gebhart/patrepeval huggingface dataset:
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca (2014)

Thermobifida fusca is a cellulolytic bacterium with potential to be used as a platform organism for sustainable industrial production of biofuels, pharmaceutical ingredients and other bioprocesses due to its capability of potential to convert plant biomass to value-added chemicals. To best develop T. fusca as a bioprocess organism, it is important to understand its native cellular processes. In the current study, we characterize the metabolic network of T. fusca through reconstruction of a genome-scale metabolic model and proteomics data. The overall goal of this study was to use multiple metabolic models generated by different methods and comparison to experimental data to gain a high-confidence understanding of the T. fusca metabolic network. We report the generation of three versions of a metabolic model of Thermobifida fusca sp. XY developed using three different approaches (automated, semi-automated, and proteomics-derived). The model closest to in vivo growth was the proteomics-derived model that consists of 975 reactions involving 1382 metabolites and account for 316 EC numbers (296 genes). The model was optimized for biomass production with the optimal flux of 0.48 doublings per hour when grown on cellobiose with a substrate uptake rate of 0.25 mmole/h. In vivo activity of the DXP pathway for terpenoid biosynthesis was also confirmed using real-time PCR. i Tfu296 provides a platform to understand and explore the metabolic capabilities of the actinomycete T. fusca for the potential use in bioprocess industries for the production of biofuel and pharmaceutical ingredients. By comparing different model reconstruction methods, the use of high-throughput proteomics data as a starting point proved to be the most accurate to in vivo growth.
The Synthesis of 2′-Deoxyadenosine <i>via</i> Stereospecific Coupling Reaction (1989)

Abstract The coupling reaction of the sodium salt of adenine, which could be easily prepared by deprotonation with sodium hydroxide or sodium methoxide, with 1-α-chloro-2-deoxyribose derivative proceeded in a good stereospecific manner in acetone as a solvent to give the β-anomer of the corresponding acylated adenosine.
A Generalized Family of Optical Receivers for Optical Interconnects (1997)

Optical energy is limited in any optical interconnect system. Therefore we require an amplifier to decrease the optical energy for data communication. Electrical power consumed by this amplifier reduces the optical power required. An optical receiver for parallel interconnected systems (e.g., optical interconnected VLSI chips) must be moderately sensitive (-30 dBm to -20 dBm), low- electrical power (< 7 dBm), and high-speed (bit rate, B, in the hundreds of Mb/s). It also needs to be low-noise. A small dynamic range (<3 dB) can usually be tolerated since the optical power level can be set to this accuracy. The challenge in VLSI optical receiver design is to meet the above requirements simultaneously [1].
Metabolic engineering of bacteria for ethanol production (1998)

Technologies are available which will allow the conversion of lignocellulose into fuel ethanol using genetically engineered bacteria. Assembling these into a cost-effective process remains a challenge. Our work has focused primarily on the genetic engineering of enteric bacteria using a portable ethanol production pathway. Genes encoding Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase have been integrated into the chromosome of Escherichia coli B to produce strain KO11 for the fermentation of hemicellulose-derived syrups. This organism can efficiently ferment all hexose and pentose sugars present in the polymers of hemicellulose. Klebsiella oxytoca M5A1 has been genetically engineered in a similar manner to produce strain P2 for ethanol production from cellulose. This organism has the native ability to ferment cellobiose and cellotriose, eliminating the need for one class of cellulase enzymes. The optimal pH for cellulose fermentation with this organism (pH 5.0–5.5) is near that of fungal cellulases. The general approach for the genetic engineering of new biocatalysts has been most successful with enteric bacteria thus far. However, this approach may also prove useful with Gram-positive bacteria which have other important traits for lignocellulose conversion. Many opportunities remain for further improvements in the biomass to ethanol processes. These include the development of enzyme-based systems which eliminate the need for dilute acid hydrolysis or other pretreatments, improvements in existing pretreatments for enzymatic hydrolysis, process improvements to increase the effective use of cellulase and hemicellulase enzymes, improvements in rates of ethanol production, decreased nutrient costs, increases in ethanol concentrations achieved in biomass beers, increased resistance of the biocatalysts to lignocellulosic-derived toxins, etc. To be useful, each of these improvements must result in a decrease in the cost for ethanol production. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:204–214, 1998.
An Improved Synthesis of 3′,4′-Dideoxykanamycin B (1979)

