gebhart/patrepeval huggingface dataset:
Isolation and Expression in Escherichia coli of a cDNA Clone Encoding Porcine Pancreatic Elastase (1986)

We have cloned a DNA that is complementary to the messenger RNA that encodes porcine pancreatic elastase 1 from pancreas using rat pancreatic elastase 1 cDNA as a probe. This complementary DNA contains the entire protein coding region of 798 nucleotides which encodes an elastase of 266 amino acids, and 22 and 136 nucleotides of the 5' and 3'-untranslated sequences. When this deduced amino acid sequence was compared with known amino acid sequences, a carboxy-terminal 240 amino acids long peptide was found to be identical with a mature form of porcine pancreatic elastase 1, except for two amino acids. The porcine enzyme contains the same number of amino acid residues as the rat enzyme, and their amino acid sequences are 85% homologous. Taking the above findings together, we conclude that the cloned cDNA encodes a mature enzyme of 240 amino acids including a leader and activation peptide of 26 amino acids. We expressed the cloned porcine pancreatic elastase 1 cDNA in E. coli as a lac-fused protein. The resulting fused protein showed enzymatic activity and immunoreactivity toward anti-elastase serum.
How to detect eosinophil ETosis (EETosis) and extracellular traps (2020)

Eosinophils are short-lived and comprise only a small population of circulating leukocytes; however, they play surprisingly multifunctional roles in homeostasis and various diseases including allergy and infection. Recent research has shed light on active cytolytic eosinophil cell death that releases eosinophil extracellular traps (EETs) and total cellular contents, namely eosinophil extracellular trap cell death (EETosis). The pathological contribution of EETosis was made more cogent by recent findings that a classical pathological finding of eosinophilic inflammation, that of Charcot-Leyden crystals, is closely associated with EETosis. Currently no gold standard methods to identify EETosis exist, but "an active eosinophil lysis that releases cell-free granules and net-like chromatin structure" appears to be a common feature of EETosis. In this review, we describe several approaches that visualize EETs/EETosis in clinical samples and in vitro studies using isolated human eosinophils. EETs/EETosis can be observed using simple chemical or fluorescence staining, immunostaining, and electron microscopy, although it is noteworthy that visualization of EETs is greatly changed by sample preparation including the extracellular space of EETotic cells and shear flow. Considering the multiple aspects of biological significance, further study into EETs/EETosis is warranted to give a detailed understanding of the roles played in homeostasis and disease pathogenesis.
Total Synthesis of (−)-Horsfiline via Asymmetric Nitroolefination (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTTotal Synthesis of (−)-Horsfiline via Asymmetric NitroolefinationGingipalli Lakshmaiah, Takeo Kawabata, Muhong Shang, and Kaoru FujiView Author Information Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan Cite this: J. Org. Chem. 1999, 64, 5, 1699–1704Publication Date (Web):February 13, 1999Publication History Received4 August 1998Published online13 February 1999Published inissue 1 March 1999https://pubs.acs.org/doi/10.1021/jo981577qhttps://doi.org/10.1021/jo981577qbrief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views2256Altmetric-Citations65LEARN 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 SUBJECTS:Alcohols,Enantioselective synthesis,Organic compounds,Organic reactions,Redox reactions Get e-Alerts
Chemisorption of polysulfides through redox reactions with organic molecules for lithium–sulfur batteries (2018)

Lithium-sulfur battery possesses high energy density but suffers from severe capacity fading due to the dissolution of lithium polysulfides. Novel design and mechanisms to encapsulate lithium polysulfides are greatly desired by high-performance lithium-sulfur batteries towards practical applications. Herein, we report a strategy of utilizing anthraquinone, a natural abundant organic molecule, to suppress dissolution and diffusion of polysulfides species through redox reactions during cycling. The keto groups of anthraquinone play a critical role in forming strong Lewis acid-based chemical bonding. This mechanism leads to a long cycling stability of sulfur-based electrodes. With a high sulfur content of ~73%, a low capacity decay of 0.019% per cycle for 300 cycles and retention of 81.7% over 500 cycles at 0.5 C rate can be achieved. This finding and understanding paves an alternative avenue for the future design of sulfur-based cathodes toward the practical application of lithium-sulfur batteries.
Modeling and Simulation of a Modern PEM Fuel Cell System (2006)

