gebhart/patrepeval huggingface dataset:
ACVR1 p.Q207E causes classic fibrodysplasia ossificans progressiva and is functionally distinct from the engineered constitutively active ACVR1 p.Q207D variant (2014)

Fibrodysplasia ossificans progressiva (FOP) is a disabling genetic disorder of progressive heterotopic ossification (HO). Here, we report a patient with an ultra-rare point mutation [c.619C>G, p.Q207E] located in a codon adjacent to the most common FOP mutation [c.617G>A, p.R206H] of Activin A Receptor, type 1 (ACVR1) and that affects the same intracellular amino acid position in the GS activation domain as the engineered constitutively active (c.a.) variant p.Q207D. It was predicted that both mutations at residue 207 have similar functional effects by introducing a negative charge. Transgenic p.Q207D-c.a. mice have served as a model for FOP HO in several in vivo studies. However, we found that the engineered ACVR1(Q207D-c.a.) is significantly more active than the classic FOP mutation ACVR1(R206H) when overexpressed in chicken limbs and in differentiation assays of chondrogenesis, osteogenesis and myogenesis. Importantly, our studies reveal that the ACVR1(Q207E) resembles the classic FOP receptor in these assays, not the engineered ACVR1(Q207D-c.a.). Notably, reporter gene assays revealed that both naturally occurring FOP receptors (ACVR1(R206H) and ACVR1(Q207E)) were activated by BMP7 and were sensitive to deletion of the ligand binding domain, whereas the engineered ACVR1(Q207D-c.a.) exhibited ligand independent activity. We performed an in silico analysis and propose a structural model for p.Q207D-c.a. that irreversibly relocates the GS domain into an activating position, where it becomes ligand independent. We conclude that the engineered p.Q207D-c.a. mutation has severe limitations as a model for FOP, whereas the naturally occurring mutations p.R206H and p.Q207E facilitate receptor activation, albeit in a reversible manner.
Method for characterizing single photon detectors in saturation regime by cw laser (2010)

We derive an analytical expression for the count probability of a single photon detector for a wide range of input optical power that includes afterpulsing effects. We confirm the validity of the expression by fitting it to the data obtained from a saturated commercial Single Photon Detector by illuminating it with a cw laser. Detector efficiency and afterpulsing probability extracted from the fits agree with the manufacture specs for low repetition frequencies.
Simultaneous measurements of electric and thermal fields utilizing an electrooptic semiconductor probe (2001)

A method to simultaneously measure electric and thermal fields with a single probe is presented in this paper. The Pockels effect is employed within a gallium-arsenide probe to measure electric fields, and the effect of photon absorption due to bandtail states in the semiconductor is used to determine temperature. The measured optical power is found to be inversely related to temperature, in agreement with theory, and experimental results demonstrate a temperature sensitivity of 0.31 /spl mu/W//spl deg/C at 25/spl deg/C and an accuracy of /spl plusmn/0.5/spl deg/C between 20/spl deg/C-60/spl deg/C. The minimum detectable electric field is 1.24/spl plusmn/0.06 V/m using a 300-ms electrical bandwidth. Temporal phase stability of /spl plusmn/3/spl deg//h is achieved through the implementation of a system phase reference channel. The invasiveness of the probe is quantified by examining the change in the characteristic impedance and capacitance per unit length of a planar transmission line. Measured and simulated data show that the effect is equivalent to a lumped shunt capacitance on the order of a few femtofarads. The examination of a monolithic microwave integrated circuit in an X-band quasi-optical power-combining array and the calibration of electric-field data that was corrupted by temperature-dependent effects inherent to the electrooptic probe demonstrate the capability of this combined electrothermal measurement technique.
Aircraft Charging and its Influence on Triggered Lightning (2019)

Abstract This paper reports on a laboratory experiment to study the effect of vehicle net charge on the inception of a positive leader from an aircraft exposed to high atmospheric electric fields. The experiment models the first stage of aircraft‐triggered lightning in which a positive leader typically develops from the vehicle and is shortly afterwards followed by a negative leader. This mechanism of lightning initiation amounts to around 90% of strikes to aircraft. Aircraft can acquire net charge levels of the order of a millicoulomb from a number of sources including corona emission, charged particles in the engine exhaust, and charge transfer by collisions with particles in the atmosphere. In addition, aircraft could potentially be artificially charged through controlled charge emission from the surface. Experiments were performed on a model aircraft with a 1m wingspan, which was suspended between two parallel electrodes in a 1.45m gap with voltage difference of a few hundred kilovolts applied across it. In this configuration, it is found that the breakdown field can vary by as much as 30% for the range of charging levels tested. The experimental results show agreement with an electrostatic model of leader initiation from aircraft, and the model indicates that the effect can be substantially stronger if additional negative charge is added to the aircraft. The results from this work suggest that flying uncharged is not optimal in terms of lightning avoidance and open up the possibility of developing risk‐reduction strategies based on net charge control.
Cube-3 (1994)

