gebhart/patrepeval huggingface dataset:
Model and verification of electrokinetic flow and transport in a micro-electrophoresis device (2005)

We investigate the electrokinetic flow and transport within a micro-electrophoresis device. A mathematical model is set up, which allows to perform two-dimensional, time-dependent finite-element simulations. The model reflects the dominant features of the system, namely electroosmosis, electrophoresis, externally-applied electrical potentials, and equilibrium chemistry. For the solution of the model equations we rely on numerical simulations of the core region, while the immediate wall region is treated analytically at leading order. This avoids extreme refinements of the numerical grid within the EDL. An asymptotic matching of both solutions and subsequent superposition, nevertheless, provides an approximation for the solution in the entire domain. The results of the simulations are verified against experimental observation and show good agreement.
Bridging VisTrails Scientific Workflow Management System to High Performance Computing (2013)

NASA Earth Exchange (NEX) is a collaboration platform whose goal is to accelerate Earth science research, by leveraging NASA's vast collections of global satellite data together with access to NASA's High-End Computing (HEC) facilities. NEX also aims to facilitate the sharing of experimental results as well as scientific processes (workflows) with the Earth science community through integration with VisTrails workflow management system. While VisTrails is used internally, it is not easily accessible from remote computers without directly logging into the NASA HEC systems through twofactor authentication and a bastion host. This paper describes the initial design of an extensible architecture that facilitates easier workflow interaction on NEX, by enabling users to develop and execute workflows in a supercomputing environment directly from their local VisTrails installation. This architecture helps domain scientists seamlessly leverage distributed computing and storage resources and it is potentially applicable to other scientific workflow management software. We further describe the architecture of the VisTrails-HEC plugin (as well as the VisTrails-Amazon plugin) and the implementation of a working prototype to demonstrate the feasibility of our solution.
Towards Automating the AI Operations Lifecycle (2020)

Today's AI deployments often require significant human involvement and skill in the operational stages of the model lifecycle, including pre-release testing, monitoring, problem diagnosis and model improvements. We present a set of enabling technologies that can be used to increase the level of automation in AI operations, thus lowering the human effort required. Since a common source of human involvement is the need to assess the performance of deployed models, we focus on technologies for performance prediction and KPI analysis and show how they can be used to improve automation in the key stages of a typical AI operations pipeline.
Texture segmentation using Voronoi polygons (1990)

Textures are defined in terms of primitives called tokens. A texture segmentation algorithm based on the Voronoi tessellation is discussed. The algorithm first builds the Voronoi tessellation of the tokens that make up the textured image. It then computes a feature vector for each Voronoi polygon. These feature vectors are used in a probabilistic relaxation labeling on the tokens, to identify the interior and the border regions of the textures. Some experimental results are shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structural basis for repurpose and design of nucleoside drugs for treating COVID-19 (2020)

SARS-CoV-2 has caused a global pandemic of COVID-19 that urgently needs an effective treatment. Nucleoside analog drugs including favipiravir have been repurposed for COVID-19 despite of unclear mechanism of their inhibition of the viral RNA polymerase (RdRp). Here we report the cryo-EM structures of the viral RdRp in complex with favipiravir and two other nucleoside inhibitor drugs ribavirin and penciclovir. Ribavirin and the ribosylated form of favipiravir share a similar ribose scaffold that is distinct from penciclovir. However, the structures reveal that all three inhibitors are covalently linked to the primer strand in a monophosphate form despite the different chemical scaffolds between favipiravir and penciclovir. Surprisingly, the base moieties of these inhibitors can form mismatched pairs with the template strand. Moreover, in view of the clinical disadvantages of remdesivir mainly associated with its prodrug form, we designed several orally-available remdesivir parent nucleoside derivatives, including VV16 that showed 5-fold more potent than remdesivir in inhibition of viral replication. Together, these results demonstrate an unexpected promiscuity of the viral RNA polymerase and provide a basis for repurpose and design of nucleotide analog drugs for COVID-19. One Sentence Summary Cryo-EM structures of the RNA polymerase of SARS-CoV-2 reveals the basis for repurposing of old nucleotide drugs to treat COVID-19.
Synthesis of antimony complexes of yeast mannan and mannan derivatives and their effect on <i>Leishmania</i>-infected macrophages (1993)

