gebhart/patrepeval huggingface dataset:
A filamentous phage display system for <i>N‐</i>linked glycoproteins (2010)

We have developed a filamentous phage display system for the detection of asparagine-linked glycoproteins in Escherichia coli that carry a plasmid encoding the protein glycosylation locus (pgl) from Campylobacter jejuni. In our assay, fusion of target glycoproteins to the minor phage coat protein g3p results in the display of glycans on phage. The glyco-epitope displayed on phage is the product of biosynthetic enzymes encoded by the C. jejuni pgl pathway and minimally requires three essential factors: a pathway for oligosaccharide biosynthesis, a functional oligosaccharyltransferase, and an acceptor protein with a D/E-X(1)-N-X(2)-S/T motif. Glycosylated phages could be recovered by lectin chromatography with enrichment factors as high as 2 × 10(5) per round of panning and these enriched phages retained their infectivity after panning. Using this assay, we show that desired glyco-phenotypes can be reliably selected by panning phage-displayed glycoprotein libraries on lectins that are specific for the glycan. For instance, we used our phage selection to identify permissible residues in the -2 position of the bacterial consensus acceptor site sequence. Taken together, our results demonstrate that a genotype-phenotype link can be established between the phage-associated glyco-epitope and the phagemid-encoded genes for any of the three essential components of the glycosylation process. Thus, we anticipate that our phage display system can be used to isolate interesting variants in any step of the glycosylation process, thereby making it an invaluable tool for genetic analysis of protein glycosylation and for glycoengineering in E. coli cells.
Helios (2009)

Helios is an operating system designed to simplify the task of writing, deploying, and tuning applications for heterogeneous platforms. Helios introduces satellite kernels, which export a single, uniform set of OS abstractions across CPUs of disparate architectures and performance characteristics. Access to I/O services such as file systems are made transparent via remote message passing, which extends a standard microkernel message-passing abstraction to a satellite kernel infrastructure. Helios retargets applications to available ISAs by compiling from an intermediate language. To simplify deploying and tuning application performance, Helios exposes an affinity metric to developers. Affinity provides a hint to the operating system about whether a process would benefit from executing on the same platform as a service it depends upon.
A Frequency-Independent Vibrational Energy Harvester using Symmetrically Charged Comb-Drive Electrodes with Heavily Doped Ion Electrets (2016)

An energy harvester has been developed to efficiently earn energy from both cyclic and impulse vibrations by using a symmetric pair of comb-electrodes that are heavily doped with potassium-ions to form electrets. By equalizing the electromechanical forces on the opposing comb-drives, energy conversion efficiency is enhanced for both impulses and broad-frequency harmonic vibrations.
Hardware/software instruction set configurability for system-on-chip processors (2001)

New application-focused system-on-chip platforms motivate new application-specific processors. Configurable and extensible processor architectures offer the efficiency of tuned logic solutions with the flexibility of standard high-level programming methodology. Automated extension of processor function units and the associated software environment - compilers, debuggers, simulators and real-time operating systems - satisfies these needs. At the same time, designing at the level of software and instruction set architecture significantly shortens the design cycle and reduces verification effort and risk. This paper describes the key dimensions of extensibility within the processor architecture, the instruction set extension description language and the means of automatically extending the software environment from that description. It also describes two groups of benchmarks, EEMBC's Consumer and Telecommunications suites, that show 20 to 40 times acceleration of a broad set of algorithms through application-specific instruction set extension, relative to high performance RISC processors.
On the Ac stability of high power factor three-phase rectifiers (2010)

This paper presents a comprehensive study of the ac stability of high power factor rectifiers, proposing a new stability criterion to assess this condition under constant power load dynamics. Specifically, based on the multivariable generalized Nyquist stability criterion developed by MacFarlane and Postlethwaite, this paper shows how the fundamental stability problem at such ac interface is indeed reduced to a single-input single-output (SISO) case. It is shown that the ac stability is fully determined by the SISO return-ratio of the d-d channel-or the power transfer channel of the desired d-q frame alignment; that is, the stability is determined by the d-d channel input and output impedances. Correspondingly, it is shown that the q-q channel trajectory on the complex plane is such that it cannot encircle the critical point (-1+j0) and therefore be the cause of instability. The ac stability at the input terminals of the rectifier can then be fully assessed using the standard SISO Nyquist stability theorem, in sheer duality of Middlebrook's criterion for dc-dc converters. Simulation results are used to verify and appraise the implications of the proposed ac system stability criterion.
Robot Would Reconfigure Modular Equipment (1993)

