gebhart/patrepeval huggingface dataset:
Crystal Structure of the Terminal Oxygenase Component of Cumene Dioxygenase from<i>Pseudomonas fluorescens</i>IP01 (2005)

ABSTRACT The crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of Pseudomonas fluorescens IP01 (CumDO) was determined at a resolution of 2.2 Å by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NphDO). The ligation of the two catalytic centers of CumDO (i.e., the nonheme iron and Rieske [2Fe-2S] centers) and the bridging between them in neighboring catalytic subunits by hydrogen bonds through a single amino acid residue, Asp231, are similar to those of NphDO. An unidentified external ligand, possibly dioxygen, was bound at the active site nonheme iron. The entrance to the active site of CumDO is different from the entrance to the active site of NphDO, as the two loops forming the lid exhibit great deviation. On the basis of the complex structure of NphDO, a biphenyl substrate was modeled in the substrate-binding pocket of CumDO. The residues surrounding the modeled biphenyl molecule include residues that have already been shown to be important for its substrate specificity by a number of engineering studies of biphenyl dioxygenases.
Construction and characterization of a bifunctional fusion enzyme of<i>Bacillus</i>-sourced Î²-glucanase and xylanase expressed in<i>Escherichia coli</i> (2006)

A chimeric gene, Glu-Xyl, encoding Bacillus amyloliquefaciens glucanase (Glu, 24.4 kDa) and Bacillus subtilis xylanase (Xyl, 21.2 kDa), was constructed via end-to-end fusion and expressed successfully in Escherichia coli. The purified fusion protein (46.1 kDa) exhibited both glucanase and xylanase activities. Compared with parental enzymes, the Glu moiety was characterized by kinetic parameters of decreased K(m) (0.66-fold) and increased K(cat) (2.75-fold), whereas the Xyl moiety had an increased K(m) (1.37-fold) and decreased K(cat) (0.79-fold). These indicate a 3.15-fold net increase and a 31% decrease in catalytic efficiency (K(cat)/K(m)) of the Glu and Xyl moieties. Activities and stabilities of both moieties at 40-90 degrees C or pH 3.0-10.0 were compared with those of the parental enzymes. Despite some variations, common optima were 40 degrees C and pH 9.0 for the Glu moiety and parent, and 50-60 degrees C and pH 9.0 for the Xyl counterparts. Thus, the fusion enzyme Glu-Xyl was bifunctional, with greatly enhanced glucanase activity associated with a decrease in xylanase activity.
Asymmetric construction of optically active 3-hydroxyalkyne functionalities (1989)

An efficient general method for the construction of optically active 3-hydroxyalkyne functionalities has been developed using optically active α,β-epoxy alcohols readily accessible from non-chiral allyl alcohol precursors.
Transformation of carbonyl compounds into gem-difluoro compounds with dibromodifluoromethane/zinc reagent (1993)

Reaction of carbonyl compounds with dibromodifluoromethane/zinc gives the gem-difluoro compounds (12 examples). It seems to be that the reaction involves the generation of difluorocarbene by reaction of dibromodifluoromethane with zinc, followed by production of the difluorocarbonyl ylide. Such an ylide then breaks down the corresponding CF2 moiety.
The Use of Corticosteroids in the Treatment of Acute Asthma (1975)

A study of 23 patients admitted to hospital with severe acute asthma is reported in which plasma cortisol level on admission was significantly correlated with the degree of acidaemia and pulse rate. Patients who had not previously received treatment with corticosteroids responded satisfactorily to repeated daily injections of tetracosactrin depot, the rate of improvement being comparable to that observed in other patients treated with intravenous hydrocortisone hemisuccinate. A prompt and sustained rise in plasma cortisol was also seen following tetracosactrin. The total daily dose of hydrocortisone required to achieve plasma cortisol levels above 100 μg/100 ml was less when given by continuous intravenous infusion compared with intermittent injections, and a regime of 3 mg/kg body weight every six hours by infusion appeared satisfactory. Most patients reported subjective improvement by about four hours after starting treatment but objective evidence did not appear until about six hours from the start. Measurements of FEV, and FVC proved to be the most reliable indices of the beginning of improvement although pulse rate was the first index to show maximum improvement. Previous maintenance treatment with corticosteroids in patients with asthma did not appear materially to affect the plasma half-life of intravenous hydrocortisone (4 mgm/kg body weight) when compared with healthy subjects or other patients with asthma who had not previously been treated with corticosteroids.
Replication and Interaction of Virus DNA and Cellular DNA in Mouse Cells Infected by a Human Adenovirus (1979)