Article Cube-3: a real-time architecture for high-resolution volume visualization Share on Authors: Hanspeter Pfister View Profile , Arie Kaufman View Profile , Tzi-Cker Chiueh View Profile Authors Info & Claims VVS '94: Proceedings of the 1994 symposium on Volume visualizationOctober 1994 Pages 75–82https://doi.org/10.1145/197938.197969Online:17 October 1994Publication History 16citation206DownloadsMetricsTotal Citations16Total Downloads206Last 12 Months2Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Time-encoded imaging of energetic radiation (2013)

Time-encoded imaging (TEI) is a new approach to directional detection of energetic radiation that produces images by inducing a time-dependent modulation of detected particles. TEI-based detectors use single-scatter events and have a low channel count, reducing complexity and cost while maintaining high efficiency with respect to other radiation imaging techniques such as double-scatter or coded aperture imaging. The scalability of TEI systems makes them a very promising detector class for weak source detection. Extension of the technique to high-resolution imaging is also under study. With a prototype time-encoding detector, we demonstrated detection of a neutron source at 60 m with neutron output equivalent to an IAEA significant quantity of WGPu. We have since designed and built a full-scale detector based on the time-encoding concept. We will present results from characterization of very large liquid scintillator cells, including pulse shape discrimination, as well as from studies of the detector system performance in weak source detection scenarios.
The LEM3 implementation of learnable evolution model and its testing on complex function optimization problems (2006)

Learnable Evolution Model (LEM) is a form of non-Darwinian evolutionary computation that employs machine learning to guide evolutionary processes. Its main novelty are new type of operators for creating new individuals, specifically, hypothesis generation, which learns rules indicating subareas in the search space that likely contain the optimum, and hypothesis instantiation, which populates these subspaces with new individuals. This paper briefly describes the newest and most advanced implementation of learnable evolution, LEM3, its novel features, and results from its comparison with a conventional, Darwinian-type evolutionary computation program (EA), a cultural evolution algorithm (CA), and the estimation of distribution algorithm (EDA) on selected function optimization problems (with the number of variables varying up to 1000). In every experiment, LEM3 outperformed the compared programs in terms of the evolution length (the number of fitness evaluations needed to achieved a desired solution), sometimes more than by one order of magnitude.
The effect of baclofen on nocturnal gastroesophageal reflux and measures of sleep quality: a randomized, cross‐over trial (2012)

In addition to reducing the number of reflux events during sleep, baclofen significantly improved several measures of sleep in patients with documented GER and sleep disturbances. Baclofen could therefore be considered as a useful adjunct therapy to proton pump inhibitors (PPIs) in patients with nighttime heartburn and sleep disturbance who continue to have heartburn and/or sleep complaints despite PPI therapy.
Role of the Leader and Structural Regions of Prelantibiotic Peptides as Assessed by Expressing Nisin-Subtilin Chimeras in Bacillus subtilis 168, and Characterization of their Physical, Chemical, and Antimicrobial Properties (1995)

Biosynthesis of lantibiotics such as nisin and subtilin involves post-translational modifications, including dehydration of serines and threonines, formation of thioether cross-linkages, translocation, cleavage of a leader sequence, and release into the medium. We have studied the cellular machinery that performs the modifications by constructing and expressing nisin-subtilin chimeric prepeptides in a strain of Bacillus subtilis 168 that possesses all of the cellular machinery for making subtilin except for the presubtilin gene. The chimeras consisted of a normal subtilin leader region (SL), fused to nisin-subtilin chimeric structural regions, one of which was SL-Nis1-11-Sub12-32, in which the N-terminal portion of the structural region was derived from nisin, and the C-terminal portion derived from subtilin. This chimera was accurately and efficiently converted to the corresponding mature lantibiotic, as established by reverse phase high performance liquid chromatography profiles, proton NMR spectroscopy, mass spectral analysis, and biological activity. A succinylated form of the chimera was also produced. Another chimera was in the reverse sense, with subtilin sequence at the N terminus and nisin sequence at the C terminus of the structural region (SL-Sub1-11-Nis12-34). It was processed into a heterogeneous mixture of products, none of which had the characteristics of a correctly processed polypeptide, but did contain a minor component that was active, with a specific activity that considerably exceeded nisin itself. These results, together with results published earlier, establish that processing requires specific recognition between the prelantibiotic peptide and the processing machinery, and in order for the processing to occur correctly, there must be an appropriate combination of the N-terminal part of the leader region and the C-terminal part of the structural region of the prepeptide.
Magnetoelectric effect in laminate composite of magnets/0.7Pb(Mg1∕3Nb2∕3)O3–0.3PbTiO3 single crystal (2006)

