gebhart/patrepeval huggingface dataset:
Abstract 3787: EphrinB1 is a novel microtubule associated protein whose expression may predict sensitivity to taxane (2015)

Abstract Mitosis is a complex sequence of highly regulated events that ensures the proper segregation of sister chromatids into daughter cells. At the heart of the mitotic machinery lie the microtubules. Microtubules (MTs) are components of the cytoskeleton made up of polymerized alpha and beta tubulin dimers. MT structure and function must be maintained throughout the cell cycle to ensure proper execution of mitosis and cellular homeostasis. It has previously been reported that the protein tyrosine phosphatase, PTPN13, localizes at centrosomes from interphase, through metaphase and dramatically shifts to the spindle midzone during anaphase. During telophase, PTPN13 accumulates at the midzone, becoming concentrated at the center of the midbody during cytokinesis. We have previously demonstrated that the HPV16 E6 oncoprotein binds PTPN13 and leads to its degradation. Given PTPN13's localization to distinct compartments during mitosis/cytokinesis, we speculated that HPV infection may affect the process of mitosis. In addition, the newly appreciated roles of the PTPN13 phosphatase substrate, EphrinB1, in oncogenesis, further prompted us to define its role in mitosis. Here we report that EphrinB1 co-localizes with MTs during all phases of the cell cycle. Specifically, unphosphorylated EphrinB1 directly binds tubulin, while its phosphorylated form lacks MT binding. These characteristics are hallmarks of microtubule associated proteins (MAPs) and suggest that EphrinB1 is a novel MAP. Importantly, we demonstrate that expression of PTPN13 correlates with sensitivity to taxanes while its absence may confer resistance. In addition, we show that EphrinB1 expression affects taxane response in vitro and in vivo. We speculate that this reflects PTPN13's modulation of EphrinB1 phosphorylation and suggest that EphrinB1 is an important contributor to taxane sensitivity/resistance phenotypes in epithelial cancers. HPV infection or functional mutations of PTPN13 in non-viral cancers may predict taxane sensitivity. Note: This abstract was not presented at the meeting. Citation Format: Paola D. Vermeer, Paul L. Colbert, Daniel W. Vermeer, Bryant G. Wieking, John H. Lee. EphrinB1 is a novel microtubule associated protein whose expression may predict sensitivity to taxane. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3787. doi:10.1158/1538-7445.AM2015-3787
Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release (1998)

Nascent RNA structures may regulate RNA chain elongation either directly through interaction with RNA polymerase or indirectly by disrupting nascent RNA contacts with polymerase or DNA. To distinguish these mechanisms we tested whether the effects of the his leader pause RNA hairpin could be mimicked by pairing of antisense DNA or RNA oligonucleotides to the nascent transcript. The his pause hairpin inhibits nucleotide addition when it forms 11 nucleotides from the transcript 3' end. It also can terminate transcription when base changes extend its stem to </=8 nucleotides from the 3' end. All oligonucleotides that disrupted the pause hairpin reduced the dwell time of RNA polymerase at the pause site dramatically, even when they mimicked the 11-nucleotide 3'-proximal RNA spacing or created a suitably positioned RNA loop. Oligonucleotides that paired </=8 nucleotides from the pause RNA 3' end could trigger transcript release, but only when added to an already paused complex. These results argue that direct interaction of a nascent RNA hairpin with RNA polymerase delays escape from a pause, but that indirect effects of a hairpin may trigger transcript release from a paused complex. Resistance of the paused complex to pyrophosphorolysis and its reversal by antisense oligonucleotides further suggest that interaction of the pause hairpin with RNA polymerase disengages the RNA 3' end from the active site.
Chemoenzymatic Asymmetric Synthesis of Pregabalin Precursors via Asymmetric Bioreduction of β-Cyanoacrylate Esters Using Ene-Reductases (2013)