Special-purpose sets of equipment, packaged in identical modules with identical interconnecting mechanisms, attached to or detached from each other by specially designed robot, according to proposal. Two-arm walking robot connects and disconnects modules, operating either autonomously or under remote supervision. Robot walks along row of connected modules by grasping successive attachment subassemblies in hand-over-hand motion. Intended application for facility or station in outer space; robot reconfiguration scheme makes it unnecessary for astronauts to venture outside spacecraft or space station. Concept proves useful on Earth in assembly, disassembly, or reconfiguration of equipment in such hostile environments as underwater, near active volcanoes, or in industrial process streams.
Homoepitaxial graphene tunnel barriers for spin transport (Presentation Recording) (2015)

Tunnel barriers are key elements for both charge-and spin-based electronics, offering devices with reduced power consumption and new paradigms for information processing. Such devices require mating dissimilar materials, raising issues of heteroepitaxy, interface stability, and electronic states that severely complicate fabrication and compromise performance. Graphene is the perfect tunnel barrier. It is an insulator out-of-plane, possesses a defect-free, linear habit, and is impervious to interdiffusion. Nonetheless, true tunneling between two stacked graphene layers is not possible in environmental conditions (magnetic field, temperature, etc.) usable for electronics applications. However, two stacked graphene layers can be decoupled using chemical functionalization. Here, we demonstrate homoepitaxial tunnel barrier devices in which graphene serves as both the tunnel barrier and the high mobility transport channel. Beginning with multilayer graphene, we fluorinate or hydrogenate the top layer to decouple it from the bottom layer, so that it serves as a single monolayer tunnel barrier for both charge and spin injection into the lower graphene transport channel. We demonstrate successful tunneling by measuring non-linear IV curves, and a weakly temperature dependent zero bias resistance. We perform lateral transport of spin currents in non-local spin-valve structures and determine spin lifetimes with the non-local Hanle effect to be commensurate with previous studies (~200 ps). However, we also demonstrate the highest spin polarization efficiencies (~45%) yet measured in graphene-based spin devices [1]. [1] A.L. Friedman, et al., Homoepitaxial tunnel barriers with functionalized graphene-on-graphene for charge and spin transport, Nat. Comm. 5, 3161 (2014).
Wavelength demultiplexing multiple quantum well photodetectors operating on a medium spectral spacing (2002)

In conclusion, we have presented two-wavelength demultiplexing photodiodes utilizing multiple quantum well material so that for wavelengths as close as 15 nm there is less that -12 dB of crosstalk. We produced two devices, one that operates at 810 and 825 nm, and the other at 840 and 855 nm. The devices may be packaged inexpensively as for ordinary photodetectors.
Purification and characterization of a novel species of ubiquitin-carrier protein, E2, that is involved in degradation of non-“N-end rule” protein substrates (1994)