Recent trends and advances in hydrogen/air Proton Exchange Membrane Fuel Cells (PEMFC) are incorporated into a dynamic control oriented model. This type of model is important for development of control systems for PEMFC powered transportation where unpredictable and widely varying changes in power demand can be expected. Self humidification and low pressure operation are the two major changes to past systems. As a result, a high pressure air compressor, air cooler, and inlet gas humidifiers are no longer required. Also, the likelihood of cathode flooding is reduced. The overall fuel cell model consists of four basic sub-models: anode, cathode, fuel cell body, and cooling. Additionally, the oxidant supply blower, cooling pump, and cooling fan are explicitly incorporated. Mass and energy conservation are applied to each using a lumped parameter control volume approach. Empirical modeling is minimized as much as possible, however it is necessary for model manageability in a control context. Interactions between each subsystem and balance of plant components are clearly defined. The overall model is capable of capturing the transient behavior of the flows, pressures, and temperatures as well as net output power. The influence of the charge double layer effect on transient performance is also explored. Numerical simulations of the system are presented which illustrate the usefulness of the model. Finally, future control work is described.
Bis[chlorobis(1,10-phenanthroline-N,N′)(thiourea-S)nickel(II)] chloride nitrate diethanol solvate (2000)

The crystal structure of the title compound, [NiCl(C12H8N2)2(CH4N2S)]2(NO3)­Cl·­2C2H6O, is formed by [Ni(phen)2(thio­urea)Cl]+ cations (phen = 1,10-phenanthroline), chloride and nitrate counter-ions, and ethanol solvate mol­ecules. The Ni atom is octahedrally coordinated to two bidentate phen ligands, a monodentate thio­urea and a chloride ion. Both the chloride and nitrate anions, which provide charge balance, are located at special positions on a twofold symmetry axis. Hydro­gen bonds play a key role in the packing and conformation of the cation and create a three-dimensional network.
Reactive surfactants in heterophase polymerization. Part XXII—incorporation of macromonomers used as stabilizers in styrene dispersion polymerization (1997)

The effect of several parameters on the incorporation yield of poly(ethylene oxide) macromonomers at the surface of the particles, for the dispersion polymerization of styrene in ethanol–water mixtures, has been studied. The reactivity of the macromonomer is a key parameter in the mechanism of stabilization of the micrometer-size polymer particles, because it partly determines the amount and the composition of the copolymer stabilizer available at any moment during the process. The polarity of the reaction medium also strongly influences the polymerization process: higher incorporation yield and grafting density were obtained in medium of lower polarity. Besides, a chain length of around 50 ethylene oxide units for the macromonomer were needed to produce stable monodisperse particles with a significant incorporation yield. Thus, an incorporation yield as high as 53% and a grafting density corresponding to a surface area of 232 Å2/molecule have been obtained in a one-step process by using a methacrylate macromonomer. In an optimized two-step process resulting in monodisperse polymer particles, 80% incorporation yield with a very high grafting density (175 Å2/molecule) were reached. The particles with high grafting density (surface area lower than 600 Å2/molecule) could be transferred in water and exposed to a freeze–thaw cycle without massive flocculation, illustrating the efficiency of the steric stabilization. © 1997 John Wiley & Sons, Ltd.
Neuronal organization of olfactory bulb circuits (2014)

