gebhart/patrepeval huggingface dataset:
DNA Replication Timing Is Maintained Genome-Wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy (2011)

Facioscapulohumeral muscular dystrophy (FSHD) is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.
Distributed and dynamic voronoi overlays for coverage detection and distributed hash tables in ad-hoc networks (2004)

In this paper we study two important problems - coverage-boundary detection and implementing distributed hash tables in ad-hoc wireless networks. These problems frequently arise in service location and relocation in wireless networks. For the centralized coverage-boundary problem we prove a /spl Omega/(n log n) lower bound for n devices. We show that both problems can be effectively reduced to the problem of computing Voronoi overlays, and maintaining these overlays dynamically. Since the computation of Voronoi diagrams requires O(n log n) time, our solution is optimal for the computation of the coverage-boundary. We present efficient distributed algorithms for computing and dynamically maintaining Voronoi overlays, and prove the stability properties for the latter - i.e., if the nodes stop moving, the overlay stabilizes to the correct Voronoi overlay. Finally, we present experimental results in the context of the two selected applications, which validate the performance of our distributed and dynamic algorithms.
−1 V bias 67 GHz bandwidth Si-contacted germanium waveguide p-i-n photodetector for optical links at 56 Gbps and beyond (2016)

We demonstrate a 67 GHz bandwidth silicon-contacted germanium waveguide p-i-n photodetector operating at -1 V with 6.8 fF capacitance. The dark current is below 4 nA. The responsivity is 0.74 A/W at 1550 nm and 0.93 A/W at 1310 nm wavelength. 56 Gbps on-off-keying data reception is demonstrated with clear open eye diagrams in both the C-band and O-band.
Electrochemical oxidation of enamines in the presence of organic anions (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochemical oxidation of enamines in the presence of organic anionsToshiro Chiba, Mitsuhiro Okimoto, Hiroshi Nagai, and Yoshiyuki TakataCite this: J. Org. Chem. 1979, 44, 20, 3519–3523Publication Date (Print):September 1, 1979Publication History Published online1 May 2002Published inissue 1 September 1979https://doi.org/10.1021/jo01334a016RIGHTS & PERMISSIONSArticle Views707Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (708 KB) Get e-Alertsclose Get e-Alerts
Why X is not our ideal window system (1990)

Extensive experience with X11 has convinced us that it represents a true advance in window systems, but that there are areas in which the X protocol is seriously deficient. The problems we describe fall into seven categories: coordinate system pitfalls, unavoidable race conditions, incomplete support for window managers, insufficient window viewability information, difficulties with interactive mouse-tracking, pop-up and redisplay inefficiencies, and exceptional condition handling. We propose solutions for most of these problems. Some solutions could be easily incorporated into the X11 protocol. Other proposals are too incompatible to be adopted, but are included for the benefit of future window system designers.
C1q/TNF‐related protein‐1 functions to protect against acute ischemic injury in the heart (2015)

Obesity is associated with an increased risk of cardiovascular disease. C1q/TNF-related protein (CTRP)-1 is a poorly characterized adipokine that is up-regulated in association with ischemic heart disease. We investigated the role of CTRP1 in myocardial ischemia injury. CTRP1-knockout mice showed increased myocardial infarct size, cardiomyocyte apoptosis, and proinflammatory gene expression after I/R compared with wild-type (WT) mice. In contrast, systemic delivery of CTRP1 attenuated myocardial damage after I/R in WT mice. Treatment of cardiomyocytes with CTRP1 led to reduction of hypoxia-reoxygenation-induced apoptosis and lipopolysaccharide-stimulated expression of proinflammatory cytokines, which was reversed by inhibition of sphingosine-1-phosphate (S1P) signaling. Treatment of cardiomyocytes with CTRP1 also resulted in the increased production of cAMP, which was blocked by suppression of S1P signaling. The antiapoptotic and anti-inflammatory actions of CTRP1 were cancelled by inhibition of adenylyl cyclase or knockdown of adiponectin receptor 1. Furthermore, blockade of S1P signaling reversed CTRP1-mediated inhibition of myocardial infarct size, apoptosis, and inflammation after I/R in vivo. These data indicate that CTRP1 protects against myocardial ischemic injury by reducing apoptosis and inflammatory response through activation of the S1P/cAMP signaling pathways in cardiomyocytes, suggesting that CTRP1 plays a crucial role in the pathogenesis of ischemic heart disease.
Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity (2016)

