gebhart/patrepeval huggingface dataset:
Subolesin expression in response to pathogen infection in ticks (2010)

Subolesin expression in infected ticks suggested that subolesin may be functionally important for tick innate immunity to pathogens, as has been reported for the akirins. However, subolesin expression and consequently subolesin-mediated innate immunity varied with the pathogen and tick tissue. Subolesin may plays a role in tick innate immunity in the salivary glands by limiting pathogen infection levels, but activates innate immunity only for some pathogen in the guts and other tissues. In addition, these results provided additional support for the role of subolesin in other molecular pathways including those required for tissue development and function and for pathogen infection and multiplication in ticks. Consequently, RNAi experiments demonstrated that subolesin knockdown in ticks may affect pathogen infection directly by reducing tick innate immunity that results in higher infection levels and indirectly by affecting tissue structure and function and the expression of genes that interfere with pathogen infection and multiplication. The impact of the direct or indirect effects of subolesin knockdown on pathogen infection may depend on several factors including specific tick-pathogen molecular interactions, pathogen life cycle in the tick and unknown mechanisms affected by subolesin function in the control of global gene expression in ticks.
Sparsity-driven distributed array imaging (2015)

We consider multi-static radar with a single transmitter and multiple, spatially distributed, linear sensor arrays, imaging an area with several targets. Assuming that the location and orientation of all the sensor arrays is known and that all measurements are synchronized, we develop compressive sensing based methods to improve imaging performance. Our approach imposes sparsity on the complex-valued reconstruction of the region of interest, with the non-zero coefficients corresponding to the imaged targets. Compared to conventional delay-and-sum approaches, which typically exhibit aliasing and ghosting artifacts due to the distributed small-aperture arrays, our sparsity-driven methods improve the imaging performance and provide high resolution. We validate our methods through numerical experiments on simulated data.
Semiconductor lasers for optoelectronic integrated circuits. (1988)

Semiconductor laser for use in optoelectronic integrated circuits has been developed. A ridge waveguide laser using the same layer with the heterojunction bipolar transitor (HBT) have been successfully integrated on a semi-insulating InP substrate. The n-cladding layer of the laser and the base of the HBT are the same epitaxial layers. This new structure has a small surface step and its fabrication process is very simple.The threshold current of the ridge-waveguide laser is 30mA, and the characteristic temperature 65K. Since the HBT has an additional narrow band gap layer at the collector side of the base. Early effect is not observed.This paper describes an analysis of the characteristics of the ridge-waveguide laser and the HBT, fabrication, and the operation of the optoelectronic integrated circuit.
Integrated measurement of the mass and surface charge of discrete microparticles using a suspended microchannel resonator (2009)

Measurements of the mass and surface charge of microparticles are employed in the characterization of many types of colloidal dispersions. The suspended microchannel resonator (SMR) is capable of measuring individual particle masses with femtogram resolution. Here, we employ the high sensitivity of the SMR resonance frequency to changes in particle position, relative to the cantilever tip, to determine the electrophoretic mobility of discrete particles in an applied electric field. When a sinusoidal electric field is applied to the suspended microchannel, the transient resonance frequency shift corresponding to a particle transit can be analyzed by digital signal processing to extract both the buoyant mass and electrophoretic mobility of each particle. These parameters, together with the mean particle density, can be used to compute the size, absolute mass, and surface charge of discrete microspheres, leading to a true representation of the mean and polydispersity of these quantities for a population. We have applied this technique to an aqueous suspension of two types of polystyrene microspheres, to differentiate them based on their absolute mass and their surface charge. The integrated measurement of electrophoretic mobility using the SMR is determined to be quantitative, based on comparison with commercial instruments, and exhibits favorable scaling properties that will ultimately enable measurements from mammalian cells.
Dual-Mode Silicon Photonic Crystal Nanocavity Modulator with Indium Oxide Gate (2018)