Ubiquitin-carrier proteins (E2s, ubiquitin-conjugating enzymes, UBCs) participate in proteolysis by catalyzing transfer of activated ubiquitin to the protein substrates, which are bound to specific ubiquitin-protein ligases (E3s). Yeast UBC2 (RAD6) and the mammalian E2(14kDa) bind to the ligase that recognizes and is involved in the degradation of certain free amino-terminal substrates ("N-end rule" substrates). As such proteins are rather scarce, the role of these E2s in general proteolysis is probably limited. Here, we report the purification and characterization of a novel 18-kDa species of E2 from rabbit reticulocytes. Unlike most members of the E2 family, this enzyme does not adsorb to anion exchange resin in neutral pH, and it is purified from the unadsorbed material (Fraction 1). Thus, it is designated E2-F1. Like all members of the E2 family, it generates a thiol ester with ubiquitin that serves as an intermediate in the conjugation reaction. Sequence analysis revealed a significant homology to many known species of E2s. The enzyme generates multiply ubiquitinated proteins in the presence of an E3 that has not been characterized yet. Most importantly, the ubiquitination via this E2 leads to the degradation of certain non-"N-end rule" substrates such as glyceraldehyde-3-phosphate dehydrogenase (Val at the NH2 terminus) and to the ubiquitination and degradation of certain N-alpha-acetylated proteins such as histone H2A, actin, and alpha-crystallin. The enzyme is also involved in the conjugation and degradation of the tumor suppressor protein p53.
New Al2O3:C,Mg crystals for radiophotoluminescent dosimetry and optical imaging (2006)

Optical and dosimetric properties of a new radiophotoluminescent material based on aluminum oxide doped with carbon and magnesium (Al2O3:C,Mg) and having aggregate oxygen vacancy defects are presented. The Al2O3:C,Mg crystals are characterized by several new optical absorption and emission bands. It is suggested that the main optical properties of this material are due to the formation of aggregate defects composed of two oxygen vacancies and two Mg-impurity atoms. Radiation-induced optical absorption bands are centered at 335 and 620 nm and produce fluorescent emission at 750 nm with a 75 +/- 5 ns lifetime. The dose measurements are performed by illumination of the Al2O3:C,Mg crystal with 335 nm or 650 nm light and by measuring the intensity of the 750 nm fluorescence. The detector material is insensitive to room light before and after the irradiation and the traps are stable up to 600 degrees C. A dose measurement range between 5 mGy and 200 Gy, suitable for therapeutic radiology applications, was demonstrated. The short luminescent lifetime and nondestructive readout is favorable for imaging applications.
Utilisation of chitosan flocculation of residual lipids and microfiltration for the production of low fat, clear <scp>WPC</scp>80 (2015)

Annato coloured cheese whey was adjusted to pH 4.5 and treated with 0.01% (w/w) chitosan to selectively precipitate residual lipids, which were removed by gravity settling and microfiltration (MF). MF permeate was concentrated by ultrafiltration/diafiltration (UF/DF) to produce whey protein concentrate with 80% protein (WPC80‐Chitosan). WPC80 samples were also produced by UF/DF only (Control), and by MF without chitosan treatment (MF). Both WPC80‐Chitosan and WPC80‐MF samples had lower fat, lower turbidity, higher foam overrun/stability and lower quantities of volatile compounds than WPC80‐Control before and after storage. WPC80‐Chitosan samples have an additional advantage of annatto removal (excellent clarity).
Automated Analysis for Free and Short-Chain Acylcarnitine in Plasma with a Centrifugal Analyzer (1992)

Abstract We describe a fully automated, spectrophotometric assay of free and total carnitine in plasma ultrafiltrates. The method, suitable for routine application in most hospital laboratories, incorporates the hydrolysis of acylcarnitines to free carnitine within the program of a Cobas Fara II centrifugal analyzer. The hydrolysis is monitored and calibrated with standard solutions containing octanoylcarnitine. Results correlated well with those from a reference isotope-dilution mass spectrometric assay. The ability to analyze a batch of samples for both free and total carnitine within 90 min enables analysis of &gt; or = 100 samples per day. Used in conjunction with acylcarnitine species identification by mass spectrometry, the Cobas assay facilitates the diagnosis of carnitine-deficiency syndromes and specific metabolic disorders.
Screening and Characterization of Protein-hyperproducing Bacteria without Detectable Exoprotease Activity (1989)

