gebhart/patrepeval huggingface dataset:
Development and Characterization of a Field-Deployable Ion-Trap Mass Spectrometer with an Atmospheric Pressure Interface (2012)

A field-deployable quadrupole ion-trap mass spectrometer with an atmospheric pressure interface is designed, built, and characterized. The instrument enclosure (48 cm × 43 cm × 42 cm) includes a roughing pump and a helium lecture bottle; the total weight of the instrument is 68 kg. Peak power consumption during the instrument operation is ∼500 W. The instrument has a mass range of m/z 30-2500, across which it provides better than unit mass resolution. The typical peak width at half height is 0.3 Th for a scan speed of 4000 Th/s. Operation of the instrument with electrospray and atmospheric-pressure matrix-assisted laser desorption ionization (AP-MALDI) ion sources is demonstrated. AP-MALDI analysis of low femtomole amounts of peptides reveals that the sensitivity of the instrument is on par with modern commercially available quadrupole ion-trap mass spectrometers. Tandem mass spectrometry capabilities of the instrument include simultaneous isolation and fragmentation of several different compounds. Two ways to reduce the size, weight, and power consumption of the portable instrument were explored, and results of these initial studies are presented. One of the ways includes utilization of hydrogen as a buffer gas for operation of the ion-trap mass analyzer in combination with a metal hydride method for storage of hydrogen in a compact rechargeable cartridge. Furthermore, careful selection of the inlet capillary dimensions allowed to eliminate the first "1 Torr" stage of the differential pumping without any significant loss of the instrument sensitivity. The elimination of this first pumping stage removed two turbo drag pumps, which substantially decreased the instrument's maximum power consumption (to ∼300 W in peak use, and ∼150 W during standby), as well as its size (to 30 cm × 43 cm × 50 cm) and weight (to 35 kg).
Silicon heterointerface photodetector (1996)

We report the demonstration of an infrared avalanche photodetector that uses an InGaAs absorption layer and a Si avalanche multiplication layer bonded by wafer fusion. Photocurrent measurements of the silicon heterointerface photodetector showed high response to 1.3 μm light and gains of up to 130. Frequency response measurements for the detectors yielded 3 dB bandwidth products of up to 81 GHz.
Micro execution (2014)

Micro execution is the ability to execute any code fragment without a user-provided test driver or input data. The user simply identifies a function or code location in an exe or dll. A runtime Virtual Machine (VM) customized for testing purposes then starts executing the code at that location, catches all memory operations before they occur, allocates memory on-the-fly in order to perform those read/write memory operations, and provides input values according to a customizable memory policy, which defines what read memory accesses should be treated as inputs.
Expression of <i>Acidothermus cellulolyticus</i> E1 endo‐β‐1,4‐glucanase catalytic domain in transplastomic tobacco (2009)

As part of an effort to develop transgenic plants as a system for the production of lignocellulose-degrading enzymes, we evaluated the production of the endo-beta-1,4-glucanase E1 catalytic domain (E1cd) of Acidothermus cellulolyticus in transplastomic tobacco. In an attempt to increase the translation efficiency of the E1cd cassette, various lengths of the N-terminus of the psbA gene product were fused to the E1cd protein. The psbA gene of the plastid genome encodes the D1 polypeptide of photosystem II and is known to encode an efficiently translated mRNA. Experiments in an Escherichia coli expression system indicated that the fusion of short (10-22 amino acid) segments of D1 to E1cd resulted in modest increases in E1cd abundance and were compatible with E1cd activity. Plastid expression cassettes encoding unmodified E1cd and a 10-amino-acid D1 fusion (10nE1cd) were used to generate transplastomic tobacco plants. Expression of the E1cd open reading frame in transplastomic tobacco resulted in very low levels of the enzyme. The transplastomic plants accumulated a high level of E1cd mRNA, however, indicating that post-transcriptional processes were probably limiting the production of recombinant protein. The accumulation of 10nE1cd in transplastomic tobacco was approximately 200-fold higher than that of unmodified E1cd, yielding 10nE1cd in excess of 12% of total soluble protein in the extracts of the lower leaves. Most importantly, the active recombinant enzyme was recovered very easily and efficiently from dried plant material and constituted as much as 0.3% of the dry weight of leaf tissue.
<title>Performance improvement with hybrid WDM and CDMA optical communications</title> (1996)

