gebhart/patrepeval huggingface dataset:
A rabbit monoclonal antibody against the antiviral and cancer genomic DNA mutating enzyme APOBEC3B (2019)

Abstract The DNA cytosine deaminase APOBEC3B (A3B) is normally an antiviral factor in the innate immune response. However, A3B has been implicated in cancer mutagenesis, particularly in solid tumors of the bladder, breast, cervix, head/neck, and lung. Here, we report data on the generation and characterization of a rabbit monoclonal antibody (mAb) for human A3B through a series of immunoblot, immunofluorescence microscopy, and immunohistochemistry experiments. Positive results indicate that one mAb, 5210-87-13, will be useful for fundamental research in virology and cancer biology and that immunohistochemical quantification of A3B enzyme levels may constitute a clinical biomarker for tumor evolvability and differential treatment.
Distribution system for ac electrical energy derived from dc energy sources (1977)

Apparatus is described for providing alternating current electrical energy to a load wherein an alternating current energy source includes one or more direct current energy sources coupled to one or more inverters each having at least one switching element therein. Switching elements are controlled to provide alternating current waveforms having a relatively low harmonic content. A preferred embodiment has two alternating current sources. The two alternating current sources are coupled to the load in a manner which causes their output voltages to be summed vectorially across the load. The phase difference between the output voltages of the two sources is controlled to regulate the resultant load voltage by controlling the operation of the switching elements in the inverters.
High-Precision D/H Measurement from Hydrogen Gas and Water by Continuous-Flow Isotope Ratio Mass Spectrometry (1995)

Two instrumental approaches are described for continuous-flow high-precision determinations of D/H ratios from hydrogen gas or via on-line reduction of water. In the first system, Ar is used as a carrier gas, with a Ni reduction furnace and a water trap to remove minor levels of unreduced water that are a potential source of memory effects. Precisions of SD < 10/1000 (delta DSMOW) over a 600/1000 range from -55 to +532/1000 are obtained for liquid water (0.4 microL). Linearity is excellent over 4 orders of magnitude of D concentration in tap water (r2 > 0.9999), although precision degrades at enrichments delta DSMOW > 5000/1000. In the second system, a heated Pd metal foil functions as a filter to admit purified hydrogen into the mass spectrometer. Hydrogen gas injections are made into flowing Ar and are directed to the Pd filter (approximately 330 degrees C) which passes hydrogen isotopes only while diverting the carrier flow to waste. Precisions of these measurements are SD < 6/1000 over the D enrichment range -213 to 340/1000, with excellent linearity (r2 > 0.9999) and accuracy (< 2/1000). Similar precision is obtained using the on-line reduction apparatus and a water trap prior to the Pd filter with injections of 0.4 microL of liquid water, with acceptable linearity (r2 > 0.999) over 3 orders of magnitude of D concentration. Neither system shows any sign of memory effects when water is analyzed. The data indicate that either one of these systems is a useful means for continuous-flow IRMS of D/H isotope ratio determinations.
Localized three-dimensional adaptive spatial-temporal processing for airborne radar (2003)

Radar space-time adaptive processing (STAP) techniques have classically focused on azimuth-Doppler adaptivity while placing minimal emphasis on elevation. Elevation adaptivity offers significant clutter suppression improvement, allowing further suppression of interference sources having identical Doppler and azimuth as the expected target. This work incorporates elevation adaptivity using two approaches: (1) a factored approach and (2) a joint domain approach, both greatly improving clutter suppression performance. The proposed concepts are validated using results based on simulated range ambiguous airborne radar data. Target detection improvements on the order of 8 dB and 10 dB (as compared to standard 2D-JDL processing) are demonstrated for the factored and joint domain approaches, respectively, using an 8 /spl times/ 8 non-uniform rectangular array.
A unified methodology for pre-silicon verification and post-silicon validation (2011)

