gebhart/patrepeval huggingface dataset:
Abstract 2492: Down-regulation of AR splice variants through XPO1 suppression contributes to the inhibition of prostate cancer progression (2018)

Abstract Increased XPO1 (a key nuclear exporter of many tumor suppressor proteins [TSPs]) expression in prostate cancer (PCa) has been found to be associated with a high Gleason score and bone metastasis. However, it is unknown whether aberrant XPO1 activity regulates AR and AR splice variants (Arv) signaling in PCa progression. In this study, using 22Rv1 and VCaP prostate cancer cells which harbor full length AR and ARv, we conduct in vitro cellular and molecular biological experiments and in vivo animal studies to elucidate the role XPO1 inhibition plays in PCa progression through regulation of XPO1/AR/ARv signaling. We found that high expression of AR splice variant 7 (AR-v7) was correlated with increased XPO1 expression. Silencing of XPO1 by RNAi or treatment with Selective Inhibitor of Nuclear Export (SINE) compounds (selinexor and KPT-8602/eltanexor) down-regulated the expression of AR, AR-v7 and ARv567es at the mRNA and protein levels. Mechanistic studies showed that XPO1 silencing also inhibited the expression of AR/ARv regulators including FOXA1, Src, Vav3, MED1 and Sam68, leading to the suppression of ARv and AR target genes, UBE2C and PSA. SINE compound treatment of cells retained the eIF4E protein (translation initiation factor and nuclear transporter of capped depended mRNAs) in nuclear compartment, leading to nuclear retention of AR-v7 and PSA mRNAs. The nuclear localization of AR-v7 mRNA resulted in the reduction in the ARv protein. Furthermore, SINE compound treatment retained TSPs including Rb, p21, p53, APC and SMAD4 in the nucleus leading to inhibition of cell proliferation and induction of apoptosis. Moreover, by targeting XPO1/ARv signaling, SINE compounds suppressed prostate cancer growth in vitro and in vivo and potentiated the anti-cancer activity of conventional chemotherapeutic agent docetaxel and anti-AR agents (enzalutamide and abiraterone) through the inhibition of AR, AR-v7, FOXA1, PSA and UBE2C. From these results, we conclude that there is a causal relationship between XPO1 and AR splice variants. High expression of both XPO1 and AR-v7 could lead to constitutively activated AR signaling, CRPC development and progression, and anti-AR drug resistance. By targeting XPO1/AR/ARv signaling and increasing anti-AR sensitivity, SINE compounds could be novel agents used in combination with conventional chemotherapeutics and AR-targeted therapy for the treatment of PCa, especially CRPC. Citation Format: Irfana Muqbil, Yiwei Li, Erkan Baloglu, William Senapedis, Yosef Landesman, Christian Argueta, Michael Kauffman, Sharon Friedlander, Hua Chang, Sharon Shacham, Elisabeth Heath, Asfar S. Azmi. Down-regulation of AR splice variants through XPO1 suppression contributes to the inhibition of prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2492.
TRPV1 promotes opioid analgesia during inflammation (2019)

Pain and inflammation are inherently linked responses to injury, infection, or chronic diseases. Given that acute inflammation in humans or mice enhances the analgesic properties of opioids, there is much interest in determining the inflammatory transducers that prime opioid receptor signaling in primary afferent nociceptors. Here, we found that activation of the transient receptor potential vanilloid type 1 (TRPV1) channel stimulated a mitogen-activated protein kinase (MAPK) signaling pathway that was accompanied by the shuttling of the scaffold protein β-arrestin2 to the nucleus. The nuclear translocation of β-arrestin2 in turn prevented its recruitment to the μ-opioid receptor (MOR), the subsequent internalization of agonist-bound MOR, and the suppression of MOR activity that occurs upon receptor desensitization. Using the complete Freund's adjuvant (CFA) inflammatory pain model to examine the role of TRPV1 in regulating endogenous opioid analgesia in mice, we found that naloxone methiodide (Nal-M), a peripherally restricted, nonselective, and competitive opioid receptor antagonist, slowed the recovery from CFA-induced hypersensitivity in wild-type, but not TRPV1-deficient, mice. Furthermore, we showed that inflammation prolonged morphine-induced antinociception in a mouse model of opioid receptor desensitization, a process that depended on TRPV1. Together, our data reveal a TRPV1-mediated signaling pathway that serves as an endogenous pain-resolution mechanism by promoting the nuclear translocation of β-arrestin2 to minimize MOR desensitization. This previously uncharacterized mechanism may underlie the peripheral opioid control of inflammatory pain. Dysregulation of the TRPV1-β-arrestin2 axis may thus contribute to the transition from acute to chronic pain.
Frontispiece: Selective Calixarene‐Directed Synthesis of MXene Plates, Crumpled Sheets, Spheres, and Scrolls (2017)