The asymmetric bioreduction of a library of β-cyanoacrylate esters using ene-reductases was studied with the aim to provide a biocatalytic route to precursors for GABA analogues, such as pregabalin. The stereochemical outcome could be controlled by substrate-engineering through size-variation of the ester moiety and by employing stereochemically pure (E)- or (Z)-isomers, which allowed to access both enantiomers of each product in up to quantitative conversion in enantiomerically pure form. In addition, stereoselectivities and conversions could be improved by mutant variants of OPR1, and the utility of the system was demonstrated by preparative-scale applications.
Molecular architecture of a miRNA-regulated 3′ UTR (2008)

Animal genomes contain hundreds of microRNAs (miRNAs), small regulatory RNAs that control gene expression by binding to complementary sites in target mRNAs. Some rules that govern miRNA/target interaction have been elucidated but their general applicability awaits further experimentation on a case-by-case basis. We use here an assay system in transgenic nematodes to analyze the interaction of the Caenorhabditis elegans lsy-6 miRNA with 3' UTR sequences. In contrast to many previously described assay systems used to analyze miRNA/target interactions, our assay system operates within the cellular context in which lsy-6 normally functions, a single neuron in the nervous system of C. elegans. Through extensive mutational analysis, we define features in the known and experimentally validated target of lsy-6, the 3' UTR of the cog-1 homeobox gene, that are required for a functional miRNA/target interaction. We describe that both in the context of the cog-1 3' UTR and in the context of heterologous 3' UTRs, one or more seed matches are not a reliable predictor for a functional miRNA/target interaction. We rather find that two nonsequence specific contextual features beyond miRNA target sites are critical determinants of miRNA-mediated 3' UTR regulation. The contextual features reside 3' of lsy-6 binding sites in the 3' UTR and act in a combinatorial manner; mutation of each results in limited defects in 3' UTR regulation, but a combinatorial deletion results in complete loss of 3' UTR regulation. Together with two lsy-6 sites, these two contextual features are capable of imparting regulation on a heterologous 3' UTR. Moreover, the contextual features need to be present in a specific configuration relative to miRNA binding sites and could either represent protein binding sites or provide an appropriate structural context. We conclude that a given target site resides in a 3' UTR context that evolved beyond target site complementarity to support regulation by a specific miRNA. The large number of 3' UTRs that we analyzed in this study will also be useful to computational biologists in designing the next generation of miRNA/target prediction algorithms.
Global brightness-variation compensation for video coding (1998)

A global brightness-variation compensation (GBC) scheme is proposed to improve the coding efficiency for video scenes that contain global brightness-variations caused by fade in/out, camera-iris adjustment, flicker, illumination change, and so on. In this scheme, a set of two brightness-variation parameters, which represent multiplier and offset components of the brightness-variation in the whole frame, is estimated. The brightness-variation is then compensated using the parameters. We also propose a method to apply the GBC scheme to component signals for video coding. Furthermore, a block-by-block on/off control method for GBC is introduced to improve the coding performance even for scenes including local variations in brightness caused by camera flashes, spotlights, and the like. Simulation results show that the proposed GBC scheme with the on/off control method improves the peak signal-to-noise ratio (PSNR) by 2-4 dB when the coded scenes contain brightness-variations.
[Sodium transport and its regulation of acutely isolated alveolar type II cells]. (2006)

Acutely isolated AT II cells can be valuable for studying electrophysiological characteristics of sodium channels even under pathological conditions.
Flattened Broadband Notch Filters Using Guided-Mode Resonance Associated With Asymmetric Binary Gratings (2006)

In this letter, the broadband notch filter exhibiting a flattened bandstop spectral response is experimentally demonstrated for the first time by using the guided-mode resonance associated with the periodic subwavelength structure possessing asymmetric binary grating profiles. The proposed filter consisting of grating and waveguide structures is realized by utilizing a single-layer poly-silicon film deposited on a quartz substrate. The asymmetric grating profile is carried out by dividing the one-filling-factor binary structure into the one with two distinct filling factors within one identical period. A flat bandstop spectral response at the central wavelength of 1.22 mum is obtained under normal incidence for transverse-electric polarization. Its transmittance of bandstop spectrum can be suppressed as low as -20dB within a broad spectral range of 85 nm and its corresponding Deltalambda/lambda is larger than 6%. The spectra under oblique incidence are demonstrated to verify the proposed filter has a high immunity for the angular deviation up to 20deg
Surface Tension Transport of Prey by Feeding Shorebirds: The Capillary Ratchet (2008)