Many biopharmaceutical products exhibit extensive structural micro-heterogeneity due to an array of co-occurring post-translational modifications. These modifications often effect the functionality of the product and therefore need to be characterized in detail. Here, we present an integrative approach, combining two advanced mass spectrometry-based methods, high-resolution native mass spectrometry and middle-down proteomics, to analyse this micro-heterogeneity. Taking human erythropoietin and the human plasma properdin as model systems, we demonstrate that this strategy bridges the gap between peptide- and protein-based mass spectrometry platforms, providing the most complete profiling of glycoproteins. Integration of the two methods enabled the discovery of three undescribed C-glycosylation sites on properdin, and revealed in addition unexpected heterogeneity in occupancies of C-mannosylation. Furthermore, using various sources of erythropoietin we define and demonstrate the usage of a biosimilarity score to quantitatively assess structural similarity, which would also be beneficial for profiling other therapeutic proteins and even plasma protein biomarkers.
The Perceptual Color Space of Digital Image Display Terminals (1983)

The geometric properties of the set of colors that can be displayed on the TV monitor of a digital image processing terminal are discussed in the framework of the Commission Internationale de l'Eclairage (CIE) 1976 (L* u* v*) color space. Quantitative results are presented for the HACIENDA image processing system. The use of lightness, chroma, and hue angle for the representation of multi-band images is briefly discussed.
Delay minimization and technology mapping of two-level structures and implementation using clock-delayed domino logic (2000)

This paper presents a new delay minimization and technology mapping algorithm for two-level structures (TLS) implemented using clock-delayed (CD) domino logic. We take advantage of CD domino's high-speed, large fan-in NOR and OR gates to increase the speed of a circuit by partial collapsing. The algorithm is delay-driven and the delays are obtained from a characterized CD domino library. The results on eight combinational MCNC benchmark circuits show an average speed improvement of 89% for CD domino with TLS, compared to static CMOS implementations generated by Synopsys. CD domino with TLS using our tools produced on average 44% faster circuits than CD domino benchmarks minimized and mapped using Synopsys. The delay results for CD domino with TLS were on average 22% better than for standard domino.
Hydride Vapor Phase Epitaxy of GaN on NdGaO<sub>3</sub> Substrate and Realization of Freestanding GaN Wafers with 2-inch Scale (2000)

GaN thick film is grown on NdGaO 3 substrate using hydride vapor phase epitaxy. To avoid decomposition of NdGaO 3 substrate by NH 3 , a low-temperature grown GaN protective layer is adopted. Using NdGaO 3 substrate and a low-temperature GaN protective layer simultaneously, 2-inch-scale GaN wafers are realized. The photoluminescence (PL) spectrum indicates strong band-edge emission without deep-level related emission. Both plan-view transmission electron microscope and cathode luminescence images suggest that the dislocation density of freestanding GaN wafers is expected to be as low as 10 6 cm -2 .
Neue 1,4‐Dipolare Cycloadditionen von 6‐Oxo‐6<i>H</i>‐1,3‐oxazin‐3‐ium‐4‐olaten und eines 6‐Oxo‐6<i>H</i>‐1,3‐thiazin‐3‐ium‐4‐olats an Keten‐Derivate und Enamine (1988)

Abstract Die Reaktionen der Keten‐Derivate 4, 7 und 9 sowie der Enamine 13 und 17 mit einigen ausgewählten Titelverbindungen werden beschrieben. In diesen Fällen sind entweder Primäraddukte vom Typ 5, 14 oder 20 als Ergebnis einer 1,4‐Dipolaren Cycloaddition faßbar, oder als Folgereaktionen treten Eliminierungen zu Produkten vom Typ 8, 11, 16 oder 18 ein. Die 2(1 H )‐Pyridinone 8 entstehen auch bei der Thermolyse von 5 , während 15a–d aus 14a–d oder 20 durch Säurebehandlung zugänglich sind. Die beobachteten Regioselektivitäten werden mit den Ergebnissen aus MNDO‐Rechnungen und der FMO‐ und PMO‐Theorie verglichen.
XMLView: Discover domain specific service description in a UDDI compliant registry (2008)

In recent years we have seen the wide adoption of Web services architecture in grid computing. Service discovery, as one of the critical tasks in Web services architecture, is addressed by the UDDI specification. However, UDDI does not gain as much popularity as other Web services specifications such as WSDL and SOAP. At the same time, a number of domain-specific service description models are developed to address the problem of service discovery in specific application domains of grid computing. In this paper, we argue that both UDDI and domain-specific service description models can complement each other, instead of replacing each other. To demonstrate this, we present a system called XMLView that is able to accommodate domain-specific service descriptions and present them in a UDDI compliant view. Queries expressed on the domain-specific model are also supported.
Integration of proximity relations under consistency constraint (2003)