Antimony(Sb)-yeast mannan complexes were synthesized as a strategy to introduce Sb into macrophages infected with Leishmania amastigotes. The complexes were taken up by endocytosis after specific recognition by alpha-D-mannosyl receptors on the macrophage membrane. About 90% of the intracellular parasites were destroyed by Sb-mannan in vitro, whereas the corresponding Sb concentration used as the pentavalent antimonial drug glucantime destroyed about 60% of the amastigotes. None of the Sb complexes prepared with mannan acid or basic derivatives was as effective as the simple Sb-mannan complex in clearing macrophage infection by Leishmania (L) amazonensis. The leishmanicidal effect of Sb-mannan was also demonstrated in vivo with infected hamsters. The alternative use of Sb-mannan complex in the treatment of human leishmaniasis is envisaged on the basis of parasite-killing efficiency and the use of a low antimony dose.
Soft Tissue Sarcoma Cells Are Highly Sensitive to AKT Blockade: A Role for p53-Independent Up-regulation of GADD45α (2008)

The AKT signaling pathway is activated in soft tissue sarcoma (STS). However, AKT blockade has not yet been studied as a potential targeted therapeutic approach. Here, we examined the in vitro and in vivo effects of AKT inhibition in STS cells. Western blot analysis was used to evaluate the expression of AKT pathway components and the effect of AKT stimulation and inhibition on their phosphorylation. Cell culture assays were used to assess the effect of AKT blockade (using a phosphatidylinositol 3-kinase inhibitor and a specific AKT inhibitor) on STS cell growth, cell cycle, and apoptosis. Oligoarrays were used to determine gene expression changes in response to AKT inhibition. Reverse transcription-PCR was used for array validation. Specific small inhibitory RNA was used to knockdown GADD45 alpha. Human STS xenografts in nude mice were used for in vivo studies, and immunohistochemistry was used to assess the effect of treatment on GADD45 alpha expression, proliferation, and apoptosis. Multiple STS cell lines expressed activated AKT. AKT inhibition decreased STS downstream target phosphorylation and growth in vitro; G(2) cell cycle arrest and apoptosis were also observed. AKT inhibition induced GADD45 alpha mRNA and protein expression in all STS cells treated independent of p53 mutational status. GADD45 alpha knockdown attenuated the G(2) arrest induced by AKT inhibition. In vivo, AKT inhibition led to decreased STS xenograft growth. AKT plays a critical role in survival and proliferation of STS cells. Modulation of AKT kinase activity may provide a novel molecularly based strategy for STS-targeted therapies.
High Survival Rates of Kidney Transplants from Spousal and Living Unrelated Donors (1995)

Spouses are an important source of living-donor kidney grafts because, despite poor HLA matching, the graft-survival rate is similar to that of parental-donor kidneys. This high rate of survival is attributed to the fact that the kidneys were uniformly healthy.
Memory reliability improvements based on maximized error-correcting codes (2012)

Error-correcting codes (ECC) offer an efficient way to improve the reliability and yield of memory subsystems. ECC-based protection is usually provided on a memory word basis such that the number of data-bits in a codeword corresponds to the amount of information that can be transferred during a single memory access operation. Consequently, the codeword length is not the maximum allowed by a certain check-bit number since the number of data-bits is constrained by the width of the memory data interface. This work investigates the additional error correction opportunities offered by the absence of a perfect match between the numbers of data-bits and check-bits in some of the most used ECCs. A method is proposed for the selection of multiple-bit errors which can become correctable with a minimal impact on decoder latency. Reliability improvements are evaluated for memories in which all errors affecting the same number of bits in a codeword are equally probable. It is shown that the application of the proposed methods to standard double-bit ECCs can improve the mean-time-to-failure (MTTF) of memories with up to 100%.
Targeting the Hsp40/Hsp70 Chaperone Axis as a Novel Strategy to Treat Castration-Resistant Prostate Cancer (2018)

