gebhart/patrepeval huggingface dataset:
Abstract A74: Proteasome subunit RPN13 as a candidate target for treatment of ovarian carcinoma. (2016)

Abstract The aberrant metabolism of ovarian cancer cells produces an excess of misfolded proteins and particular sensitivity to proteasome inhibition. Blockade of proteasome 19S regulatory particle (RP) deubiquitinase and/or 20S subunit proteolytic function results in a rapid buildup of denatured protein aggregates and triggers a p53-independent cell death. However, treatment of ovarian cancer with the licensed proteasome inhibitor bortezomib did not produce sufficient benefit to warrant further development. This setback led us to develop second generation inhibitors representing a distinct class of molecule and new mechanism of proteasome inhibition. We have developed novel bis-benzylidine piperidones, RA183 and RA190, which bind covalently to the RPN13 subunit of the 19S RP. RPN13 acts as an ubiquitin receptor and promotes the deubiquitinase activity of its binding partner UCH37. RA183 and RA190 cause rapid accumulation of very high molecular weight poly-ubiquitinated proteins, higher and more rapid than seen with bortezomib treatment, suggesting they inhibit RPN13 function, and thus deubiquitination by the 19S regulatory particle and 20S catalytic subunit activity. The accumulation of polyubiquitinated proteins triggered by RA183 or RA190 causes endoplasmic reticulum (ER) stress and an unresolved unfolded protein response that rapidly triggers apoptosis. RA190 and RA183 are active against multiple high-grade ovarian carcinoma cell lines in vitro and ovarian cancer models in mice. In nude mice carrying intraperitoneal ES2-luciferase xenografts, RA190 treatment (10mg/kg) significantly inhibited tumor growth. RPN13 is amplified in a subset of high grade ovarian cancers (10-20%), but its amplification did not correlate with a change in the sensitivity of ovarian carcinoma cell lines to RPN13 inhibitor. Sensitivity to RA190 also did not correlate with the level of pre-treatment stress or protein poly-ubiquitination. Knockdown of RPN13 expression in mouse ovarian cell line, ID8, increased its sensitivity to RA190. However attempts to generate knockout of RPN13 by CRISPR in NIH:OVCAR-3 failed and appeared to reflect toxicity. RPN13 mRNA was detected by chromogenic RNA in situ hybridization in all high grade serous carcinoma (HGSC) cases tested and matched precursor serous tubal intraepithelial carcinomas(n=16), and was overexpressed in all relative to adjacent normal fallopian tube epithelium. We conclude that RPN13 has promise as a target for treatment of ovarian carcinomas and possibly HGSC precursor STIC lesions, and that further development of RPN13 inhibitors warranted. Citation Format: Rosie T. Jiang, Ravi K. Anchoori, Anna V. Yemelyanova, Chien-fu Hung. Proteasome subunit RPN13 as a candidate target for treatment of ovarian carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A74.
Noncataleptic potential neuroleptics: 2-Methyl-10-(4-methylpiperazino)- and -10-[4-(2-hydroxyethyl)piperazino]-10,11-dihydrodibenzo[b,f]thiepin (1979)

[5-Methyl-2-(phenylthio)phenyl]acetic acid ( XV ) was synthesized on the one hand from the acid VIII using the known homologization technique via the alcohol X and nitrile XII , on the other from 5-methyl-2-(phenylthio)acetophenone ( XIII ) by means of the Willgerodt reaction. Via the intermediates XIX and XX , the synthesis led to 10-chloro-2-methyl-10,11-dihydrodibenzo[ b,f ]thiepin ( XXI ), giving by treatment with 1-methylpiperazine and 1-(2-hydroxyethyl)piperazine the title compounds III and IV . These compounds have low cataleptic and high central depressant activity; on the other hand, they do not influence the levels of dopamine metabolites in the rat brain which is considered an indication of their lacking the neuroleptic character.
<title>Simple segmentation algorithm for mixed raster contents image representation</title> (2001)

