gebhart/patrepeval huggingface dataset:
Distinct Conformational Changes Induced by 20-epi Analogues of 1α,25-Dihydroxyvitamin D3 Are Associated with Enhanced Activation of the Vitamin D Receptor (1995)

The relative affinities of the 1 alpha,25-dihydroxyvitamin D3 (1,25-D3) analogues 20-epi-1 alpha,25-dihydroxyvitamin D3 (IE) and 20-epi-22-oxa-24a,26a,27a-tri-homo-1 alpha,25-dihydroxyvitamin D3 (ID) to the nuclear vitamin D receptor (VDR) are similar to that of 1,25-D3, but their antiproliferative action is 1000-fold greater. We tested whether the greater antiproliferative effect of these analogues is due to a differential activation of the VDR. In ROS 17/2.8 cells, the effective doses required to produce 50% maximal stimulation (ED50) of transfected reporter genes driven by either the osteocalcin or the osteopontin vitamin D-response elements (VDRE) were 5 x 10(-9) M, 10(-10) M, and 10(-11) M for 1,25-D3, ID, and IE, respectively. Similar results were obtained when recombinant human VDR was cotransfected into CV-1 cells with an osteocalcin VDRE-reporter plasmid. We found that in vitro the sensitivity of 1,25-D3-induced and analogue-induced receptors to proteases was different. The ED50 for binding to VDRE, as determined by electrophoretic mobility shift assays, was significantly higher for 1,25-D3-induced than for analogue-induced VDR. The concentration of retinoid X receptor (RXR) was significantly lower in 1,25-D3-induced than analogue-induced VDR complexes with VDRE. We therefore conclude that IE and ID augment transcriptional activity of VDR more than 1,25-D3 does, by producing conformational changes that enhance dimerization of VDR with RXR. We suggest that these conformational changes are due to differences in the contact sites of the 20-epi analogues and 1,25-D3 with the VDR.
Developing a Hydrate-Monitoring System (2008)

Summary A major challenge in offshore development is to ensure unimpeded flow of hydrocarbons. Managing solids such as hydrates is the key to the viability of developing a deepwater prospect. Common methods to prevent and reduce hydrate risks are generally based on injection of thermodynamic inhibitors to prevent hydrate formation, or use of kinetic hydrate inhibitors to sufficiently delay hydrate nucleation/growth. Currently, the amount of inhibitor required is either calculated and/or determined based on lab experiments. The amount of inhibitor depends on various parameters, including, water cut, inhibitor loss to hydrocarbon phases, aqueous and non-aqueous fluid compositions, operating conditions. Generally, a safety factor is considered and the resulting inhibitor is injected upstream without much downstream measurements. Despite the usual safety margins, gas hydrates are formed, which could result in serious operational and safety concerns. This is mainly caused by changes in the system conditions (e.g., rates and water cut) and/or malfunction of the equipment. In most cases, the amount of inhibitor is more than necessary and is not adjusted with seasonal changes, affecting CAPEX/OPEX. As a result of a joint industry project, several novel techniques, based on downstream and online measurements, have been developed. These techniques could be divided into the following categories: Monitoring hydrate safety margin to optimize inhibitor injection rates. The system determines the amount of inhibitor in the aqueous phase and the degree of inhibition they can offer. Detecting initial hydrate formation, as an early warning system against hydrate blockage. The system detects the changes in the system caused by hydrate formation with the aim of giving the operator enough time to prevent a blockage. The main advantages of these techniques include minimizing the amount of inhibitor required and preventing pipeline blockages caused by hydrates, hence the cost of inhibitor; impact on the environment; cost of remedial actions; and deferred production. A number of techniques have been investigated during this project, with some techniques selected for prototype development. The developed prototypes have been tested in the project sponsors’ laboratories and some in commercial production. In this paper, an update on the latest results of this new approach in flow assurance control is presented.
General time-, space-, and frequency-multiplexed acoustooptic correlator (1985)

A time-, space-, and frequency-multiplexed time-integrating acoustooptic correlator is described. Its general functional use is emphasized in communication applications. The applications considered are synchronization of long duration signals with an infinite range delay search required and the parallel demodulation of many possible message codes.
Formation Evaluation in Thin Sand/Shale Laminations (2007)

