gebhart/patrepeval huggingface dataset:
Hole Schottky barrier height enhancement and its application to metal–semiconductor–metal photodetectors (2001)

Hole Schottky barrier heights on GaAs have been studied experimentally by using a conventional metal–semiconductor–metal photodetector (MSMPD) structure. The Schottky barrier height for holes was obtained directly by the hole-current dominated dark current measurement of the MSMPD. With a thin, highly doped surface layer, control of the Schottky barrier heights for holes from 0.48 to 0.79 eV was obtained. By using these engineered Schottky contacts in the MSMPDs, over three orders of magnitude reduction in the dark currents of the MSMPDs was achieved.
Successful classroom deployment of a social document annotation system (2012)

NB is an in-place collaborative document annotation website targeting students reading lecture notes and draft textbooks. Serving as a discussion forum in the document margins, NB lets users ask and answer questions about their reading material as they are reading. NB users can read and annotate documents using their web browsers, without any special plug-ins. We describe the NB system and its evaluation in real class environment, where students used it to submit their reading assignments, ask questions and get or provide feedback. We show that this tool can be and has been successfully incorporated into a number of different classes at different institutions. To understand how and why, we focus on a particularly successful class deployment where the instructor adapted his teaching style to take students' comment into account. We analyze the annotation practices that were observed - including the way geographic locality was exploited in ways unavailable in traditional forums - and discuss general design implications for online annotation tools in academia.
Epigenetics: differential DNA methylation in mammalian somatic tissues (2008)

Epigenetics refers to heritable phenotypic alterations in the absence of DNA sequence changes, and DNA methylation is one of the extensively studied epigenetic alterations. DNA methylation is an evolutionally conserved mechanism to regulate gene expression in mammals. Because DNA methylation is preserved during DNA replication it can be inherited. Thus, DNA methylation could be a major mechanism by which to produce semi-stable changes in gene expression in somatic tissues. Although it remains controversial whether germ-line DNA methylation in mammalian genomes is stably heritable, frequent tissue-specific and disease-specific de novo methylation events are observed during somatic cell development/differentiation. In this minireview, we discuss the use of restriction landmark genomic scanning, together with in silico analysis, to identify differentially methylated regions in the mammalian genome. We then present a rough overview of quantitative DNA methylation patterns at 4600 NotI sites and more than 150 differentially methylated regions in several C57BL/6J mouse tissues. Comparative analysis between mice and humans suggests that some, but not all, tissue-specific differentially methylated regions are conserved. A deeper understanding of cell-type-specific differences in DNA methylation might lead to a better illustration of the mechanisms behind tissue-specific differentiation in mammals.
Animal models and the prediction of efficacy in clinical trials of analgesic drugs: A critical appraisal and call for uniform reporting standards (2008)

Rice, Andrew S.C.; Cimino-Brown, Dorothy; Eisenach, James C.; Kontinen, Vesa K.; Lacroix-Fralish, Michael L.; Machin, Ian; Mogil, Jeffrey S.; Stöhr, Thomas (on behalf of the Preclinical Pain Consortium) Author Information
Silicon nanoridge array waveguides for nonlinear and sensing applications (2015)

We fabricate and characterize waveguides composed of closely spaced and longitudinally oriented silicon ridges etched into silicon-on-insulator wafers. Through both guided mode and bulk measurements, we demonstrate that the patterning of silicon waveguides on such a deeply subwavelength scale is desirable for nonlinear and sensing applications alike. The proposed waveguide geometry simultaneously exhibits comparable propagation losses to similar schemes proposed in literature, an enhanced effective third-order nonlinear susceptibility, and high sensitivity to perturbations in its environment.
Capricate (2015)

3D printing is widely used to physically prototype the look and feel of 3D objects. Interaction possibilities of these prototypes, however, are often limited to mechanical parts or post-assembled electronics. In this paper, we present Capricate, a fabrication pipeline that enables users to easily design and 3D print highly customized objects that feature embedded capacitive multi-touch sensing. The object is printed in a single pass using a commodity multi-material 3D printer. To enable touch input on a wide variety of 3D printable surfaces, we contribute two techniques for designing and printing embedded sensors of custom shape. The fabrication pipeline is technically validated by a series of experiments and practically validated by a set of example applications. They demonstrate the wide applicability of Capricate for interactive objects.
Solution Structure of the Viral Receptor Domain of Tva and Its Implications in Viral Entry (2002)