The variability of bird beak morphology reflects diverse foraging strategies. One such feeding mechanism in shorebirds involves surface tension-induced transport of prey in millimetric droplets: By repeatedly opening and closing its beak in a tweezering motion, the bird moves the drop from the tip of its beak to its mouth in a stepwise ratcheting fashion. We have analyzed the subtle physical mechanism responsible for drop transport and demonstrated experimentally that the beak geometry and the dynamics of tweezering may be tuned to optimize transport efficiency. We also highlight the critical dependence of the capillary ratchet on the beak's wetting properties, thus making clear the vulnerability of capillary feeders to surface pollutants.
Novel fabrication method of highly-nonlinear silica holey fibres (2006)

We present a novel and simple method of producing small core silica holey fibres with nonlinearity close to the maximum achievable. An effective area of 1.6 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with a loss of 0.18 dB/m at 1.55 mum were achieved.
A combined LLC/MAC traffic analysis of the radio interface in TDMA-based third generation mobile systems (2003)

Packet reservation multiple access (PRMA) is a TDM-based multiple access protocol for third generation mobile radio systems capable of a accommodating synchronous and asynchronous traffic and enabling efficient spectrum usage. However, a traffic performance analysis of the protocol has been only carried out for speech traffic. The analysis is extended to a traffic mixture comprising speech and data applications. Error detection/recovery functionalities as exercised at the data link layer are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Two Cheers for the Monetary Control Act1 (2010)

This article explains how the Monetary Control Act (MCA) of 1980 paved the way for the transition away from paper to electronic check clearing and processing, ultimately leading to the successful implementation of the Check Clearing for the 21st Century Act (Check 21) in 2003.
Optimal Finite Horizon Sensing for Wirelessly Powered Devices (2019)

We are witnessing a significant advancements in the sensor technologies which has enabled a broad spectrum of applications. Often, the resolution of the produced data by the sensors significantly affects the output quality of an application. We study a sensing resolution optimization problem for a wireless powered device (WPD) that is powered by wireless power transfer (WPT) from an access point (AP). We study a class of harvest-first-transmit-later type of WPT policy, where an access point (AP) first employs RF power to recharge the WPD in the down-link, and then, collects the data from the WPD in the up-link. The WPD optimizes the sensing resolution, WPT duration and dynamic power control in the up-link to maximize an application dependant utility at the AP. The utility of a transmitted packet is only achieved if the data is delivered successfully within a finite time. Thus, we first study a finite horizon throughput maximization problem by jointly optimizing the WPT duration and power control. We prove that the optimal WPT duration obeys a time-dependent threshold form depending on the energy state of the WPD. In the subsequent data transmission stage, the optimal transmit power allocations for the WPD is shown to posses a channel-dependent fractional structure. Then, we optimize the sensing resolution of the WPD by using a Bayesian inference based multi armed bandit problem with fast convergence property to strike a balance between the quality of the sensed data and the probability of successfully delivering it.
Mechanism for bistability in organic memory elements (2004)

We demonstrate that the resistive switching phenomenon observed in organic semiconductor layers containing granular metal particles conforms to a charge storage mechanism described by Simmons and Verderber [Proc. R. Soc. A 391, 77 (1967)]. The space-charge field due to the stored charge inhibits further charge injection from the electrodes. The equilibrium current–voltage curve is N shaped and the low and high resistance states are obtained by applying voltage close to the local maximum and minimum, respectively.
Effects of Insulating Layers and Active Layer on ZnS:Tb, F Thin-Film Electroluminescent Devices (1993)

