most known metalloproteins function and we possess enough insight to quickly assess the modus operandi of newly discovered ones. However, translating this knowledge into an ability to construct functional metalloproteins from scratch represents a challenge at a whole different level: it is one thing to know how an automobile works; it is another to build one. In our quest to build new metalloproteins, we have taken an original approach in which folded, monomeric proteins are used as ligands or synthons for building supramolecular complexes through metal-mediated self-assembly (MDPSA, Metal-Directed Protein Self-Assembly). The interfaces in the resulting protein superstructures are subsequently tailored with covalent, noncovalent, or additional metal-coordination interactions for stabilization and incorporation of new functionalities (MeTIR, Metal Templated Interface Redesign). In an earlier Account, we had described the proof-of-principle studies for MDPSA and MeTIR, using a four-helix bundle, heme protein cytochrome cb<sub>562</sub> (cyt cb<sub>562</sub>), as a model building block. By the end of those studies, we were able to demonstrate that a tetrameric, Zn-directed cyt cb<sub>562</sub> complex (Zn<sub>4</sub>:M1<sub>4</sub>) could be stabilized through computationally prescribed noncovalent interactions inserted into the nascent protein-protein interfaces. In this Account, we first describe the rationale and motivation for our particular metalloprotein engineering strategy and a brief summary of our earlier work. We then describe the next steps in the "evolution" of bioinorganic complexity on the Zn<sub>4</sub>:M1<sub>4</sub> scaffold, namely, (a) the generation of a self-standing protein assembly that can stably and selectively bind metal ions, (b) the creation of reactive metal centers within the protein assembly, and (c) the coupling of metal coordination and reactivity to external stimuli through allosteric effects.
Segmentation using Deformable Spatial Priors with Application to Clothing (2010)

We present a method for segmenting the parts of multiple instances of a known object category exhibiting large variations in projected shape and colour. The method builds on an existing MRF formulation incorporating a prior shape model and colour distributions for the constituent parts. We propose a novel shape model consisting of a deformable spatial prior probability for the part-label at each pixel. We also make a simple extension to the MRF formulation to deal simultaneously with multiple objects within a global optimisation. Finally, we evaluate the method for the task of segmenting individual items of clothing in images depicting groups of people, and demonstrate improved performance against the state of the art for this task.
Silicon Porosification: State of the Art (2010)

This review is devoted to the analysis of the problems related to fabrication of the Si porous layers. The review was motivated by a great interest to Si-based porous materials from nano- to macro-scale for various applications in electronics, optoelectronics, photonics, chemical sensors, biosensors, etc. The peculiarities of the silicon porosification and the principles of preparing porous layers are considered in the present article. Various methods used for Si porosification such as chemical stain etching, chemical vapor etching, laser-induced etching, metal-assisted etching, spark processing and reactive ion (plasma) etching were analyzed. However, the main attention was focused on electrochemical porosification of Si. The review discusses in detail the influence of parameters such as electrolyte composition and pH, current density, etching time, temperature, wafer doping and orientation, lighting, magnetic field, and ultrasonic agitation on the process of Si porosification. It was shown that the structure of porous silicon strongly depends on both technological parameters of electrochemical etching and the parameters of the semiconductor subject to treatment. This review also addresses the main properties of porous silicon, porous multilayer and 3D structure formation, oxidation of porous Si, release of the porous layer, drying, storage, etching, filling and surface functionalizing of porous Si. Features of III-V compound porosification are also briefly analyzed.
The potential of nano-structured silicon oxide type coatings deposited by PACVD for control of aquatic biofouling (2008)

SiO(x)-like coatings were deposited on glass slides from a hexamethylsiloxane precursor by plasma-assisted CVD (PACVD). Surface energies (23.1-45.7 mJ m(-1)) were correlated with the degree of surface oxidation and hydrocarbon contents. Tapping mode AFM revealed a range of surface topologies with Ra values 1.55-3.16 nm and RMS roughness 1.96-4.11 nm. Settlement of spores of the green alga Ulva was significantly less, and detachment under shear significantly more on the lowest surface energy coatings. Removal of young plants (sporelings) of Ulva under shear was positively correlated with reducing the surface energy of the coatings. The most hydrophobic coatings also showed good performance against a freshwater bacterium, Pseudomonas fluorescens, significantly reducing initial attachment and biofilm formation, and reducing the adhesion strength of attached bacterial cells under shear. Taken together the results indicate potential for further investigation of these coatings for applications such as heat exchangers and optical instruments.
Computer-Aided High-Throughput Cloning of Bacteria in Liquid Medium (2011)