It is well known that either Wavelength Division Multiplexing (WDM) or pulsed Code Division Multiple Accessing (CDMA) can be used as a basic accessing format in structuring an optical communication network or high speed parallel data processor. Each such system has its own inherent advantages and disadvantages when used as the principle format. When the two concepts are combined into a single hybrid WDM/CDMA format, some of the disadvantages of each format can be offset by the presence of the other, producing a more robust networking system with improved communication performance. In this paper these hybrid concepts are presented, and some of their hardware and architecture impacts are developed.
FK-506, a potent novel immunosuppressive agent, binds to a cytosolic protein which is distinct from the cyclosporin A-binding protein, cyclophilin. (1989)

A novel macrolide antibiotic, FK-506, isolated from Streptomyces tsukubaensis, has been shown to be a potent immunosuppressive agent in vivo and in vitro. FK-506 shares a number of immunosuppressive properties with the cyclic peptide, cyclosporin A (CsA), although 10 to 100 times more potent in this regard. These similarities suggest that both agents may share a similar mechanism(s) of action at the biochemical level. We have identified a cytoplasmic binding protein for FK-506 in the human T cell line, JURKAT, using [3H]FK-506. The FK-506 binding protein has a mr of 10 to 12 kDa (as determined by gel filtration), is heat stable and does not bind CsA. This contrasts with the CsA binding protein, cyclophilin, in that cyclophilin is heat labile and has a mr of 15 to 17 kDa. Our data suggest that FK-506 binds to a low m.w. protein(s) in JURKAT cells, which is distinct from cyclophilin. This protein may mediate the immunosuppressive effects of FK-506 in T cells. In addition, our results suggest that the immunosuppressive activity of FK-506, as with CsA, is mediated by an intracellular mechanism.
Newly Developed SNP-Based Identification Method of Hop Varieties (2014)

AbstractTwenty-one hop varieties in Europe and the United States were successfully identified by DNA analysis, based on single nucleotide polymorphisms (SNPs) as identification markers. Several dozen Mb of transcriptome sequencing data were obtained by next generation sequencer (NGS) from three hop varieties, respectively, and compared to search the regions, which contained many SNPs (including indel sequence). Consequently, four SNP-rich regions were selected as candidates for identification markers of hop varieties. Sequence data of these regions in all varieties tested here were obtained by the normal Sanger method and compared in terms of SNPs. Combination of these SNPs could work well for identification of 21 hop varieties. Moreover, the mixture of two varieties could be correctly evaluated by this method. Hop pellet samples of two different varieties were mixed at various ratios and DNA sequencing was carried out. As a result, the coexisting variety at even a 5% level could be detected by examining electropherograms of the SNP positions. A more quantitative method for mixture evaluation can be expected by DNA techniques, such as quantitative real-time PCR. Because this SNP-based identification method utilizes the DNA sequence itself, it could be an accurate and reproducible tool for the identification of hop varieties.KeywordsHopIdentificationNGSSNPTranscriptomeVariety
Pseudomonad Cyclopentadecanone Monooxygenase Displaying an Uncommon Spectrum of Baeyer-Villiger Oxidations of Cyclic Ketones (2006)

