gebhart/patrepeval huggingface dataset:
Magnesium-Agarose Electrophoretic Mobility Shift Assay (EMSA) of Transcription Factor IID Binding to DNA (2010)

The general transcription factor IID (TFIID) is a key target for regulation because its binding to a core promoter is the nucleating step in transcription complex assembly. Many eukaryotic activators stimulate recruitment of the TFIID when its concentration is made limiting at a promoter in vitro. Magnesium-agarose gels can separate large complexes containing TFIID, TFIIA (the DA complex), and TFIIB (the DAB complex) and permit a quantitative measurement of how activators stimulate assembly of such complexes. The advantage of the electrophoretic mobility shift assay (EMSA) is that the reactions can be performed under subsaturating conditions where a TFIID footprint might not be observed. Typically, the activator is incubated with a 32P-labeled DNA template, recombinant TFIIA purified from Escherichia coli, and immunopurified TFIID. After incubation, the samples are electrophoresed on magnesium-containing agarose gels, dried onto DEAE-cellulose paper, and autoradiographed. The DNA-protein complexes containing TFIID migrate with reduced mobility on magnesium-agarose gels both because of the large size of the complex and because the TATA-binding protein (TBP) subunit induces a sharp bend in the DNA, causing altered mobility. By comparing the binding of TFIID over a wide concentration range, with and without activator, one can assess whether the activator interacts with TBP or with one of the TBP-associated factors (TAFIIs). Additional factors such as TFIIA and TFIIB can be added subsequently to quantify their contributions to assembly of the transcription complex.
Controlled Synthesis of Polyenes by Catalytic Methods. Progress Report for the period December 1, 1989 - November 30, 1992 (1992)

A more direct approach to polyenes by the direct polymerization of acetylenes has been achieved. We were able to show that polymerization of acetylene itself can be controlled with a well- characterized alkylidene catalyst, but only if a base such as quinuclidine is present in order to slow down the rate of propagation relative to initiation. (Quinuclidine may also stabilize vinylalkylidene intermediates formed in the reaction). Unfortunately, living polyenes'' were no more stable than isolated polyenes, and so this approach had its limitations. Direct polymerization of acetylene by Mo(CH-t-Bu)(NAr)(O-t-Bu){sub 2} was more successful, but inherent polyene instability was still a problem. The most important result of the past grant period is the finding that dipropargyl derivatives (HC=CCH{sub 2}XCH{sub 2}C=CH; X = CH{sub 2}, C(CO{sub 2}R){sub 2}, SiR{sub 2}, etc.), which have been reported to be cyclopolymerized by various classical catalysts by as yet unknown mechanisms, are polymerized by Mo(CH-t-Bu)(NAr)(OCMe(CF{sub 3}){sub 2}){sub 2} in dimethoxyethane. We speculate that intramolecular formation of a five-membered ring in the product of {alpha} addition is fast enough to yield another terminal alkylidene on the time scale of the polymerization reaction, while a six-membered ring is formed in a reaction involving a more reaction terminal alkylidene. Either intermediate alkylidene, but most likely the terminal alkylidene, could react with additional monomer to lead to growth of a chain having dangling'' triple bonds that eventually could be employed to form crosslinks.
Video-Based Point-Cloud-Compression Standard in MPEG: From Evidence Collection to Committee Draft [Standards in a Nutshell] (2019)

The widespread adoption of new 3D sensor and authoring technologies has made it possible to capture 3D scenes and models in real time with decent visual quality. As an example, Microsoft's Kinect and Apple's PrimeSense technology are now being used in a wide variety of interactive 3D mobile applications, including gaming and augmented reality applications. The latest smartphones are equipped with multiple cameras, which can be readily used to generate depth images. Some of the latest smartphones also include depth-ranging sensors that can be used for 3D model generation. Light-based detection and ranging (lidar) technologies are yet another field where 3D depth acquisition is important. Realtime 3D scenery detection and ranging has become an important issue for the emerging field of autonomous navigation and driving applications.
Animal models of chronic pain: Advances and challenges for clinical translation (2016)

