gebhart/patrepeval huggingface dataset:
PKU mutation (D143G) associated with an apparent high residual enzyme activity: Expression of a kinetic variant form of phenylalanine hydroxylase in three different systems (1996)

We have used three complementary in vitro systems to express the human phenylalanine hydroxylase (PAH) gene at high levels. Recombinant PAH was expressed in Escherichia coli (as a fusion protein), in human kidney cells and in a cell-free in vitro transcription-translation system. These systems were used to characterize a novel kinetic variant form (D143G) of the enzyme. The recombinant D143G mutant enzyme had the same physicochemical properties as the wild-type PAH and was stable when expressed in eukaryotic cells. Enzyme activity studies of the D143G mutant enzyme, produced in the three expression systems, revealed a kinetic variant form with reduced affinity for L-Phe (about 2.4-fold increase in the S0.5 value) as well as reduced affinity for tetrahydrobiopterin (BH4) (about 2-fold increase in the apparent Km). At standard assay conditions (1 mM L-Phe, t5 microM BH4) the residual activity of the mutant enzyme was high and variable (52%, 33%, and 102%) when analysed in the three different systems. The high residual activities of the mutant enzyme obtained at these conditions were not in agreement with the classical PKU phenotype found in a patient compound heterozygous for the termination mutation G272X and the novel D143G mutation. However, when the D143G mutant enzyme was assayed at lower concentrations of L-Phe (100-300 microM) and BH4 (10 microM) the residual activities were compatible with severely reduced hydroxylation of L-Phe and the classical PKU phenotype.
Comparison of Decoding Strategies for CTC Acoustic Models (2017)

Connectionist Temporal Classification has recently attracted a lot of interest as it offers an elegant approach to building acoustic models (AMs) for speech recognition. The CTC loss function maps an input sequence of observable feature vectors to an output sequence of symbols. Output symbols are conditionally independent of each other under CTC loss, so a language model (LM) can be incorporated conveniently during decoding, retaining the traditional separation of acoustic and linguistic components in ASR. For fixed vocabularies, Weighted Finite State Transducers provide a strong baseline for efficient integration of CTC AMs with n-gram LMs. Character-based neural LMs provide a straight forward solution for open vocabulary speech recognition and all-neural models, and can be decoded with beam search. Finally, sequence-to-sequence models can be used to translate a sequence of individual sounds into a word string. We compare the performance of these three approaches, and analyze their error patterns, which provides insightful guidance for future research and development in this important area.
The role of oxygen in the hydroxylation reaction of benzene with Fenton's reagent. Oxygen 18 tracer study (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe role of oxygen in the hydroxylation reaction of benzene with Fenton's reagent. Oxygen 18 tracer studyAtsutaka. Kunai, Shintaro. Hata, Sotaro. Ito, and Kazuo. SasakiCite this: J. Am. Chem. Soc. 1986, 108, 19, 6012–6016Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://pubs.acs.org/doi/10.1021/ja00279a057https://doi.org/10.1021/ja00279a057research-articleACS PublicationsRequest reuse permissionsArticle Views717Altmetric-Citations121LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Fiber-optic acoustic pressure sensor based on large-area nanolayer silver diaghragm (2014)

A fiber-optic acoustic pressure sensor based on a large-area nanolayer silver diaphragm is demonstrated with a high dynamic pressure sensitivity of 160 nm/Pa at 4 kHz frequency. The sensor exhibits a noise limited detectable pressure level of 14.5 μPa/Hz(1/2). Its high dynamic pressure sensitivity and simple fabrication process make it an attractive tool for acoustic sensing and photo-acoustic spectroscopy.
Extreme Discordant Sib Pairs for Mapping Quantitative Trait Loci in Humans (1995)

