gebhart/patrepeval huggingface dataset:
Isolation from recombinant Escherichia coli and characterization of CMP-Kdo synthetase, involved in the expression of the capsular K5 polysaccharide (K-CKS) (1995)

In Escherichia coli with group II capsules, the synthesis of capsular polysaccharide and its cellular expression are encoded by the kps gene cluster, which is composed of three regions.The central region 2 encodes proteins involved in polysaccharide synthesis, and the flanking regions 1 and 3 direct the translocation of the finished polysaccharide across the cytoplasmic membrane and its surface expression.The kps genes of E. coli with the group II capsular K5 polysaccharide, have been cloned and sequenced.Region 1 contains the kpsE, D, U, C and S genes.In this communication we describe the overexpression of the @D and @psU genes as well as the isolation of the KpsU protein from the recombinant bacteria by chloroform treatment.The purified KpsU protein exhibited CMP-Kdo-synthetase activity.The N-terminal sequence and two internal peptide sequences of the isolated protein are in agreement with that previously predicted from the DNA sequence of the kpsU gene.The kinetic data of the CMP-Kdo-synthetase participating in K5 capsule expression (K-CMP-Kdo-synthetase) differ from those described for the CMP-Kdo-synthetase, participating in lipopolysaccharide synthesis (L-CMP-Kdo-synthetase).
Enhancing the ENSO Predictability beyond the Spring Barrier (2020)

El Niño-Southern Oscillation (ENSO) is the dominant interseasonal-interannual variability in the tropical Pacific and substantial efforts have been dedicated to predicting its occurrence and variability because of its extensive global impacts. However, ENSO predictability has been reduced in the 21<sup>st</sup> century, and the impact of extratropical atmosphere on the tropics has intensified during the past 2 decades, making the ENSO more complicated and harder to predict. Here, by combining tropical preconditions/ocean-atmosphere interaction with extratropical precursors, we provide a novel approach to noticeably increase the ENSO prediction skill beyond the spring predictability barrier. The success of increasing the prediction skill results mainly from the longer lead-time of the extratropical-tropical ocean-to-atmosphere interaction process, especially for the first 2 decades of the 21<sup>st</sup> century.
<sup>1</sup>H and <sup>13</sup>C HR‐MAS spectroscopy of intact biopsy samples <i>ex vivo</i> and <i>in vivo</i><sup>1</sup>H MRS study of human high grade gliomas (2004)

High-resolution magic angle spinning (HR-MAS) one- and two-dimensional 1H and 13C nuclear magnetic resonance (NMR) spectroscopy has been used to study intact glioblastoma (GBM) brain tumour tissue. The results were compared with in vitro chemical extract and in vivo spectra. The resolution of 1H one-dimensional, 1H TOCSY and 13C HSQC HR-MAS spectra is comparable to that obtained on perchloric extracts. 13C HSQC HR-MAS spectra have been particularly useful for the identification of 37 different metabolites in intact biopsy tumours, excluding water and DSS components. To our knowledge, this is the most detailed assignment of biochemical compounds obtained in intact human tissue, in particular in brain tumour tissue. Tissue degradation during the recording of the NMR experiment was avoided by keeping the sample at a temperature of 4 degrees C. Detailed metabolical compositions of 10 GBM (six primary, two secondary and two unclassified) were obtained. A good correlation between ex vivo and in vivo MRS has been found.
Adaptive postbeamformer interference canceler with improved performance in the presence of broadband directional sources (1991)