Though the data integration problem of relational databases has been well studied, little work addresses the problem in the context of fuzzy relational databases. The fuzzy relational model relies on the specification of either a similarity relation or a proximity relation for each scalar domain in the fuzzy database. Without the constraint of max-min transitivity, proximity relations can be defined in an intuitive way. This paper states a resolution in integrating multiple proximity relations. First, the closure property of weighted combination of multiple proximity relations is shown. Then, the notion of consistency constraint is defined. It has been proved that the weighted combination of proximity relations under such constrain is still consistent with each of the proximity relations prior to their integration.
Noninvasive red and near‐infrared wavelength‐induced photobiomodulation: promoting impaired cutaneous wound healing (2016)

The innumerable intricacies associated with chronic wounds have made the development of new painless, noninvasive, biophysical therapeutic interventions as the focus of current biomedical research. Red and near-infrared light-induced photobiomodulation therapy appears to emerge as a promising drug-free approach for promoting wound healing, reduction in inflammation, pain and restoration of function owing to penetration power in conjunction with their ability to positively modulate the biochemical and molecular responses. This review will describe the physical properties of red and near-infrared light and their interaction with skin and highlight their efficacy of wound repair and regeneration. Near-infrared (800-830 nm) was found to be the most effective and widely studied wavelength range followed by red (630-680 nm) and 904 nm superpulsed light exhibiting beneficial photobiomodulatory effects on impaired dermal wound healing.
SEISMIC RETROFIT OF BRIDGE COLUMNS (1990)

Research is currently being conducted to investigate techniques for retrofitting existing bridge columns to improve their seismic performance. The objectives of the research are to develop and evaluate retrofit methods for increasing the shear strength and ductility capacity of rectangular bridge columns.
HIV‐1 Infection in the Female Reproductive Tract: Role of Interactions between HIV‐1 and Genital Epithelial Cells (2011)

Despite recent progress in understanding the mucosal transmission of human immunodeficiency virus (HIV)-1, the immediate events following transmission in the female genital tract are incompletely understood. Recent in vivo studies in primate models indicate that HIV-1 transmission may occur in the upper or lower genital tract and the initial HIV-1 replication occurs primarily in the target T cells and in some subsets of DCs localized in the genital tract. However, the principal mechanism(s) that allow the virus to cross the primary barrier of genital epithelial cells (GECs) are still unclear. A number of pathways have been proposed as possible ways that HIV-1 could use to cross the epithelium. However, little attention has been paid to the response of GECs to HIV-1. We recently demonstrated that exposure to HIV-1 rapidly upregulates a wide array of pro-inflammatory cytokine production by GECs. Among these cytokines, tumour necrosis factor (TNF)-α impaired the tight junction barrier allowing HIV-1 and luminal bacteria to translocate across the epithelium. This study illustrated that GECs are dynamically active cells that mount rapid host responses to HIV-1, independent of viral replication. Cytokine responses of GECs could play a critical role in HIV transmission and replication. Further understanding of GEC responses to HIV-1 and their regulation could be critical to understanding HIV-1 transmission dynamics during heterosexual transmission.
Coordinated interconnect: a philosophical change in the design and construction of power electronic converters (2002)

A wiring harness or buswork has been typically used to interconnect the components in power-electronic converters. Many design and manufacturing problems originate in the interconnect. This paper proposes a change in the design philosophy of power electronic converters using a system of "coordinated interconnect". With coordinated interconnect, components connect directly to each other without the intervening wiring harness or buswork. This paper describes one possible implementation of coordinated interconnect and outlines the requirements for such a system.
A thixotropic molecular hydrogel selectively enhances Flk1 expression in differentiated murine embryonic stem cells (2011)

Hydrogels are considered as promising materials for maintenance and directed differentiation of embryonic stem (ES) cells. We designed and synthesized a molecular gelator, which was a collagen mimic related to sequence. The hydrogel was found to be thixotropic and it was characterized by different techniques in detail, including rheometery, TEM, CD, FT-IR, and fluorescence spectrometery. More importantly, we demonstrated that our molecular hydrogel supported the differentiation of murine ES cells, and could selectively enhance Flk1 expression in differentiated mES cells. Flk1-positive cells derived from ES cells had been demonstrated as vascular progenitors that support the formation of vascular system. Thus, our hydrogel had great potentials for the preparation of a pure population of Flk1-positive cells, which could be used for the study of vascular formation. Our study is the first example of using molecular hydrogels for mES cell differentiation, which will promote future application of both molecular hydrogels and stem cells in regenerative medicine.
Narrowed TCR repertoire and viral escape as a consequence of heterologous immunity (2006)