Bacterial cloning was first introduced over a century ago and has since become one of the most useful procedures in biological research, perhaps paralleled in its ubiquity only by PCR and DNA sequencing. However, unlike PCR and sequencing, cloning has generally remained a manual, labor-intensive, low-throughput procedure. Here we address this issue by developing an automated, computer-aided bacterial cloning method using liquid medium that is based on the principles of (i) limiting dilution of bacteria, (ii) inference of colony forming units (CFUs) based on optical density (OD) readings, and (iii) verification of monoclonality using a mixture of differently colored fluorescently labeled bacteria for transformation. We demonstrate the high-throughput utility of this method by employing it as a cloning platform for a DNA synthesis process.
A 32nm SRAM design for low power and high stability (2008)

A SRAM cell must meet stringent requirements for operation in the sub-micron/nano ranges. A nine transistor (9T) cell at a 32nm feature size in CMOS is proposed to accomplish improvements in stability, power dissipation and performance compared with previous designs for low-power memory operation. Initially, this paper presents the optimal transistor sizing for this 9T SRAM cell considering stability, energy consumption, and delay. A write bitline balancing scheme is proposed to reduce the leakage current of the SRAM cell. By optimizing size and employing the proposed write circuitry scheme, a saving of 32% in power dissipation is achieved in memory array operation compared with a conventional 6T SRAM based design. The impact of process variations is investigated in detail, and the HSPICE simulation shows that the 9T SRAM cell has an excellent tolerance to process variations.
Mapping extracellular pH in rat brain gliomas in vivo by 1H magnetic resonance spectroscopic imaging: comparison with maps of metabolites. (2001)

The value of extracellular pH (pH(e)) in tumors is an important factor in prognosisand choice of therapy. We demonstrate here that pH(e) can be mappedin vivo in a rat brain glioma by (1)H magnetic resonance spectroscopic imaging (SI) of the pH buffer (+/-)2-imidazole-1-yl-3-ethoxycarbonylpropionic acid (IEPA). (1)H SI also allowed us to map metabolites, and, to better understand the determinants of pH(e), we compared maps of pH(e), metabolites, and the distribution of the contrast agent gadolinium1,4,7,10-tetraazacyclododecane-N,N',N",N"'-tetraaceticacid (Gd-DOTA). C6 cells injected in caudate nuclei of four Wistar rats gave rise to gliomas of approximately 10 mm in diameter. Three mmols of IEPA were injected in the right jugular vein from t = 0 to t = 60 min. From t = 50 min to t = 90 min, spin-echo (1)H SI was performed with an echo time of 40 ms in a 2.5-mm slice including the glioma (nominal voxel size, 2.2 microl). IEPA resonances were detected only within the glioma and were intense enough for pH(e) to be calculated from the chemical shift of the H2 resonance in almost all voxels of the glioma. (1)H spectroscopic images with an echo time of 136 ms were then acquired to map metabolites: lactate, choline-containing compounds (tCho), phosphocreatine/creatine, and N-acetylaspartate. Finally, T(1)-weighted imaging after injection of a bolus of Gd-DOTA gave a map indicative of extravasation. On average, the gradient of pH(e) (measured where sufficient IEPA was present) from the center to the periphery was not statistically significant. Mean pH(e) was calculated for each of the four gliomas, and the average was 7.084 +/- 0.017 (+/- SE; n = 4 rats), which is acid with respect to pH(e) of normal tissue. After normalization of spectra to their water peak, voxel-by-voxel comparisons of peak areas showed that N-acetylaspartate, a marker of neurons, correlated negatively with IEPA (P < 0.0001) and lactate (P < 0.05), as expected of a glioma surrounded by normal tissue. tCho (which may indicate proliferation) correlated positively with pH(e) (P < 0.0001). Lactate correlated positively with tCho (P < 0.0001), phosphocreatine/creatine (P < 0.001), and Gd-DOTA (P < 0.0001). Although lactate is exported from cells in association with protons, within the gliomas, no evidence was observed that pH(e) was significantly lower where lactate concentration was higher. These results suggest that lactate is produced mainly in viable, well-perfused, tumoral tissue from which proton equivalents are rapidly cleared.
Adipocyte-macrophage interaction may mediate LPS-induced low-grade inflammation: Potential link with metabolic complications (2011)