We report an ultra-efficient indium oxide gated silicon photonic crystal nanocavity electro-optical modulator, which is based on a dual-mode operation of resonance tuning and electro-absorption. With only 0.35μm long electrode, we achieved a tuning efficiency of 250pm/V and a modulation strength of 4dB/V with 35% from electro-absorption.
Photoacoustic microscopy of a three-dimensional arbitrary trajectory (2014)

We have developed three-dimensional arbitrary trajectory (3-DAT) scanning, which can rapidly image vessels of interest over a large field of view (FOV) and maintain a high signal-to-noise ratio (SNR) along the depth direction. The concept of 3-DAT scanning was demonstrated by imaging a human hair within a FOV of 3.5 × 2.0 mm<sup>2</sup>. Further, we showed that hemoglobin oxygen saturation (sO<sub>2</sub>) and blood flow can be measured simultaneously. The frame rate was 67 times faster than a traditional two-dimensional raster scan. We also observed sO<sub>2</sub> dynamics in response to a switch between systemic hyperoxia and hypoxia.
Rapid Detection of Fluoroquinolone-Resistant and Heteroresistant Mycobacterium tuberculosis by Use of Sloppy Molecular Beacons and Dual Melting-Temperature Codes in a Real-Time PCR Assay (2010)

Fluoroquinolones (FQ) are important second-line drugs to treat tuberculosis; however, FQ resistance is an emerging problem. Resistance has been mainly attributed to mutations in a 21-bp region of the Mycobacterium tuberculosis gyrA gene, often called the quinolone resistance-determining region (QRDR). We have developed a simple, rapid, and specific assay to detect FQ resistance-determining QRDR mutations. The assay amplifies the M. tuberculosis gyrA QRDR in an asymmetrical PCR followed by probing with two sloppy molecular beacons (SMBs) spanning the entire QRDR. Mutations are detected by melting temperature (T(m)) shifts that occur when the SMBs bind to mismatched sequences. By testing DNA targets corresponding to all known QRDR mutations, we found that one or both of the SMBs produced a T(m) shift of at least 3.6°C for each mutation, making mutation detection very robust. The assay was also able to identify mixtures of wild-type and mutant DNA, with QRDR mutants identified in samples containing as little as 5 to 10% mutant DNA. The assay was blindly validated for its ability to identify the QRDR mutations on DNA extracted from clinical M. tuberculosis strains. Fifty QRDR wild-type samples, 34 QRDR mutant samples, and 8 heteroresistant samples containing mixtures of wild-type and mutant DNA were analyzed. The results showed 100% concordance to conventional DNA sequencing, including a complete identification of all of the mixtures. This SMB T(m) shift assay will be a valuable molecular tool to rapidly detect FQ resistance and to detect the emergence of FQ heteroresistance in clinical samples from tuberculosis patients.
Robust determination of the anisotropic polarizability of nanoparticles using coherent confocal microscopy (2008)

A coherent confocal microscope is proposed as a means to fully characterize the elastic scattering properties of a nanoparticle as a function of wavelength. Using a high numerical aperture lens, two-dimensional scanning, and a simple vector-beam shaper, the rank-2 polarizability tensor is estimated from a single confocal image. A method for computationally efficient data processing is described, and numerical simulations show that this algorithm is robust to noise and uncertainty in the focal plane position. The proposed method is a generalization of techniques that provide an estimate of a limited set of scattering parameters, such as a single orientation angle for rodlike particles. The measurement of the polarizability obviates the need for a priori assumptions about the nanoparticle.
A Highly Scalable Capacitor-Less Cell Having a Doubly Gated Vertical Channel (2010)

A double-gate transistor structure with a vertical channel is proposed and demonstrated via three-dimensional device simulations to be well suited for dynamic random access memory (DRAM) application. The double-gate transistor structure with a vertical channel (DGVC) cell occupies 4F 2 area, provides for good retention characteristics (with immunity to disturbances), and is compatible with conventional memory process flows for stand-alone DRAM memories. In comparison with previous cell designs, the DGVC cell is more scalable, so that it is an excellent candidate for the continued scaling of DRAM technology to the 22-nm node and beyond.
Synthetic nano-fibrillar extracellular matrices with predesigned macroporous architectures (2000)