Abstract Formation evaluation in thin sand-shale lamination seeks first to determine sand resistivity, volume fraction, and porosity. Afterwards, saturation and volume are simple Archie applications. Resistivity anisotropy techniques can provide estimates of sand resistivity and volume fraction, but good results depend on the choice of the anisotropic shale point. The same shale point should be used in the determination of sand porosity. Difficulties will arise when anisotropy is not caused by sand-shale laminations, when no sand-shale point exists, or when the nearby thick sand-shale is not representative of the sand-shale in the laminations. In producing fields that have undergone several waterfloods, water resistivity is often unknown in the swept thick sands and might not be representative of the water in the unswept thin sands. As discussed previously, NMR offers useful insights into the petrophysics of thin sand-shale laminations. Typically, 1D high-resolution data is acquired to estimate sand volume fraction, porosity, and permeability, and 3D fluids data is used to evaluate the hydrocarbon type and content in the thin sands. However, shallow depth of investigation, slow logging speed, and sometimes unfavorable signal-to-noise ratios limit the applicability of the NMR technique. In this paper we first demonstrate the variability of sand resistivity, volume fraction, and porosity output depending on the input parameters. Next, we show the complementary aspects of the resistivity anisotropy and NMR techniques. Since several are the same or determined independently, using both datasets ensures more plausible results in thin beds than either stand-alone technique could provide. Field examples of a straightforward case with a well-defined anisotropic shale point, as well as a difficult case with multiple shale points, are used to demonstrate the new workflow. In general we see improvements in the estimation of the hydrocarbon in place; however, not all thin beds offer large hydrocarbon volumes.
A 16-Channel Nonparametric Spike Detection ASIC Based on EC-PC Decomposition (2015)

In extracellular neural recording experiments, detecting neural spikes is an important step for reliable information decoding. A successful implementation in integrated circuits can achieve substantial data volume reduction, potentially enabling a wireless operation and closed-loop system. In this paper, we report a 16-channel neural spike detection chip based on a customized spike detection method named as exponential component-polynomial component (EC-PC) algorithm. This algorithm features a reliable prediction of spikes by applying a probability threshold. The chip takes raw data as input and outputs three data streams simultaneously: field potentials, band-pass filtered neural data, and spiking probability maps. The algorithm parameters are on-chip configured automatically based on input data, which avoids manual parameter tuning. The chip has been tested with both in vivo experiments for functional verification and bench-top experiments for quantitative performance assessment. The system has a total power consumption of 1.36 mW and occupies an area of 6.71 mm (2) for 16 channels. When tested on synthesized datasets with spikes and noise segments extracted from in vivo preparations and scaled according to required precisions, the chip outperforms other detectors. A credit card sized prototype board is developed to provide power and data management through a USB port.
Mining the Web for IP Address Geolocations (2007)

In this paper, we observe that many Web pages contain ge-olocation information (address, zipcode, and telephone area code) and many of these geolocation items are directly re-lated to the locations of the IP addresses that host the Web pages. We then design Structon, a system that mines Web pages for IP address geolocations. In Structon, we first ex-tract geolocation information from every crawledWeb pages, we then devise a serial of information clustering, false-inform-ation filtering, error-correction, and location inferring algo-rithms to map IP addresses to geolocations. We have run our algorithms on top of a set of 74M Chinese Web pages, from which we are able to identify the geolocations for 8.2M IP addresses, which contain addresses for not only Web servers but also client hosts. We have verified our result with an IP address location table of a major Chinese ISP, the ver-ification shows that the accuracy of Structon is 94.4 % at province level. 1.
RFID security and privacy (2008)

RFID technology has raised a number of both real and imagined security and privacy fears and concerns. Since roughly 2001, a number of researchers have stepped up to the plate and proposed techniques for strengthening RFID security and privacy, while others have focused on attacking (and demonstrating weaknesses in) currently deployed RFID systems. Despite a few PhD theses devoted to this topic, it remains to be seen whether there are any new long-term fundamental issues involved in RFID security & privacy. Therefore, this panel's goal is to present and debate the panelists' diverse perspectives on the future (or lack thereof) of RFID security and privacy research.
Neutralizing antibodies induced by recombinant vaccinia virus expressing varicella-zoster virus gpIV (1991)

Monoclonal antibodies generated against varicella-zoster virus (VZV) glycoprotein I (gpI) also recognize VZV gpIV (A. Vafai, Z. Wroblewska, R. Mahalingam, G. Cabirac, M. Wellish, M. Cisco, and D. Gilden, J. Virol. 62:2544-2551, 1988). To determine whether the virus-neutralizing activity of these antibodies belongs to gpI, gpIV, or both, the open reading frame encoding gpIV was inserted into the vaccinia virus genome. Immunoprecipitation of recombinant vaccinia virus-infected cells with anti-gpIV monoclonal antibody yielded synthesis and processing of gpIV similar to those expressed in VZV-infected cells. Antibodies raised against VVgpIV in a rabbit recognized both native gpI and gpIV and neutralized VZV infectivity. In addition, antibodies raised against recombinant vaccinia virus carrying VZV gpI neutralized VZV infection. These results indicate a structural relationship between VZV gpI and gpIV and show that gpI and gpIV each induce virus-neutralizing antibody.
Coreference Aware Representation Learning for Neural Named Entity Recognition (2019)