Castration-resistant prostate cancer (CRPC) is characterized by reactivation of androgen receptor (AR) signaling, in part by elevated expression of AR splice variants (ARv) including ARv7, a constitutively active, ligand binding domain (LBD)-deficient variant whose expression has been correlated with therapeutic resistance and poor prognosis. In a screen to identify small-molecule dual inhibitors of both androgen-dependent and androgen-independent AR gene signatures, we identified the chalcone C86. Binding studies using purified proteins and CRPC cell lysates revealed C86 to interact with Hsp40. Pull-down studies using biotinylated-C86 found Hsp40 present in a multiprotein complex with full-length (FL-) AR, ARv7, and Hsp70 in CRPC cells. Treatment of CRPC cells with C86 or the allosteric Hsp70 inhibitor JG98 resulted in rapid protein destabilization of both FL-AR and ARv, including ARv7, concomitant with reduced FL-AR- and ARv7-mediated transcriptional activity. The glucocorticoid receptor, whose elevated expression in a subset of CRPC also leads to androgen-independent AR target gene transcription, was also destabilized by inhibition of Hsp40 or Hsp70. <i>In vivo</i>, Hsp40 or Hsp70 inhibition demonstrated single-agent and combinatorial activity in a 22Rv1 CRPC xenograft model. These data reveal that, in addition to recognized roles of Hsp40 and Hsp70 in FL-AR LBD remodeling, ARv lacking the LBD remain dependent on molecular chaperones for stability and function. Our findings highlight the feasibility and potential benefit of targeting the Hsp40/Hsp70 chaperone axis to treat prostate cancer that has become resistant to standard antiandrogen therapy.<b>Significance:</b> These findings highlight the feasibility of targeting the Hsp40/Hsp70 chaperone axis to treat CRPC that has become resistant to standard antiandrogen therapy. <i>Cancer Res; 78(14); 4022-35. ©2018 AACR</i>.
An orthogonal 6F/sup 2/ trench-sidewall vertical device cell for 4 Gb/16 Gb DRAM (2002)

This paper describes a novel 6F/sup 2/ trench-capacitor DRAM with a trench-sidewall vertical-channel array transistor. The cell features a line/space pattern for the active area, single-sided buried-strap node contact, vertical transistor channel formed along the upper region of the trench capacitor, a device active area bounded by the isolation trench and capacitor collar, and a single bit contact per cell.
Tensile and compressive strain measurement in the lab and field with the distributed Brillouin scattering sensor (2001)

The structural strain measurement of tension and compression in the steel beam was demonstrated with a distributed fiber-optic sensor system based on Brillouin scattering. The experiments were conducted both in the laboratory and outdoors. When it is in the outdoor environment, the temperature compensation has been taken into account for the strain measurement due to sunlight radiation. The compressive strain has been measured, without needing pretension on the fiber with a Brillouin scattering-based distributed sensor system, when the fiber is glued to the steel beam at every point. The dynamic range in the strain measurement has been increased, due to the elimination of the pretension requirement. The spatial resolution of the strain measurement is 0.5 m. The strain measurement accuracy is /spl plusmn/10 /spl mu//spl epsi/(/spl mu/m/m) in the laboratory environment with nonuniform-distributed strain. With uniform strain distribution, the strain accuracy for this system can be. /spl sim//spl plusmn/5 /spl mu//spl epsi/. These results were achieved with the introductions of a computer-controlled polarization controller, a fast digitizer-signal averager, a pulse duration control, and the electrical optical modulator bias setting in the software.
Liquid-crystal-tunable metasurface antennas (2017)