Chronic low-grade infection has been suggested to be associated with metabolic disorder such as diabetes. However, the molecular mechanism underlying this important association is largely unknown. The only clue established so far is that many subjects exhibit elevated levels of C-reactive protein as measured by highly sensitive assay. Here, we hypothesized that adipocyte-macrophage interaction plays a key role in amplifying such low grade infection to the level of influencing metabolic disorders. The presence of macrophages in abdominal adipose tissues was investigated by immunohistochemistry. To see whether molecules associated with acute phase protein, LPS signaling, and persistent recruitment of monocytes, are produced at higher amounts in adipocytes co-cultured with macrophages stimulated with low concentration of LPS (1 ng/ml), we measured serum amyloid A (SAA), LPS binding protein (LBP), soluble CD14 (sCD14), and RANTES levels in culture supernatant of co-cultures. Lastly, we investigated in vivo effect of low-grade LPS infusion on the production of these molecules using obese model mice. The macrophages were certainly identified in abdominal adipose tissues. Investigated molecules, especially LBP, SAA, and RANTES were produced at higher amounts in co-cultures stimulated with LPS compared with the cells without LPS. The ob/ob, and high-fat diet-induced obesity mice produced higher amounts of LBP, SAA, and RANTES one day after LPS infusion (1 ng/ml/g body weight) compared with ob/- and normal-fat fed control mice. Thus, adipocytes and infiltrated macrophages, and their interaction with low endotoxin stimulation appear to play an important role in amplifying and maintaining LPS-induced low-grade inflammation.
Intramolecular Cycloaddition Reactions of Furo[3,4-<i>b</i>]indoles for Alkaloid Synthesis (2014)

Model studies dealing with the Cu(II)- or Rh(II)-catalyzed carbenoid cyclization/cycloaddition cascade of several α-diazo indolo amido esters have been carried out as an approach to the alkaloid scandine. The Cu(II)-catalyzed reaction of an α-diazo indolo diester that contains a tethered oxa-pentenyl side chain was found to give rise to a reactive benzo[c]furan which undergoes a subsequent [4 + 2]-cycloaddition across the tethered π-bond. The reaction proceeds by the initial generation of a copper carbenoid intermediate which cyclizes onto the adjacent carbonyl group to give a reactive benzo[c]furan which in certain cases can be isolated. Disappointingly, the analogous reaction with the related amido indolo ester failed to take place, even when the tethered π-bond contained an electron-withdrawing carbomethoxy group. It would seem that the geometric requirements for the intramolecular cycloaddition of the furo[3,4-b]indole system with the tethered π-bond imposes distinct restrictions upon the bond angles of the reacting centers to prevent the cycloaddition reaction from occurring. However, the incorporation of another carbonyl group on the nitrogen atom of the tethered alkenyl diazo amido indolo ester seemingly provides better orbital overlap between the reacting π-systems and allows the desired cycloaddition reaction to occur.
Infection of colonic epithelial cell lines by type 1 human immunodeficiency virus is associated with cell surface expression of galactosylceramide, a potential alternative gp120 receptor. (1993)

The gastrointestinal tract plays a major role in the pathogenesis and pathophysiology of infection by the type 1 human immunodeficiency virus (HIV-1). It is a potential route for viral entry and it is the site of a number of complications, including both opportunistic infections and a primary HIV-induced enteropathy. Correspondingly, both in vivo and in vitro studies have demonstrated HIV infection of gastrointestinal cells of lymphoid and epithelial origin. HT-29, a human colonic epithelial cell line that is infectable with many HIV-1 strains, does not express CD4 protein or mRNA. Recent studies showed that antibodies recognizing a neutral glycolipid related to galactosylceramide (GalCer) in HT-29 cells inhibited HIV-1 infection of this cell line, extending previous findings in neural cells. In the current studies, we further analyzed the neutral glycolipids of HT-29 cells and showed that they contained authentic GalCer and that recombinant gp120 bound to this glycolipid. Moreover, by analyzing GalCer expression in clones derived from HT-29 and Caco-2 (another human colonic cell line), we observed that the level of expression of this glycolipid was associated with the sensitivity to HIV-1 infection. Subclones of Caco-2 did not express GalCer and were not infectable with any of three HIV-1 strains. These results strengthen the possibility that GalCer is an alternative receptor in CD4- cell lines. Furthermore, since GalCer is a major glycolipid in epithelial cells of the small intestine and colon, these results provide a structural basis for the binding of HIV-1 by gastrointestinal epithelial cells and the entry of the virus into those cells.
<scp>ADX</scp>71441, a novel, potent and selective positive allosteric modulator of the <scp>GABA<sub>B</sub></scp> receptor, shows efficacy in rodent models of overactive bladder (2013)