Recent neural network models have achieved state-of-the-art performance on the task of named entity recognition (NER). However, previous neural network models typically treat the input sentences as a linear sequence of words but ignore rich structural information, such as the coreference relations among non-adjacent words, phrases or entities. In this paper, we propose a novel approach to learn coreference-aware word representations for the NER task at the document level. In particular, we enrich the well-known neural architecture ``CNN-BiLSTM-CRF'' with a coreference layer on top of the BiLSTM layer to incorporate coreferential relations. Furthermore, we introduce the coreference regularization to ensure the coreferential entities to share similar representations and consistent predictions within the same coreference cluster. Our proposed model achieves new state-of-the-art performance on two NER benchmarks: CoNLL-2003 and OntoNotes v5.0. More importantly, we demonstrate that our framework does not rely on gold coreference knowledge, and can still work well even when the coreferential relations are generated by a third-party toolkit.
MRI detection of glycogen <i>in vivo</i> by using chemical exchange saturation transfer imaging (glycoCEST) (2007)

Detection of glycogen in vivo would have utility in the study of normal physiology and many disorders. Presently, the only magnetic resonance (MR) method available to study glycogen metabolism in vivo is (13)C MR spectroscopy, but this technology is not routinely available on standard clinical scanners. Here, we show that glycogen can be detected indirectly through the water signal by using selective radio frequency (RF) saturation of the hydroxyl protons in the 0.5- to 1.5-ppm frequency range downfield from water. The resulting saturated spins are rapidly transferred to water protons via chemical exchange, leading to partial saturation of the water signal, a process now known as chemical exchange saturation transfer. This effect is demonstrated in glycogen phantoms at magnetic field strengths of 4.7 and 9.4 T, showing improved detection at higher field in adherence with MR exchange theory. Difference images obtained during RF irradiation at 1.0 ppm upfield and downfield of the water signal showed that glycogen metabolism could be followed in isolated, perfused mouse livers at 4.7 T before and after administration of glucagon. Glycogen breakdown was confirmed by measuring effluent glucose and, in separate experiments, by (13)C NMR spectroscopy. This approach opens the way to image the distribution of tissue glycogen in vivo and to monitor its metabolism rapidly and noninvasively with MRI.
Tamper-resistant whole program partitioning (2003)

Due to limited available memory (of the order of Kilobytes) on embedded devices (such as smart cards), we undertake an approach of partitioning the whole program when it does not fit in the memory. The program partitions are downloaded from the server on demand into the embedded device just before execution. We devise a method of partitioning the code and data of the program such that no information regarding the control flow behavior of the program is leaked out. This property is called tamper resistance and it is very important for secure embedded devices such as smart cards which could hold sensitive information and/or carry out critical computation such as financial transactions. A preliminary solution to this problem was proposed in our earlier work [1]. This work proposes a new and more comprehensive solution to the problem. First, we propose a new policy which is based on keeping nothing in terms of partitions on the smart card. This policy is unlike the one in previous work which mandated keeping partitions in memory to which control flow was guaranteed to return. Based on this new policy, a new partitioning algorithm is proposed for minimal safe partitions which reduces their memory requirements over previous work. The drawback of this new policy is however lower execution speed due to frequent communication encountered. In order to not significantly degrade performance, we propose caching frequently executed functions on the smart card without violation of tamper resistance. A framework is designed to determine the set of functions to be cached in conjunction with specific minimal safe partitions. Further reduction in memory requirements is achieved due to the data partitioning.The decrease in memory footprint over the previous method is 27% for code memory and 32.4% for data memory on average. The speed-up over the old method is quite significant when applied to whole programs in large benchmarks (500 times on average). The conclusion is that previous method [1] is not suitable as a whole program partitioning strategy whereas the new proposed method is a viable solution.
Design considerations for a limited angle, dedicated breast, TOF PET scanner (2008)