Tva is the cellular receptor for subgroup A avian sarcoma and leukosis virus (ASLV-A). The viral receptor function of Tva is determined by a 40-residue, cysteine-rich motif called the LDL-A module. Here we report the solution structure of the LDL-A module of Tva, determined by nuclear magnetic resonance (NMR) spectroscopy. Although the carboxyl terminus of the Tva LDL-A module has a structure similar to those of other reported LDL-A modules, the amino terminus adopts a different conformation. The LDL-A module of Tva does not contain the signature antiparallel beta-sheet observed in other LDL-A modules, and it is more flexible than other reported LDL-A modules. The LDL-A structure of Tva provides mechanistic insights into how a simple viral receptor functions in retrovirus entry. The side chains of H38 and W48 of Tva, which have been identified as viral contact residues by mutational analysis, are solvent exposed, suggesting that they are directly involved in EnvA binding. However, the side chain of L34, another potential viral contact residue identified previously, is buried inside of the module and forms the hydrophobic core with other residues. Thus L34 likely stabilizes the Tva structure but is not a viral interaction determinant. In addition, we propose that the flexible amino-terminal region of Tva plays an important role in determining specificity in the Tva-EnvA interaction.
Implement role based access control with attribute certificates (2004)

Nowadays more and more activities are performed over the Internet. But as more people are involved in the transaction circle, security and authorization control becomes one of the biggest concerns. Hence, We are motivated by the need 10 manage and to enforce a strong authorization mechanism in large-scale web-environment. Role based access control (RBAC) provides some flexibility to security management. Public key infrastructure (PKI) can provide a strong authentication. Privilege management infrastructure (PMI) as a new technology can provide strong authorization. In order to satisfy mentioned security requirements, we have established a role based access control infrastructure and developed a prototype that uses X.509 public key certificates (PKCs) and attribute certificates (ACs). Access control is performed by access control policies that are written in XML. Policies and roles are stored in ACs. PKCs and AO are all stored in LDAP servers. A new solution for policy management is described. The main components of the prototype are administration tool and access control engine. The access control engine provides a service that mediates the data between the users and the resources, which is also responsible for authentication and authorization. The administration tool can create key pairs, PKCs and ACs, manage users' information, and so on.
Gelcasting superalloy powders (1995)

Gelcasting is a process for forming inorganic powders into complex shapes. It was originally developed for ceramic powders. A slurry of powder and a monomer solution is poured in to mold and polymerized in-situ to form gelled parts. Typically, only 2-4 wt % Polymer is used. The process has both aqueous and nonaqueous versions. Gelcasting is a generic process and has been used to produce ceramic parts from over a dozen different ceramic compositions ranging from alumina-based refractories to high-performance silicon nitride. Recently, gelcasting has been applied to forming superalloy powders into complex shapes. This application has posed several challenges not previously encountered in ceramics. In particular, problems were caused by the larger particle size and the higher density of the particles. Additional problems were encountered with binder removal. How these problems were overcome will be described.
Internal architecture of the core nucleosome: fluorescence energy transfer studies at methionine-84 of histone H4 (1986)

