gebhart/patrepeval huggingface dataset:
Proteins encoded by the DpnI restriction gene cassette. Hyperproduction and characterization of the DpnI endonuclease. (1988)

Insertion mutations in the DpnI gene cassette of Streptococcus pneumoniae indicated that the two genes it contains, dpnC and dpnD, were transcribed from an adjacent promoter and that only dpnC was necessary for expression of the DpnI endonuclease.Large amounts of the DpnI endonuclease were produced from the cloned cassette in an Escherichia coli expression system, and the enzyme was purified to homogeneity.The DpnI endonuclease is composed of a single polypeptide of 30 kDa, which, as shown by NH2terminal sequencing of the protein, is encoded by the entire dpnC open reading frame.The native protein sedimented as a monomer of 30 kDa in 0.5 M NaCl.A protein composed of a 20-kDa polypeptide, which is presumably encoded by dpnD, was also produced in large amounts.It was partially purified, but its function is unknown.Examination of the predicted amino acid sequence of DpnI revealed a potential metal-containing, DNA-binding finger structure.It is suggested that this structure provides the specificity for recognition of the methylated DNA sequence, 5"GmATC-3', that is cleaved by the DpnI endonuclease.Strains of Streptococcus pneumoniae can harbor one of two restriction systems, DpnI or DpnII (reviewed in Lacks et al., 1987).The two systems are complementary in specificity and mutually exclusive (Lacks and Greenberg, 1977; Muckerman et at., 1982).Both systems enable the cells to resist bacteriophage attack by reducing viral infectivity to (Muckerman et al., 1982).The genetic basis of the phenotypic variation in restriction systems in S. pneumoniae depends on a cassette mechanism, in which alternative gene clusters are positioned at a specific location in the chromosome (Lacks et al., 1986b).The DpnII cassette confers a typical restriction system in the sense that the restriction endonuclease recognizes and cleaves the DNA sequence 5'-GATC-3' when it is not methylated.However, the organization of genes in the DpnII cassette is not typical.The system consists of an operon composed of three genes (dpnM, dpnA, and dpnB) under
Instrumentation System Diagnoses a Thermocouple (2008)

An improved self-validating thermocouple (SVT) instrumentation system not only acquires readings from a thermocouple but is also capable of detecting deterioration and a variety of discrete faults in the thermocouple and its lead wires. Prime examples of detectable discrete faults and deterioration include open- and short-circuit conditions and debonding of the thermocouple junction from the object, the temperature of which one seeks to measure. Debonding is the most common cause of errors in thermocouple measurements, but most prior SVT instrumentation systems have not been capable of detecting debonding. The improved SVT instrumentation system includes power circuitry, a cold-junction compensator, signal-conditioning circuitry, pulse-width-modulation (PWM) thermocouple-excitation circuitry, an analog-to-digital converter (ADC), a digital data processor, and a universal serial bus (USB) interface. The system can operate in any of the following three modes: temperature measurement, thermocouple validation, and bonding/debonding detection. The software running in the processor includes components that implement statistical algorithms to evaluate the state of the thermocouple and the instrumentation system. When the power is first turned on, the user can elect to start a diagnosis/ monitoring sequence, in which the PWM is used to estimate the characteristic times corresponding to the correct configuration. The user also has the option of using previous diagnostic values, which are stored in an electrically erasable, programmable read-only memory so that they are available every time the power is turned on.
Novel sst<sub>4</sub>-Selective Somatostatin (SRIF) Agonists. 2. Analogues with β-Methyl-3-(2-naphthyl)alanine Substitutions at Position 8 (2003)