Baeyer-Villiger monooxygenases (BVMOs) are biocatalysts that offer the prospect of high chemo-, regio-, and enantioselectivity in the organic synthesis of lactones or esters from a variety of ketones. In this study, we have cloned, sequenced, and overexpressed in Escherichia coli a new BVMO, cyclopentadecanone monooxygenase (CpdB or CPDMO), originally derived from Pseudomonas sp. strain HI-70. The 601-residue primary structure of CpdB revealed only 29% to 50% sequence identity to those of known BVMOs. A new sequence motif, characterized by a cluster of charged residues, was identified in a subset of BVMO sequences that contain an N-terminal extension of approximately 60 to 147 amino acids. The 64-kDa CPDMO enzyme was purified to apparent homogeneity, providing a specific activity of 3.94 micromol/min/mg protein and a 20% yield. CPDMO is monomeric and NADPH dependent and contains approximately 1 mol flavin adenine dinucleotide per mole of protein. A deletion mutant suggested the importance of the N-terminal 54 amino acids to CPDMO activity. In addition, a Ser261Ala substitution in a Rossmann fold motif resulted in an improved stability and increased affinity of the enzyme towards NADPH compared to the wild-type enzyme (K(m) = 8 microM versus K(m) = 24 microM). Substrate profiling indicated that CPDMO is unusual among known BVMOs in being able to accommodate and oxidize both large and small ring substrates that include C(11) to C(15) ketones, methyl-substituted C(5) and C(6) ketones, and bicyclic ketones, such as decalone and beta-tetralone. CPDMO has the highest affinity (K(m) = 5.8 microM) and the highest catalytic efficiency (k(cat)/K(m) ratio of 7.2 x 10(5) M(-1) s(-1)) toward cyclopentadecanone, hence the Cpd designation. A number of whole-cell biotransformations were carried out, and as a result, CPDMO was found to have an excellent enantioselectivity (E > 200) as well as 99% S-selectivity toward 2-methylcyclohexanone for the production of 7-methyl-2-oxepanone, a potentially valuable chiral building block. Although showing a modest selectivity (E = 5.8), macrolactone formation of 15-hexadecanolide from the kinetic resolution of 2-methylcyclopentadecanone using CPDMO was also demonstrated.
Polar copolymer-surface-modified precipitated silica (1996)

To improve the performance of rubber compounds using precipitated silica as a reinforcing filler, the silica surface was directly modified by (1) adsorption of a surfactant onto the surface, (2) adsolubilization of an organic monomer, (3) in situ polymerization of the monomer in the surfactant bilayer, and (4) partial surfactant removal. Silica was thus modified using copolymers of isoprene or 1,3-butadiene with vinyl acetate, acrylonitrile, 4-methoxystyrene, 4-chlorostyrene, and methyl methacrylate on the silica surface. 4-Methoxystyrene/butadiene modification afforded the most promising candidate based on evaluation in a silica-filled, natural/styrene-butadiene rubber shoe sole compound that also has been used as a model tire compound. Physical testing showed that cure times were decreased, and break strength, tear energy, elongation to break, and cut growth resistance were increased. Thus, surface modification of silica by the in situ polymerization of organic monomers has been shown to be a flexible process capable of producing unique materials useful in improving rubber cure properties and the cured compound physical properties. © 1996 John Wiley & Sons, Inc.
An advanced transmit/receive 3D ceramic hybrid circuit module for space applications (2015)

Active Electronically Steerable Antenna (AESA) systems for space applications demand continuous performance improvement in terms of increased bandwidth, wider electronic scanning in azimuth, mass reduction, multi-polarization capability and higher transmitted power. At electronic front-end sub-system level, such goals can be achieved by increasing the density of the radiating patch elements of the antenna through a shrinking of such planar elements, which in turn leads to a reduction of transmit/receive (T/R) hybrid modules footprint. As a consequence, the use of suitable technology to take advantage of the modules “third dimension” (z-axis) connectivity becomes mandatory: active components have to be assembled also on the package lid, and means to implement reliable interconnections along the z-axis have to be devised.
Joint Multicell Beamforming and Client Association in OFDMA Small-Cell Networks (2015)