Abstract A new synthetic route has been exploited for the large scale production of 3′,4′-dideoxykanamycin B starting with kanamycin B. The key stage in the synthesis involves the formation in excellent yield of the 3′,4′-anhydro-4′-epi derivative (5) followed by convertion to the 3′-ene derivative through the iodohydrin. Compound 5 was prepared by the treatment of 3′,2″-di-O-benzoyl-4″,6″-O-cyclohexylidene-4′-O-methylsulfonyl-penta-N-t-butoxycarbonyl-kanamycin B with sodium methoxide.
A Sex Attractant for the Adult Males of Variegated Cutworm,Peridroma saucia2 (1976)

Field testing of a large number of synthetic compounds and combinations thereof revealed that male moths of the variegated cutworm, Peridroma saucia (Hübner), were attracted to combinations of Z -9-tetradecen-1-yl acetate and Z -11-hexadecen-1-yl acetate. The greatest number of males were attracted to ratios of 1:1 to 1:2 and this attractant may be improved by the inclusion of anyone of E 9-14:OH, E 9-14:Ac, E 11-14:OH, or E 11-16:OH.
Concatenated peak-to-average power ratio reduction scheme with threshold limited selection for coded orthogonal frequency-division multiplexing (2008)

The authors propose a concatenated scheme to reduce the peak-to-average power ratio (PAPR) in coded orthogonal frequency-division multiplexing (OFDM) systems. First, they employ a label-bits-inserted encoder of a random-like code to achieve selected mapping (SLM). Then they set a threshold at the selector to limit the number of candidate sequences. Both analytical and numerical results show that the complexity of the SLM implemented by the label-bit-inserted encoder can be significantly reduced by threshold limited selection. With the same complexity, the performance of PAPR reduction is improved. The proposed concatenated PAPR reduction scheme enjoys many advantages including low-complexity, small overhead, no side information transmission and no performance loss or additional complexity at the receiver.
A Fast Organic-on-Inorganic Semiconductor Photodetector (1988)

It has been shown that certain crystalline organic semiconductors such as 3,4,9,10 perylenetetracarboxylic dianhydride (PTCDA) form rectifying energy bariers 1 when deposited onto inorganic semiconductor substrates; for example, Si, GaAs and InP. The organic-on-inorganic semiconductor (OI) heterostructure devices are particularly useful in fabricating many novel devices such as organic-on-inorganic semiconductor transistors 2 due to the low reverse leakage current. The high index of refraction and high transmittance in the organic material also enable them to be used for optoelectronic device applications such as optical waveguides and photodetectors. In particular, since PTCDA is transparent in the infrared region it is very useful for waveguide, and various other optoelectronic device applications.
Synapse Effect of Waveguide Modulator with a Nematic Liquid Crystal Cladding for Optical Neural Computing (1992)