A magnetoelectric (ME) laminate composite was fabricated by sandwiching one 0.7Pb(Mg1∕3Nb2∕3)O3–0.3PbTiO3 (PMN-PT) piezoelectric single crystal layer between two NdFeB magnet layers along the thickness direction. The high ME effect was obtained by the product of the magnetic attractive-repellent effect in the magnet layers and the piezoelectric effect in the piezoelectric layer. The magnetoelectric voltage coefficient of the composite was measured to be ∼12.5mV∕cmOe with a flat frequency response in the range of 0.1–20kHz. The induced ME voltage showed an excellent linear relationship to the applied ac magnetic field with field amplitude varying from 10−3to10Oe. Other advantages included low heat generation, no bias magnetic field required, and high scale-down capability. These made the composite to be a promising ME material for realizing high-performance, small-size, and low-cost magnetic sensors.
Retroviral Replication (2006)

Abstract Retroviruses are enveloped animal ribonucleic acid (RNA) viruses that replicate via a deoxyribonucleic acid (DNA) intermediate, which is integrated into host cell chromosomal DNA. Expression of viral RNA and proteins from the DNA intermediate utilizes the normal transcription and translation machinery of the host.
Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities (2004)

We describe the construction, structural properties and enzymatic substrate abilities of a series of circular DNA oligonucleotides that are entirely composed of the C-rich human telomere repeat, (CCCTAA)n. The nanometer-sized circles range in length from 36 to 60 nt, and act as templates for synthesis of human telomere repeats in vitro. The circles were constructed successfully by the application of a recently developed adenine-protection strategy, which allows for cyclization/ligation with T4 DNA ligase. Thermal denaturation studies showed that at pH 5.0, all five circles form folded structures with similar stability, while at pH 7.0 no melting transitions were seen. Circular dichroism spectra at the two pH conditions showed evidence for i-motif structures at the lower pH value. The series was tested as rolling circle templates for a number of DNA polymerases at pH = 7.3-8.5, using 18mer telomeric primers. Results showed that surprisingly small circles were active, although the optimum size varied from enzyme to enzyme. Telomeric repeats >>1000 nt in length could be synthesized in 1 h by the Klenow (exo-) DNA polymerase. The results establish a convenient way to make long human telomeric repeats for in vitro study of their folding and interactions, and establish optimum molecules for carrying this out.
Multi-Layer Network Performance and Reliability Analysis (2009)

The authors describe a methodology for evaluating the performability (combined performance and reliability) of large communications networks. Networks are represented by a 4-level hierarchical model, consisting of traffic matrix, network graph, “components” representing failure modes, and reliability information. Network states are assignments of modes to the network components, which usually represent network elements and their key modules, although they can be more abstract. The components can be binary or multi-modal, and each of their failure modes may change a set of attributes of the graph (e.g. the capacity or cost of a link). Their methodology also captures the effect of automatic restoration against network failures by including two common rerouting methods. To compute network performability measures, including upper and lower bounds on their cumulative distribution functions, we augment existing probabilistic state-space generation algorithms with our new “hybrid” algorithm. To characterize the network failures of highest impact, we compute the Pareto boundaries of the network’s risk space. The authors have developed a network analysis tool called nperf that embodies this methodology. To illustrate the methodology and the practicality of the tool, they describe a performability analysis of three design alternatives for a large commercial IP backbone network.
An area-efficient differential input ADC with digital common mode rejection (1999)

This paper presents a differential input flash ADC with digital common mode rejection (DCMR) and dithered, noise shaped requantization used in a high-performance, single-poly CMOS ADC /spl Delta//spl Sigma/ modulator IC. By avoiding the use of metal-metal capacitors, the DCMR flash ADC required 14% less area than a switched-capacitor implementation and avoided circuit implementation problems. Measurements and analysis show that the DCMR flash ADC rejects common mode noise without generating spurious tones. In the absence of common mode noise, its quantization noise power is equivalent to a conventional flash ADC.
Efficient Techniques for High-Speed Elliptic Curve Cryptography. (2010)

Abstract. In this paper, a thorough bottom-up optimization process (field, point and scalar arithmetic) is used to speed up the computation of elliptic curve point multiplication and report new speed records on modern x86-64 based processors. Our different implementations include elliptic curves using Jacobian coordinates, extended Twisted Edwards coordinates and the recently proposed Galbraith-Lin-Scott (GLS) method. Compared to state-of-the-art implementations on identical platforms the proposed techniques provide up to 30 % speed improvements. Additionally, compared to the best previous published results on similar platforms improvements up to 31 % are observed. This research is crucial for advancing high speed cryptography on new emerging processor architectures.
Performance of Fluids in a Silicon-based Continuous Inkjet Printhead Using Asymmetric Heating (2001)