Chicken histone H4, labeled separately at Met-84 with N-[[(iodoacetyl)amino]ethyl]-5-naphthylamine-1-sulfonic acid and 5-(iodoacetamido)fluorescein, was reassociated with unlabeled histones H2A, H2B, and H3 and 146 base pairs of DNA to produce fluorescently labeled nucleosomes having physical characteristics virtually the same as those of native core particles. Four types of particles were prepared containing respectively unlabeled H4, dansylated H4, fluoresceinated H4, and a mixture of the two labeled H4 molecules. Quantitative singlet-singlet energy-transfer measurements were carried out to determine changes in the distance between the two Met-84 H4 sites within the same nucleosome following conformational transitions which we have reported earlier. In the ionic strength range 0.1-100 mM NaCl, the distance between these sites is less than 2 nm except at 1 mM. Between 100 and 600 mM monovalent salt the distance separating the donor and acceptor fluors at Met-84 H4 increases to 3.8 nm. The conformational change centered around 200 mM NaCl is cooperative. Our results and those of others indicate that there is little unfolding of the histone octamer, at least around Met-84 H4, in the entire ionic strength range studied. A mechanism involving the rotation of the globular portion of H4 is proposed to account for this transition which occurs at physiological ionic strengths.
Low loss broadband transmission in optimized core-shape Kagome Hollow-Core PCF (2010)

A Kagome-lattice hollow-core photonic crystal fiber with a hypocycloid-shaped core enhances the coupling-inhibition between the core- and cladding-modes, thus providing an optical attenuation <250dB/km. This rivals the state-of-the-art photonic bandgap hollow-core fibers is demonstrated.
Effective Fades and Flashlight Detection Based on Accumulating Histogram Difference (2006)

Scene change detection is a fundamental step in automatic video indexing, browsing and retrieval. Fade in and fade out are two kinds of gradually changing scenes which are difficult to be detected in comparison with the abruptly changing scenes. The salient character of flashlight effect is the luminance change, which is caused by abrupt appearance or disappearance of the illumination source. Performance of shot boundary detection is not satisfactory for the video sequences containing flashlights, if no flashlight discrimination strategy is adopted. In this paper, an effective fades and flashlight detection method is proposed for both the compressed and uncompressed videos, based on the accumulating histogram difference (AHD). This fades detection method is proposed in terms of their mathematical models. AHDs of all the two consecutive frames during fades transitions can be classified into six cases. The flashlight detection method is proposed based on the AHD and the energy variation characters. AHD and energy variation characters for the starting and ending frames of a flashlight have certain regularities, which can also be expressed by cases. Thus the fades and flashlight detection problems are converted into cases matching ones. Experimental results on several test video sequences with different bit rates show the effectiveness of the proposed AHD based fades and flashlight detection method
Effect of BaCeO<tex>$_3$</tex>and BaSnO<tex>$_3$</tex>Additives on Microstructural Development and Critical Current Density of Melt Textured YBa<tex>$_2$</tex>Cu<tex>$_3$</tex>O<tex>$_7-x$</tex> (2005)

Improvement of superconducting properties, such as critical current density J/sub c/ and trapped magnetic field, of melt textured YBa/sub 2/Cu/sub 3/O/sub 7-x/ (Y123) require introducing of effective pinning sites, e.g., nonsuperconducting inclusions, twin boundaries and other defects. It has been shown that addition of small quantities of BaCeO/sub 3/ (<0.5 wt%) into Y123 results in an increase of the J/sub c/. However, higher cerium concentrations affect the solidification process and inhibit the growth of melt textured Y123 single crystals. In this study, the effect of BaCeO/sub 3/ additions on the growth and microstructural development of melt textured Y123 single crystals were investigated. The relationship between the solidification kinetics, microstructural development and superconducting properties of Y123 melt textured single crystals with cerium additives is discussed.
Radiating and Nonradiating Classical Current Distributions and the Fields They Generate (1973)

Several general theorems are established relating to well-behaved, localized, monochromatic current distributions and the fields that they generate. In particular, a necessary and sufficient condition for such a current distribution to be nonradiating is established and a general expression for all nonradiating current distributions of this class is obtained.
Hide-and-Seek: The Challenge of Viral Persistence in HIV-1 Infection (2007)