A postbeamformer interference canceler (PIC) is a beam space processor that processes the signals derived from an antenna array by forming two beams using fixed beamforming weights. One beam, referred to as the signal beam, is formed to have a fixed response in the known signal direction. The processed output of the second beam, referred to as the interference beam, is subtracted from the output of the signal beam to form the output of the PIC. In the presence of broadband directional sources, the formation of a beam is usually carried out by a set of steering delays followed by a weight and sum network. For this case, the processing of the interference beam output is carried out by a tapped delay line filter. When the two beams of the PIC are formed using conventional weights and the tapped delay line filter weights are adjusted to minimize the mean output power of the PIC, a substantial amount of the signal gets suppressed. It is due to the presence of signal component in the interference channel. This paper considers a frequency domain structure of the PIC (FDPIC) in the presence of broadband directional sources; derives conditions required for the performance of the FDPIC to be equal to the performance of the time-domain structure of the PIC (TDPIC); presents an algorithm to calculate the fixed weights of the two beams at each frequency bin such that the FDPIC maintains a specified frequency response in the signal direction and its optimized performance is better than that of the TDPIC using conventional beam weights; and suggests a scheme to select a gradient step size, which allows the misadjustment of the convergence time constant of the iterative gradient algorithm to be specified.
Rate of clinical progression in Parkinson's disease. A prospective study (2007)

Few prospective data on the clinical progression of Parkinson's disease (PD) in patient groups outside treatment trials in selected patients are available, and controversy exists on the rate of clinical disease progression with advancing disease. In this study, we investigated the rate of clinical progression of PD in a clinic-based sample of 145 patients over 1 year and in a community-based sample of 124 patients over 4 years. Depending on the sample and clinical scale used, mean deterioration of motor and disability scores ranged from 2.4 to 7.4% of the maximum possible score per year, and standard deviations indicated that there was considerable variability of progression rates between individuals. The progression of motor scores decreased with follow-up over 4 years and significantly decreased in more advanced disease stages. Deterioration of disability scores did not differ between disease stages; this may reflect the increasing rate of disease complications, which contribute to increasing disability in addition to motor impairment alone, in more advanced disease. Thus, motor fluctuations, hallucinations, depression, memory problems, and bladder symptoms were all reported more often at follow-up in the community-based sample (all P < 0.01), and dyskinesias, motor fluctuations, falls, and hallucinations were more common and cognitive and depression scores worse in higher disease stages in the clinic-based sample (all P < 0.001). We conclude that progression of motor scores in PD decreases with advancing disease in PD. However, disability continues to deteriorate with advancing disease and with the development of disease complications that are likely to be related to additional extrastriatal pathology.
Efficient Stereoselective Synthesis of <i>o</i>-Functionalized P-Chirogenic Phosphines Applied to Asymmetric Catalysis (2015)

GRAPHICAL ABSTRACT
Study on Privacy Risk Measurement Model of Cloud Computing (2018)

Background: Problems of cloud user privacy leaks have already hindered the further development of cloud computing, as described in various patents. Therefore, the comprehensive analysis and measurement of cloud computing privacy risks factors is an effective way to control and identify risks. However, the researches about this issue have not yet been discovered, so the relevant issues have been focused in this paper. Methods: This paper combines Analytic Hierarchy Process(AHP) with Information Entropy theory to identify and measure the privacy security risks of cloud computing. Results: This paper constructs a privacy risk attribute model of cloud computing with 20 privacy risk factors, based on the model, a cloud computing privacy risk measurement model has been designed. Conclusion: In order to effectively identify the defects and weakness on privacy protection, this paper can calculate the value and level of privacy risk factors of the attribute model by measuring model. The measurement results can provide a reference for cloud service providers to protect the privacy of users. Then the correctness of the model is verified by relevant simulation experiments. Keywords: Cloud computing, privacy risks, risk measurement, information entropy, Analytic Hierarchy Process(AHP), privacy protection.
Validation of a PicoGreen-Based DNA Quantification Integrated in an RNA Extraction Method for Two-Dimensional and Three-Dimensional Cell Cultures (2011)