A new type of waveguide-like nervous mode, in which the nematic liquid crystal (NLC) layer is used as the electrically controlled active material cladding and the channel waveguides are passive, is suggested. Its synaptic weight effect is discussed theoretically with a specific numerical example, and a preliminary experiment shows the results supporting this idea.
Correction to Synthesis and Biological Evaluation of the First Dual Tyrosyl-DNA Phosphodiesterase I (Tdp1)–Topoisomerase I (Top1) Inhibitors (2012)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to Synthesis and Biological Evaluation of the First Dual Tyrosyl-DNA Phosphodiesterase I (Tdp1)–Topoisomerase I (Top1) InhibitorsTrung Xuan Nguyen, Andrew Morrell, Martin Conda-Sheridan, Christophe Marchand, Keli Agama, Alun Bermingham, Andrew G. Stephen, Adel Chergui, Alena Naumova, Robert Fisher, Barry R. O'Keefe, Yves Pommier, and Mark Cushman*Cite this: J. Med. Chem. 2012, 55, 16, 7297Publication Date (Web):August 14, 2012Publication History Published online14 August 2012Published inissue 23 August 2012https://pubs.acs.org/doi/10.1021/jm301167vhttps://doi.org/10.1021/jm301167vcorrectionACS PublicationsCopyright © 2012 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1052Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (146 KB) Get e-Alertsclose Get e-Alerts
Selenate Reduction to Elemental Selenium by Anaerobic Bacteria in Sediments and Culture: Biogeochemical Significance of a Novel, Sulfate-Independent Respiration (1989)

Interstitial water profiles of SeO(4), SeO(3), SO(4), and Cl in anoxic sediments indicated removal of the seleno-oxyanions by a near-surface process unrelated to sulfate reduction. In sediment slurry experiments, a complete reductive removal of SeO(4) occurred under anaerobic conditions, was more rapid with H(2) or acetate, and was inhibited by O(2), NO(3), MnO(2), or autoclaving but not by SO(4) or FeOOH. Oxidation of acetate in sediments could be coupled to selenate but not to molybdate. Reduction of selenate to elemental selenium was determined to be the mechanism for loss from solution. Selenate reduction was inhibited by tungstate and chromate but not by molybdate. A small quantity of the elemental selenium precipitated into sediments from solution could be resolublized by oxidation with either nitrate or FeOOH, but not with MnO(2). A bacterium isolated from estuarine sediments demonstrated selenate-dependent growth on acetate, forming elemental selenium and carbon dioxide as respiratory end products. These results indicate that dissimilatory selenate reduction to elemental selenium is the major sink for selenium oxyanions in anoxic sediments. In addition, they suggest application as a treatment process for removing selenium oxyanions from wastewaters and also offer an explanation for the presence of selenite in oxic waters.
Imferon agar: improved medium for isolation of pathogenic Neisseria (1977)

Imferon, an iron-dextran complex, enhances the growth of Neisseria gonorrhoeae and N. meningitidis. The use of Imferon as a replacement for ferric nitrate, in a defined supplement for GC agar significantly increased the average colony sizes of both gonococci and meningococci. In comparison with Thayer-Martin medium, Imferon agar increased the speed and rate of isolation of gonococci from clinical specimens.
High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories (2012)

Dynamic tracking of human sperms across a large volume is a challenging task. To provide a high-throughput solution to this important need, here we describe a lensfree on-chip imaging technique that can track the three-dimensional (3D) trajectories of > 1,500 individual human sperms within an observation volume of approximately 8-17 mm(3). This computational imaging platform relies on holographic lensfree shadows of sperms that are simultaneously acquired at two different wavelengths, emanating from two partially-coherent sources that are placed at 45° with respect to each other. This multiangle and multicolor illumination scheme permits us to dynamically track the 3D motion of human sperms across a field-of-view of > 17 mm(2) and depth-of-field of approximately 0.5-1 mm with submicron positioning accuracy. The large statistics provided by this lensfree imaging platform revealed that only approximately 4-5% of the motile human sperms swim along well-defined helices and that this percentage can be significantly suppressed under seminal plasma. Furthermore, among these observed helical human sperms, a significant majority (approximately 90%) preferred right-handed helices over left-handed ones, with a helix radius of approximately 0.5-3 μm, a helical rotation speed of approximately 3-20 rotations/s and a linear speed of approximately 20-100 μm/s. This high-throughput 3D imaging platform could in general be quite valuable for observing the statistical swimming patterns of various other microorganisms, leading to new insights in their 3D motion and the underlying biophysics.
Bayesian estimation of multicomponent relaxation parameters in magnetic resonance fingerprinting (2017)