Scaffolding plays a pivotal role in tissue engineering. To mimic the architecture of a natural extracellular matrix component-collagen, nona-fibrous matrices have been created with synthetic biodegradable polymers in our laboratory using a phase-separation technique. To improve the cell seeding, distribution, mass transport, and new tissue organization, three-dimensional macroporous architectures are built in the nano-fibrous matrices. Water-soluble porogen materials are first fabricated into three-dimensional negative replicas of the desired macroporous architectures. Polymer solutions are then cast over the porogen assemblies in a mold, and are thermally phase-separated to form nano-fibrous matrices. The porogen materials are leached out with water to finally form the synthetic nano-fibrous extracellular matrices with predesigned macroporous architectures. In this way, synthetic polymer matrices are created with architectural features at several levels, including the anatomical shape of the matrix, macroporous elements (100 microm to millimeters), interfiber distance (microns), and the diameter of the fibers (50-500 nm). These scaffolding materials circumvent the concerns of pathogen transmission and immuno-rejection associated with natural collagen. With the flexibility in the design of chemical structure, molecular weight, architecture, degradation rate, and mechanical properties, these novel synthetic matrices may serve as superior scaffolding for tissue engineering.
Orthonormal Polynomials in Wavefront Analysis: Error Analysis (2006)

This paper formulates the error arising when Zernike polynomials are used in wavefront analysis of non-circular pupils. Numerical examples illustrate how the error varies as the number of terms and shapes of the apertures vary.
The Effect Of Glass Composition On The Performance Of Er <sup> 3+ </sup> Fiber Amplifiers (1990)

Despite the excellent performance that has been demonstrated for Er<sup>3+</sup>-doped fiber amplifiers at 1.5 µ m, they have several shortcomings that remain concerns in practical applications. The efficiency, gain, and signal/noise ratio of three-level devices are quite sensitive to the magnitude and spectrum of the cross sections. These, in turn, depend on the glass composition used as host. We report an investigation which determined the relevant cross sections for a variety of glasses and used them to predict performance trends for fiber amplifiers. Glasses have been identified which have advantages over silica, particularly for pumping with AlGaAs diode lasers at 800 nm.
Pattern-based Policy Configuration for SOA Applications (2008)

Service Component Architecture (SCA) defines a component model that allows for a late binding with a concrete implementation. Similarly, the SCA policy framework defines a policy mechanism that uses intents, which are high-level declarations of desired nonfunctional features that are bound to concrete policies at a later time. The definitions of intents are simple, but the actual intent application is complex. Meeting policy requirements requires application of intents at many points in an assembly, and presumes domain knowledge about the semantics and constraints related to using a particular combination of intents. We propose pattern based policy configuration to resolve these difficulties. Our proposed configuration system has two features: policy intent patterns and pattern application rules. Domain knowledge is encoded as roles and role constraints in policy intent patterns. Pattern application rules can be used to define how patterns are applied automatically. This paper takes the original approach of thinking about policy application from a compositional perspective; this reduces the complexity of meeting nonfunctional requirements for SCA assemblies and provides a validation framework for applied intents.
Practical Fault Localization with Combinatorial Test Design (2019)

Combinatorial test design is a well-known effective technique for test planning. However, in order to fully realize its potential in industrial settings, it needs to be considered as an integral part of the end to end testing flow rather than as an isolated component. In this work, we present an automated end to end solution for CTD-based test optimization, generation, execution and fault localization, implemented in an industrial framework. We further report on our initial promising experience in applying it to an industrial product.
Liquid-vapor thermodynamic equilibrium in Fischer-Tropsch synthesis products (2008)