As the result of extensive screening, we isolated 37 protein-hyperproducing bacteria. Their protein productivities were highly stimulated by polypepton, but not by yeast extract or meat extract. These bacteria produced 4.5 ~ 11.5 g/l of cell bound and extracellular proteins under appropriate cultural conditions. Many of the selected bacteria showed characteristics of Bacillus brevis or species related to it as to cellular morphology and physiology. The bacteria which seemed to be B. brevis mostly accumulated one or two major high-molecular-weight protein species. Several strains were found to have excellent ability to produce proteins and showed no detectable extracellular protease activity. Such bacteria are expected to be potential hosts for the production of foreign proteins through recombinant DNA technology.
Decoding Techniques For Fine-Fine Geometry Multi-Anode Microchannel Arrays (1988)

The Multi-Anode Microchannel Array (MAMA) is a photon counting detector which decodes the position of an event through coincidence discrimination. The decoding algorithm which associates a given event with the appropriate pixel is determined by the geometry of the array. The decoding process can be divided into two tasks: anode encoding and pixel decoding. Techniques for performing both tasks are described and contrasted in light of application requirements. Decode times of 75 nanoseconds have been achieved, and considerably faster decoders are possible given new architectures and technologies.
10'-Desmethoxystreptonigrin, a novel analog of streptonigrin. (1992)

10'-Desmethoxystreptonigrin, a novel analog of streptonigrin produced by Streptomyces albus, was discovered in a screen for inhibitors of farnesylation of RAS p21 protein. The compound was isolated from the fermentation broth and its structure determined. It is markedly cytotoxic to several human tumor cell lines and also exhibits potent broad-spectrum antibacterial activity.
Polybacterial Periodontal Pathogens Alter Vascular and Gut BH4/nNOS/NRF2-Phase II Enzyme Expression (2015)

Periodontal disease is a highly prevalent chronic inflammatory disease and is associated with complex microbial infection in the subgingival cavity. Recently, American Heart Association supported a century old association between periodontal disease and atherosclerotic vascular disease. We have recently shown that polybacterial periodontal infection led to aortic atherosclerosis and modulation of lipid profiles; however the underlying mechanism(s) has not been yet demonstrated. Altered nitric oxide (NO) synthesis and tetrahydrobiopterin (BH4), a cofactor for nitric oxide synthases (NOS) has long been shown to be associated with vascular dysfunction and gastrointestinal motility disorders. We sought to examine the mechanism of periodontal infection leading to altered vascular and gastrointestinal smooth muscle relaxation, focusing on the BH4/nNOS pathways. In addition, we also have investigated how the antioxidant system (NRF2-Phase II enzyme expression) in vascular and GI specimens is altered by oral infection. Eight week old male ApoEnull mice were either sham-infected or infected orally for 16 weeks with a mixture of major periodontal bacteria Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia to induce experimental periodontitis. Serum, vascular (mesenteric), stomach, and colon specimens were collected at the end of periodontal pathogen infection. Bacterial infection induced significant (p<0.05) reductions in the levels of BH4,in ratio of BH4:BH2+B and also in nitric oxide levels compared to sham-infected controls. In addition, we identified a significant (p<0.05) reduction in eNOS dimerization, nNOS dimerization and protein expression of BH4 biosynthesis enzymes; GCH-1, DHFR and NRF2 & Phase II enzymes in infected mice versus controls in both mesenteric artery and colon tissues. However, we found no differences in nNOS/BH4 protein expression in stomach tissues of infected and sham-infected mice. This suggests that a polybacterial infection can cause significant changes in the vascular and colonic BH4/nNOS/NRF2 pathways which might lead to impaired vascular relaxation and colonic motility.
Analysis on the Inception of the Magnetohydrodynamic Flow Instability in the Annular Linear Induction Pump Channel (2021)