The Bayesian framework and algorithm shown provide accurate solutions for the partial-volume problem in magnetic resonance fingerprinting. The flexibility of the method will allow further study into different priors and hyperpriors that can be applied in the model. Magn Reson Med 80:159-170, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Improved Max-Log-MAP Turbo Decoding by Maximization of Mutual Information Transfer (2005)

The demand for low-cost and low-power decoder chips has resulted in renewed interest in low-complexity decoding algorithms. In this paper, a novel theoretical framework for improving the performance of turbo decoding schemes that use the max-log-MAP algorithm is proposed. This framework is based on the concept of maximizing the transfer of mutual information between the component decoders. The improvements in performance can be achieved by using optimized iteration-dependent correction weights to scale the a priori information at the input of each component decoder. A method for the offline computation of the correction weights is derived. It is shown that a performance which approaches that of a turbo decoder using the optimum MAP algorithm can be achieved, while maintaining the advantages of low complexity and insensitivity to input scaling inherent in the max-log-MAP algorithm. The resulting improvements in convergence of the turbo decoding process and the expedited transfer of mutual information between the component decoders are illustrated via extrinsic information transfer (EXIT) charts.
PMD Compensation in Polarization-Multiplexed Multilevel Modulations by Turbo Equalization (2009)

We propose the multilevel maximum a posteriori probability (MAP) detector suitable for use in polarization-multiplexed optical communications using multilevel modulation and coherent detection. The proposed multilevel MAP detection scheme considers two symbols transmitted over two orthogonal polarization states as a two-component symbol. We demonstrate experimentally that the proposed MAP scheme is effective in eliminating the bit-error-ratio (BER) floor phenomenon introduced by the conventional MAP equalizer, which considers the symbols transmitted over both polarizations independently. To improve further tolerance to optical fiber polarization-mode dispersion, we iterate extrinsic soft information between the MAP detector and soft-iterative decoder, in a turbo equalization fashion. Penalty of less than 1.5 dB at 20 Gb/s (and BER of 10-6 ) for differential group delay of 100 ps is reported.
An alternative formulation for predicting sound radiation from a vibrating object (1998)

An alternative formulation is derived for predicting acoustic radiation from a vibrating object in an unbounded fluid medium. The radiated acoustic pressure is shown to be expressible as a surface integral of the particle velocity, which is determinable by using a nonintrusive laser velocimeter. This approach is in contrast with the Kirchhoff integral formulation which requires the knowledge of both the normal component of the surface velocity and the surface acoustic pressure prior to predicting the radiated acoustic pressure. Solutions thus obtained are unique. Moreover, the efficiency of numerical computations is high because the surface integration can be readily implemented numerically by using standard Gaussian quadratures. This alternative formulation may be desirable to analyze the acoustic and vibration responses of a lightweight, a flexible, or a structure under an adverse environment for which a nonintrusive laser measurement technique must be used. Validations of this alternative formulation are demonstrated both analytically and numerically for vibrating spheres and right circular cylinders.
Conversion of just-continuous metallic films to large particulate substrates for metal-enhanced fluorescence (2008)

We report the effects of thermally annealing, non-, just-, and thick continuous silver films for their potential applications in metal-enhanced fluorescence, a near-field concept which can alter the free-space absorption and emissive properties of close-proximity fluorophores (excited states). We have chosen to anneal a noncontinuous particulate film 5 nm thick and two thicker continuous films, 15 and 25 nm thick, respectively. Our results show that the annealing of the 25 nm film has little effect on close-proximity fluorescence when coated with a monolayer of fluorophore-labeled protein. However, the 15 nm continuous film cracks upon annealing, producing large nanoparticles which are ideal for enhancing the fluorescence of close-proximity fluorophores that are indeed difficult to prepare by other wet-chemical deposition processes. The annealing of 5 nm noncontinuous particulate films (a control sample) has little influence on metal-enhanced fluorescence, as expected.
A new time-domain measurement technique for microwave devices (2002)