Chronic pain is a global problem that has reached epidemic proportions. An estimated 20% of adults suffer from pain, and another 10% are diagnosed with chronic pain each year (Goldberg and McGee, ). Despite the high prevalence of chronic pain (an estimated 1.5 billion people are afflicted worldwide), much remains to be understood about the underlying causes of this condition, and there is an urgent requirement for better pain therapies. The discovery of novel targets and the development of better analgesics rely on an assortment of preclinical animal models; however, there are major challenges to translating discoveries made in animal models to realized pain therapies in humans. This review discusses common animal models used to recapitulate clinical chronic pain conditions (such as neuropathic, inflammatory, and visceral pain) and the methods for assessing the sensory and affective components of pain in animals. We also discuss the advantages and limitations of modeling chronic pain in animals as well as highlighting strategies for improving the predictive validity of preclinical pain studies. © 2016 Wiley Periodicals, Inc.
Data Supplement from Optimal Effector Functions in Human Natural Killer Cells Rely upon Autocrine Bone Morphogenetic Protein Signaling (2023)

&lt;p&gt;Supplemental Figure S5. Effects of DMH1 on NK cells IFN-y production and killing capacity upon target cell engagement.&lt;/p&gt;
Near-Infrared Surface-Enhanced Raman Spectroscopy (NIR-SERS) for the Identification of Eosin Y: Theoretical Calculations and Evaluation of Two Different Nanoplasmonic Substrates (2012)

This work demonstrates the development of near-infrared surface-enhanced Raman spectroscopy (NIR-SERS) for the identification of eosin Y, an important historical dye. NIR-SERS benefits from the absence of some common sources of SERS signal loss including photobleaching and plasmonic heating, as well as an advantageous reduction in fluorescence, which is beneficial for art applications. This work also represents the first rigorous comparison of the enhancement factors and the relative merits of two plasmonic substrates utilized in art applications; namely, citrate-reduced silver colloids and metal film over nanosphere (FON) substrates. Experimental spectra are correlated in detail with theoretical absorption and Raman spectra calculated using time-dependent density functional theory (TDDFT) in order to elucidate molecular structural information and avoid relying on pigment spectral libraries for dye identification.
Broad band dispersion slope compensation of dispersion shifted fiber using negative slope fiber (2002)

The dispersion of zero and/or non-zero dispersion shifted fiber (DSF) at 1550 nm was compensated to be flat about 30 nm band-range, by connecting with dispersion slope compensating fiber, with negative slope of 20 times larger absolute value than DSF.
Search for new phenomena in final states with large jet multiplicities and missing transverse momentum at $ \sqrt{s}=8 $ TeV proton-proton collisions using the ATLAS experiment (2013)

A bstract A search is presented for new particles decaying to large numbers (7 or more) of jets, with missing transverse momentum and no isolated electrons or muons. This analysis uses 20.3 fb −1 of pp collision data at $ \sqrt{s}=8 $ TeV collected by the ATLAS experiment at the Large Hadron Collider. The sensitivity of the search is enhanced by considering the number of b -tagged jets and the scalar sum of masses of large-radius jets in an event. No evidence is found for physics beyond the Standard Model. The results are interpreted in the context of various simplified supersymmetry-inspired models where gluinos are pair produced, as well as an mSUGRA/CMSSM model.
Port Restricted IP Address Assignment (2012)

With the foreseen scarcity of public IPv4 addresses and the hesitation
and technical difficulties to deploy IPv6, the transition scenarios
which assumed that migration to IPv6 happens before the run-out of
IPv4 addresses, need to be revisited. This document defines a method
to allocate the same IPv4 address to multiple hosts, thus prolonging
the availability of public IPv4 addresses for as long as it takes for
IPv6 to take over the demand for IPv4. The document also describes the
deployment scenarios where this method is applicable.
In Vivo Imaging of Amyloid Deposition in Alzheimer Disease Using the Radioligand 18F-AV-45 (Flobetapir F 18) (2010)