We present a family of human sst(4)-selective, high-affinity (IC(50) = 2-4 nM) cyclic somatostatin (SRIF) octapeptides. These peptides result from the substitution of dTrp(8) in H-c[Cys(3)-Phe(6)-Phe(7)-DTrp(8)-Lys(9)-Thr(10)-Phe(11)-Cys(14)]-OH (SRIF numbering) (ODT-8) by one of the four conformationally biased stereoisomers of beta-methyl-3-(2-naphthyl)alanine (beta-Me2Nal). Whereas H-c[Cys-Phe-Phe-DNal-Lys-Thr-Phe-Cys]-OH (ODN-8, 2) has high affinity and marginal selectivity for human sst(3) (Reubi et al., Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13973-13978), H-c[Cys-Phe-Tyr-D-threo-beta-Me2Nal-Lys-Thr-Phe-Cys]-OH (5) has high affinity for all sst's except for sst(1); H-c[Cys-Phe-Tyr-L-threo-beta-Me2Nal-Lys-Thr-Phe-Cys]-OH (6) has high affinity for sst(4) (IC(50) = 2.1 nM), with more than 50-fold selectivity toward the other receptors. Analogues 7 and 8, containing d- and l-erythro-beta-Me2Nal instead of the corresponding threo derivatives at position 8, are essentially inactive at all receptors. Substitution of Tyr(7) in 5 and 6 by Aph(7) resulted in 9 and 10 with similar affinity patterns overall yet lowered affinity. The substitution of DCys(3) for Cys(3) in 5 and 6 yielded H-c[DCys-Phe-Tyr-D-threo-beta-Me2Nal-Lys-Thr-Phe-Cys]-OH (11) and H-c[DCys-Phe-Tyr-L-threo-beta-Me2Nal-Lys-Thr-Phe-Cys]-OH (12), with biological profiles almost identical to those of their parents 5 and 6 (i.e., high affinity for sst(2-5) for 11 and high affinity and selectivity for sst(4) for 12). Analogue 12, with high sst(4) affinity combined with the highest sst(4) selectivity among all tested compounds, is an agonist in the cAMP accumulation assay (EC(50) = 1.29 nM). Cold monoiodination of 12 yielded 14, with loss of sst(4) selectivity and loss of high affinity (IC(50) = 21 nM). Introduction of Tyr(2) in 9 and 10 and substitution of Cys(3) by dCys(3), to yield 15 and 16 (IC(50) = 9.8 and 61 nM, respectively, for sst(4) and limited selectivity), failed to generate a high-affinity (125)iodinatable sst(4)-selective ligand. Substitution of Phe by Tyr at position 11 in H-c[DCys-Phe-Phe-L-threo-beta-Me2Nal-Lys-Thr-Phe-Cys]-OH yielded 18 (IC(50) = 11.8 nM at sst(4)), with limited sst(4) selectivity (30-fold or greater at the other receptors) yet only slightly improved affinity over that of 14. Cold monoiodination of 18 yielded 20 (IC(50) = 30 nM at sst(4) and high selectivity). Whereas we were able, in this study, to identify a new family of sst(4)-selective, high-affinity compounds, our additional goal, to identify highly potent and sst(4)-selective ligands amenable to (125)iodination, could not be achieved satisfactorily. On the other hand, some of the diastereomers identified in this study, such as 5, 11, 17, and 19, are very potent ligands at all receptors but sst(1).
Two‐Photon Fluorescent Probes for Long‐Term Imaging of Calcium Waves in Live Tissue (2008)

2-Acetyl-6-(dimethylamino)naphthalene-derived two-photon fluorescent Ca2+ probes (ACa1-ACa3) are reported. They can be excited by a 780 nm laser beam, show 23-50-fold enhancement in one- and two-photon excited fluorescence in response to Ca2+, emit fourfold stronger two-photon excited fluorescence than Oregon Green 488 BAPTA-1 upon complexation with Ca2+, and can selectively detect intracellular free Ca2+ ions in live cells and living tissues with minimum interference from other metal ions and membrane-bound probes. Moreover, these probes are capable of monitoring calcium waves at a depth of 120-170 microm in live tissues for 1100-4000 s using two-photon microscopy with no artifacts of photobleaching.
A bio-inspired, chemo-responsive polymer nanocomposite for mechanically dynamic microsystems (2009)

This paper reports the development of a biologically-inspired, variable-modulus nanocomposite material for mechanically dynamic biomedical microsystems. This nanocomposite is comprised of a poly(vinyl acetate) matrix polymer that is reinforced with rigid cellulose nanofibers, and becomes very flexible when exposed to water. A direct-write CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> laser was used to pattern structures in this chemical- and temperature-sensitive material. Tensile testing of laser-cut, micron-scale nanocomposite beams was performed using a custom-built tensile tester. These samples displayed a significant reduction in Young's modulus from 4.1 GPa to 6.1 MPa when the nanocomposite was exposed to phosphate buffered saline. Additionally, the modulus change was observed to be reversible upon drying of soaked tensile samples. As a well-suited application of this nanocomposite, cortical probes utilizing this material as a substrate were fabricated. Gold-coated, dual-shank cortical probes utilizing this nanocomposite as a substrate were shown to record action potentials from a single neuron in a cockroach brain.
Image derived second-order differential microphones (1992)