The growing importance of post-silicon validation in ensuring functional correctness of high-end designs increases the need for synergy between the pre-silicon verification and post-silicon validation. We propose a unified functional verification methodology for the pre- and post-silicon domains. This methodology is based on a common verification plan and similar languages for test-templates and coverage models. Implementation of the methodology requires a user-directable stimuli generation tool for the post-silicon domain. We analyze the requirements for such a tool and the differences between it and its pre-silicon counterpart. Based on these requirements, we implemented a tool called Threadmill and used it in the verification of the IBM POWER7 processor chip with encouraging results.
Deletion of the ASFV dUTPase Gene E165R from the Genome of Highly Virulent African Swine Fever Virus Georgia 2010 Does Not Affect Virus Replication or Virulence in Domestic Pigs (2022)

African swine fever (ASF) is a frequently lethal disease of domestic and wild swine currently producing a pandemic affecting pig production in Eurasia. The causative agent, ASF virus (ASFV) is a structurally complex virus with a large genome harboring over 150 genes. One of them, <i>E165R</i>, encodes for a protein belonging to the dUTPase family. The fine structure of the purified protein has been recently analyzed and its dUTPase activity tested. In addition, it has been reported that a BA71 mutant virus, adapted to growth in Vero cells, lacking the <i>E165R</i> gene presented a drastic decreased replication in swine macrophages, its natural target cell. Herein, we report the development of a recombinant virus, ASFV-G-∆E165R, harboring the deletion of the <i>E165R</i> gene from the genome of the highly virulent field isolate ASFV Georgia 2010 (ASFV-G). Interestingly, ASFV-G-∆E165R replicates in primary swine macrophage cultures as efficiently as the parental virus ASFV-G. In addition, ASFV-G-∆E165R also replicates in experimentally inoculated domestic pigs with equal efficacy as ASFV-G and produced a lethal disease almost indistinguishable from that induced by the parental virus. Therefore, results presented here clearly demonstrated that <i>E165R</i> gene is not essential or important for ASFV replication in swine macrophages nor disease production in domestic pigs.
Synthesis of 9-Deoxo-4‘‘-deoxy-6,9-epoxyerythromycin Derivatives:  Novel and Acid-Stable Motilides (1998)

In our quest toward the discovery of highly potent and acid-stable motilides, novel 4"-deoxy derivatives of 9-deoxo-6, 9-epoxyerythromycin were designed, synthesized, and evaluated for their gastrointestinal prokinetic activities. These compounds, in their 9R configuration, were more potent than their 6,9-enol ether homologues in inducing well-coordinated smooth muscle contractions in an in vitro rabbit duodenal assay: e.g., (9R), (8S)-9-deoxo-4"-deoxy-3'-N-desmethyl-3'-N-ethyl-6, 9-epoxyerythromycin A (10) and (9R), (8S)-9-deoxo-4"-deoxy-3'-N-desmethyl-3'-N-ethanol-6, 9-epoxyerythromycin A (15) had a pED50 of 8.54 and 8.11 compared to a pED50 of 7.22 for compound 2 (ABT-229). Reduction of the 6,9-enol ether, which was aimed at improving the acid stability, afforded the most stable motilides to date with t1/2 of 5.5 h for 10 and 15. Compounds 10 and 15 bind specifically to rabbit antral smooth muscle motilin receptors with pIC50 values of 8.52 and 8.70.
Bioactive glass fiber/polymeric composites bond to bone tissue (1998)