Analysis of differences between siblings (sib pair analysis) is a standard method of genetic linkage analysis for mapping quantitative trait loci, such as those contributing to hypertension and obesity, in humans. In traditional designs, pairs are selected at random or with one sib having an extreme trait value. The majority of such pairs provide little power to detect linkage; only pairs that are concordant for high values, low values, or extremely discordant pairs (for example, one in the top 10 percent and the other in the bottom 10 percent of the distribution) provide substantial power. Focus on discordant pairs can reduce the amount of genotyping necessary over conventional designs by 10- to 40-fold.
[Mechanisms of neutral red transport through the mucosa of the gastrointestinal tract]. (1981)

The conditions of the passage of neutral red into the cavity of gastro--intestinal tract were investigated during the atropine blockade of the stomach secretory activity in the dogs with fundal, antral and duodenal fistulas. The neutral red begins to cross the gastric mucosa only after the PH of the perfusing solution has achieved 2.5 and for intestine--5.0. The intensity of the neutral red passage increases with further decrease of the perfusing solution pH. During perfusion of acid solutions through the stomach and particularly through the duodenum, retrodiffusion of H+ occurs into the mucosa. The excretion of neutral red into the cavity of gastro--intestinal tract seems to be a process of passive diffusion. The role of the H+ retrodiffusion in this process is discussed.
Endonuclease A degrades chromosomal and plasmid DNA of Escherichia coli present in most preparations of single stranded DNA from phagemids. (1992)

With E. coli, large and variable amounts of chromosomal and plasmid DNAs are observed in the supernatants of overnight cultures when the cells carry an endA mutation, but are not detected by gel electrophoresis when the cells carry the wild type allele of endA. Significant amounts of nuclease activity in DH11S endA+ supernatants were detected by two simple assays; the rapid degradation of added pBR322 plasmid DNA, as judged by agarose gel electrophoresis, and a decrease of more than 100000 fold in transformation efficiency of the added pBR322 plasmid DNA. By employing isogenic endA mutant and wild type strains of DH11S and DH10B/F' proAB+ laclq Z delta M15, it was shown that detectable levels of chromosomal and plasmid DNAs are observed only in the endA mutant strains. These results indicate that Endonuclease I activity is responsible for degradation of chromosomal and plasmid DNA usually present in preparations of ssDNA. Therefore, a wild type endA gene is useful for the rapid and simple production of highly purified ssDNA from cells containing phagemid vectors.
Joint Beamforming and Power Splitting for MISO Interference Channel With SWIPT: An SOCP Relaxation and Decentralized Algorithm (2014)

This paper considers a power splitting-based MISO interference channel for simultaneous wireless information and power transfer (SWIPT), where each single antenna receiver splits the received signal into two streams of different power for decoding information and harvesting energy separately. We aim to minimize the total transmission power by joint beamforming and power splitting (JBPS) under both the signal-to-interference-plus-noise ratio (SINR) constraints and energy harvesting (EH) constraints. The JBPS problem is nonconvex and has not yet been well addressed in the literature. Moreover, decentralized algorithm design for JBPS based on local channel state information (CSI) and limited information exchange remains open. In this paper, we first propose a novel relaxation method named second-order cone programming (SOCP) relaxation to address the JBPS problem. We formulate the relaxed problem as an SOCP and present two sufficient conditions under which the SOCP relaxation is tight. For the case when the SOCP solution is not necessarily optimal to the JBPS problem, a closed-form feasible-solution-recovery method is provided. Then, we develop a distributed algorithm for the JBPS problem based on primal-decomposition (PD) method. The PD-based distributed algorithm consists of a master problem and a set of subproblems. The former is solved by using subgradient method while the latter are solved using coordinate descent method. Finally, numerical results validates the efficiency of the proposed algorithms.
Biochemical Characterization of Arterivirus Nonstructural Protein 11 Reveals the Nidovirus-Wide Conservation of a Replicative Endoribonuclease (2009)