Second-order differential (SOD) toroidal and uniaxial microphones derived using a first-order differential (FOD) sensor and a reflecting plane are described. For a uniaxial implementation a dipole FOD sensor is positioned with its axis perpendicular to and suspended a few centimeters from a large acoustically reflecting surface. The resulting sensor image is phase reversed resulting in a transducer that is a linear quadrupole. The linear quadrupole can be described by two dimensions, the distance corresponding to the FOD sensor dipole distance and the distance from the reflecting plane. If the reflecting surface is large enough, or if the wall of an enclosure is used, the resulting microphone becomes a SOD axial microphone. The close match between the sensor and its image from a good acoustic reflector results in a uniaxial SOD microphone with a 3-dB beamwidth of 66°. The sensor will operate as a differential microphone at frequencies below 3 kHz for a 2.5-cm spacing between the sensor and reflecting surface. A wall-mounted toroid can be formed by using two FOD sensors at right angles to each other and with the axis of each sensor at 45° to the reflecting surface. Also, the spacing between sensors is twice the height of the sensors from the reflecting plane. Measurements show that these transducers can be realized with existing commercially available electret condenser dipole sensors.
Sequential Antibody Affinity Chromatography of Human Leukocyte Interferon (1977)

Antibodies to crude leukocyte interferon (CIF) were bound to Sepharose 4B, and CIF was chromatographed. A relationship between recovered interferon and percentage binding of the antibodies to Sepharose 4B was observed. Highest recovery was obtained when only 50%-85% of th- antibodies were bound. When CIF was subjected to normal affinity chromatography, specific activity of 1-5 X 10(6) interferon units (IFU) (69/19B-units)/mg protein was obtained. When this purified preparation was further chromatographed on a column mainly directed against normal cellular proteins and then concentrated by normal affinity chromatography, a tenfold increase in 'direct' specific activity was obtained. It is suggested that the 'indirect' specific activity is about 2 X 10(8) IFU/mg protein.
High-Speed and Unified ECC Processor for Generic Weierstrass Curves over GF(p) on FPGA (2021)

In this paper, we present a high-speed, unified elliptic curve cryptography (ECC) processor for arbitrary Weierstrass curves over GF(p), which to the best of our knowledge, outperforms other similar works in terms of execution time. Our approach employs the combination of the schoolbook long and Karatsuba multiplication algorithm for the elliptic curve point multiplication (ECPM) to achieve better parallelization while retaining low complexity. In the hardware implementation, the substantial gain in speed is also contributed by our <i>n</i>-bit pipelined Montgomery Modular Multiplier (pMMM), which is constructed from our <i>n</i>-bit pipelined multiplier-accumulators that utilizes digital signal processor (DSP) primitives as digit multipliers. Additionally, we also introduce our unified, pipelined modular adder/subtractor (pMAS) for the underlying field arithmetic, and leverage a more efficient yet compact scheduling of the Montgomery ladder algorithm. The implementation for 256-bit modulus size on the 7-series FPGA: Virtex-7, Kintex-7, and XC7Z020 yields 0.139, 0.138, and 0.206 ms of execution time, respectively. Furthermore, since our pMMM module is generic for any curve in Weierstrass form, we support multi-curve parameters, resulting in a unified ECC architecture. Lastly, our method also works in constant time, making it suitable for applications requiring high speed and SCA-resistant characteristics.
Novel Acyl Derivatives from Karanja Oil: Alternative Renewable Lubricant Base Stocks (2014)