(18)F-AV-45 was well tolerated, and PET showed significant discrimination between AD patients and HCs, using either a parametric reference region method (DVR) or a simplified SUVR calculated from 10 min of scanning 50-60 min after (18)F-AV-45 administration.
Information retrieval and knowledge discovery utilising a biomedical Semantic Web (2005)

Although various ontologies and knowledge sources have been developed in recent years to facilitate biomedical research, it is difficult to assimilate information from multiple knowledge sources. To enable researchers to easily gain understanding of a biomedical concept, a biomedical Semantic Web that seamlessly integrates knowledge from biomedical ontologies, publications and patents would be very helpful. In this paper, current research efforts in representing biomedical knowledge in Semantic Web languages are surveyed. Techniques are presented for information retrieval and knowledge discovery from the Semantic Web that extend traditional keyword search and database querying techniques. Finally, some of the challenges that have to be addressed to make the vision of a biomedical Semantic Web a reality are discussed.
On time-optimal anti-sway controller design for bridge cranes (2014)

In this paper, we analyze and discuss the time optimal control problem for bridge cranes. Specifically, we employ the geometric approach introduced in [12] to address the control issue without computing the analytic trajectory of the costate. As a second contribution, we show that an alternative approach based on a proportional controller accounting for the limits of the control action can be tuned to resemble to the time-optimal solution, but with simpler and more robust implementation. The above ideas are validated by means of some simulation examples.
ESPRIT And Uniform Linear Arrays (1989)

Ã¢â‚¬â€?ESPRIT is a recently developed and patented technique for high-resolution estimation of signal parameters. It exploits an invariance structure designed into the sensor array to achieve a reduction in computational requirements of many orders of magnitude over previous techniques such as MUSIC, Burg&apos;s MEM, and Capon&apos;s ML, and in addition achieves performance improvement as measured by parameter estimate error variance. It is also manifestly more robust with respect to sensor errors (e.g. gain, phase, and location errors) than other methods as well. Whereas ESPRIT only requires that the sensor array possess a <i>single invariance</i> best visualized by considering two identical but other-wise arbitrary arrays of sensors displaced (but not rotated) with respect to each other, many arrays currently in use in various applications are uniform linear arrays of identical sensor elements. Phased array radars are commonplace in high-resolution direction finding systems, and uniform tapped delay lines (i.e., constant rate A/D converters) are the rule rather than the exception in digital signal processing systems. Such arrays possess many invariances, and are amenable to other types of analysis, which is one of the main reasons such structures are so prevalent. Recent developments in high-resolution algorithms of the signal/noise subspace genre including total least squares (TLS) ESPRIT applied to uniform linear arrays are summarized. ESPRIT is also shown to be a generalization of the root-MUSIC algorithm (applicable only to the case of uniform linear arrays of omni-directional sensors and unimodular cisoids). Comparisons with various estimator bounds, including CramerRao bounds, are presented.
Laser-induced "two-atom" coherence (1984)

Our analysis shows that if an electromagnetic field excites a coherent superposition of states of two different types of atoms, then the results of a collision of those two atoms can be quite different from the usual dephasing that a coherently excited atom suffers upon collision with another atom. We present the concept of "two-atom" coherence as one feature of this interaction where the field of a given wavelength may interact with the system coherently over a wide range of internuclear distances.
Overall survival and competing risks of death in patients with Waldenström macroglobulinaemia: an analysis of theSurveillance,Epidemiology andEndResults database (2014)

Waldenström macroglobulinaemia (WM) is a rare and incurable lymphoma. Given that the survival of WM patients can be prolonged, our objective was to describe trends in overall survival (OS) and analyse competing risks of death in patients with WM. The analysis included 5784 patients diagnosed with WM between 1991 and 2010 from the Surveillance, Epidemiology and End Results (SEER) database. Multivariate hazard models for OS and cumulative incidence of death were fitted according to epoch of diagnosis (1991-2000 vs. 2001-10) while adjusting for age, sex, race, histology, site of involvement and registry. Median OS for the 1991-2000 and the 2001-10 cohorts was 6 and 8 years, respectively (P < 0·001). In the multivariate analysis, better OS [hazard ratio (HR) 0·73, 95% confidence interval (CI) 0·67-0·79; P < 0·001] was seen in the 2001-10 cohort. Survival benefits were identified, for the 2001-10 cohort, in almost every stratum analysed, with the exception of patients aged <50 years and blacks. In the multivariate competing-risk analysis, the 2001-10 cohort experienced lower rates of WM-related (HR 0·57, 95% CI 0·49-0·66; P < 0·001) and non-WM-related deaths (HR 0·72, 95% CI 0·66-0·79; P < 0·001). In conclusion, there have been significant improvements in OS, WM-related and non-WM-related mortality in patients with WM diagnosed in the last decade.
Abstract 510: Novel glutamine antagonist JHU-395 suppresses MYC-driven medulloblastoma growth and induces apoptosis (2020)