Development of partial ring, dedicated breast positron emission tomography (PET) scanners is an active area of research. Due to the limited angular coverage, generation of distortion and artifact-free, fully 3D tomographic images is not possible without rotation of the detectors. With time-of-flight (TOF) information, it is possible to achieve the 3D tomographic images with limited angular coverage and without detector rotation. We performed simulations for a breast scanner design with a ring diameter and an axial length of 15 cm and comprising a full (180 degrees in-plane angular coverage), 2/3 (120 degrees in-plane angular coverage) or 1/2 (90 degrees in-plane angular coverage) ring detector. Our results show that as the angular coverage decreases, improved timing resolution is needed to achieve distortion-free and artifact-free images with TOF. The contrast recovery coefficient (CRC) value for small hot lesions in a partial ring scanner is similar to a full ring non-TOF scanner. Our results indicate that a timing resolution of 600 ps is needed for a 2/3 ring scanner, while a timing resolution of 300 ps is needed for a 1/2 ring scanner. We also analyzed the ratio of lesion CRC to the background pixel noise (SNR) and concluded that TOF improves the SNR values of the partial ring scanner, and helps to compensate for the loss in sensitivity due to reduced geometric sensitivity in a limited angle coverage PET scanner. In particular, it is possible to maintain similar SNR characteristic in a 2/3 ring scanner with a timing resolution of 300 ps as in a full ring non-TOF scanner.
Text/Conference Paper (2019)

Learning time-series models is useful for many applications, such as simulation and forecasting. In this study, we consider the problem of actively learning time-series models while taking given safety constraints into account. For time-series modeling we employ a Gaussian process with a nonlinear exogenous input structure. The proposed approach generates data appropriate for time series model learning, i.e. input and output trajectories, by dynamically exploring the input space. The approach parametrizes the input trajectory as consecutive trajectory sections, which are determined stepwise given safety requirements and past observations. We analyze the proposed algorithm and evaluate it empirically on a technical application. The results show the effectiveness of our approach in a realistic technical use case.
Underwater sound generator (1986)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation George D. Hugus, A. Mark Young; Underwater sound generator. J. Acoust. Soc. Am. 1 July 1986; 80 (1): 372. https://doi.org/10.1121/1.394478 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
Refractive index and absorption detector for liquid chromatography based on Fabry-Perot interferometry (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRefractive index and absorption detector for liquid chromatography based on Fabry-Perot interferometrySteven D. Woodruff and Edward S. YeungCite this: Anal. Chem. 1982, 54, 7, 1174–1178Publication Date (Print):June 1, 1982Publication History Published online1 May 2002Published inissue 1 June 1982https://doi.org/10.1021/ac00244a036RIGHTS & PERMISSIONSArticle Views260Altmetric-Citations67LEARN 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 (692 KB) Get e-Alerts Get e-Alerts
Strand displacement amplification—an isothermal,<i>in vitro</i>DNA amplification technique (1992)

Strand Displacement Amplification (SDA) is an isothermal, in vitro nucleic acid amplification technique based upon the ability of HincII to nick the unmodified strand of a hemiphosphorothioate form of its recognition site, and the ability of exonuclease deficient klenow (exo- klenow) to extend the 3'-end at the nick and displace the downstream DNA strand. Exponential amplification results from coupling sense and antisense reactions in which strands displaced from a sense reaction serve as target for an antisense reaction and vice versa. In the original design (G. T. Walker, M. C. Little, J. G. Nadeau and D. D. Shank (1992) Proc. Natl. Acad. Sci 89, 392-396), the target DNA sample is first cleaved with a restriction enzyme(s) in order to generate a double-stranded target fragment with defined 5'- and 3'-ends that can then undergo SDA. Although effective, target generation by restriction enzyme cleavage presents a number of practical limitations. We report a new target generation scheme that eliminates the requirement for restriction enzyme cleavage of the target sample prior to amplification. The method exploits the strand displacement activity of exo- klenow to generate target DNA copies with defined 5'- and 3'-ends. The new target generation process occurs at a single temperature (after initial heat denaturation of the double-stranded DNA). The target copies generated by this process are then amplified directly by SDA. The new protocol improves overall amplification efficiency. Amplification efficiency is also enhanced by improved reaction conditions that reduce nonspecific binding of SDA primers. Greater than 10(7)-fold amplification of a genomic sequence from Mycobacterium tuberculosis is achieved in 2 hours at 37 degrees C even in the presence of as much as 10 micrograms of human DNA per 50 microL reaction. The new target generation scheme can also be applied to techniques separate from SDA as a means of conveniently producing double-stranded fragments with 5'- and 3'-sequences modified as desired.
A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF (2021)

We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer-small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF-TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein-protein interactions.