C57 black mouse cells infected with human adenovirus type 5 (Ad5) produced large amounts of early virus proteins, small amounts of late virus proteins and less than 0.2 infectious units (i.u.)/cell of infectious virus. Many cells died but the cultures recovered. Virus DNA and cellular DNA were synthesized. Some Ad5 DNA sedimented with cell DNA in alkaline sucrose, but virus DNA was rapidly lost from the culture after recovery and none of 28 unselected cloned survivors contained detectable amounts of virus DNA or antigens. Ad5 ts36 was temperature-sensitive for virus DNA replication in mouse cells, but ts125 was detective at 32.5 degrees C as well as at 39.9 degrees C. No difference was detected in the percentage of virus DNA that sedimented in alkali with cell DNA, in mouse cells infected by Ad5 ts+, ts36 or ts125 at 32.5 or 39.9 degrees C. All parts of the virus genome were equally represented in virus DNA that sedimented with cell DNA, in mouse cells infected by Ad5 ts+ or ts36 at either temperature.
Ultrasonic Degradation of Hydroxypropyl Cellulose Solutions in Water, Ethanol, and Tetrahydrofuran (1982)

Abstract Ultrasonic degradations of hydroxypropyl cellulose (HPC) have been carried out in water, ethanol, and tetrahydrofuran (THF) solutions. In the HPC-water system, cavitation intensity did not increase linearly with ultrasound intensity because of a lower threshold of ultrasonic intensity below which cavitation does not occur. At 27°C the rate of degradation in the three solvents followed the order water > ethanol > THF which is not in line with their characteristic impedance values. The rate of degradation for 20 kHz, 70 W ultrasound intensity was found to increase with a decrease in solution volumes, concentration of HPC, and temperature. Increased rate of degradation at lower temperatures supports the concept based on sonoluminescence experiments that it is the cavitation in a polymer solution that is responsible for ultrasonic degradations and the dissolved polymer molecules do not act as cavitation nuclei. Increased surface tension and density of the solvent are thought to be responsible for improved cavitation at low temperatures. Infrared spectroscopy and x-ray analysis of HPC subjected to ultrasonic treatments remained unchanged, suggesting that there were no chemical or structural (e.g., degree of order) changes on irradiation. The decreases in molecular weights on irradiation arise due to random chain scission whereas similar decreases in Huggins coefficients can be attributed to physical changes (decrease in molecular weight or branching) in the degraded HPC samples.
Cationic porphyrins: novel delivery vehicles for antisense oligodeoxynucleotides (1998)

Cationic porphyrins form stable complexes with oligodeoxynucleotides. To evaluate delivery, we used a 20mer phosphorothioate oligomer (Isis 3521) targeted to the 3'-untranslated region of the PKC-alpha mRNA, and complexed it with porphyrin. The expression of PKC-alpha protein and mRNA in T24 bladder carcinoma cells was reduced by approximately 80 +/- 10% at a concentration of oligomer of 3 microM, and 9 microM porphyrin. The expression of PKC-beta1, -delta and -straightepsilon isoforms was unaffected by this treatment, but elimination of PKC-zeta protein and mRNA were observed. However, treatment with the porphyrin complex of Isis 3522, an oligomer which is directed at the 5' coding region of the PKC-alpha mRNA, was equally effective as Isis 3521 with respect to PKC-alpha, but did not affect PKC-zeta protein or mRNA levels. Since Isis 3521 has an 11-base region of complementarity with the PKC-zeta mRNA, wheras Isis 3522 has only a 4-base region, the effect of Isis 3521 on PKC-zeta protein and mRNA expression may be due to irrelevant cleavage. Depending upon the desired application, this new strategy may offer several advantages over other methods of antisense oligodeoxynucleotide delivery including efficiency, stability, solubility, relatively low toxicity and serum compatibility. Porphyrins may thus be a potentially useful delivery vehicle for antisense therapeutics and/or target validation.
APPLICATION OF A GENETIC ALGORITHM TO QUANTITATIVE ANALYSIS OF OVERLAPPED FTIR SPECTRA<sup>*</sup> (2001)