DNA measurement and RNA extraction are two frequently used methods for cell characterization. In the conventional protocols, they require similar, but separate samples and in most cases, different pretreatments. The few combined protocols that exist still include time-consuming steps. Hence, to establish an efficient combined RNA extraction and DNA measurement protocol for two-dimensional (2D) and three-dimensional (3D) cell cultures, a PicoGreen-based DNA measurement was integrated in an existing RNA extraction protocol. It was validated by analysis of the influence of different lysis buffers, RLT, RA1, or Trizol, used for RNA extraction on the measured DNA concentration. The DNA cell yield was evaluated both in cell suspensions (2D) and on 3D cell-seeded scaffolds. Results showed that the different RNA lysis buffers caused a concentration-dependent perturbation of the PicoGreen signal. The measured DNA concentrations in 2D and 3D using RLT and RA1 buffer were comparable, also to the positive control. We, therefore, concluded that RNA extraction protocols using RA1 or RLT buffer allow the integration of a DNA quantification step without the buffer influencing the results. Hence, the combined DNA measurement and RNA extraction offer an alternative for DNA measurement techniques that is time and sample saving, for both 2D cell cultures and specific 3D constructs.
Performance Analysis and Design of On-Demand Electric Aircraft Concepts (2012)

The work presented in this paper is part of a larger NASA study focused on investigating the characteristics and feasibility of an on-demand air transportation system that consists of a eet of small, electrically-powered, general aviation aircraft. The present paper focuses on the performance and design implications of using electric propulsion systems for these on-demand aircraft. As a part of this study, a procedure to create aircraft performance models has been developed. The procedure is used to model a Cirrus SR-22 aircraft to serve as a point of comparison and to establish condence in the approach for application to electric concepts. Simple performance and sizing tools are developed for battery electric concepts, and calculations are performed using these tools to study the feasibility of fully electric aircraft for on-demand missions. Results indicate that designing electric aircraft through simple modications of existing airframes are not likely to produce aircraft with practical range capability in the near term; however, innovative vehicle concepts designed to leverage specic opportunities available with battery-electric propulsion show promise in meeting performance targets as soon as 2015.
IBUOV, A Provably Secure Identity-Based UOV Signature Scheme (2013)

Multivariate Public Key Cryptosystem (MPKC) is one of post-quantum cryptosystems which can potentially resist quantum computer attacks. It has increasingly been seen by some as a possible alternative to public key cryptosystems RSA, ECC, etc., which are widely in use today. Moreover, MPKC schemes are in general much more computationally efficient than number theoretic-based schemes. However, the oversize key poses obstacle on the calculation and transmission in MPKC. We notice the feature and benefit of the identity-based cryptography - the public key is directly gained from the user's identity information. Based on this, we consider introducing the identity-based semantics to MPKC, and it can cut down the size of public key of MPKC. Using the idea of constructing certificate-based Identity-Based Signature (IBS), we propose a novel and secure Identity-Based Unbalanced Oil-Vinegar (IBUOV) signature scheme based on the ordinary Unbalanced Oil-Vinegar (UOV) signature scheme. We provide the provable security to explain that our proposal is secure.
Past, present, and future for biologic intervention in atopic dermatitis (2015)

Atopic dermatitis (AD) is a debilitating disease that significantly alters the quality of life for one in four children and one in 10 adults. Current management of AD utilizes combinations of treatments to symptomatically alleviate disease by suppressing the inflammatory response and restoring barrier function in the skin, reducing disease exacerbation and flare, and preventing secondary skin infections. Resolution is temporary and long-term usage of these treatments can be associated with significant side-effects. Antibody therapies previously approved for inflammatory diseases have been opportunistically evaluated in patients with atopic dermatitis; however, they often failed to demonstrate a significant clinical benefit. Monoclonal antibodies currently in development offer hope to those individuals suffering from the disease by specifically targeting immune and molecular pathways important for the pathogenesis of atopic dermatitis. Here, we review the underlying biological pathways and the state of the art in therapeutics in AD.
Training Restricted Boltzmann Machines on Word Observations (2012)