MXenes are a rapidly emerging new class of 2D laminar materials with unique properties. This work is the first example of templated morphological change beyond sheets of the thinnest member of the MXenes class of materials, Ti2C, leading to plates, crumpled sheets, spheres and scrolls. This has been achieved by taking advantage of the inherent properties of a family of calixarene derivatives. This advancement opens up wider avenues of discovery/design for new morphologies from the wider family of MXenes beyond Ti2C, along with opportunities to exploit any new physico-chemical properties proffered. For more information see Communication by S. Kellici and co-workers on page 8128 ff. Artwork by Rodrigo F. P. de Carvalho.
O1‐08‐02: AGE‐RELATED WHITE MATTER PATHOGENESIS IN A MOUSE MODEL OF TAUOPATHY (2014)

Progressive tau pathology is associated with neuronal loss and white matter (WM) pathology in Alzheimer's disease. WM degeneration in AD has been known from postmortem examinations. Diffusion tensor imaging (DTI) has provided significant insight into AD-associated reductions in WM integrity. Microstructural damage in WM may contribute the finding from DTI. However, a direct causal relation between DTI indices and specific AD-related pathologies is not established yet. Age-related alterations in WM diffusion anisotropy using in vivo DTI at 11.1 Tesla was measured in a mouse model of human tauopathy (rTg4510) and non-transgenic (non-tg) control mice at 2.5, 4.5, 8 months of age. Tau pathology in corpus callosum of transgenic mice was examined by immunohistochemistry and immunogold electron microscopy (IEM). The conformation specific tau antibody MC1-positive tau pathology in cortex and hippocampus was appeared as early as 1.5-2.5 months of age. However, there is no noticeable staining for MC1 antibody in corpus callosum of rTg4510 mice until 6 month-old. By IEM, aggregates of tau-positive filaments were detected in axons and swollen unmyelinated processed in 4 month-old and older rTg4510 mice. By DTI, 8 month-old rTg4510 mice showed lower fractional anisotropy (FA) values in WM structures than non-tg. The corpus callosum of 2.5 month-old rTg4510 mice showed a significantly reduced mode of anisotropy compared to non-tg controls. Our data support a role for the progression of tau pathology in reduced WM integrity measured by DTI. In vivo DTI studies in this mouse model provide better understanding for the mechanisms of WM pathogenesis and the specific role of tau during neurodegeneration.
Bounded arbitration algorithm for QoS-supported on-chip communication (2006)

Time-critical multi-processor systems require guaranteed services in terms of throughput, bandwidth etc. in order to comply to hard real-time constraints. However, guaranteed-service schemes suffer from low resource utilization.To the best of our knowledge, we are presenting the first approach for on-chip communication that provides a high resource utilization under a transaction-specific, flexible (i.e. different classifications on data exchange) communication scheme. It does provide tight time-related guarantees. Hence, we are presenting our bounded arbitration scheme considering lower and upper bounds for each type of transaction level. We demonstrate its advantages by means of a complete MPEG4 decoder case study and achieve under these constraints a bandwidth utilization of up to 100%, on an average 97% with a guaranteed (100%) bandwidth.
The optical design of the six-meter CCAT-prime and Simons Observatory telescopes (2018)

A common optical design for a coma-corrected, 6-meter aperture, crossed-Dragone telescope has been adopted for the CCAT-prime telescope of CCAT Observatory, Inc., and for the Large Aperture Telescope of the Simons Observatory. Both are to be built in the high altitude Atacama Desert in Chile for submillimeter and millimeter wavelength observations, respectively. The design delivers a high throughput, relatively flat focal plane, with a field of view 7.8 degrees in diameter for 3 mm wavelengths, and the ability to illuminate &gt;100k diffraction-limited beams for &lt; 1 mm wavelengths. The optics consist of offset reflecting primary and secondary surfaces arranged in such a way as to satisfy the Mizuguchi-Dragone criterion, suppressing first-order astigmatism and maintaining high polarization purity. The surface shapes are perturbed from their standard conic forms in order to correct coma aberrations. We discuss the optical design, performance, and tolerancing sensitivity. More information about CCAT-prime can be found at ccatobservatory.org and about Simons Observatory at simonsobservatory.org.
Formal Derivation of Direct Torque Control for Induction Machines (2006)