The success of highly active antiretroviral therapy (HAART) for HIV-1 infection has sparked interest in mechanisms by which the virus can persist despite effectively suppressive therapy. Latent HIV-1 reservoirs established early during infection not only prevent sterilizing immunity but also represent a major obstacle to virus eradication. When HIV-1 gains a foothold in the immunologic memory or in certain inaccessible compartments of the human body, it cannot be easily purged by HAART and is able to replenish systemic infection on treatment interruption. Because latently infected cells are indistinguishable from uninfected cells, deliberate activation of latent infection combined with intensified HAART seems to be the best strategy to combat latent infection. Initial hypothesis-driven clinical trials did not achieve their ultimate goal, although they provided valuable insight for the design of future eradication protocols. A more detailed understanding of the basic mechanisms underlying the establishment and long-term maintenance of HIV-1 reservoirs will be critical in developing new eradication approaches.
Local Temperature Rises Influence In Vivo Electroporation Pore Development: A Numerical Stratum Corneum Lipid Phase Transition Model (2007)

Electroporation is an approach used to enhance transdermal transport of large molecules in which the skin is exposed to a series of electric pulses. Electroporation temporarily destabilizes the structure of the outer skin layer, the stratum corneum, by creating microscopic pores through which agents, ordinarily unable to pass into the skin, are able to pass through this outer barrier. Long duration electroporation pulses can cause localized temperature rises, which result in thermotropic phase transitions within the lipid bilayer matrix of the stratum corneum. This paper focuses on electroporation pore development resulting from localized Joule heating. This study presents a theoretical model of electroporation, which incorporates stratum corneum lipid melting with electrical and thermal energy equations. A transient finite volume model is developed representing electroporation of in vivo human skin, in which stratum corneum lipid phase transitions are modeled as a series of melting processes. The results confirm that applied voltage to the skin results in high current densities within the less resistive regions of the stratum corneum. The model captures highly localized Joule heating within the stratum corneum and subsequent temperature rises, which propagate radially outward. Electroporation pore development resulting from the decrease in resistance associated with lipid melting is captured by the lipid phase transition model. As the effective pore radius grows, current density and subsequent Joule heating values decrease.
Percutaneous lumbar discectomy: a new adjunct to open surgery. (1991)

Percutaneous automated lumbar discectomy is a new and alternative method to open operations for lumbar disc disease. The procedure and indications for the procedure are explained in this article. The results of the first 24 such procedures performed at the Indiana University Medical Center will be examined and discussed.
Applications of Spatial Light Modulators in Raman Spectroscopy (2019)

Advances in consumer display screen technologies have historically been adapted by researchers across the fields of optics as they can be used as electronically controlled spatial light modulators (SLMs) for a variety of uses. The performance characteristics of such SLM devices based on liquid crystal (LC) and digital micromirror device (DMD) technologies, in particular, has developed to the point where they are compatible with increasingly sensitive instrumental applications, for example, Raman spectroscopy. Spatial light modulators provide additional flexibility, from modulation of the laser excitation (including multiple laser foci patterns), manipulation of microscopic samples (optical trapping), or selection of sampling volume (adaptive optics or spatially offset Raman spectroscopy), to modulation in the spectral domain for high-resolution spectral filtering or multiplexed/compressive fast detection. Here, we introduce the benefits of different SLM devices as a part of Raman instrumentation and provide a variety of recent example applications which have benefited from their incorporation into a Raman system.
Central Hypotensive Effects of the α <sub>2a</sub> -Adrenergic Receptor Subtype (1996)

alpha2-Adrenergic receptors (alpha2ARs) present in the brainstem decrease blood pressure and are targets for clinically effective antihypertensive drugs. The existence of three alpha2AR subtypes, the lack of subtype-specific ligands, and the cross-reactivity of alpha2AR agonists with imidazoline receptors has precluded an understanding of the role of individual alpha2AR subtypes in the hypotensive response. Gene targeting was used to introduce a point mutation into the alpha2aAR subtype in the mouse genome. The hypotensive response to alpha2AR agonists was lost in the mutant mice, demonstrating that the alpha2aAR subtype plays a principal role in this response.
Antagonism of cytotoxic T lymphocyte‐mediated lysis by natural HIV‐1 altered peptide ligands requires simultaneous presentation of agonist and antagonist peptides (1997)