Mixed Raster Contents (MRC) is a powerful image representation concept in achieving high compression ratios while maintaining high reconstructed image quality. By decomposing an image into different planes, each plane of the raster data can be compressed by different coding schemes according to its individual attributes. This paper presents a simple segmentation algorithm for implementing the MRC model. The segmentation is performed block by block. Each image block is segmented according to its local statistics as well as its surrounding context. The latter is determined by a Markov model.
A Reliable and Predictable Scratchpad-centric OS for Multi-core Embedded Systems (2017)

The reliable use of multi-core platforms for designing safety-critical systems still represents an open challenge. Recently, the FAA [1] has formally expressed its concern towards the use of multi-core systems in avionics. The sharing of hardware resources introduces non-trivial timing dependencies between logically independent components (e.g. cores); additionally, the increase in size of circuitry, memory resources, and transistor density makes these platforms more susceptible to transient memory (soft) errors. This work addresses the problem of memory soft errors and their recovery at an OS/platform level on commercial multi-core systems. Proposed strategy considers the schedulability impact of recovery procedures on hard real-time workloads. Finally, the implementation of a SPM-centric OS with the proposed OS-level strategies was performed by using a commercially available multi-core platform. The design has been validated and evaluated using a combination of synthetic and realistic (EEMBC) benchmarks.
Channel management policies for handovers in cellular networks (2002)

A major criterion in evaluating a cellular system is the handover failure probability — the probability that a mobile call in progress will be forced to abort during a handover because it could not be allocated a radio channel in the new cell. One factor that influences the handover failure probability is the channel allocation policy within each cell. This policy is used to determine how to allocate the limited set of available channels in the cell to two kinds of calls: new calls originating within the cell, and handovers that migrate into the cell from neighboring cells. Two classes of such policies are explored in this paper — nonreserving and reservation-based. Nonreserving policies do not set aside resources for exclusive use by handover calls, whereas reservation-based policies do reserve resources. For the former class, this paper presents an optimal policy and, for the latter, an adaptive traffic-driven reservation policy that improves on static guard channel policies. Analytic and simulation results are provided for policies in each class.
Nanotube Phonon Waveguide (2007)

We find that the high thermal conductivity of carbon nanotubes remains intact under severe structural deformations while the corresponding electrical resistance and thermoelectric power show compromised responses. Similar robust thermal transport against bending is found for boron nitride nanotubes. Surprisingly, for both systems the phonon mean free path exceeds the characteristic length of structural ripples induced by bending and approaches the theoretical limit set by the radius of curvature. The robustness of heat conduction in nanotubes refines the ultimate limit that is far beyond the reach of ordinary materials.
Nanometer-scale imaging and ablation with Extreme Ultraviolet lasers (2007)

The short wavelength and high brightness of compact extreme ultraviolet lasers is shown to enable the development of microscopes with spatial resolution of tens of nanometers and new types of nanoprobes.
Particle size limits when using optical trapping and deflection of particles for sorting using diode laser bars (2009)

We explore a simple, inexpensive approach to large particle manipulation using diode laser bar optical trapping. This method overcomes limitations that prevent conventional point laser traps from effectively directing large particles. Expanding a previously developed line optical trap model into larger particle regimes, we verify and examine the advantages and limitations of diode laser bar trapping for manipulating particles greater than 100 microm in diameter within fluidic environments for biochemical, biological, and biomedical applications.
Automated Yeast Transformation Protocol to Engineer <i>Saccharomyces cerevisiae</i> Strains for Cellulosic Ethanol Production with Open Reading Frames That Express Proteins Binding to Xylose Isomerase Identified Using a Robotic Two-Hybrid Screen (2009)