Abstract Medulloblastoma is the most common malignant pediatric brain tumor. Genomic amplification of MYC is a hallmark of a subset of poor-prognosis medulloblastoma. MYC upregulates glutamine metabolism, and medulloblastoma tumors with evidence of high glutamate have a poor prognosis. We modified the naturally occurring glutamine analog 6-diazo-5-oxo-l-norleucine (DON) to increase its lipophilicity and its stability in plasma, creating a prodrug termed JHU-395. We hypothesized that this prodrug would have enhanced cell penetration compared to DON and would kill MYC-expressing medulloblastoma. JHU-395 treatment caused decreased growth and increased apoptosis in human MYC-expressing medulloblastoma cell lines at lower concentrations than DON. In D283MED for example IC50 for DON is 20 uM while JHU 395 IC50 is 1 uM (p value &amp;lt; 0.05). Similar results were obtained with other high-MYC medulloblastoma cell lines, including D425MED and D341MED. JHU-395 induced apoptosis at low micromolar concentrations as measured by cleaved PARP Western blot and cleaved caspase 3 (CC3) immunofluorescence (60% CC3+ cells compared to 30% CC3+ in control p&amp;lt;0.05). Parenteral administration of JHU-395 in Nu/Nu mice led to the accumulation of micromolar concentrations of DON in brain as measured by mass spectrometry. These data suggest that JHU-395 may have activity against high MYC medulloblastoma in vivo, and testing this prodrug against MYC-driven medulloblastoma orthotopic xenografts is currently underway. Citation Format: Khoa Pham, Micah Maxwell, Heather Sweeney, Jesse Alt, Rana Rais, Barbara S. Slusher, Charles G. Eberhart, Eric H. Raabe. Novel glutamine antagonist JHU-395 suppresses MYC-driven medulloblastoma growth and induces apoptosis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 510.
Adaptive State Estimation for Power Systems Measured by PMUs With Unknown and Time-Varying Error Statistics (2021)

Measurement error is a crucial factor that determines the accuracy of state estimation (SE). Conventional estimators have fixed models, and can yield optimal performance only when the measurement error statistics exactly meet the assumptions. In reality, however, the error distribution is usually unknown and time-varying, resulting in suboptimal state estimates in most cases. This paper develops the concept of adaptive SE for power systems measured by phasor measurement units (PMUs). First, the Gaussian-Laplacian Mixture (GLM) model is developed to fit the body and tail of unknown measurement error distributions. Then, an adaptive estimation framework is proposed based on the Expectation-Maximization (EM) algorithm. It is capable of tracking the actual error statistics online, and adjusting the parameters of SE to maintain near-optimality of state estimates under complex measurement error conditions. Simulation results demonstrate that the proposed adaptive estimator yields more accurate state estimates than the well-known Weighted Least Squares (WLS) and Weighted Least Absolute Value (WLAV) estimators by adapting itself to the variations of measurement error statistics.
<title>Conjugate Cassegrain telescopes for thermal source FTIR spectral radiometric calibration</title> (1998)