Nidoviruses (arteriviruses, coronaviruses, and roniviruses) are a phylogenetically compact but diverse group of positive-strand RNA viruses that includes important human and animal pathogens. Nidovirus RNA synthesis is mediated by a cytoplasmic membrane-associated replication/transcription complex that includes up to 16 viral nonstructural proteins (nsps), which carry common enzymatic activities, like the viral RNA polymerase, but also unusual and poorly understood RNA-processing functions. Of these, a conserved endoribonuclease (NendoU) is a major genetic marker that is unique to nidoviruses. NendoU activity was previously verified in vitro for the coronavirus nsp15, but not for any of its distantly related orthologs from other nidovirus lineages, like the arterivirus nsp11. Here, we show that the bacterially expressed nsp11 proteins of two arteriviruses, equine arteritis virus and porcine respiratory and reproductive syndrome virus, possess pyrimidine-specific endoribonuclease activity. RNA cleavage was independent of divalent cations in vitro and was greatly reduced by replacement of residues previously implicated in catalysis. Comparative characterization of the NendoU activity in arteriviruses and severe acute respiratory syndrome coronavirus revealed common and distinct features of their substrate requirements and reaction mechanism. Our data provide the first biochemical evidence of endoribonuclease activity associated with arterivirus nsp11 and support the conclusion that this remarkable RNA-processing enzyme, whose substrate in the infected cell remains to be identified, distinguishes nidoviruses from all other RNA viruses.
Distinct Adenosine 3′,5′-Monophosphate and Phorbol Ester-Responsive Signal Transduction Pathways Converge at the Level of Transcriptional Activation by the Interactions of DNA-Binding Proteins (1989)

Evidence is presented that distinct cellular signal transduction pathways involving cAMP-dependent protein kinase-A and phorbol ester-stimulated protein kinase-C coordinately modulate gene transcription through common as well as distinct cis-acting elements and DNA-binding proteins. When transfected and expressed in HeLa and placental JEG-3 cells, fusion reporter plasmids that differ only by a single base deletion or addition to interconvert the octameric cAMP-responsive element TGACGTCA (CRE) to form the heptameric phorbol ester-responsive element TGACTCA (TRE) are differentially regulated by cAMP and phorbol esters [12-O-tetradecanoyl phorbol-14-acetate (TPA)]. Transcription directed by the CRE is stimulated by cAMP and not TPA, although the basal expression mediated by this element in JEG-3 and HeLa cells is augmented by endogenous protein kinase-C activity. In contrast, TRE mediates transcriptional responses to both cAMP and TPA, and the two agents together give synergistic responses. Inhibition of cAMP-dependent protein kinase-A by expression of a minigene encoding a peptide inhibitor of A-kinase abolishes the response of TRE to cAMP alone as well as the cAMP-induced component of the synergistic response to treatment with both TPA and cAMP. Desensitization of the protein kinase-C dependent pathway by prolonged exposure of cells to phorbol esters eliminates the TPA-induced transcription by TRE and inhibits the TPA-induced component of the synergistic response to both cAMP and TPA. Therefore, both protein kinases, A and C, are involved in transcriptional activation by the TRE; the function of either kinase alone results in a moderate level of activity, but the combined results of both functionally stimulated kinases are synergistically positive. Electrophoretic mobility shift assays using whole extracts of JEG-3 cells indicate that a common factor(s) binds both TRE and CRE; however, another factor(s) that binds to the CRE will not bind to the TRE. Further, a latent regulatory enhancer element (URE) located upstream of the CRE's in the human alpha gonadotropin gene, although inactive when paired alone with the alpha 100 promoter, induces basal and stimulated transcriptional activity of both CRE and TRE on the average of 10- to 20-fold. The data support the existence of a gene regulatory network consisting of related cis-acting elements and DNA-binding proteins whose transcriptional activities are regulated by the convergent actions of protein kinases-C and -A.
Selective emitters design and optimization for thermophotovoltaic applications (2012)

Among several solutions to exploit solar energy, thermophotovoltaics have been popularized and have known great breakthroughs during the past two decades. Yet, existing systems still have low efficiencies since the wavelength range of optimal photovoltaic (PV) conversion is very small compared to the emitter spectral range. Selective emitters are a very promising solution to this problem. We developed numerical tools to design and optimize such emitters. Some of the resulting structures composed of two or four layers of metals and semiconductors are presented in this paper. We also show that the usual PV devices efficiency limits (30% for crystalline silicon under solar radiation, according to Shockley-Queisser model) can be easily overcome thanks to these structures.
The application of real-time PCR to the analysis of T cell repertoires (2008)