Olfactory sensory neurons extend their axons solely to the olfactory bulb, which is dedicated to odor information processing. The olfactory bulb is divided into multiple layers, with different types of neurons found in each of the layers. Therefore, neurons in the olfactory bulb have conventionally been categorized based on the layers in which their cell bodies are found; namely, juxtaglomerular cells in the glomerular layer, tufted cells in the external plexiform layer, mitral cells in the mitral cell layer, and granule cells in the granule cell layer. More recently, numerous studies have revealed the heterogeneous nature of each of these cell types, allowing them to be further divided into subclasses based on differences in morphological, molecular, and electrophysiological properties. In addition, technical developments and advances have resulted in an increasing number of studies regarding cell types other than the conventionally categorized ones described above, including short-axon cells and adult-generated interneurons. Thus, the expanding diversity of cells in the olfactory bulb is now being acknowledged. However, our current understanding of olfactory bulb neuronal circuits is mostly based on the conventional and simplest classification of cell types. Few studies have taken neuronal diversity into account for understanding the function of the neuronal circuits in this region of the brain. This oversight may contribute to the roadblocks in developing more precise and accurate models of olfactory neuronal networks. The purpose of this review is therefore to discuss the expanse of existing work on neuronal diversity in the olfactory bulb up to this point, so as to provide an overall picture of the olfactory bulb circuit.
Endogenous microRNAs induced by heat‐shock reduce myocardial infarction following ischemia–reperfusion in mice (2008)

We investigated the role of microRNAs (miRNA) in protection against ischemia/reperfusion (I/R) injury in heart. Mice subjected to cytoprotective heat-shock (HS) showed a significant increase of miRNA-1, miRNA-21 and miRNA-24 in the heart. miRNAs isolated from HS mice and injected into non-HS mice significantly reduced infarct size after I/R injury, which was associated with the inhibition of pro-apoptotic genes and increase in anti-apoptotic genes. Chemically synthesized miRNA-21 also reduced infarct size, whereas a miRNA-21 inhibitor abolished this effect. Overall, these studies for the first time provide evidence for the potential role of endogenously synthesized miRNA's in cardioprotection following I/R injury.
Specific and sensitive detection of nucleic acids and RNases using gold nanoparticle–RNA–fluorescent dye conjugates (2007)

Gold nanoparticles were modified with RNA and utilized to detect specific DNA sequences and various RNA nucleases.
Case Histories: Real-Time Downhole Data Increase Drilling Efficiency (2010)

Abstract With current trends in exploration, drilling operations are becoming more complicated and cost-intensive. Although the focus is often on reducing non-productive time (NPT) and invisible lost time (ILT) in these high-tech wells, little time is spent on benchmarking for the time taken during common drilling and non-drilling procedures.Today’s downhole MWD systems are able to transmit information in real time, such as weight on bit (WOB), torque on bit (TOB), downhole azimuthal bending moments, downhole RPM and drilling dynamics diagnostics. However, decisions in wells ranging from simple to complex are still made using traditional surface-acquired drilling data. This paper includes cases where the use of downhole drilling data increases drilling efficiency. Six case histories describe four different applications where a downhole optimization sub’s (DHOS) real-time data was used to improve drilling operations.
Molecular dynamics simulation of Lewis blood groups and related oligosaccharides (1991)

Molecular dynamics simulations without explicit inclusion of solvent molecules have been performed to study the motions of Lewisa and Lewisb blood group oligosaccharides, and two blood group A tetrasaccharides having type I and type II core chains. The blood group H trisaccharide has also been studied and compared with the blood group A type II core chain. The potential energy surface developed by Rasmussen and co-workers was used with the molecular mechanics code CHARMM. The lowest energy minima of the component disaccharide fragments were obtained from conformational energy mapping. The lowest energy minima of these disaccharide fragments were used to build the tri- and tetrasaccharides that were further minimized before the actual heating/equilibration and dynamics simulations. The trajectories of the disaccharide fragments, e.g., Fuc alpha- (1----4)GlcNAc, Gal beta-(1----4)GlcNAc, etc., show transitions among various minima. However, the oligosaccharides were found to be dynamically stable and no transitions to other minimum energy conformations were observed in the time series of the glycosidic dihedral angles even during trajectories as long as 300 ps. The stable conformations of the glycosidic linkages in the oligosaccharides are not necessarily the same as the minimum energy conformation of the corresponding isolated disaccharides. The average fluctuations of the glycosidic angles in the oligosaccharides were well within the range of +/- 15 degrees. The results of these trajectory calculations were consistent with the relatively rigid single-conformation models derived for these oligosaccharides from 1H-nmr data.
ETS (Efficient, Transparent, and Secured) Self-healing Service for Pervasive Computing Applications (2007)