Direct torque control (DTC) is an induction motor control technique that has been successful because it explicitly considers the inverter stage and uses few machine parameters, while being more robust to parameter uncertainty than field-oriented control (FOC). This paper presents a formal derivation of DTC based on singular perturbation and nonlinear control tools. The derivation elaborates an explicit relationship between DTC performance and machine characteristics; low-leakage machines are expected to perform better under DTC. It is shown that DTC is a special case of a sliding-mode controller based on the multiple time-scale properties of the induction machine. The known troublesome machine operating regimes are predicted and justified. Explicit conditions to guarantee stability are presented. DTC is shown to be a suboptimal controller because it uses more control effort than is required for flux regulation. Finally, compensation strategies that extend DTC are discussed. The derivation does not require space vector concepts thus, it is established that the traditional link between DTC and space vectors is not fundamental
3D sonar system based on mills cross antenna configuration (2014)

A special aperture for a 3D sonar system is the so called Mills Cross antenna configuration. The Mills Cross arrangement looks like a “T” in which both antennas have a special function. In our work one antenna, consisting of 128 piezoelectric transducer elements, is used to transmit sound into a volume of interest. The second one, also made of 128 piezoelectric transducers, is used for receiving the reflections from objects or surfaces in the vicinity of the antennas. Each transducer element has a convex curvature to cover at least 30° of the elevational direction. With that a volume defined by sector angles of 30° × 30° can be measured. To achieve fast volumetric imaging a frequency coding is used to transmit signals in different directions at the same time. The received signals are decoded to determine the different signals coming from the different directions. In this work we present the basic working principals of the system and the first measurement results.
Search methods in P2P-networks of process control systems (2005)

This contribution describes a decentrally organized procedure for loss-robust networking of hierarchically structured object clusters and a search procedure according to the so gained networking structure. The objects form a hierarchically structured group in accordance with usual plant identification systems, in which every object corresponds to a defined node in the plant hierarchy. The procedure is in particular intended for the employment in process control systems in the environment of operational networks and can be realized technically through adding further software components into the process control systems
Modeling and Observer Design for Polypyrrole Conducting Polymer Actuator Control Systems (2006)

A state observer for estimating and predicting the internal state of polypyrrole conducting polymer actuators is presented. Polypyrrole actuators can produce large stresses (>5 MPa) with large associated strains (>12%), which leads to a high energy density. However, care must be taken since conducting polymers degrade quickly when exposed to overcharged or over-strain conditions. Unfortunately, charge and other internal state variables relevant to degradation of the actuator material are not directly measurable in real-time control systems. To cope with this difficulty, this paper presents the design of a dynamic state observer to estimate the internal state of the polymer actuator from available sensor information. First, a reduced-order model of a polypyrrole conducting polymer actuator is obtained. A state observer is then designed based on the dynamic model. Subsequently, a method is presented for real-time identification of key model parameters from the measured data. Lastly, a novel control system is presented which utilizes the estimated internal states of the actuator to slow its performance degradation. Preliminary experiments and simulation are presented to demonstrate the proposed approach
Supplemental Table S1 from The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs (2023)

&lt;p&gt;Supplemental Table S1: Cell lines and growth medium.&lt;/p&gt;
In Situ Sem Analysis of Lithium Metal Polymer Battery (2006)

Abstract not Available.
Implementation of a multiagent system for competitive environments on the WWW (2002)

Abstract Agents have been receiving a lot of attention as software which behaves autonomously and efficiently on a network and supports human social interactions. Various agent systems have already been proposed. A conventional agent‐based system is based on the assumption that all interacting agents are trustworthy. In practice, however, there are many instances in which agents must compete in an environment in which the other agents cannot be trusted. Thus, in this paper the authors discuss the development of an electronic commerce system which uses agents that behave competitively. The agents in this system can determine autonomously the level of uncertainty in a transaction, then make decisions flexibly. In addition, the authors argue for the validity of their system using operational examples in which their system is used in various market scenarios. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 34–49, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/scj.10032
Machine Learning of Protein Interactions in Fungal Secretory Pathways (2016)

In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker’s yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities.
Benzocyclobutene in Polymer Synthesis (1988)

A number of blends were prepared from a bisbenzocyclobutene monomer (BCB) and various bisdienophiles (Kerimid 353; dicyanates such as bisphenol A dicyanate, tetramethylbisphenol F dicyanate and thiodiphenol dicyanate; and bisphenyl-acetylenes: 1,3-PPP0 and PhATI) in 1:1 molar ratio. Nonstoichiometric mixtures were also concocted from BCB and K-353. All were completely compatible, as evidenced by a single initial Tg, except the BCB/dicyanate blends, which showed small exothermic transitions attributable to crystallization phenomenon. The results from the thermal analyses of these blend systems, in particular the K353/BCB system, lend credence to our belief that curing via Diels-Alder cycloaddition may predominate. As such, the blend systems were more stable toward thermooxidative degradation than their pure bisdienophile components.
Synthesis, properties, and solvatochromism of 1,3‐dimethyl‐5‐{(thien‐2‐yl)‐[4‐(1‐piperidyl) phenyl]methylidene}‐(1H,3H)‐pyrimidine‐2,4,6‐trione (2007)