The diversity of T-cell populations is determined by the spectrum of antigen-specific T-cell receptors (TCRs) that are heterodimers of alpha and beta subunits encoded by rearranged combinations of variable (AV and BV), joining (AJ and BJ), and constant region genes (AC and BC). We have developed a novel approach for analysis of beta transcript diversity in mice with a real-time PCR-based method that uses a matrix of BV- and BJ-specific primers to amplify 240 distinct BV-BJ combinations. Defined endpoints (Ct values) and dissociation curves are generated for each BV-BJ combination and the Ct values are consolidated in a matrix that characterizes the beta transcript diversity of each RNA sample. Relative diversities of BV-BJ combinations in individual RNA samples are further described by estimates of scaled entropy. A skin allograft system was used to demonstrate that dissection of repertoires into 240 BV-BJ combinations increases efficiency of identifying and sequencing beta transcripts that are overrepresented at inflammatory sites. These BV-BJ matrices should generate greater investigation in laboratory and clinical settings due to increased throughput, resolution and identification of overrepresented TCR transcripts.
An efficient apparatus for studying cathodoluminescence in the scanning electron microscope (1974)

This apparatus is designed to collect as much as possible of the light emitted from the surface of a solid specimen, while giving a minimum unwanted signal due to backscattered electrons. The light collector is a mirror in the shape of an ellipsoid of revolution, with the specimen at one focus and an optical microscope objective lens below the other focus. From the lens the light is led out of the vacuum by fibre optic light guides. For studies at room temperature, a wide-band spectrometer has been used in the range 400-700 nm. This spectrometer, which is based on a continuous interference filter, gives a minimum loss of light intensity.
Collaborative WHO xylitol field studies in Hungary IV. Saliva levels of<i>Streptococcus mutans</i> (1985)

Salivary Streptococcus mutans was quantified to detect possible age-, sex-, and group-dependent differences at the end of a 3-year field study assessing the value of partial substitution of sucrose with xylitol (X group) in comparison with systemic administration of fluoride (F group) and restorative treatment solely (C group). The material of this substudy consisted of 390 institutionalized children aged 9-14 years. S. mutans was determined through the spatula technique and grouped into categories 0, less than 10(5), 10(5)-10(6), and and greater than 10(6) CFU/ml saliva. Zero to less than 10(5) values included more than 80% of the subjects of the X group. The cross-sectional comparison between groups showed lower S. mutans values in the X group than in the F and C groups. These differences between groups were highly significant. S. mutans was not dependent on age or sex.
<i>Salmonella</i> SirA is a global regulator of genes mediating enteropathogenesis (1999)

SirA of Salmonella typhimurium is known to regulate the hilA and prgH genes within Salmonella pathogenicity island 1 (SPI1). To identify more members of the SirA regulon, we screened 10,000 random lacZY fusions (chromosomal MudJ insertions) for regulation by SirA and identified 10 positively regulated fusions. Three fusions were within the SPI1 genes hilA (an SPI1 transcriptional regulator), spaS (a component of the SPI1 type III export apparatus) and sipB (a substrate of the SPI1 export apparatus). Two fusions were within the sopB gene (also known as sigD). sopB is located within SPI5, but encodes a protein that is exported via the SPI1 export apparatus. In addition, five fusions were within genes of unknown function that are located in SPI4. As spaS and sipB were likely to be hilA dependent, we tested all of the fusions (except hilA) for hilA dependence. Surprisingly, we found that all of the fusions require hilA for expression and that plasmid-encoded SirA cannot bypass this requirement. Therefore, SirA regulates hilA, the product of which regulates genes within SPI1, SPI4 and SPI5. Both sirA and hilA mutants are dramatically attenuated in a bovine model of gastroenteritis, but have little or no effect in the mouse model of typhoid fever. This study establishes the SirA/HilA regulatory cascade as the primary regulon controlling enteropathogenic virulence functions in S. typhimurium. Because S. typhimurium causes gastroenteritis in both cattle and humans, we believe that this information may be directly applicable to the human disease.
Abstract 14609: {beta}3-Adrenoceptor Antagonist SR 59230A Attenuates the Imbalance of Systemic Oxygen Transport Induced by Dopamine in Newborn Lambs (2011)