Lubricant base stocks of acylated oil and its derivatives, namely, propionylated, butanoylated, and hexanoylated karanja oil and fatty acid methyl esters, were synthesized from renewable nonedible source karanja oil (Pongamia glabra). The reaction was carried out by Prilezhaev dihydroxylation, an in situ peroxyformic acid generated using hydrogen peroxide and formic acid. The hydroxylated derivatives were acylated with three acid anhydrides (C3, C4, and C6). All of the synthesized products were examined for their purity by GC and GC-MS and characterized by IR and 1H NMR spectral studies. The acylated derivatives were evaluated for physicochemical and lubricant properties. Propionylated and butanoylated esters of KFAME were found suitable as IS: 3098 hydraulic fluids in ISO VG 46 and ISO VG 68 categories, respectively. In addition, propionylated esters of KFAME are also suitable as IS: 8406 gear oils (R&O type). Other lubrication properties such as viscosity, viscosity index of all products belonging to group III, category of base fluids as per API classification, Cu corrosion value, weld point, and air release value were found to be good. These base stocks may find applications in hydraulic fluids and metal-working fluids.
Flow-induced gelation of microfiber suspensions (2017)

The flow behavior of fiber suspensions has been studied extensively, especially in the limit of dilute concentrations and rigid fibers; at the other extreme, however, where the suspensions are concentrated and the fibers are highly flexible, much less is understood about the flow properties. We use a microfluidic method to produce uniform concentrated suspensions of high aspect ratio, flexible microfibers, and we demonstrate the shear thickening and gelling behavior of such microfiber suspensions, which, to the best of our knowledge, has not been reported previously. By rheological means, we show that flowing the suspension triggers the irreversible formation of topological entanglements of the fibers resulting in an entangled water-filled network. This phenomenon suggests that flexible fiber suspensions can be exploited to produce a new family of flow-induced gelled materials, such as porous hydrogels. A significant consequence of these flow properties is that the microfiber suspension is injectable through a needle, from which it can be extruded directly as a hydrogel without any chemical reactions or further treatments. Additionally, we show that this fiber hydrogel is a soft, viscoelastic, yield-stress material.
Minimization of detection volume by surface plasmon-coupled emission (2006)

Surface plasmon-coupled emission (SPCE) has been used to reduce the detection volume in fluorescence measurements. The effective fluorescence volume (detection volume) in SPCE experiments depends on two near-field factors: the depth of evanescent wave excitation and a distance-dependent coupling of excited fluorophores to the surface plasmons. With the excitation through the glass prism at SPR angle (Kretschmann configuration), the detection volume is a composition (product) of evanescent wave penetration depth and distance-dependent coupling. In addition, the detection volume is further reduced by a metal quenching of excited fluorophores at a close proximity (below 10 nm). The height of the detected volume size is 40-70 nm, depending on the orientation of the excited dipoles. We show that using Kretchmann configuration in a microscope with high numerical aperture objective (1.45) together with confocal detection, the detection volume can be reduced to 1-2 attoL, which is necessary to observe a single cross-bridge in the muscle. The strong dependence of the coupling to the surface plasmons on the orientation of excited dipoles can be also used to study the small conformational changes of macromolecules.
Implantation approach to SEU suppression in GaAs (1999)

It is shown that oxygen-implanted GaAs with oxygen concentrations of 1020 cm–3 (or 1019 cm–3 if co-implanted with Al), annealed in the 500 – 850°C temperature range, can result in highly resistive layers with subpicosecond free-carrier lifetimes. It is suggested that such layers can be used to suppress single event upsets (SEUs) in GaAs digital circuits.
High efficiency reflective liquid crystal polarization gratings (2009)

We experimentally demonstrate a reflective-mode liquid crystal polarization grating with high reflectance, small grating period, and subms switching times. This switchable optical element can diffract ∼100% into a single order, have highly polarization-sensitive first orders, and have a polarization-insensitive zero order. Here we introduce an absorbing layer that overcomes the reflection of the (ultraviolet) holographic beams, which otherwise prevents high quality fabrication. At a grating period of 2.1 μm, we report 98% diffraction efficiency, 90% reflectance, ∼600:1 contrast-ratio, and ∼3000:1 polarization contrast. These elements can therefore be configured as polarization-independent modulators or switchable polarizing beam splitters, for use in telecommunications, displays, spatial-light modulators, and polarimetry.
CDMA coverage, capacity and pole capacity (2002)