Why some virus-specific CD8 TCR repertoires are diverse and others restricted or "oligoclonal" has been unknown. We show here that oligoclonality and extreme clonal dominance can be a consequence of T cell cross-reactivity. Lymphocytic choriomeningitis virus (LCMV) and Pichinde virus (PV) encode NP(205-212) epitopes that induce different but highly cross-reactive diverse TCR repertoires. Homologous viral challenge of immune mice only slightly skewed the repertoire and enriched for predictable TCR motifs. However, heterologous viral challenge resulted in a narrow oligoclonal repertoire with dominant clones with unpredictable TCR sequences. This shift in clonal dominance varied with the private, i.e., unique, specificity of the host's TCR repertoire and was simulated using affinity-based computer models. The skewing differences in TCR repertoire following homologous versus heterologous challenge were observed within the same private immune system in mice adoptively reconstituted with memory CD8 T cell pools from the same donor. Conditions driving oligoclonality resulted in an LCMV epitope escape variant in vivo resembling the natural Lassa virus sequence. Thus, T cell oligoclonality, including extremes in clonal dominance, may be a consequence of heterologous immunity and lead to viral escape. This has implications for the design of peptide-based vaccines, which might unintentionally prime for skewed TCR responses to cross-reactive epitopes.
ADVANCED COMPRESSOR ENGINE CONTROLS TO ENHANCE OPERATION, RELIABILITY AND INTEGRITY (2004)

This document provides a mid-term update for the ''Advanced Compressor Engine Controls to Enhance Operation, Reliability, and Integrity'' project. SwRI is conducting this project for DOE in conjunction with Cooper Energy Services, under DOE contract number DE-FC26-03NT41859. The objective of this one-year project is to develop, evaluate, and demonstrate advanced engine control technologies and hardware, specifically, closed-loop NO{sub x} emissions control on a two-stroke integral reciprocating engine/compressor used for pipeline gas transmission service. This work uses a Cooper-Bessemer GMVH-6 laboratory engine owned by Cooper Energy Services (CES) and installed in a test facility at Southwest Research Institute (SwRI). The gas transmission industry operates over 4,000 integral engine compressors, the majority being two-stroke, with a median age of 45 years and a median size of 2000 horsepower. These engines have historically exhibited poor performance and high emissions, due in part to poor engine control. The end results are misfires and partial burns that lead to increased fuel usage and exhaust emissions. Many of the slow-speed integral engines in the gas compression industry utilize control systems that are outdated, slow, and suffer from poor resolution. Research into more advanced control systems for integral compressor engines has increased tremendously in recent years. The recent advancements in control logic are being reviewed and analyzed in this program to understand the effectiveness of each. In addition, the application of a real-time NO{sub x} sensor feedback for closed-loop control is being investigated. To date, the strategies involving fuel/air equivalence ratio for a NO{sub x} prediction algorithm have been reviewed and analyzed. A hierarchy of control strategies will be outlined at the conclusion of this program. This hierarchy will range from the simplest and least expensive closed-loop control to an advanced system utilizing individual cylinder control. The ultimate control strategy is thought to be one that integrates both compressor and engine control, with the engine control based on individual power cylinders. The hierarchy of engine control may be desirable for the variety of engines in various locations that are subject to varying regulated levels of NO{sub x} emissions. The engines in non-attainment areas will require the maximum level of complexity in engine controls.
Single image multimaterial estimation (2012)

Estimating the reflectance and illumination from a single image becomes particularly challenging when the object surface consists of multiple materials. The key difficulty lies in recovering the reflectance from sparse angular samples while correctly assigning them to different materials. We tackle this problem by extracting and fully leveraging reflectance priors. The idea is to strongly constrain the possible solutions so that the recovered reflectance conform with those of real-world materials. We achieve this by modeling the parameter space of a directional statistics BRDF model and by extracting an analytical distribution of the subspace that real-world materials span. This is used, with other priors, in a layered MRF-based formulation that models material regions and their spatially varying reflectance with continuous latent layers. The material regions and their reflectance, and the direction and strength of a single point source are jointly estimated. We demonstrate the effectiveness of the method on real and synthetic images.
Automation of user-specific ASIC library development (2002)

Discusses a method to develop a user-specific standard cell library using advanced library development tools. The tools described support library engineering, development, quality assurance and productization. The tools can also automatically support multiple vendor ASIC design tools, including VHDL and Verilog, schematic entry tools, simulators, logic synthesizers, datapath compilers, and other compilation tools.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Spread-Spectrum Road-Automobile Communications (1991)

There are several issues relevant for spread spectrum communications between roadside beacons and moving vehicles. The goal to achieve a desired error-probability performance and communicate a given amount of information between a beacon and moving vehicles imposes certain requirements on the power, bandwidth, and complexity. These requirements are studied under some worst case scenario.