A new time-domain measurement technique for repetitive microwave signals is described. The microwave signal is converted to baseband before measurement, improving the accuracy compared to measurements at the carrier frequency. Applications include nonlinear device and modulator measurements, for the purpose of model generation and verification.
Channel guiding for advanced accelerators (1996)

The recent demonstration of optical guiding of high intensity laser pulses in plasma waveguides [C. G. Durfee III and H. M. Milchberg, Phys. Rev. Lett 71, 2409 (1993)] has opened the way to new advances in the development of compact laser‐driven electron particle accelerators. We review plasma waveguide properties relevant to intense pulse guiding and electron acceleration and show that the shock driven channels described here are well suited for stabilization of a large class of laser‐plasma instabilities deleterious to high intensity guiding over long distances.
Inhibition of membrane-type 1 matrix metalloproteinase tyrosine phosphorylation blocks tumor progression in mice. (2010)

We recently reported that membrane-type 1 matrix metalloproteinase (MT1-MMP) is phosphorylated on its unique cytoplasmic tyrosine residue but the contribution of this event to tumor progression remains unclear. In this work, we show that the non phosphorylizable cell-permeable peptide antennapedia-coupled cytoplasmic MMP-14 (ACM-14), consisting of the mutated (Y573F) cytoplasmic domain of MT1-MMP coupled to antennapedia, inhibits tyrosine phosphorylation of the enzyme and markedly reduces tumor cell proliferation within 3D type I collagen matrices. Interestingly, administration of ACM-14 to mice markedly delays tumor progression and increases survival, these antitumor actions being associated with the induction of extensive tumor necrosis. Overall, these findings suggest that inhibition of MT1-MMP tyrosine phosphorylation may represent an attractive strategy for the development of novel anticancer drugs.
Characterization of a genotype previously designated as CYP2A6 D-type:CYP2A6 *4B, another entire gene deletion allele of the CYP2A6 gene in Japanese (2002)

CYP2A6 is known as an enzyme responsible for the metabolism of several clincally used drugs such as tegafur. Previously, we found two novel genotypes of the CYP2A6 gene, D-type and E-type, and the E-type was clarified to be homozygous for the CYP2A6*4A allele. On the other hand, since the D-type was reported to lack regions from at least intron 5 to a part of exon 9 of the CYP2A6 gene, it caused a misunderstanding that the D-type would be a partial CYP2A6 gene-deleted allele. In this paper, we demonstrate that the D-type is a genotype heterozygous for the CYP2A6*4A and another novel entire CYP2A6 gene-deleted allele, CYP2A6*4B, by analyzing a Japanese family including parents genotyped as the CYP2A6*4A/4A and CYP2A6*1A/*4B, respectively.
Development of a Variable-Speed Residential Air-Source Integrated Heat Pump (2014)

A residential air-source integrated heat pump (AS-IHP) is under development in partnership with a U.S. manufacturer. A nominal 10.6 kW (3-ton) cooling capacity variable-speed unit, the system provides both space conditioning and water heating. This multi-functional unit can provide domestic water heating (DWH) in either full condensing (FC) (dedicated water heating or simultaneous space cooling and water heating) or desuperheating (DS) operation modes. Laboratory test data were used to calibrate a vapor-compression simulation model for each mode of operation. The model was used to optimize the internal control options for efficiency while maintaining acceptable comfort conditions and refrigerant-side pressures and temperatures within allowable operating envelopes. Annual simulations were performed with the AS-IHP installed in a well-insulated house in five U.S. climate zones. The AS-IHP is predicted to use 45 to 60% less energy than a DOE minimum efficiency baseline system while meeting total annual space conditioning and water heating loads. Water heating energy use is lowered by 60 to 75% in cold to warmer climates, respectively. Plans are to field test the unit in Knoxville, TN.