This paper describes the effects of insulating layers and active layer on the ZnS:Tb,F thin-film electroluminescent (TFEL) devices. A green-colored device, deposited by the RF-magnetron system, having doubly-stacked insulating layers has been developed to elucidate the role of insulators. It is shown that the semi-insulating layer, HfO 2 film, deposited adjacent to an active layer acts as a carrier injector due to Poole-Frenkle emission, while the insulating SiO 2 films act as a carrier limiter. In addition, improvement on device performance, such as crystalline quality of the ZnS:Tb,F thin film and the relative amount of fluorine to terbium, F/Tb, is also discussed.
Remote augmented reality for multiple players over network (2007)

Augmented Reality (AR) in multimedia gaming is a dynamic and exciting field of research. One of the challenges is to have multiple users interacting in the networked augmented reality environment. In recent years, camera-based body motion capturing console games, which captures the player's body movement to control the objects rendered by the computer, have been developed. In this paper, we present a system called, Tele-Table which allows multiple users to interact with each other through the network using real objects. Each player's set-up consists of an overhead mounted camera perceiving real objects, a plasma TV placed horizontally to act as a game table, and a computer. One of the most challenging tasks is data synchronization between two terminals. There are mainly three synchronization tasks we need to handle. They are temporal synchronization, spatial synchronization, and game states synchronization between the two terminals. We present these difficulties and present solutions and discussion to solve them. The design goals of the Tele-Table are real-time and realistic user experience. The features of the system are changeable background, using real objects, and real-time augmented reality gaming between two terminals. We outline the system, present the detailed description, and discuss current achievements.
Should We Try to Prevent Hyperthermia After Cardiac Arrest? (2000)

Dealing with the sequelae of cardiac arrest or asphyxia in a previously normal adult or child is always very difficult, for the pediatrician as much as the family. We now know that following resuscitation there can be a “latent” phase with transient recovery of cerebral energy metabolism, before a secondary phase of deterioration as determined by seizures, cytotoxic edema,1 and cerebral energy failure.2 ,3 This latent phase may persist as long as 6 to 15 hours after reperfusion in infants.3 It is highly likely that the processes active during this latent period involve activation of the intracytoplasmic phase of programmed …
c‐TiS<sub>2</sub>, a New Modification of Titanium Disulfide with Cubic Structure (1985)

A metastable modification of TiS 2 has been prepared by a topotactic solid‐state reaction at room temperature in which CuTi 2 S 4 working electrodes were anodically oxidized in aprotic copper( I ) electrolytes. On the basis of X‐ray powder data, it can be determined that the new phase belongs to a very seldom AB 2 structural type. This cubic TiS 2 is of interest, inter alia, as a material for reversible electrodes in secondary batteries. It has advantages over hexagonal TiS 2 (layer lattice).
Activation of CaMKIV by soluble amyloid-β <sub>1–42</sub> impedes trafficking of axonal vesicles and impairs activity-dependent synaptogenesis (2017)

The prefibrillar form of soluble amyloid-β (sAβ<sub>1-42</sub>) impairs synaptic function and is associated with the early phase of Alzheimer's disease (AD). We investigated how sAβ<sub>1-42</sub> led to presynaptic defects using a quantum dot-based, single particle-tracking method to monitor synaptic vesicle (SV) trafficking along axons. We found that sAβ<sub>1-42</sub> prevented new synapse formation induced by chemical long-term potentiation (cLTP). In cultured rat hippocampal neurons, nanomolar amounts of sAβ<sub>1-42</sub> impaired Ca<sup>2+</sup> clearance from presynaptic terminals and increased the basal Ca<sup>2+</sup> concentration. This caused an increase in the phosphorylation of Ca<sup>2+</sup>/calmodulin-dependent protein kinase IV (CaMKIV) and its substrate synapsin, which markedly inhibited SV trafficking along axons between synapses. Neurons derived from a transgenic AD mouse model had similar defects, which were prevented by an inhibitor of CaMK kinase (CaMKK; which activates CaMKIV), by antibodies against Aβ<sub>1-42</sub>, or by expression a phosphodeficient synapsin mutant. The CaMKK inhibitor also abolished the defects in activity-dependent synaptogenesis caused by sAβ<sub>1-42</sub> Our results suggest that by disrupting SV reallocation between synapses, sAβ<sub>1-42</sub> prevents neurons from forming new synapses or adjusting strength and activity among neighboring synapses. Targeting this mechanism might prevent synaptic dysfunction in AD patients.
A Review of Developments in Computer-Based Systems to Image Teeth and Produce Dental Restorations. (1987)