Objective: The increase in O2 delivery (DO2) by dopamine may be offset by a greater increase in O2 consumption (VO2) in neonates due to β adrenergic receptors in abundant brown fat tissue, particul...
A parallel discrete event IP network emulator (2002)

Testing distributed applications over the Internet is fraught with problems: due to the inability to control a wide area network consistent, reproducible performance experiments are not possible. A system is described that uses a parallel discrete event simulator that can act as a real-time network emulator. Real Internet Protocol (IP) traffic generated by application programs running on user workstations can interact with modelled traffic in the emulator; thus providing a controlled test environment for distributed applications. Parallel execution enables the emulator to simulate large virtual networks and to model traffic interactions that could not be done in real-time sequentially. This paper gives an overview of the emulator and explores the various external data routing methods that the emulator supports. These routing methods allow the emulator to be operated in shared environments with certain constraints, as well as in dedicated test environments. Preliminary performance results are included.
Optimal decision making in a complex business simulation (2003)

The author provides insights into the possibility of inculcating the next generation of management with a commitment to consider optimization of management decision models. The approach used was to integrate the Business Management Laboratory/Systems Laboratory for Information Management (BML/SLIM) and the Interactive Financial Planning System/Optimum (IFPS/Optimum) in a semester-long course on decision support and expert systems. Eight groups of three second-year MBA students participated for a series of three trial decisions and 12 'real' decisions with the conceptual goal of optimizing the firm's operations. The research method was a complex case-study approach modified to fit a classroom situation. One insight indicates that optimization may follow a similar trend in usage as discounted cash-flow techniques experienced in financial analysis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ground Vehicle Spectral and Polarization Imaging Sensor (2007)

This paper summarizes the design of an Imaging Spectropolarimeter that operates in the visible wavelength region. The sensor uses computed tomographic imaging techniques to instantaneously form an object cube (spectral and spatial image) during each frame time. This computed tomographic imaging spectrometer (CTIS) is then combined with a channeled spectropolarimeter (CHSP) to form a computed tomography imaging channeled spectropolarimeter (CTICS)) which can simultaneously obtain image spatial and spectral information as well as polarization Stokes vectors at each resolution element in a single focal plane array (FPA) integration time with no moving parts. The work described in this paper is being performed by I Technology Applications and the The University of Arizona Optical Sciences Center. Calibration techniques as well as reconstruction investigations are discussed. Spectral and polarization measurement results are described. The applications of the sensor include target detection and recognition as well as navigation and environmental monitoring.
Improved Metal Gate Process by Simultaneous Gate-Oxide Nitridation during W/WN<sub>x</sub> Gate Formation (2000)

The improvement of gate dielectric reliability by simultaneous gate dielectric nitridation during W/WN x gate sputtering deposition was investigated. The time-to-breakdown ( t bd ) of the W/WN x gate metal-oxide-semiconductor (MOS) capacitor was improved compared to that of the W gate by increasing the N 2 flow ratio ( R N ) during the reactive sputtering deposition of the WN x gate with an N 2 –Ar gas mixture. The surface nitridation of the gate dielectric of the W/WN x gate MOS capacitor was confirmed to occur simultaneously with the reactive sputtering deposition of the WN x layer. The improvement of the gate dielectric reliability was achieved by the nitridation, which terminated the dangling bonds formed in the gate dielectric surface during the metal gate sputtering process. Other characteristics of the W/WN x gate electrode were also demonstrated. The W/WN x gate provides low resistivity, a near-mid-gap work function and a good gate etch profile.