This paper presents a new concept of electronically tunable metasurface using nematic liquid crystal. The proposed metasurface is a high impedance surface that contains electrically small scatterers loaded with liquid crystal, distributed in a periodic two-dimensional plane with a relatively small periodicity as compared to the operating wavelength. Distribution of reflection phase on the metasurface is reconfigurable by varying DC control voltages on unit cells across the metasurface. This tunable metasurface concept can be useful for development of relatively large, dual linearly polarized, electronically tunable, beam steering antennas, especially for millimeter wave applications.
Embedded Planar Power Inductor in an Organic Interposer for Package-Level DC Power Grid (2014)

To realize the basic technology of a package-level dc power grid for the next generation power delivery to large scale integrated circuits (LSIs), two types of planar spiral inductors embedded in an organic interposer, for several tens of megahertz switching power supply integrated in LSI package, have been proposed. One is a Zn-Fe ferrite core spiral inductor, and another is a hybrid core spiral inductor, with quasi closed magnetic circuit consisting of the bottom Zn-Fe ferrite core and top carbonyl-iron/epoxy composite core. In this paper, the two types of planar spiral inductors have been fabricated and evaluated. From the experimental results, it was found that the hybrid core planar spiral inductor exhibited higher Q-factor and larger rating dc current than the Zn-Fe ferrite core inductor.
Egr1 Promotes Growth and Survival of Prostate Cancer Cells (2003)

In the majority of aggressive tumorigenic prostate cancer cells, the transcription factor Egr1 is overexpressed. We provide new insights of Egr1 involvement in proliferation and survival of TRAMP C2 prostate cancer cells by the identification of several new target genes controlling growth, cell cycle progression, and apoptosis such as cyclin D2, P19ink4d, and Fas. Egr1 regulation of these genes, identified by Affymetrix microarray, was confirmed by real-time PCR, immunoblot, and chromatin immunoprecipitation assays. Furthermore we also showed that Egr1 is responsible for cyclin D2 overexpression in tumorigenic DU145 human prostate cells. The regulation of these genes by Egr1 was demonstrated using Egr1 antisense oligonucleotides that further implicated Egr1 in resistance to apoptotic signals. One mechanism was illustrated by the ability of Egr1 to inhibit CD95 (Fas/Apo) expression, leading to insensitivity to FasL. The results provide a mechanistic basis for the oncogenic role of Egr1 in TRAMP C2 prostate cancer cells.
Security Assessment of the Transmission Control Protocol (TCP) (2009)

This document contains a security assessment of the IETF
specifications of the Transmission Control Protocol (TCP), and of a
number of mechanisms and policies in use by popular TCP
implementations. It is based on the results of a project carried out
by the UK's Centre for the Protection of National Infrastructure
(CPNI).
A Processing Method for Measuring Data of 3-D Welding Seam Based on Active Framework (2011)

In order to realize precise laser welding of the large-scale aerospace structure,a 5+2 axes laser welding measuring system,as well as a processing method for measured data based on the active framework were developed.According to homogeneous coordinate transformation,local position and normal of 3-D welding seam were converted into global data to establish its geometric model which was reflected on the machine tool's reference coordinate.Then,the machine tool's geometric errors were analyzed and compensated.Finally,a welding experiment based on the aerospace structure simulacrum was carried out.Through online measurement,data processing,geometric modeling,and actual welding,the proposed method was verified to meet the requirements.
Frames-Based Denoising in 3D Confocal Microscopy Imaging (2005)

In this paper, we propose a novel denoising method for 3D confocal microscopy data based on robust edge detection. Our approach relies on the construction of a non-separable frame system in 3D that incorporates the Sobel operator in dual spatial directions. This multidirectional set of digital filters is capable of robustly detecting edge information by ensemble thresholding of the filtered data. We demonstrate the application of our method to both synthetic and real confocal microscopy data by comparing it to denoising methods based on separable 3D wavelets and 3D median filtering, and report very encouraging results.
Chaperonins facilitate the in vitro folding of monomeric mitochondrial rhodanese (1991)