Abstract Flow instability is the intricate phenomenon in the annular linear induction pump (ALIP) when the pump runs at off-design working condition. A three-dimensional (3D) numerical model is built to simulate the flow in the pump channel. The pump heads at different flow rates are accurately predicted by comparing with experiment. The simulation results show the fluid velocity is circumferentially nonuniform in the pump channel even at the nominal flow rate. The flow in the middle sector continuously decelerates to nearly zero with the reducing flow rate. Reversed flow occurs in the azimuthal plane, followed by vortex flow. The reason for the heterogeneous velocity field is attributed to the mismatch between nonuniform Lorentz force and relatively even pressure gradient. It is seen that the flow in the region of small Lorentz force has to sacrifice its velocity to match with the pressure gradient. An analytic expression of the axial Lorentz force is then developed and it is clearly demonstrated the Lorentz force could be influenced by the profiles of velocity and radial magnetic flux density. The coupling between velocity and magnetic field is studied by analyzing the magnitudes of different terms in the dimensionless magnetic induction equation. It is found the dissipation term is determined by not only the magnetic Reynolds number but also the square of wave number of the disturbance in each direction. The smaller disturbing wave number weakens the dissipating effect, resulting in the larger nonuniform magnetic field and axial Lorentz force.
Robust latch mapping for combinational equivalence checking (1998)

Article Free Access Share on Robust latch mapping for combinational equivalence checking Authors: Jerry R. Burch Cadence Berkeley Labs Cadence Berkeley LabsView Profile , Vigyan Singhal Cadence Berkeley Labs Cadence Berkeley LabsView Profile Authors Info & Claims ICCAD '98: Proceedings of the 1998 IEEE/ACM international conference on Computer-aided designNovember 1998 Pages 563–569https://doi.org/10.1145/288548.289087Published:01 November 1998Publication History 11citation233DownloadsMetricsTotal Citations11Total Downloads233Last 12 Months19Last 6 weeks1 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 SiteeReaderPDF
Asymmetric Distances for Binary Embeddings (2013)

In large-scale query-by-example retrieval, embedding image signatures in a binary space offers two benefits: data compression and search efficiency. While most embedding algorithms binarize both query and database signatures, it has been noted that this is not strictly a requirement. Indeed, asymmetric schemes that binarize the database signatures but not the query still enjoy the same two benefits but may provide superior accuracy. In this work, we propose two general asymmetric distances that are applicable to a wide variety of embedding techniques including locality sensitive hashing (LSH), locality sensitive binary codes (LSBC), spectral hashing (SH), PCA embedding (PCAE), PCAE with random rotations (PCAE-RR), and PCAE with iterative quantization (PCAE-ITQ). We experiment on four public benchmarks containing up to 1M images and show that the proposed asymmetric distances consistently lead to large improvements over the symmetric Hamming distance for all binary embedding techniques.
Nanophotonic quantum sensing with engineered spin‐optic coupling (2023)

Nitrogen vacancy centers in diamond provide a spin-based qubit system with long coherence time even at room temperature, making them suitable ambient-condition quantum sensors for quantities including electromagnetic fields, temperature, and rotation. The optically addressable level structures of NV spins allow transduction of spin information onto light-field intensity. The sub-optimal readout fidelity of conventional fluorescence measurement remains a significant drawback for room-temperature ensemble sensing. Here, we discuss nanophotonic interfaces that provide opportunities to achieve near-unity readout fidelity based on IR absorption via resonantly enhanced spin-optic coupling. Spin-coupled resonant nanophotonic devices are projected to particularly benefit applications that utilize micro- to nanoscale sensing volume and to outperform present methods in their volume-normalized sensitivity.
Backside Defect Monitoring Strategy and Improvement in the Advanced Semiconductor Manufacturing (2021)

Traditionally, control the defect on the front of wafer can improve equal yield because all chips located wafer's upper part. That's why wafer manufacturing engineers always focus on front side and bevel of wafer. However, with the rapid development of semiconductor technology, slight variation of backside condition may induce yield loss. Against this backdrop, monitoring the backside of wafer will be extremely important. Monitoring method include visual inspection (VI), macroscopic inspection (MAI), microscopically inspection (MII) and hyper fine inspection (HFI). All the above methods cross banded by different process characteristic build a multi-stage monitor system. There are a lot of challenges in backside inspection result from scanning algorithm. Monitor arrangement scientifically was elaborated in this paper. Meanwhile, graphic recognition system was introduced which can quantify the backside scan image and distinguish exceptions. Finally, the scan result can check and clear a fault after compare with the Backside Database (BDB). Certainly, use ingenious printing to collect the BDB was also discussed in this content.