Technique for the quantitative analysis in FTIR spectrometer by Genetic Algorithm is studied without the help of more widespread methods, such as PLS and Kalman filtering. Individuals are expressed with decimal digit instead of the traditional expression—binary digit. The effect of the probability of crossover and the establishment of objective function are discussed. The method of step size mutation is used. Compared with the Kalman filtering, the Genetic Algorithm has excellent nonlinear ability of solution. The results are exciting. Mean relative error of each result is really small, generally not bigger than 1%, if the conditions are properly controlled.
Hearables: feasibility of recording cardiac rhythms from head and in-ear locations (2017)

Mobile technologies for the recording of vital signs and neural signals are envisaged to underpin the operation of future health services. For practical purposes, unobtrusive devices are favoured, such as those embedded in a helmet or incorporated onto an earplug. However, these locations have so far been underexplored, as the comparably narrow neck impedes the propagation of vital signals from the torso to the head surface. To establish the principles behind electrocardiogram (ECG) recordings from head and ear locations, we first introduce a realistic three-dimensional biophysics model for the propagation of cardiac electric potentials to the head surface, which demonstrates the feasibility of head-ECG recordings. Next, the proposed biophysics propagation model is verified over comprehensive real-world experiments based on head- and in-ear-ECG measurements. It is shown both that the proposed model is an excellent match for the recordings, and that the quality of head- and ear-ECG is sufficient for a reliable identification of the timing and shape of the characteristic P-, Q-, R-, S- and T-waves within the cardiac cycle. This opens up a range of new possibilities in the identification and management of heart conditions, such as myocardial infarction and atrial fibrillation, based on 24/7 continuous in-ear measurements. The study therefore paves the way for the incorporation of the cardiac modality into future 'hearables', unobtrusive devices for health monitoring.
An <i>in vivo</i> binding assay for RNA-binding proteins based on repression of a reporter gene (2017)

ABSTRACT We employ a reporter assay and Selective 2′-hydroxyl acylation analysed by primer extension sequencing (SHAPE-seq) to study translational regulation by RNA-binding proteins, in bacteria. We designed 82 constructs, each with a single hairpin based on the binding sites of the RNA-binding coat proteins of phages MS2, PP7, GA, and Qβ, at various positions within the N-terminus of a reporter gene. In the absence of RNA-binding proteins, the translation level depends on hairpin location, and exhibits a three-nucleotide periodicity. For hairpin positions within the initiation region, we observe strong translational repression in the presence of its cognate RNA-binding protein. In vivo SHAPE-seq results for a representative construct indicate that the repression phenomenon correlates with a wide-swath of protection, including the hairpin and extending past the ribosome binding site. Consequently, our data suggest that the protection provided by the RBP-hairpin complex inhibits ribosomal initiation. Finally, utilizing the repression phenomenon for quantifying protein-RNA binding affinity in vivo , we both observe partially contrasting results to previous in vitro and in situ studies, and additionally, show that this method can be used in a high-throughput assay for a quantitative study of protein-RNA binding in vivo .
Postexposure Protective Efficacy of T-705 (Favipiravir) Against Sudan Virus Infection in Guinea Pigs (2018)

Filoviruses such as Ebola virus (EBOV), Marburg virus (MARV), and Sudan virus (SUDV) cause deadly viral hemorrhagic fever in humans, with high case-fatality rates; however, no licensed therapeutic agent or vaccine has been clinically approved to treat or prevent infection. T-705 (favipiravir) is a novel antiviral drug that has been approved for the treatment of influenza in Japan. T-705 exhibits broad-spectrum antiviral activity against different viruses, including MARV and EBOV, and here, we are the first to report the in vitro and in vivo antiviral activity of T-705 against SUDV. T-705 treatment reduced SUDV replication in Vero E6 cells. Subcutaneous administration of T-705, beginning 1-4 days after infection and continuing for 7 days, significantly protected SUDV-infected guinea pigs, with a survival rate of 83%-100%. Viral RNA replication and infectious virus production were also significantly reduced in the blood, spleen, liver, lungs, and kidney. Moreover, early administration of low-dose T-705 and late administration (at 5 days after infection) of higher-dose T-705 also showed partial protection. Overall, our study is the first to demonstrate the antiviral activity of T-705 against SUDV, suggesting that T-705 may be a potential drug candidate for use during outbreaks.
MIND China (China) (2020)