Two Cassegrain telescopes were constructed to function as sender and receiver for an FTIR spectrometer primarily for the purpose of obtaining spectral data for analysis of military night vision emission targets, and spectral calibration of external variable temperature thermal radiation sources, utilizing freezing-point type blackbodies for primary radiation temperature standards. The sender and receiver telescopes, F/7 and F/5, respectively, each employ 0.30 m (12 in) diameter primary and 0.15 m (6 in) diameter secondary, protected Ag coated Zerodur mirrors. In operation, a thermal target image formed by the sender, whose optical axis is aligned with that of the receiver and spectrometer, is transmitted to and brought to a focus at the spectrometer entrance aperture by the receiver telescope. With (lambda) /8 p-v optical surface accuracy at 633 nm, telescope system tests indicate near diffraction- limited performance in the visible, and 2.81 mrad (full) FOV with further reduction achieved with field stops. Wavelength range capability of the commercially available FTIR instrument employed is approximately 0.22 micrometers (55000 cm<SUP>-1</SUP>) to 22 micrometers (450 cm<SUP>-1</SUP>) with wavenumber resolution of about 0.013 cm<SUP>-1</SUP> in the IR to 0.769 micrometers (13000 cm<SUP>-1</SUP>). In this paper, the techniques and tests employed for the telescope mirror construction are described. An innovative technique for secondary alignment for Hindle's tests of a Cassegrain utilizing a He-Ne laser is presented. Telescope mountings for positioning and alignment with the FTIR are briefly discussed, as well as radiometric and calibration parameters for the integrated system.
Consistent detection of age-dependent variations of the longitudinal relaxation time in cortical brain regions investigated by MP2RAGE at 9.4T: influence of correcting for a non-uniform transmit field (2016)

Accurate and precise determination of T1 values is of central importance in clinical studies and for tissue segmentation based on the myeloarchitecture that transcends T1. Here we investigate whether well-described age-dependent changes can be detected by high field T1 relaxometry, and how different transmit field correction methods influence the results. We found that the intrinsic bias correction of the MP2RAGE technique is not sufficient to achieve reliable quantification of T1 at ultra high magnetic fields. But, provided that a correction for transmit field inhomogeneity is performed, T1 maps that consistently reveal age-related changes can be generated. The technique holds promise for investigation of local myeloarchitectonics for neuroscientific and clinical studies.
Effect of cross-phase-modulation-induced polarization scattering on optical polarization mode dispersion compensation in wavelength-division-multiplexed systems (2003)

Interchannel cross-phase-modulation-induced polarization scattering (XPMIPS) and its effect on the performance of optical polarization mode dispersion (PMD) compensation in wavelength-division-multiplexed (WDM) systems are studied. The level of XPMIPS in long-haul WDM transmission systems is theoretically quantified, and its effect on optical PMD compensation is evaluated with numerical simulations. We show that in 10-Gbit/s ultra-long-haul dense WDM systems XPMIPS could reduce the PMD compensation efficiency by 50%, whereas for 40-Gbit/s systems the effect of XPMIPS is smaller.
On convergence constrained precoder design for iterative frequency domain MIMO detector (2009)

This paper proposes a novel linear precoder design technique for single carrier single-user multiple input multiple output (MIMO) systems with frequency-domain (FD) soft cancellation (SC) minimum mean squared error (MMSE) iterative equalization where the convergence properties of the equalizer are taken into account. The proposed precoder design technique, convergence constrained precoding (CCP), minimizes the transmission power while it achieves the target mutual information for each stream after the iterations at the receiver side. We show that the optimality criterion for the proposed design can be formulated as a convex optimization problem. The results demonstrate that our proposed technique outperforms the existing linear precoding techniques by ensuring the convergence with a reduced transmission power. Furthermore, we show that with CCP we can adjust transmission according to convergence properties of the iterative equalizer in a more flexible way than, e.g., minimum sum mean squared error (MinSumMSE) and maximum information rate (MaxRate) precoding.
Turbine Engine Temperature Pattern Factor Control System Based on Fuel Modulation and Passive Optical Sensors (2010)

We present preliminary results for a new passive optical sensor that is the basis for a temperature pattern factor control system. The sensor uses the natural combustion radiance in several spectral bands to deduce the local pre-combustion equivalence ratio, which is correlated with local combustor exit temperature. The sensor was applied in an arc-sector combustor and in a closed-loop control system in a four-way laboratory burner.