The main contribution of this work is the explicit calculation of the qualitatively known tradeoff between coverage and capacity in CDMA systems. The analysis of the paper permits prediction of coverage for a projected capacity, for any given admission policy used to achieve that capacity. Furthermore, our approach allows us to arrive at a good approximation for pole capacity, defined to be the limit of the number of users a cell can support as the coverage shrinks to zero.
Arginyltransferase, Its Specificity, Putative Substrates, Bidirectional Promoter, and Splicing-derived Isoforms (2006)

Substrates of the N-end rule pathway include proteins with destabilizing N-terminal residues. Three of them, Asp, Glu, and (oxidized) Cys, function through their conjugation to Arg, one of destabilizing N-terminal residues that are recognized directly by the pathway's ubiquitin ligases. The conjugation of Arg is mediated by arginyltransferase, encoded by ATE1. Through its regulated degradation of specific proteins, the arginylation branch of the N-end rule pathway mediates, in particular, the cardiovascular development, the fidelity of chromosome segregation, and the control of signaling by nitric oxide. We show that mouse ATE1 specifies at least six mRNA isoforms, which are produced through alternative splicing, encode enzymatically active arginyltransferases, and are expressed at varying levels in mouse tissues. We also show that the ATE1 promoter is bidirectional, mediating the expression of both ATE1 and an oppositely oriented, previously uncharacterized gene. In addition, we identified GRP78 (glucose-regulated protein 78) and protein-disulfide isomerase as putative physiological substrates of arginyltransferase. Purified isoforms of arginyltransferase that contain the alternative first exons differentially arginylate these proteins in extract from ATE1(-/-) embryos, suggesting that specific isoforms may have distinct functions. Although the N-end rule pathway is apparently confined to the cytosol and the nucleus, and although GRP78 and protein-disulfide isomerase are located largely in the endoplasmic reticulum, recent evidence suggests that these proteins are also present in the cytosol and other compartments in vivo, where they may become N-end rule substrates.
Superconducting High-Resolution Low-Pass Analog-to-Digital Converters (2007)

HYPRES has developed a high-resolution, dynamically programmable analog-to-digital converter (ADC) for radar and communications applications. The ADC uses the phase modulation-demodulation low-pass architecture and on-chip digital filtering. Detailed experimental results at 20 GHz clock frequency of the ADC chip fabricated with a 1 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Nb process are presented and discussed. In addition to the standard ADC configuration, different ADC modifications are described. In the multi-rate ADC, the modulator sampling frequency is the twice the clock frequency for the time-interleaved digital filter. In addition to the standard parallel-output ADC, a serial output ADC and its interface to room temperature electronics are developed. This serial ADC chip fabricated with the advanced HYPRES 4.5 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> process operated up to 34 GHz clock. As a major step toward commercialization of superconducting electronics, an ADC chip was successfully packaged on a cryocooler where it showed reduced performance up to 11.52 GHz clock.
Permission re-delegation: attacks and defenses (2011)

Modern browsers and smartphone operating systems treat applications as mutually untrusting, potentially malicious principals. Applications are (1) isolated except for explicit IPC or inter-application communication channels and (2) unprivileged by default, requiring user permission for additional privileges. Although inter-application communication supports useful collaboration, it also introduces the risk of permission redelegation. Permission re-delegation occurs when an application with permissions performs a privileged task for an application without permissions. This undermines the requirement that the user approve each application’s access to privileged devices and data. We discuss permission re-delegation and demonstrate its risk by launching real-world attacks on Android system applications; several of the vulnerabilities have been confirmed as bugs. We discuss possible ways to address permission redelegation and present IPC Inspection, a new OS mechanism for defending against permission re-delegation. IPC Inspection prevents opportunities for permission redelegation by reducing an application’s permissions after it receives communication from a less privileged application. We have implemented IPC Inspection for a browser and Android, and we show that it prevents the attacks we found in the Android system applications. 1
Handheld instrument for the measurement of Macular Pigment Optical Density using structured light (2021)

A handheld, standalone optical instrument was developed for the in-vivo assessment of the eye’s macular pigment optical density. The instrument is based on the reflectometry method, where the retina is illuminated with light of the appropriate spatial, temporal, and spectral characteristics and the reflected light from the fundus is collected using a high-speed photodetector. The collected light is then analysed and the corresponding value for macular pigment in the eye is computed.