Abstract Background Epidemiologic studies have estimated that around one‐third of dementia patients worldwide might be attributable to seven modifiable risk factors. This implies that interventions to improve the control of modifiable risk factors may delay the onset of age‐related cognitive disorders such as dementia. We presented the study design and progress of the ongoing randomized controlled multimodal interventions to delay dementia and disability in rural China (MIND‐CHINA). Methods MIND‐CHINA is designed as a 2‐year cluster‐randomized, controlled, multimodal intervention study, which targets people who are aged 60‐79 years and living in the rural communities of Yanlou Town, western Shandong Province, China. Following the baseline examination, 52 villages in Yanlou Town are randomly (cluster‐randomization) divided into three groups: control group (regular primary health care service), vascular intervention group, and multimodal intervention group. The multimodal intervention program consists of four modules that are sensitive to Chinese lifestyle and sociocultural tradition; medical control of vascular risk factors; lifestyle and nutritional guidelines; group physical exercise and personalized leisure activities; and cognitive training. Results In March‐October 2018, we carried out baseline assessment for MIND‐CHINA that integrated our special examinations with the National Primary Health Care Services, during which 5764 persons were examined. We collected the following data through face‐to‐face interviews, clinical examination, testing, and laboratory tests: epidemiological, clinical, and biochemical data as well as physical function, cognitive function, mild cognitive impairment, and dementia. In May‐September 2019, the pilot study was completed to test the feasibility of the intervention programs and the implementation procedure in 7 villages (2 villages in control group, 3 villages in vascular intervention group, and 2 villages in multimodal intervention group). Recruitment of participants for interventions started in Oct/November 2019, and 2265 participants have been successfully recruited so far. Conclusion It is feasible to integrate a comprehensive health examination program with local primary health care services in rural‐dwelling elderly Chinese people. MIND‐CHINA will be likely to address whether multimodal interventions sensitive to Chinese lifestyle and socioculture help maintain cognitive and physical functioning among community‐dwelling elderly people in rural areas.
High power narrow-linewidth linearly-polarized 1610 nm Er:Yb all-fiber MOPA (2016)

We developed a narrow-linewidth linearly-polarized all-PM-fiber MOPA at the wavelength of 1610 nm. The MOPA consists of a DFB laser diode seed source and three amplifier stages with three different gain fibers. The first amplifier stage employed an Er doped fiber and the second and third amplifier stages employed Er:Yb co-doped fibers. The maximum output power was 8 W. Linewidth of 25 MHz and polarization extinction ratio of 28 dB was obtained. At the maximum output power, no ASE component around 1.55 μm or 1μm was observed.
New non-linear decision feedback equalizers based on the functional-link neural network (1994)

This paper presents a new approach for the Decision Feedback Equalizer using the Functional Link Network (DFFLE) for channel equalization in digital communication systems. Results show that the new non-linear DFFLE structures offer superior performance to the Multi-Layered perceptron (MLP) based DFE and the conventional DFE-LMS which are two widely used decision feedback equalizers. The performance has been evaluated in terms of the equalizers' speed of convergence and bit error rates.
Fast Erasure Coding for Data Storage (2020)

Various techniques have been proposed in the literature to improve erasure code computation efficiency, including optimizing bitmatrix design and computation schedule, common XOR (exclusive-OR) operation reduction, caching management techniques, and vectorization techniques. These techniques were largely proposed individually, and, in this work, we seek to use them jointly. To accomplish this task, these techniques need to be thoroughly evaluated individually and their relation better understood. Building on extensive testing, we develop methods to systematically optimize the computation chain together with the underlying bitmatrix. This led to a simple design approach of optimizing the bitmatrix by minimizing a weighted computation cost function, and also a straightforward coding procedure—follow a computation schedule produced from the optimized bitmatrix to apply XOR-level vectorization. This procedure provides better performances than most existing techniques (e.g., those used in ISA-L and Jerasure libraries), and sometimes can even compete against well-known but less general codes such as EVENODD, RDP, and STAR codes. One particularly important observation is that vectorizing the XOR operations is a better choice than directly vectorizing finite field operations, not only because of the flexibility in choosing finite field size and the better encoding throughput, but also its minimal migration efforts onto newer CPUs.
Duchenne smile, emotional experience, and autonomic reactivity: A test of the facial feedback hypothesis. (2002)