Computer-aided design and manufacturing (CAD/CAM) make it possible to automate the creation of dental restorations. Currently practiced techniques are described. Three automated systems currently under development are described and compared. Advances in computer-aided design and computer-aided manufacturing (CAD/CAM) provide a new option for dentistry, creating an alternative technique for producing dental restorations. It is possible to create dental restorations that are automatically produced and meet or exceed current requirements for fit and occlusion.
A New Framework of a Heteroleptic Iridium(III)–Carbene Complex as a Triplet Emitting Material (2012)

A new framework for a dark red emitting heteroleptic failed cyclometalated iridium(III) carbene complex as an intermediate with a short triplet lifetime has been synthesized. A crystal structure has been determined by X-ray structure analysis. The photophysical behavior of this complex has been studied experimentally through UV–vis spectroscopy and photoluminescence studies with a view toward organic light-emitting diode (OLED) applications. The determination of HOMO/LUMO levels has been carried out by differential pulse voltammetry.
Synthesis of Knowledge from Woody Biomass Removal Case Studies (2008)

Interest in woody biomass from forests has increased because of rising fossil fuel costs, concerns about greenhouse gas emissions from fossil fuels, and the threat of catastrophic wildfires. However, getting woody biomass from the forest to the consumer presents economic and logistical challenges. Woody biomass is the lowest-value material removed from the forest, usually logging slash, small-diameter trees, tops, limbs, or trees that can not be sold as timber. This report brings together 45 case studies of how biomass is removed from forests and used across the country to demonstrate the wide variety of successful strategies, funding sources, harvesting operations, utilization outlets, and silvicultural prescriptions. The case studies are available at http://biomass.forestguild.org. Seven main themes emerged from collecting and comparing the biomass removal case studies: objectives, collaboration, ecology, fire, economics, implementation, and regional differences. Biomass removal projects tend to combine multiple objectives such as ecological restoration, wildfire hazard reduction, forest-stand improvement, rural community stability, employment, and habitat improvement. Collaboration, with both the interested public and contractors, is a key element in successful projects. Stewardship contracting presents a flexible way to develop partnerships and invite constructive public involvement. The Ecological impacts of biomass removals, both positive and negative, need more research. States and non-governmental organizations are creating guidelines for biomass harvesting that may help to protect forests and alleviate concerns about the impact of removals. Fire is the main driver of many biomass projects. In many cases, the goal of biomass removals is to reduce forest fuels and wildfire hazard. Biomass removal provides substantial ecological benefits when it helps to re-establish natural fire regimes. The economics of biomass removal are challenging. The case studies demonstrate that biomass removal projects are rarely a source of income. However, some managers generated a profit by combining multiple forest products in the removal, taking advantage of fluctuations in the biomass market, and selling to established outlets. The implementation of biomass harvests benefit from mechanization as well as dividing the harvesting and handling of forest products among multiple contractors. New technologies were tested in some case studies, and others on the horizon offer the potential for further cost reductions. The case studies reveal regional differences and the importance of designing projects to fit the biophysical conditions and social context of each site. Taken together, these case studies show that all aspects of woody biomass removals, from markets to mechanization, are evolving. This report identifies the building blocks for successful biomass projects—including public involvement, partnerships with contractors, and judicious mechanization of harvest operations—that are present in the management of many forests across the country.