The restricted Boltzmann machine (RBM) is a flexible tool for modeling complex data, however there have been significant computational difficulties in using RBMs to model high-dimensional multinomial observations. In natural language processing applications, words are naturally modeled by K-ary discrete distributions, where K is determined by the vocabulary size and can easily be in the hundreds of thousands. The conventional approach to training RBMs on word observations is limited because it requires sampling the states of K-way softmax visible units during block Gibbs updates, an operation that takes time linear in K. In this work, we address this issue by employing a more general class of Markov chain Monte Carlo operators on the visible units, yielding updates with computational complexity independent of K. We demonstrate the success of our approach by training RBMs on hundreds of millions of word n-grams using larger vocabularies than previously feasible and using the learned features to improve performance on chunking and sentiment classification tasks, achieving state-of-the-art results on the latter.
Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling (2009)

Comparative proteomics is a powerful analytical method for learning about the responses of biological systems to changes in growth parameters. To make confident inferences about biological responses, proteomics approaches must incorporate appropriate statistical measures of quantitative data. In the present work we applied microarray-based normalization and statistical analysis (significance testing) methods to analyze quantitative proteomics data generated from the metabolic labeling of a marine bacterium (Sphingopyxis alaskensis). Quantitative data were generated for 1,172 proteins, representing 1,736 high confidence protein identifications (54% genome coverage). To test approaches for normalization, cells were grown at a single temperature, metabolically labeled with (14)N or (15)N, and combined in different ratios to give an artificially skewed data set. Inspection of ratio versus average (MA) plots determined that a fixed value median normalization was most suitable for the data. To determine an appropriate statistical method for assessing differential abundance, a -fold change approach, Student's t test, unmoderated t test, and empirical Bayes moderated t test were applied to proteomics data from cells grown at two temperatures. Inverse metabolic labeling was used with multiple technical and biological replicates, and proteomics was performed on cells that were combined based on equal optical density of cultures (providing skewed data) or on cell extracts that were combined to give equal amounts of protein (no skew). To account for arbitrarily complex experiment-specific parameters, a linear modeling approach was used to analyze the data using the limma package in R/Bioconductor. A high quality list of statistically significant differentially abundant proteins was obtained by using lowess normalization (after inspection of MA plots) and applying the empirical Bayes moderated t test. The approach also effectively controlled for the number of false discoveries and corrected for the multiple testing problem using the Storey-Tibshirani false discovery rate (Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A. 100, 9440-9445). The approach we have developed is generally applicable to quantitative proteomics analyses of diverse biological systems.
Spatial Analysis of<i>Arabidopsis thaliana</i>Gene Expression in Response to<i>Turnip mosaic virus</i>Infection (2007)

Virus-infected leaf tissues comprise a heterogeneous mixture of cells at different stages of infection. The spatial and temporal relationships between sites of virus accumulation and the accompanying host responses, such as altered host gene expression, are not well defined. To address this issue, we utilized Turnip mosaic virus (TuMV) tagged with the green fluorescent protein to guide the dissection of infection foci into four distinct zones. The abundance of Arabidopsis thaliana mRNA transcripts in each of the four zones then was assayed using the Arabidopsis ATH1 GeneChip oligonucleotide microarray (Affymetrix). mRNA transcripts with significantly altered expression profiles were determined across gradients of virus accumulation spanning groups of cells in and around foci at different stages of infection. The extent to which TuMV-responsive genes were up- or downregulated primarily correlated with the amount of virus accumulation regardless of gene function. The spatial analysis also allowed new suites of coordinately regulated genes to be identified that are associated with chloroplast functions (decreased), sulfate assimilation (decreased), cell wall extensibility (decreased), and protein synthesis and turnover (induced). The functions of these downregulated genes are consistent with viral symptoms, such as chlorosis and stunted growth, providing new insight into mechanisms of pathogenesis.
Presence of a DNA demethylating activity in the nucleus of murine erythroleukemic cells. (1982)