This study examined the modulatory function of Duchenne and non-Duchenne smiles on subjective and autonomic components of emotion. Participants were asked to hold a pencil in their mouth to either facilitate or inhibit smiles and were not instructed to contract specific muscles. Five conditions--namely lips pressing, low-level non-Duchenne smiling, high-level non-Duchenne smiling, Duchenne smiling, and control--were produced while participants watched videoclips that were evocative of positive or negative affect. Participants who displayed Duchenne smiles reported more positive experience when pleasant scenes and humorous cartoons were presented. Furthermore, they tended to exhibit different patterns of autonomic arousal when viewing positive scenes. These results support thefacial feedback hypothesis and suggest that facial feedback has more powerful effects when facial configurations represent valid analogs of basic emotional expressions.
A highly specific pathogen‐responsive promoter element from the immediate‐early activated <i>CMPG1</i> gene in <i>Petroselinum crispum</i> (2001)

Within the complex signalling network from pathogen-derived elicitor perception to defense-related gene activation, some immediate-early responding genes may have pivotal roles in downstream transcriptional regulation. We have identified the parsley (Petroselinum crispum) ELI17 gene as a particularly fast-responding gene possessing a new type of W box-containing, elicitor-responsive promoter element, E17. Highly selective E17-mediated reporter gene expression at pathogen infection sites in transgenic Arabidopsis thaliana plants demonstrated the potential of this promoter element for designing new strategies in resistance breeding as well as for further analysis of the early components of defense-related gene activation mechanisms. The protein encoded by the ELI17 gene exhibits various structural characteristics of established transcription factors and is designated as a CMPG protein according to the first four strictly conserved amino acids defining a newly emerging class of plant-specific proteins.
Filtering surface waves using 2D discrete wavelet transform (1999)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1999Filtering surface waves using 2D discrete wavelet transformAuthors: Minh‐Quy NguyenJéro⁁me MarsMinh‐Quy NguyenLaboratoire des Images et des Signaux, ENSIEG, FRANCE and Jéro⁁me MarsLaboratoire des Images et des Signaux, ENSIEG, FRANCEhttps://doi.org/10.1190/1.1820728 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1820728FiguresReferencesRelatedDetailsCited ByEstimating observation error covariance matrix of seismic data from a perspective of image denoising28 November 2016 | Computational Geosciences, Vol. 21, No. 2Joint Wavelet Frequency-Division and Radial Trace Transform for Surface Wave AttenuationRidgelet Domain Method of Ground-Roll Suppression31 May 2013 | Chinese Journal of Geophysics, Vol. 50, No. 4Physical Wavelet Frame DenoisingRongfeng Zhang and Tadeusz J. Ulrych27 February 2003 | GEOPHYSICS, Vol. 68, No. 1 SEG Technical Program Expanded Abstracts 1999ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1999 Pages: 2061 publication data© 1999 Copyright © 1999 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 04 Jan 2005 CITATION INFORMATION Minh‐Quy Nguyen and Jéro⁁me Mars, (1999), "Filtering surface waves using 2D discrete wavelet transform," SEG Technical Program Expanded Abstracts : 1228-1230. https://doi.org/10.1190/1.1820728 Plain-Language Summary PDF DownloadLoading ...
Study of the angular fluorescence distribution of bioaerosol particles: modelling and experiment (2012)

The results of numerical modelling of the angular fluorescence distribution of the individual particles of a bioaerosol are compared with experimental data obtained by a flowthrough-optical method when studying particles of the protein ovalbumin, as well as of Bacillus subtilis spores. It is shown that the experimental data agree on the whole with the results of the model computations.