Small cells form a critical component of next generation cellular networks, where spatial reuse is the key to higher spectral efficiencies. Interference management in the spatial domain through beamforming allows for increased reuse without having to sacrifice resources in the time or frequency domain. Existing beamforming techniques for spatial reuse, being coupled with client scheduling, face a key limitation in practical realization, especially with OFDMA small cells. In this context, we argue that for a practical spatial reuse system with beamforming, it is important to decouple beamforming from client scheduling. Further, we show that jointly addressing client association with beamforming is critical to maximizing the reuse potential of beamforming. Towards our goal, we propose ProBeam - a system for multi-cell beamforming and client association in OFDMA small cell networks. ProBeam incorporates two key components - a low complexity, highly accurate SINR estimation module that helps determine interference dependencies for beamforming between small cells; and an efficient, low complexity joint client association and beam selection algorithm for the small cells that accounts for scheduling at the small cells without being coupled with it. We have prototyped ProBeam on a WiMAX-based network of four small cells. Our evaluations reveal the accuracy of our SINR estimation module to be within 1 dB, and the reuse gains from joint client association and beamforming to be as high as 115 percent over baseline approaches.
Coherence filters and their uses. I. Basic theory and examples (1997)

Abstract The phenomenon of correlation-induced spectral changes, discovered several years ago and extensively studied since then, is shown to offer the possibility of contructing novel types of spectral filter which have several properties that are not achievable with conventional filters. For example such filters can have different prescribed filtering properties in different directions of observation. In this paper the underlying theory is discussed and is illustrated by a few examples.
BASE (2001)

Software errors are a major cause of outages and they are increasingly exploited in malicious attacks. Byzantine fault tolerance allows replicated systems to mask some software errors but it is expensive to deploy. This paper describes a replication technique, BASE, which uses abstraction to reduce the cost of Byzantine fault tolerance and to improve its ability to mask software errors. BASE reduces cost because it enables reuse of off-the-shelf service implementations. It improves availability because each replica can be repaired periodically using an abstract view of the state stored by correct replicas, and because each replica can run distinct or non-deterministic service implementations, which reduces the probability of common mode failures. We built an NFS service where each replica can run a different off-the-shelf file system implementation, and an object-oriented database where the replicas ran the same, non-deterministic implementation. These examples suggest that our technique can be used in practice --- in both cases, the implementation required only a modest amount of new code, and our performance results indicate that the replicated services perform comparably to the implementations that they reuse.
An efficient filter-based approach for combinational verification (1999)

We have developed a lter-based f r amework where several fundamentally di erent techniques can be c ombined to provide fully automated and e cient heuristic solutions to veri cation and possibly other NP-complete problems. Such an integrated methodology is far more robust and e cient than any single existing technique on a wide variety of circuits. Our methodology has been applied to verify the ISCAS 85 benchmark circuits and e cient veri cation results have been presented o n a large set of industrial circuits which could not be veried using several published t e chniques and commercial veri cation tools available to us.
Probabilistic data association for semantic SLAM (2017)

Traditional approaches to simultaneous localization and mapping (SLAM) rely on low-level geometric features such as points, lines, and planes. They are unable to assign semantic labels to landmarks observed in the environment. Furthermore, loop closure recognition based on low-level features is often viewpoint-dependent and subject to failure in ambiguous or repetitive environments. On the other hand, object recognition methods can infer landmark classes and scales, resulting in a small set of easily recognizable landmarks, ideal for view-independent unambiguous loop closure. In a map with several objects of the same class, however, a crucial data association problem exists. While data association and recognition are discrete problems usually solved using discrete inference, classical SLAM is a continuous optimization over metric information. In this paper, we formulate an optimization problem over sensor states and semantic landmark positions that integrates metric information, semantic information, and data associations, and decompose it into two interconnected problems: an estimation of discrete data association and landmark class probabilities, and a continuous optimization over the metric states. The estimated landmark and robot poses affect the association and class distributions, which in turn affect the robot-landmark pose optimization. The performance of our algorithm is demonstrated on indoor and outdoor datasets.
Construction of a Vector Plasmid for Use in<i>Gluconobacter oxydans</i> (2003)