In vitro refolding of the monomeric mitochondrial enzyme, rhodanese (thiosulfate sulfurtransferase; EC 2.8.1.1) is facilitated by molecular chaperonins. The four components: two proteins from Escherichia coli, chaperonin 60 (groEL) and chaperonin 10 (groES), MgATP, and K+, are necessary for the in vitro folding of rhodanese. These were previously shown to be necessary for the in vitro folding of ribulose-1,5-bisphosphate carboxylase at temperatures in excess of 25 degrees C (Viitanen, P. V., Lubben, T. H., Reed, J., Goloubinoff, P., O'Keefe, D. P., and Lorimer, G. H. (1990) Biochemistry 29, 5665-5671). The labile folding intermediate, rhodanese-I, which rapidly aggregates at 37 degrees C in the absence of the chaperonins, can be stabilized by forming a binary complex with chaperonin 60. The discharge of the binary chaperonin 60-rhodanese-I complex, results in the formation of active rhodanese, and requires the presence of chaperonin 10. Optimal refolding is associated with a K(+)-dependent hydrolysis of ATP. At lower protein concentrations and 25 degrees C, where aggregation is reduced, a fraction of the rhodanese refolds to an active form in the absence of the chaperonins. This spontaneous refolding can be arrested by chaperonin 60. There is some refolding (approximately equal to 20%) when ATP is replaced by nonhydrolyzable analogs, but there is no refolding in the presence of ADP or AMP. ATP analogs may interfere with the interaction of rhodanese-I with the chaperonins. Nondenaturing detergents facilitate rhodanese refolding by interacting with exposed hydrophobic surfaces of folding intermediates and thereby prevent aggregation (Tandon, S., and Horowitz, P. (1986) J. Biol. Chem. 261, 15615-15618). The chaperonin proteins appear to play a similar role in as much as they can replace the detergents. Consistent with this view, chaperonin 60, but not chaperonin 10, binds 2-3 molecules of the hydrophobic fluorescent reporter, 1,1'-bi(4-anilino)naphthalene-S,5'-disulfonic acid, indicating the presence of hydrophobic surfaces on chaperonin 60. The number of bound probe molecules is reduced to 1-2 molecules when chaperonin 10 and MgATP are added. The results support a model in which chaperonins facilitate folding, at least in part, by interacting with partly folded intermediates, thus preventing the interactions of hydrophobic surfaces that lead to aggregation.
The frequency synthesizer (1943)

This paper describes a frequency synthesizer which enables any frequency that is harmonically related to a sub-multiple of a standard frequency to be generated by means of a decade system involving a synthesis process. The adjacent harmonic interference is substantially independent of the order of the harmonic and can be extremely small.The paper is divided into two Parts. The limitations of the present technique as applied to frequency measurements and the means of overcoming them are given in Part 1, while Part 2 outlines the principles of the frequency synthesizer and gives a detailed description of a typical example with some applications of its uses as a source.
Software Analytics for Mobile Applications--Insights &amp; Lessons Learned (2013)

Mobile applications, known as apps, are software systems running on handheld devices, such as smartphones and tablet PCs. The market of apps has rapidly expanded in the past few years into a multi-billion dollar business. Being a new phenomenon, it is unclear whether approaches to maintain and comprehend traditional software systems can be ported to the context of apps. We present a novel approach to comprehend apps from a structural and historical perspective, leveraging three factors for the analysis: source code, usage of third-party APIs, and historical data. We implemented our approach in a web-based software analytics platform named SAMOA. We detail our approach and the supporting tool, and present a number of findings obtained while investigating a corpus of mobile applications. Our findings reveal that apps differ significantly from traditional software systems in a number of ways, which calls for the development of novel approaches to maintain and comprehend them.