Bioactive glass fibers were investigated for use as a fixation vehicle between a low modulus, polymeric composite and bone tissue. In an initial pilot study, bioactive glass fiber/polysulfone composites and all-polysulfone control rods were implanted into the rabbit tibia; the study was subsequently expanded with implantation into the rabbit femur. Bone tissue exhibited direct contact with the glass fibers and adjacent polymer matrix and displayed a mechanical bond between the composite and bone tissue after six weeks implantation. Interfacial bond strengths after six weeks implantation averaged 12.4 MPa, significantly higher than those of the all-polymer controls. Failure sites for the composite at six weeks generally occurred in the bone tissue or composite, whereas the failure site for the polymer implants occurred exclusively at the implant/tissue interface. The bioactive glass fiber/polysulfone composite achieved fixation to bone tissue through a triple mechanism: a bond to the bioactive glass fiber, mechanical interlocking between the tissue and glass fibers, and close apposition and possible chemical bond between the portions of the polymer and bone tissue. This last mechanism resulted from an overspill of bioactivity reactions from the fibers onto the surface of the surrounding polymer which we call the “halo” effect. © 1998 John Wiley & Sons, Inc. J Biomed Mater Res, 39, 161–170, 1998.
Evaluation of Redundancy Driven Provisioning for Hypervisors with Locally Attached Storage (2011)

Virtualized data centers became ubiquitous and led to invention of new delivery model called cloud computing. Cloud service providers pursue high degree of automation for the management processes in order to make their services responsive and inexpensive. One of such critical processes is virtual machine provisioning. This article reports on our on-going research to evaluate the efficiency of the provisioning process that leverages virtual machine similarity to reduce the amount of data that has to be transferred from the storage server to the hyper visor on which the virtual machine is being instantiated. The simulation experiments point to conclusion that the redundancy based provisioning can provide very substantial reduction in terms of amount of data that needs to be copied from the storage server.
First Experimental Demonstration of Optical Parametric Chirped Pulse Amplification in an Optical Fiber (2010)

Optical parametric chirped pulse amplification is experimentally demonstrated in an all fibered optical system. A single chirped fiber Bragg grating achieving the stretching/compression stages is combined to a continuous wave pumped Fiber optical parametric amplifier.
Fabrication and performance of diffractive optics for quantum well infrared photodetectors (1998)

Diffractive optical elements (microlenses) for quantum well infrared photodetectors (QWIPs) were fabricated by two techniques: (1) standard lithography of a binary optical structure and (2) PMMA pattern transfer for an analog diffractive optic structure. The binary lenses were fabricated by sequential contact lithography and etching using two binary masks. The analog diffractive lenses were fabricated in PMMA by direct-write e-beam lithography followed by acetone development. The resulting PMMA surface relief profile was transferred into the GaAs by dry etching. Both types of lenses were etching into GaAs using an electron cyclotron resonance (ECR) microwave plasma etching system. Although the lenses were fabricated accurately, the performance of the QWIPs was not improved as much as expected due to the angle-of-incidence sensitivity of the QWIP light-coupling grating. The lenses would have likely improved the performance of detectors capable of absorbing normally incident light.
Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin (2016)

Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity to acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels.
CMOS Image Sensors (2022)

This book explores the operating principles of complementary metal oxide semiconductor (CMOS) image sensors, their architecture, readout circuits, and characterisation techniques. The book focusses on the pinned photodiode (4T) pixel and also describes the three transistor (3T) design and other pixel architectures. Device operation is explained throughout with the support of technology computer-aided design (TCAD) semiconductor simulations. Characterisation techniques of CMOS image sensors are discussed in detail, including the use of the photon transfer curve (PTC) for determining the many device parameters. Solved examples are included with the purpose of helping readers gain an understanding of the practical use of the formulas. The main audience includes physicists and engineers in image sensor characterisation and development. Key features • Includes many semiconductor device and circuit simulations as a tool to illustrate the operating principles. • Covers both the semiconductor physics and the most important electronic circuits comprising a CMOS image sensor. • Presents solved examples and a list of the most important ‘take-aways’ within each chapter. • Discusses some specialised topics, such as charge collection, sources of dark current, reflective barriers, backside illumination and potential gradients. • Provides detailed analysis of the noise sources and the readout techniques in CMOS image sensors. • Covers the on-chip readout circuits at transistor level and presents the essential off-chip electronics with practical examples.
Fourier-interpolation superresolution optical fluctuation imaging (fSOFi)(Conference Presentation) (2016)