A modified Peng-Robinson equation of state is used to develop the methods for calculating the liquid-vapor thermodynamic equilibrium in Fischer-Tropsch synthesis products. The critical thermodynamic parameters of paraffin and olefin hydrocarbons with a number of carbon atoms higher than 20 are determined using the correlations proposed in the present paper. The calculated results are compared with literature data and the data obtained in the Integrated Research and Development Center.
Modification of seldomycin factor 5 at C-3'. (1978)

Attempted removal of the 3'-hydroxyl group of seldomycin factor 5 via displacement of a sulfonate ester has led to 3'-epi-seldomycin factor 5. Removal of the hydroxyl group has been effected by the Barton procedure. The antibacterial activity of 3'-epi- and 3'-deoxyseldomycin factor 5 against various aminoglycoside-resistant strains is discussed.
A Closed-Loop Optogenetic Platform (2021)

Neuromodulation is an established treatment for numerous neurological conditions, but to expand the therapeutic scope there is a need to improve the spatial, temporal and cell-type specificity of stimulation. Optogenetics is a promising area of current research, enabling optical stimulation of genetically-defined cell types without interfering with concurrent electrical recording for closed-loop control of neural activity. We are developing an open-source system to provide a platform for closed-loop optogenetic neuromodulation, incorporating custom integrated circuitry for recording and stimulation, real-time closed-loop algorithms running on a microcontroller and experimental control via a PC interface. We include commercial components to validate performance, with the ultimate aim of translating this approach to humans. In the meantime our system is flexible and expandable for use in a variety of preclinical neuroscientific applications. The platform consists of a Controlling Abnormal Network Dynamics using Optogenetics (CANDO) Control System (CS) that interfaces with up to four CANDO headstages responsible for electrical recording and optical stimulation through custom CANDO LED optrodes. Control of the hardware, inbuilt algorithms and data acquisition is enabled via the CANDO GUI (Graphical User Interface). Here we describe the design and implementation of this system, and demonstrate how it can be used to modulate neuronal oscillations <i>in vitro</i> and <i>in vivo</i>.
A molecular basis for opiate action (1998)

Opioid receptors mediate the strong analgesic and addictive actions of exogenous opiates, the prototype of which is morphine. The opioid system consists of a family of endogenous opioid peptides and three receptor types, m, d and k. It is widely distributed throughout the CNS and regulates a large diversity of physiological functions, including pain perception and mood control. The recent cloning of opioid receptors has opened up a new era in opioid research. The molecular basis of opioid action may now be addressed by in vitro structure-function studies of recombinant receptors and by in vivo gene targeting. Novel drug design strategies based on data obtained from molecular approaches will be developed in order to generate the long-sought non-addictive analgesic.
Estimation of Cooldown Time in Cryocooled Superconducting Magnet System (2010)

A cooldown time is one of the major factors in many cryocooler applications, especially for the design of conduction-cooled superconducting apparatus. The estimation of cooldown seeks the elapsed time to cool thermal object by a cryocooler during initial cooldown process. This procedure includes the dimension of cold mass, heat transfer analysis for cryogenic load and available refrigerating capacity of a cryocooler. This method is applied to the specific cooling system for a 3 Tesla superconducting magnet cooled by a two-stage GM cryocooler. The result is compared with that of experiment, showing that the results of proposed method have a good agreement with experiments during initial cooling of superconducting magnet.
Real-time control of laser-hybrid welding using weld quality attributes (2004)