A host vector system in Gluconobacter oxydans was constructed. An Acetobacter-Escherichia coli shuttle vector was introduced with the efficiency of 10(4) transformants/microg of DNA. Next, aiming for a self-cloning vector, we found a cryptic plasmid (which we named pAG5) of 5648 bp in G. oxydans strain IFO 3171, and sequenced the nucleotides. The plasmid seemed to have only one open reading flame (ORF) for a possible replication protein. Shuttle vectors of Gluconobacter-E. coli were constructed with the plasmid pAG5 and an E. coli vector, pUC18.
Recent Advances in AlInAs Avalanche Photodiodes (2007)

We present practical planar AlInAs APDs, which have large gain-bandwidth products, low noise, and high reliability. The APD receivers had a sensitivity of -28.6 dBm at 10 Gb/s and -37.0 dBm at 2.5 Gb/s.
Development of a Species-Specific PCR Assay for Detection of <i>Leishmania donovani</i> in Clinical Samples from Patients with Kala-Azar and Post-Kala-Azar Dermal Leishmaniasis (2001)

ABSTRACT We have developed a PCR assay that is capable of amplifying kinetoplast DNA (kDNA) of Leishmania donovani in a species-specific manner among Old World leishmanias. With Indian strains and isolates of L. donovani the assay was sensitive enough to detect kDNA in an amount equivalent to a single parasite or less. The extreme sensitivity of the assay was reflected in its ability to detect parasite DNA from small volumes of peripheral blood of patients with kala-azar (KA) and from skin lesions from patients with post-KA dermal leishmaniasis (PKDL). A total of 107 clinical leishmaniasis samples were analyzed. Of these 102 (95.3%) were positive by PCR. The test provided a diagnosis of KA with 96% sensitivity using patient whole-blood samples instead of bone marrow or spleen aspirates that are obtained by invasive procedures. The assay was also successful in the diagnosis of 45 of 48 PKDL cases (93.8%). Cross-reactions with pathogens prevalent in the area of endemicity, viz., Mycobacterium tuberculosis, Mycobacterium leprae , and Plasmodium spp., could be ruled out. Eighty-one control samples, including dermal scrapings from healthy portions of skin from patients with PKDL were all negative. Two of twenty controls from the area of endemicity were found positive by PCR assay; however, there was a good possibility that these two were asymptomatic carriers since they were serologically positive for KA. Thus, this PCR assay represents a tool for the diagnosis of KA and PKDL in Indian patients in a noninvasive manner, with simultaneous species identification of parasites in clinical samples.
In vivo selective cancer-tracking gadolinium eradicator as new-generation photodynamic therapy agent (2014)

In this work, we demonstrate a modality of photodynamic therapy (PDT) through the design of our truly dual-functional--PDT and imaging--gadolinium complex (Gd-N), which can target cancer cells specifically. In the light of our design, the PDT drug can specifically localize on the anionic cell membrane of cancer cells in which its laser-excited photoemission signal can be monitored without triggering the phototoxic generation of reactive oxygen species--singlet oxygen--before due excitation. Comprehensive in vitro and in vivo studies had been conducted for the substantiation of the effectiveness of Gd-N as such a tumor-selective PDT photosensitizer. This treatment modality does initiate a new direction in the development of "precision medicine" in line with stem cell and gene therapies as tools in cancer therapy.
Tris(pyrazolyl)methane<sup>99m</sup>Tc tricarbonyl complexes for myocardial imaging (2008)

Novel ether-containing tris(pyrazolyl)methane chelators stabilize thefac-[99mTc(CO)3]+ moiety providing complexes with significant, fast and stable heart uptake, together with a extremely fast liver clearance.
Separation of Inorganic Salts From Supercritical Water by Cross-Flow Microfiltration (1995)

Abstract A cross-flow microfilter capable of operating at elevated temperatures and pressures was evaluated for its ability to remove inorganic salts from supercritical water (SCW). The separation characteristics of molten sodium nitrate were investigated. The overall performance of the cross-flow microfilter and the effects of process variables on the separation efficiency were evaluated. Separation efficiencies up to 85% were observed. An empirical model was developed for the prediction of the filtrate salt concentration and the fluidized cake resistance as a function of the salt solubility and salt flux to the filter. Physical principles governing the separation process were defined.