Stochastic Optical Fluctuation Imaging (SOFI) is a superresolution fluorescence microscopy technique which allows to enhance the spatial resolution of an image by evaluating the temporal fluctuations of blinking fluorescent emitters. SOFI is not based on the identification and localization of single molecules such as in the widely used Photoactivation Localization Microsopy (PALM) or Stochastic Optical Reconstruction Microscopy (STORM), but computes a superresolved image via temporal cumulants from a recorded movie. A technical challenge hereby is that, when directly applying the SOFI algorithm to a movie of raw images, the pixel size of the final SOFI image is the same as that of the original images, which becomes problematic when the final SOFI resolution is much smaller than this value. In the past, sophisticated cross-correlation schemes have been used for tackling this problem. Here, we present an alternative, exact, straightforward, and simple solution using an interpolation scheme based on Fourier transforms. We exemplify the method on simulated and experimental data.
Synthesis of [11C]oxazolidinone via rhodium-mediated carbon-yaltion reaction using [11C]carbon monoxide and [11C]isocyanate intermediate (2006)

Methods for the 11C-labeling of carbonyl compounds applicable in the preparation of radiotracers for Positron Emission Tomography (PET) are described. To this end [11C]carbon monoxide at low concentration was used in transition metal- mediated reactions.Stille couplings were employed in the synthesis of [carbonyl-11C]ketones from methyl and aryl halides with [11C]carbon monoxide. The synthesized [carbonyl-11C]ketones were obtained from the corresponding organostannanes with analytical radiochemical yields up to 98%.A number of synthetic routes were designed using [11C]carbon monoxide and rhodium complexes. Nitrene intermediates were generated from azides and reacted via a rhodium-mediated carbonylation reaction as a general synthetic route to [carbonyl-11C]isocyanates, versatile precursors. [carbonyl-11C]Isocyanate reacted via nucleophilic attack of an amine to form N,N’-diphenyl[11C]urea in 82% analytical radiochemical yield, ethyl phenyl[11C]carbamate was synthesized by the same route, using ethanol as the nucleophile, in 70% radiochemical yield. [11C]Isocyanate was also able to react in a [2+3] cycloaddition with ethylene oxide to form 3-phenyl[carbonyl-11C]oxazolidin-2-one in over 80% analytical radiochemical yield. This method was applied to the synthesis of a potential efflux system tracer [11C]hydroxyurea in 38% isolated radiochemical yield and the derivative 1-hydroxy-3-phenyl[11C]urea in 35% isolated radiochemical yield. Carbene intermediates, generated from diazo compounds, were reacted with [11C]carbon monoxide in the rhodium-mediated synthesis of [carbonyl-11C]ketenes. [carbonyl-11C]Ketene intermediates were utilised in the synthesis of diethyl[carbonyl-11C]malonate, from ethyl diazoacetate and ethanol. The product was obtained with a 20% isolated radiochemical yield. Alkylation of diethyl[carbonyl-11C]malonate, with ethyliodide and tetrabutylammonium fluoride, was successfully accomplished and diethyl diethyl[carbonyl-11C]malonate was synthesized in 50% analytical radiochemical yield. Several (carbonyl-13C)compounds were also synthesized using the described methods as a way of characterizing the position of the label using 13C-NMR.
A metasurface antenna for space application (2012)

We present the main results of a study on the use of anisotropic metasurfaces to realize an antenna radiating a circularly polarized field in an isoflux shaped beam pattern, suitable for LEO satellite application. We summarize the theory on which the design process is founded and provide a numerical validation relevant to an already manufactured antenna prototype. Measurement results will be presented during the oral session.
Self-Assembled Polyaniline Nanofibers/Nanotubes (2007)