Applied Thermal Sciences, Inc is developing and validating an automated, large-scale laser GMAW-assisted welding process that can be utilized to fabricate high-precision lightweight structural shapes for shipbuilding and other industries. At the heart of this laser welding process is a real-time, adaptive Process Control System (PCS). This PCS is unique in that it utilizes weld quality attributes as process control variables. The system integrates these weld quality variables along with the more traditional process parameters such as laser power, wire feed, GMAW voltage and active seam tracking. This PCS has sufficient bandwidth and response time to achieve welding speeds up to 600 inches/minute. The high degree of integration of the various subsystems allows the PCS to coordinate and accurately regulate all of the necessary tasks in real-time during the laser welding process. In addition to process control, the weld quality attributes are also extracted and provide immediate documentation of weld quality. Thus, the system performs, at high speed, weld quality inspections that were previously manually performed offline. By eliminating manual inspection, product throughput is increased and product costs are reduced. This paper describes the laser welding PCS designed for a fully integrated prototype facility. While the prototype facility uses a 25 kW CO2 laser, the PCS is adaptable to any type, power and wavelength of laser, and will be integrated with a high power Ytterbium fiber laser in the near future.
Inference and enforcement of data structure consistency specifications (2006)

Corrupt data structures are an important cause of unacceptable program execution. Data structure repair (which eliminates inconsistencies by updating corrupt data structures to conform to consistency constraints) promises to enable many programs to continue to execute acceptably in the face of otherwise fatal data structure corruption errors. A key issue is obtaining an accurate and comprehensive data structure consistency specification. We present a new technique for obtaining data structure consistency specifications for data structure repair. Instead of requiring the developer to manually generate such specifications, our approach automatically generates candidate data structure consistency properties using the Daikon invariant detection tool. The developer then reviews these properties, potentially rejecting or generalizing overly specific properties to obtain a specification suitable for automatic enforcement via data structure repair. We have implemented this approach and applied it to three sizable benchmark programs: CTAS (an air-traffic control system), BIND (a widely-used Internet name server) and Freeciv (an interactive game). Our results indicate that (1) automatic constraint generation produces constraints that enable programs to execute successfully through data structure consistency errors, (2) compared to manual specification, automatic generation can produce more comprehensive sets of constraints that cover a larger range of data structure consistency properties, and (3) reviewing the properties is relatively straightforward and requires substantially less programmer effort than manual generation, primarily because it reduces the need to examine the program text to understand its operation and extract the relevant consistency constraints. Moreover, when evaluated by a hostile third party "Red Team" contracted to evaluate the effectiveness of the technique, our data structure inference and enforcement tools successfully prevented several otherwise fatal attacks.
Polysiloxanes with a Phenol Moiety for Bilayer Photoresist Applications (1989)

Novel Polysiloxanes with a phenol pendant group were synthesized and applied to bilayer photoresists for g-line and deep-UV (248 nm) lithography. These polymers had adequate aqueous-base solubility and oxygen-RIE resistance to serve as the base resin component for top imaging resists in bilayer resist systems. One of these polysiloxanes was synthesized from chlorodiethoxyphenylsilane and m-trimethylsiloxychlobenzene. Others were synthesized from dichlorophenylsilane and phenol and phenols with a double bond moiety (eugenol, isoeugenol and m-isopropenylphenol). These polysiloxanes had from 9.8 wt.% to 13.1 wt.X Si content and displayed an oxygen-RIE resistance 10 times greater than novolak resin. The m.p. values for these polymers ranged from 30°C to 90°C. The UV transmittance value (at 248 nm, 1 micron thickness) were from 7 % to 76 X. Resists were prepared from these polysiloxanes and sensitizers. In g-line lithography, the sensitizer was naphthoquinonediazide. In deep-UV (248 nm) lithography, the sensitizer was selected from naphtoquinonediazide, diazide and diazo compounds. 0.5 micron line and space patterns were obtained, when the resist was exposed using a g-line stepper, and using a tetramethylammonium hydroxide solution (ca. 1.3 %). 0.4 micron line and space patterns were resolved, when the resist was exposed using a KrF excimer laser stepper, and developed using the same solution. The top layer pattern could be transferred to the bottom layer (hard baked positive resist OFPR-5000) using oxygen-RIE. The etching rate for the silicon containing resist was 35 nm/min, while that for OFPR-5000 was 555 nm/min. These polysiloxanes make it possible to obtain the fine pattern resolution required in VLSI processing.