Mutations in human immunodeficiency virus (HIV) cluster in cytotoxic T lymphocyte (CTL) epitopes (Phillips, R. E. et al., Nature 1991. 354: 453) and are subject to immune-mediated positive selection (Price, D. A. et al., Proc. Natl. Acad. Sci. USA 1997. 94: 1890). We studied the effects of naturally occurring mutations in the HIV-1 p17 Gag HLA A2 restricted epitope SLYNTVATL on recognition by anti-HIV CTL. Most of these naturally occurring mutants escaped killing by one CTL line and the majority acted as CTL antagonists. We also investigated whether CTL exposed to a strict antagonist peptide restricted by HLA A2 were unresponsive when exposed to targets presenting the wild-type sequence. The results show that antagonism of anti-HIV CTL killing requires the simultaneous presence of agonist and antagonist peptide. We found no evidence that CTL exposed to an antagonist received a functionally negative signal since these CTL retained an unimpaired capacity to lyse targets bearing wild-type peptide.
Automated Particle Electrophoresis:  Modeling and Control of Adverse Chamber Surface Properties (1998)

Electrophoretic analysis of colloidal particles is adversely affected by a host of surface phenomena, including electroosmosis, phase wall wetting, and sample or air bubble adsorption. Neutral, hydrophilic polymer coatings control such phenomena on a variety of surfaces. Poly(ethylene glycol)-poly(ethylene imine) (PEG-PEI) conjugates significantly reduce electroosmosis and positively control adsorption and wetting in the glass sample chambers (5 mm × 3 mm × 1 mm i.d.) employed in a representative commercial electrophoresis apparatus (Coulter DELSA 440). The reduction in electroosmosis (e.g., 80% in 7.5 mM solution at pH 11) was similar to that exhibited by coated 2-mm-i.d. quartz capillaries in a Rank MK I manual apparatus. PEG-PEI coatings significantly reduce electroosmosis over a wide range of pH (2-11) and ionic strength (1-100 mM) and can be stable for weeks under normal laboratory conditions. They greatly enhance ease of operation and accuracy (sample mean electrophoretic mobility ± SD) of the DELSA 440. The latter results from reduced electroosmosis flow profile gradients near the chamber center-axis stationary levels, where particle mobility is typically measured. Such flow profiles may also be affected by chamber wall surface asymmetries. A hydrodynamic description of electroosmotic fluid flow in rectangular chambers was adapted in order to analyze the propagation of errors due to both nonideal focusing and chamber surface asymmetry. The analysis indicated that the accuracy of rectangular chambered devices may be improved by measuring particle mobility at stationary levels different than chamber center-axes. As a result, some rectangular chambers may confer accuracy advantages over cylindrical chambers.
B Cell Receptor Cross-Linking Triggers a Caspase-8- Dependent Apoptotic Pathway That Is Independent of the Death Effector Domain of Fas-Associated Death Domain Protein (2001)

We have previously reported that B cell receptors, depending on the degree to which they are cross-linked, can promote apoptosis in various human B cell types. In this study, we show that B cell receptors can trigger two apoptotic pathways according to cross-linking and that these pathways control mitochondrial activation in human Burkitt's lymphoma cells. Whereas soluble anti-mu Ab triggers caspase-independent mitochondrial activation, cross-linked anti-mu Ab induces an apoptotic response associated with a caspase-dependent loss of mitochondrial transmembrane potential. This B cell receptor-mediated caspase-dependent mitochondrial activation is associated with caspase-8 activation. We show here that caspase-8 inhibitors strongly decrease cross-linking-dependent B cell receptor-mediated apoptosis in Burkitt's lymphoma BL41 cells. These inhibitors act upstream from the mitochondria as they prevented the loss of mitochondrial membrane potential observed in B cell receptor-treated BL41 cells. Caspase-8 activation in these cells was also evident from the detection of cleaved fragments of caspase-8 and the cleavage of specific substrates, including Bid. Our data show that cross-linked B cell receptors induced an apoptotic pathway involving sequential caspase-8 activation, loss of mitochondrial membrane potential, and the activation of caspase-9 and caspase-3. Cells expressing a dominant negative mutant of Fas-associated death domain protein were sensitive to cross-linked B cell receptor-induced caspase-8 activation and apoptosis; therefore, this caspase-8 activation was independent of the death effector domain of Fas-associated death domain protein.