A facile chemical polymerization is introduced to synthesize relatively long polyaniline nanofibers/nanotubes via self-assembly. 1-D elongation is achieved through the rapid formation of a substantial amount of dimer cation−radicals using excess initiator. 1-D nanostructures can be altered into 3-D hollow micro-/nanospheres in the presence of surfactant or counterion additives.
Formation of insoluble perylenetetracarboxylic diimide films by electro- or photo-crosslinking of pyrrole units (2005)

Perylenetetracarboxylic diimide derivatives bearing 2- or 4-peripheral pyrrole pendants could be efficiently crosslinked to form an insoluble film either by electropolymerization or visible light induced oxidative photopolymerization of the pyrrole units.
Fast techniques for computing finite-length MIMO MMSE decision feedback equalizers (2006)

Multiple-input multiple-output (MIMO) digital communication systems have received great attention due to their potential of increasing the overall system throughput. In such systems, MIMO decision feedback equalization (DFE) schemes are often used to mitigate intersymbol interference (ISI) resulting from channel multipath propagation. In this context, the existing computationally efficient methods for exact estimation of the DFE filters under minimum mean-square-error criteria (MMSE-DFE) rely on fast Cholesky decomposition and backsubstitution or Levinson techniques. These methods may still present several difficulties in implementation as the demand on higher transmission rates increases, and thus a simple solution is necessary. In this paper, new procedures for fast computation of the MIMO-MMSE-DFE are presented. The new algorithms are obtained from a simple observation, namely, that the optimal feedforward filter (FFF) is related to the well-known Kalman gain matrix, commonly encountered in fast recursive least squares adaptive algorithms-for which fast recursions exist and are readily applicable. Moreover, the feedback filter can be easily computed via stable fast MIMO convolution techniques. As a result, the proposed method is less complex, more structured, and can be as reliable in finite precision as known approaches in the literature.
Analytical noise and slice-sensitivity-profile models for multislice helical CT (2003)

Multi-slice computed tomography (MSCT) is one of the most recent technological advancements in CT. Several experimental studies have been conducted in the last few years on the peformance of MSCT. However, there is a lack of theoretical analysis on the slice sensitivity profile (SSP) and noise performance. In this paper, we derive several closed-form expressions to characterize these performance parameters under different detector configurations and acquisition modes. Following the common practice, the expressions are explicitly described for regions near the iso-center, although the same approach can be used to describe system performances away from the iso-center. Our models are validated against phantom experiments.
Very Large Fabrication Tolerance of VCSELs Using High- Contrast Subwavelength Grating (2007)

A very large fabrication tolerance for the high-index-contrast subwavelength grating (HCG) integrated VCSELs is experimentally demonstrated, with similar performance over as large as ±20% variation in HCG critical dimension.
Wide pressure range operation of air-coupled CMUTs (2012)

We present measurement results of capacitive micromachined ultrasonic transducers (CMUTs) in permanent contact mode over a wide pressure range (1 - 8 atm). The CMUT plates are in contact with the bottom of the cavities due to atmospheric pressure, even without any dc bias voltage. The electrical input impedance at various dc bias voltages are measured at elevated pressure to characterize individual devices. The open and short circuit resonant frequencies are extracted from the impedance data, and the acoustic performance of pairs of devices is evaluated by performing pitch-catch measurements. A frequency matching method is proposed and used to determine the optimal dc bias voltages for the transmitting and receiving CMUTs individually. Our electrical impedance results show good agreement with the finite element model results (modal and harmonic analysis performed with ANSYS) over the entire pressure range. Moreover, the pitch-catch measurement results validate the proposed frequency matching method for an optimal biasing scheme, and a received signal with good signal-to-noise ratio of 45 dB was observed at a pressure of 7 atm. In conclusion, the behavior of CMUTs in permanent contact mode can be predicted well with our FEA, and they are indeed a promising solution in providing ultrasonic transducers that can operate over a wide pressure range.