Our findings demonstrate, for the first time, that a GABAB PAM has potential as a novel approach for the treatment of OAB.
Error Estimates in Some Commonly Used Earthquake Location Programs (1984)

Research Article| April 01, 1984 Error Estimates in Some Commonly Used Earthquake Location Programs Thomas M. Boyd; Thomas M. Boyd Virginia Tech Seismological Observatory, Department of Geological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 *Presently at Lamont-Doherty Geological Observatory, of Columbia University, Palisades, New York 10964 Search for other works by this author on: GSW Google Scholar J. Arthur Snoke J. Arthur Snoke Virginia Tech Seismological Observatory, Department of Geological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 Search for other works by this author on: GSW Google Scholar Seismological Research Letters (1984) 55 (2): 3–6. https://doi.org/10.1785/gssrl.55.2.3 Article history first online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation Thomas M. Boyd, J. Arthur Snoke; Error Estimates in Some Commonly Used Earthquake Location Programs. Seismological Research Letters 1984;; 55 (2): 3–6. doi: https://doi.org/10.1785/gssrl.55.2.3 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietySeismological Research Letters Search Advanced Search Abstract Most earthquake location programs provide the user with some estimate of the error in the calculated hypocentral solution. Because the criteria used in estimating these errors differ, a cross-reference guide of error estimates is provided herein for some of the more widely used programs (HYPOELLIPSE, FASTHYPO, HYPO71, and HYPOINVERSE).In all the programs considered, an individual confidence interval is given for the depth error. For the epicentral error, HYPO71 and HYPOINVERSE provide only individual confidence estimates, while the other programs provide epicentral joint confidence regions. The programs differ in the type of statistic used: a x2 statistic (HYPOELLIPSE), or no explicitly assumed statistic (HYPO71, HYPOINVERSE, FASTHYPO). There are also differences in confidence levels: 83% (HYPOELLIPSE epicentral region), 94% (HYPOELLIPSE depth interval), 39% (FASTHYPO epicentral region assuming a x2, value of 1.0), and 68% (FASTHYPO, HYPO71, and HYPOINVERSE depth intervals assuming a x2 value of 1.0). In almost all cases, confidence intervals and regions can be rescaled to a common reference. This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Progress in the design of a radiation-hard plastic scintillator (1991)

The authors present an update on research started three years ago with the goal of developing plastic scintillators able to endure annual doses of 10/sup 4/ to 10/sup 5/ Gy or more. Attention is given to radiation damage to plastic scintillators, techniques to improve radiation resistance (wavelength shifting and radiation-tolerant plastic bases), and other issues. It is concluded that, although the studies of scintillators must continue in order to define the limits of current capabilities, there is a need to move beyond the study of 'naked' scintillators (whether as plates or optical fibres) and to study them 'dressed' within a detector system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Production of GST-SOD fusion protein by recombinantE coli XL1 Blue (2000)

A recombinant plasmid was constructed by inserting a DNA fragment with the coding region of Cu/Zn–superoxide dismutase (Cu/Zn–SOD) cDNA from sweet potato, Ipomoea batatas (l) Lam cv Tainong 57, into the 3′ end of the open reading frame of the glutathione S-transferase (GST) gene in an expression vector, pGEX-2T. The constructed plasmid was transformed into E coli XL1 Blue. Fusion proteins of Cu/Zn–SOD and GST (GST–SOD) were produced from the recombinant E coli. About 6 mg of GST–SOD fusion proteins could be obtained from 1 dm3 of cultural broth after induction with 0.075 mmol dm−3 Isopropyl-β-D-thiogalactoside (IPTG). Lactose was not an efficient inducer. High cell density culture was performed by fed-batch fermentation using a glucose analyzer to control glucose concentration at 1 g dm−3. The cell density of the fed-batch culture reached an OD600 of 30, the total amount of GST–SOD fusion protein was 100 mg dm−3 which is about 14 times more than that of the batch culture. Most of the fusion proteins were shown to be in an active monomeric form, and the molecular weight was estimated to be 45 kDa by SDS–PAGE and 47 kDa by gel filtration. The specific activity of the purified fusion proteins was about 1200 mg−1 and equal to 3200 unit per mg of SOD domain only. © 2000 Society of Chemical Industry