Abstract A new merocyanine dye, 1,3‐Dimethyl‐5‐{(thien‐2‐yl)‐[4‐(1‐piperidyl)phenyl]methylidene}‐ (1 H , 3 H )‐pyrimidine‐2,4,6‐trione 3 , has been synthesized by condensation of 2‐[4‐(piperidyl)benzoyl]thiophene 1 with N,N′ ‐dimethyl barbituric acid 2 . The solvatochromic response of 3 dissolved in 26 solvents of different polarity has been measured. The solvent‐dependent long‐wavelength UV/Vis spectroscopic absorption maxima, v max , are analyzed using the empirical Kamlet–Taft solvent parameters π * (dipolarity/polarizability), α (hydrogen‐bond donating capacity), and β (hydrogen‐bond accepting ability) in terms of the well‐established linear solvation energy relationship (LSER): The solvent independent coefficients s , a , and b and ( v max ) 0 have been determined. The McRae equation and the empirical solvent polarity index, E T (30) have been also used to study the solvatochromism of 3 . Copyright © 2007 John Wiley &amp; Sons, Ltd.
Ultra-thin oxynitride gate dielectrics by pulsed-RF DPN for 65 nm general purpose CMOS applications (2004)

This paper investigates the use of pulsed-RF decoupled plasma nitridation (DPN) for the growth of oxynitride gate dielectrics for 65 nm general purpose (GP) applications. The effects of several DPN plasma parameters, base oxide thickness and post-nitridation anneal (PNA) conditions on device performance were evaluated. Significant gate leakage reduction and improved trade-off between the equivalent-oxide-thickness (EOT) and mobility, for scaled EOT, have been found in devices with oxynitrides grown from thicker base oxides and optimized DPN/PNA processing conditions. DPN oxynitrides with 1.1-1.4 nm EOT have maximum operating voltages above 0.8 V, as extrapolated for a 10 year lifetime.
Double-Stranded Ligation Assay for the Rapid Multiplex Quantification of MicroRNAs (2015)

MicroRNAs are auspicious candidates for a new generation of biomarkers. The detection of microRNA panels in body fluids promises early diagnosis of many diseases, including cancer or acute coronary syndrome. For a fast, sensitive, and specific detection of microRNA panels on the bedside, medical point-of-care systems that measure those biomarkers are required. As microchips are promising technical tools for a robust signal measurement at biochemical interfaces, we developed an assay for the electrochemical multiplex quantification of microRNAs on a CMOS chip with interdigitated gold electrode sensor positions. The method is based on the formation of a tripartite hybridization complex and subsequent both-sided ligation of the target nucleic acid to a reporter and capture strand. With a time to results of 30 min, the reported assay achieves a limit of detection below 1 pM, at a specificity down to single mismatch discrimination. It also offers very good signal dynamics between 1 pM and 1 nM, thus, allowing reliable quantification of the detected microRNAs and easy implementation into automated devices due to a simple workflow.
FLT3 and MLL intragenic abnormalities in AML reflect a common category of genotoxic stress (2003)

MLL rearrangements in acute myeloid leukemia (AML) include translocations and intragenic abnormalities such as internal duplication and breakage induced by topoisomerase II inhibitors. In adult AML, FLT3 internal tandem duplications (ITDs) are more common in cases with MLL intragenic abnormalities (33%) than those with MLL translocation (8%). Mutation/deletion involving FLT3 D835 are found in more than 20% of cases with MLL intragenic abnormalities compared with 10% of AML with MLL translocation and 5% of adult AML with normal MLL status. Real-time quantification of FLT3 in 141 cases of AML showed that all cases with FLT3 D835 express high level transcripts, whereas FLT3-ITD AML can be divided into cases with high-level FLT3 expression, which belong essentially to the monocytic lineage, and those with relatively low-level expression, which predominantly demonstrate PML-RARA and DEK-CAN. FLT3 abnormalities in CBF leukemias with AML1-ETO or CBFbeta-MYH11 were virtually restricted to cases with variant CBFbeta-MYH11 fusion transcripts and/or atypical morphology. These data suggest that the FLT3 and MLL loci demonstrate similar susceptibility to agents that modify chromatin configuration, including topoisomerase II inhibitors and abnormalities involving PML and DEK, with consequent errors in DNA repair. Variant CBFbeta-MYH11 fusions and bcr3 PML-RARA may also be initiated by similar mechanisms.