Commercialization of fuel ethanol production from lignocellulosic biomass has focused on engineering the glucose-fermenting industrial yeast Saccharomyces cerevisiae to use pentose sugars. Because S. cerevisiae naturally metabolizes xylulose, one approach involves introducing xylose isomerase (XI), which catalyzes conversion of xylose to xylulose. In this study, an automated two-hybrid interaction protocol was used to find yeast genes encoding proteins that bind XI to identify potential targets for improving xylose utilization by S. cerevisiae. A pDEST32 vector re-engineered for TRP selection and containing the Gal4 binding domain fused with the Piromyces sp. E2 XI open reading frame (ORF) was used as bait with a library of LEU-selectable pOAD vectors containing the Gal4 activation domain in fusion with members of the S. cerevisiae genome ORF collection. Binding of a yeast ORF protein to XI activates two chromosomally located reporter genes in a PJ69–4 yeast strain to give selective growth. Five genes, including ADHI, were identified in the two-hybrid screen, suggesting the proteins encoded by these genes bind to XI. The effect of ADHI overexpression was examined using the pSUMOduoHisADHI vector in an automated protocol to transform eight previously identified yeast strains that showed anaerobic growth on xylose. One transformant consumed all available glucose, xylose, and arabinose during growth on wheat straw hydrolysate.
A comparative review on the wireless implantable medical devices privacy and security (2014)

Nowadays wireless communication is playing a vital role in implantable medical devices (IMDs) on health-care applications. It has many advantages in remote health monitoring, treatment and prediction for critical cases. However, any drawback in security of these devices against malicious attacks may lead to serious problems, such as theft of private information, wrong treatment and even death. In this paper, a comparative review of the current literature on IMD security research is provided to have a better understanding of the state of the art and the gaps in this direction.
Photorefractive device using self-assembled monolayer coated indium-tin-oxide electrodes (2014)

We present here the optimized photorefractive (PR) device based on methyl-substituted poly(triarylamine) (PTAA). The PR performance of PTAA-based PR device was demonstrated using chemically modified electrodes (CMEs) of selfassembled monolayer (SAM) coated indium-tin-oxide (ITO) electrodes. The SAM-ITO electrodes successfully suppressed dark current which blocks the formation of space-charge field and also causes the dielectric breakdown, which result in the remarkable response time faster than video rate of 16 ms. Our approach will widen the usage of higher mobility materials to photorefractive field and give us more favorable materials to achieve the best performance of photorefractivity in the future.
PREPARATION OF HOP EXTRACTS WITHOUT USING ORGANIC SOLVENTS (1977)

Extraction of hops with liquid carbon dioxide at ambient temperature provides an attractive means of producing hop extracts which are rich in α-acids and free from hard resins, polyphenols, pigments and residual organic solvents. The resulting yellow extracts give beer with a clean bitter flavour when they are added during wort boiling. Manufacturing costs using the process are likely to be substantially less than in a conventional hop extraction plant.
Design Of A Transform Coder For High Quality Audio Signals (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
Imperfect and unmatched CSIT is still useful for the frequency correlated MISO broadcast channel (2013)

Since Maddah-Ali and Tse showed that the completely stale transmitter-side channel state information (CSIT) still benefits the Degrees of Freedom (DoF) of the Multiple-Input-Multiple-Output (MISO) Broadcast Channel (BC), there has been much interest in the academic literature to investigate the impact of imperfect CSIT on DoF region of time correlated broadcast channel. Even though the research focus has been on time correlated channels so far, a similar but different problem concerns the frequency correlated channels. Indeed, the imperfect CSIT also impacts the DoF region of frequency correlated channels, as exemplified by current multi-carrier wireless systems. This contribution, for the first time in the literature, investigates a general frequency correlated setting where a two-antenna transmitter has imperfect knowledge of CSI of two single-antenna users on two adjacent subbands. A new scheme is derived as an integration of Zero-Forcing Beamforming (ZFBF) and the scheme proposed by Maddah-Ali and Tse. The achievable DoF region resulted by this scheme is expressed as a function of the qualities of CSIT.
X-ray dark-field and phase-contrast imaging using a grating interferometer (2009)

In this letter, we report results obtained with a recently developed approach for grating-based x-ray dark-field imaging [F. Pfeiffer et al., Nat. Mater. 7, 134 (2008)]. Since the image contrast is formed through the mechanism of small-angle scattering, it provides complementary and otherwise inaccessible structural information about the specimen at the micron and submicron length scales. Our approach is fully compatible with conventional transmission radiography and the grating-based hard x-ray phase-contrast imaging scheme [F. Pfeiffer et al., Nat. Phys. 2, 258 (2006)]. Since it can be used with standard x-ray tube sources, we envisage widespread applications to x-ray medical imaging, industrial nondestructive testing, or security screening.
Comparative Whole-Genome Hybridization Reveals Genomic Islands in<i>Brucella</i>Species (2004)

Brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and Malta fever in humans. Based on host preference, the genus is divided into six species. Brucella abortus, B. melitensis, and B. suis are pathogenic to humans, whereas B. ovis and B. neotomae are nonpathogenic to humans and B. canis human infections are rare. Limited genome diversity exists among Brucella species. Comparison of Brucella species whole genomes is, therefore, likely to identify factors responsible for differences in host preference and virulence restriction. To facilitate such studies, we used the complete genome sequence of B. melitensis 16M, the species highly pathogenic to humans, to construct a genomic microarray. Hybridization of labeled genomic DNA from Brucella species to this microarray revealed a total of 217 open reading frames (ORFs) altered in five Brucella species analyzed. These ORFs are often found in clusters (islands) in the 16M genome. Examination of the genomic context of these islands suggests that many are horizontally acquired. Deletions of genetic content identified in Brucella species are conserved in multiple strains of the same species, and genomic islands missing in a given species are often restricted to that particular species. These findings suggest that, whereas the loss or gain of genetic material may be related to the host range and virulence restriction of certain Brucella species for humans, independent mechanisms involving gene inactivation or altered expression of virulence determinants may also contribute to these differences.
Heat-transfer dynamics during cryogen spray cooling of substrate at different initial temperatures (2004)

Cryogen spray cooling (CSC) is used to minimize the risk of epidermal damage during laser dermatologic therapy. However, the dominant mechanisms of heat transfer during the transient cooling process are incompletely understood. The objective of this study is to elucidate the physics of CSC by measuring the effect of initial substrate temperature (T0) on cooling dynamics. Cryogen was delivered by a straight-tube nozzle onto a skin phantom. A fast-response thermocouple was used to record the phantom temperature changes before, during and after the cryogen spray. Surface heat fluxes (q") and heat-transfer coefficients (h) were computed using an inverse heat conduction algorithm. The maximum surface heat flux (q"max) was observed to increase with T0. The surface temperature corresponding to q"max also increased with T0 but the latter has no significant effect on h. It is concluded that heat transfer between the cryogen spray and skin phantom remains in the nucleate boiling region even if T0 is 80 degrees C.
Simultaneous Targeting of IL-1 and IL-18 Is Required for Protection against Inflammatory and Septic Shock (2014)

Our data point toward the therapeutic potential of neutralizing IL-1 and IL-18 simultaneously in sepsis, rather than inhibiting the upstream inflammatory caspases.
Bamboo fiber-reinforced polypropylene composites: A study of the mechanical properties (1998)

A new type of bamboo fiber-reinforced polypropylene (PP) composite was prepared and its mechanical properties were tested. To enhance the adhesion between the bamboo fiber and the polypropylene matrix, maleic anhydride-grafted polypropylene (MAPP) was prepared and used as a compatibilizer for the composite. The maleic anhydride content of the MAPP was 0.5 wt %. It was found that with 24 wt % of such MAPP being used in the composite formulation, the mechanical properties of the composite such as the tensile modulus, the tensile strength, and the impact strength all increased significantly. The new composite has a tensile strength of 32–36 MPa and a tensile modulus of 5–6 GPa. Compared to the commercially available wood pulp board, the new material is lighter, water-resistant, cheaper, and more importantly has a tensile strength that is more than three times higher than that of the commercial product. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 69: 1891–1899, 1998
Implementing interactive analysis of attack graphs using relational databases (2008)