In this paper, we study the performance of a variety of fluids in a new continuous inkjet printhead that employs asymmetrical heating of a jet of fluid to cause it to deflect. The basic design and operation of the printhead is described in a companion paper in this same conference. We focus mainly on the performance of non-aqueous fluids, with some discussion of the performance of water mixed with common humectants.By examining the performance of a variety of fluids, we try to understand the mechanism causing the deflection. We compare our experimental results to the output of a Computational Fluid Dynamics (CFD) model of the device that is solved using finite difference Volume of Fluid (VOF) code. With our choice of fluids, we focus on the role played by the temperature dependence of the fluid viscosity on magnitude of the jet deflection.
A Dexterous Surgical Manipulation Tool Using Self-Sensing Magnetoelectric Actuators (2010)

In this paper, a dexterous surgical manipulation tool is developed, and characterized using a magnetoelectric self-sensing actuator. The magnetoelectric actuator is made up of three magnetoelectric cantilevers, which are mounted in a specific configuration. Each of the magnetoelectric cantilevers is composed of Galfenol and PZT-5H. The device consists of a single larger magnetoelectric cantilever that is capable of producing an up-down movement upon remote application of a magnetic field to the magnetostrictive layer. Towards one of the ends of this actuator two smaller magnetoelectric cantilevers are attached that are capable of producing a deflection in a side-ways direction making them well suited for gripping action. The shape-anisotropy of the magnetostrictive layers is designed to ensure a controlled sequence of gripping action and up-down movement when these cantilevers are actuated via a remote magnetic field which induces bending in them. The electrical signal generated by the piezoelectric layer is used to provide a sensing signal for both tactile sensing (and gripping) and deflection. This can be used in a closed loop control system.
Pulverized and Intermixed Elements Sintering Method for (Bi, Sb)<sub>2</sub>(Te, Se)<sub>3</sub> based <i>n</i>-type Thermoelectric Devices (1991)

The Pulverized and Intermixed Elements Sintering (PIES) method, which can eliminate the use of a powder consisting of fully reacted alloys, is successfully achieved for the preparing of n-type (Bi, Sb)2(Te, Se)3 based thermoelectric devices for the first time. Hence the PIES method can substantially reduce the manufacturing cost of thermoelectric devices such as (Bi, Sb)2(Te, Se)3 based one.It is proved that the solid solution formation of PIES device is occurred in the sintering process and in order to get the useful thermoelectric performance a strong intermixing force such as a large centrifugal force in a planetary ball mill is necessary by X-ray diffractometory and measurement of thermoelectric properties.The thermoelectric figure of merit of PIES devices is about 1.7×10-31/K at 300K, and there is plenty of room for improvement in the PIES method to obtain higher figure of merit.
Antibody-based inhibitors of HIV infection (2006)

The demand for new treatment options against HIV is becoming increasingly desperate as the side effects and the expansion and spread of drug-resistant virus within the infected population limit the clinical benefits provided by available anti-HIV drugs. Preparations of polyclonal antibodies have a long history of proven clinical utility against some viruses; however, they have enjoyed very limited success against HIV. Recent clinical trials and in vitro experiments suggest that monoclonal antibodies against HIV may have promise clinically. These antibodies and antibody-based reagents target either the viral envelope glycoprotein, the receptor (CD4) or coreceptor (CCR5) molecules, or transition-state structures that appear during viral entry. The challenge is whether an antibody-based therapy can be identified (with or without their small molecule brethren) that presents long-term clinical efficacy, low toxicity and minimal risk of clinical failure from viral resistance.
Enhancing Mobile IPv6 Route Optimization Mode with Secure Social Dimension (2011)

This memo describes an enhancement to Mobile IPv6 route optimization
mode which is derived from introducing a social dimension within the
home network.
A Parametric Model for Characterizing Seabed Textures in Synthetic Aperture Sonar Images (2010)

High-resolution synthetic aperture sonar (SAS) systems yield finely detailed images of sea bottom environments. SAS image texture models must be capable of representing a wide variety of sea bottom environments including sand ripples, coral or rock formations, and flat hardpack. In this paper, a parameterized model for SAS image textures is derived from the autocorrelation functions (ACFs) of the SAS imaging point spread function (PSF) and the ACF of the seabed texture sonar cross section (SCS). The proposed texture mixture model is analytically tractable and parameterized by component mixing parameters, mixture component correlation lengths, the single-point intensity image statistical shape parameter, and the rotation of the ACF mixture components in the 2-D imaging plane. An iterative parameter estimation algorithm based on the expectation-maximization (EM) algorithm for truncated data is presented and tested against various synthetic and real SAS image textures. The performance of the algorithm is compared and discussed for synthetically generated data across various image sizes and texture characteristics. The model fit is also compared against a small set of real SAS survey images and is shown to accurately fit the imaging PSF and seabed SCS ACF for these textures of interest.