Nucleoplasm prepared from murine erythroleukemia cells was assayed from enzymatic activity which removes methyl groups from DNA methylated at the internal C of the sequence 5'-CCGG-3' (Hpa II sites). Under the conditions of assay, the release of methyl groups was linear with time for 1 h, and up to 2 pmol could be released per microgram of extract protein. The activity was proportional to the amount of added extract and was sensitive to heat ant to proteinase K exposure. The initial velocity was hyperbolic with increasing amounts of substrate, and the Km for methyl groups was estimated to be between 1 and 1.5 microM. These results show that DNA demethylation catalyzed by extracts from cell nuclei can occur in vitro where no DNA synthesis is occurring and suggest that such a process might occur in vivo to alter DNA methylation during differentiation.
A Review of Outcome Measurements for Voice Disorders (2002)

There has been great interest in the medical and associated communities in the development and use of patient-based outcome measures such as quality-of-life and handicap indexes. This area of assessment of initial disability and response to subsequent treatment is especially applicable to the field of laryngology and voice disorders given the limitations of perceptual analysis and objective vocal function studies. In this review, we outline the development and importance of patient-based outcome measures in general, and their application for voice disorders specifically. In addition, several voice-specific instruments are discussed in detail and provided. One of the primary goals of this review is to educate and facilitate the future use of these simple but important patient-based outcome instruments for otolaryngologists who care for patients with voice disorders.
Development of reactive topical skin protectants against sulfur mustard and nerve agents (1999)

The potential for highly reactive nanoparticles (RNP) to absorb destructively, i.e. to neutralize highly toxic substances such as the warfare agents GA, GB, HD and VX, has been demonstrated in the laboratory. Reactive nanoparticles represent a new class of nanoscale particles of metals and metal oxides that differ from other nanoparticles in reactivity and crystalline morphology. The potential for incorporating RNP into a protective barrier skin cream also has been demonstrated. Preliminary studies indicate that RNP are physically and chemically compatible with a base cream provided by the Army Medical Research Office and, importantly, remain reactive with chemical agents while promising to be compatible with skin contact.
Use of Pharmacokinetics and Pharmacodynamics to Optimize Antimicrobial Treatment of Pseudomonas aeruginosa Infections (2005)

The study of pharmacodynamics has greatly enhanced our understanding of antimicrobials and has enabled us to optimize dosing regimens. Applying this knowledge to the clinical setting can be critical for the treatment of Pseudomonas aeruginosa infections. Because of its selectively permeable outer membrane and multiple efflux pump mechanisms, P. aeruginosa has high intrinsic resistance to many available antimicrobials. Numerous studies have established pharmacodynamic values for concentration-dependent agents (maximum serum concentration : minimum inhibitory concentration [MIC] and area under the serum concentration-time curve : MIC) and concentration-independent agents (i.e., percentage of time that the drug concentration remains greater than the MIC) that help predict the probability of a successful outcome. Current therapies attempt to meet these target values. However, to reduce the risk of clinical failures, combination therapy (typically, a β-lactam with an aminoglycoside or fluoroquinolone) is commonly used to enhance eradication rates and decrease the risk of developing resistance. Although combination therapy ensures a greater chance of selection of appropriate treatment, timely initial administration of antimicrobial therapy remains a key factor for reducing the likelihood of death for these patients.
High extinction ratio in-fiber polarizers based on 45° tilted fiber Bragg gratings (2005)

We report a near-ideal in-fiber polarizer implemented by use of 45 degrees tilted fiber Bragg grating structures that are UV inscribed in hydrogenated Ge-doped fiber. We demonstrate a polarization-extinction ratio of 33 dB over a 100-nm operation range near 1550 nm. We further show an achievement of 99.5% degree of polarization for unpolarized light with these gratings. We also theoretically investigate tilted grating structures based on the Green's function calculation, therein revealing the unique polarization characteristics, which are in excellent agreement with experimental data.
Excimer laser projection lithography (1984)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text K. Jain and R. T. Kerth, "Excimer laser projection lithography," Appl. Opt. 23, 648-650 (1984) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article