An attack graph models the causal relationships between vulnerabilities. Attack graphs have important applications in protecting critical resources in networks against sophisticated multi-step intrusions. Currently, analyses of attack graphs largely depend on proprietary implementations of speciali zed algorithms. However, developing and implementing algorithms causes a delay to the availability of new analyses. The delay is usually unacceptable due to rapidly-changing needs in defending against network intrusions. An administrator may want to revise an analysis as soon as its outcome is observed. Such an interactive analysis, similar to that in decision support systems, is desirable but difficult with current approaches based on proprietary implementations of algorithms. This paper addresses the above issue through a relational approach. Specifically, we devise a relational model for representing necessary inputs, such as network configurations and domain knowledge, and we generate attack graphs from these inputs as relational views. We show that typical analyses can be supported through different type of searches in an attack graph, and these searches can be realized as relational queries. Our approach eliminates the needs for implementing algorithms, because an analysis is now simply a relational query. The interactive analysis of attack graphs becomes possible, since relational queries can be dynamically constructed and revised at run time. As a side effect, experimental results show that the mature optimization techniques in relational databases can transparently improve the performance of the analysis.
Molecular imaging of breast tumors using a near‐infrared fluorescently labeled clusterin binding peptide (2011)

Several reports have shown that secreted clusterin (sCLU) plays multiple roles in tumor development and metastasis. Here, we report on a 12-mer sCLU binding peptide (designated P3378) that was identified by screening a phage-display peptide library against purified human sCLU. Differential resonance perturbation nuclear magnetic resonance using P3378 and a scrambled control peptide (designated P3378R) confirmed the P3378-sCLU interaction and demonstrated that it was sequence specific. P3378 and P3378R peptides were conjugated to an Alexa680 near infrared fluorophore (NIRF) and assessed for their tumor homing abilities in in vivo time-domain fluorescence optical imaging experiments using living 4T1 tumor bearing BALB/c mice. When injected in separate animals, both peptides accumulated at the tumor site, however the NIRF-labeled P3378 peptide was retained for a significant longer period of time than the P3378R peptide. Similar observations were made after simultaneously injecting the same tumor-bearing animal with a peptide mixture of P3378 DyLight (DL)680 and the P3378R-DL800. Coinjection of P3378-DL680 with excess unlabeled P3378 blocked tumor accumulation of fluorescent signal while excess P3378R control peptide did not confirming the sequence specificity of the tumor accumulation. Finally, ex vivo fluorescence microscopy of these tumors confirmed the presence of P3378-DL680 in the tumor and its colocalization with CLU. These results confirm the tumor targeting specificity of the P3378 CLU-binding peptide and suggest its usefulness for the in vivo monitoring of solid tumors secreting detectable levels of CLU.
Behavior And Corrections Of Constant Modulus Equalization With A Dc Offset (2002)

Publication in the conference proceedings of EUSIPCO, Toulouse, France, 2002
Probing lung physiology with xenon polarization transfer contrast (XTC) (2000)

One of the major goals of hyperpolarized-gas MRI has been to obtain 129Xe dissolved-phase images in humans. So far, this goal has remained elusive, mainly due to the low concentration of xenon that dissolves in tissue. A method is proposed and demonstrated in dogs that allows information about the dissolved phase to be obtained by imaging the gas phase following the application of a series of RF pulses that selectively destroy the longitudinal magnetization of xenon dissolved in the lung parenchyma. During the delay time between consecutive RF pulses, the depolarized xenon rapidly exchanges with the gas phase, thus lowering the gas polarization. It is demonstrated that the resulting contrast in the 129Xe gas image provides information about the local tissue density. It is further argued that minor pulse-sequence modifications may provide information about the alveolar surface area or lung perfusion. Magn Reson Med 44:349–357, 2000. © 2000 Wiley-Liss, Inc.
Whole body adhesion: hierarchical, directional and distributed control of adhesive forces for a climbing robot (2007)

We describe the design and control of a new bio-inspired climbing robot designed to scale smooth vertical surfaces using directional adhesive materials. The robot, called Stickybot, draws its inspiration from geckos and other climbing lizards and employs similar compliance and force control strategies to climb smooth vertical surfaces including glass, tile and plastic panels. Foremost among the design features are multiple levels of compliance, at length scales ranging from centimeters to micrometers, to allow the robot to conform to surfaces and maintain large real areas of contact so that adhesive forces can support it. Structures within the feet ensure even stress distributions over each toe and facilitate engagement and disengagement of the adhesive materials. A force control strategy works in conjunction with the directional adhesive materials to obtain sufficient levels of friction and adhesion for climbing with low attachment and detachment forces.