To ensure smooth functioning of numerous handheld devices anywhere anytime, the importance of self-healing mechanism cannot be overlooked. Incorporation of efficient fault detection and recovery in device itself is the quest for long but there is no existing self-healing scheme for devices running in pervasive computing environments that can be claimed as the ultimate solution. Moreover, the highest degree of transparency, security and privacy attainability should also be maintained. ETS Self-healing service, an integral part of our developing middleware named MARKS (Middleware Adaptability for Resource discovery, Knowledge usability, and Self-healing), holds promise for offering all of those functionalities.
Are Nano-Composite Coatings the Key for Photovoltaic Panel Self-Maintenance: An Experimental Evaluation (2018)

This article shows the influence of an anti-fouling nano-coating on the electrical energy produced by a string of photovoltaic modules. The coating effect was evaluated comparing the energy produced by two strings of the same PV power plant: one of them was cleaned and the other was cleaned and treated with the coating before the monitoring campaign. The PV plant is located in Modena, north of Italy. A first monitoring campaign of nine days after the treatment shows that the treatment increases the energy production on the PV arrays by about 1.82%. Results indicate that the increase is higher during sunny days with respect to cloudy days. A second monitoring campaign of the same length, but five months later, shows that the energy gain decreases from 1.82% to 0.69% due to the aging of the coating, which is guaranteed for one year by the manufacturer. A technical-economical analysis demonstrates that at the moment the yearly economic gain is 0.43 € per square meter of panel and the cost of the treatment is about 1 € per square meter. However, large scale diffusion can reduce the production cost and thus increase the affordability of the coating.
VISUALIZATION TECHNIQUES FOR THE STUDY OF ULTRASONIC WAVE PROPAGATION IN THE RAILWAY INDUSTRY (1984)

This article describes two visualization techniques that make ultrasonic tests of railway equipment more relevant to engineering needs. One relies on Schlieren optics; a special mirror makes possible closed-circuit television recordings of tests of liquids. The other technique makes use of photoelasticity for studying wave propagation in glass models. Display facilities have been enhanced, and a quantified assessment of the wave stresses can be made. Sample tests of railroad equipment are described.
P2‐055: Cellular prion protein and class‐specific Aβ oligomers mediate plaque‐associated cytopathology in a mouse model of Alzheimer's disease (2015)

Increasing evidence indicates that plaque-associated amyloid-β (Aβ) oligomers might be responsible for neuronal architecture changes occurring in the vicinity of amyloid deposits in Alzheimer's disease. However, the underlying mechanism regulating these changes remains unclear. Cellular prion protein (PrPC) has recently been proposed to act as a receptor for Aβ oligomers that mediates amyloid toxicity. We here investigate whether PrPCmediates oligomeric Aβ-induced cytopathology associated with amyloid plaques. To understand whether PrPC mediates plaque-associated neuronal architectural abnormalities, we stained dense-core Aβ plaques using thioflavin S and axonal structure using SMI-312, a monoclonal anti-neurofilament antibody, in brain sections of 12-month-old hAPP-J20 and hAPP-J20/PrP-null mice. Neuronal morphology analyses were performed to assess axonal curvature ratios and the numbers of dystrophic neurites per plaque. Using conformation-sensitive antibodies OC and A11, which recognize distinct structural epitopes of amyloid proteins, we performed co-immunoprecipitation assays on water-soluble brain extracts of hAPP-J20 mice to identify what class of brain-derived Aβ oligomers might bind to PrPC. Finally, unbiased stereology and non-denaturing immunoblotting were used to evaluate the consequence of Prnpgene ablation on amyloid burden and oligomeric Aβ levels in hAPP-J20 and hAPP-J20/PrP-null mice. Genetic ablation of PrPC ameliorated neuronal architecture abnormalities in the vicinity of plaques in hAPP-J20 mice. PrPC immunoprecipitated with Aβ oligomers immunoreactive to OC antibodies, known to recognize the in-register, parallel β-sheet structure of amyloid fibrils. In contrast, PrPC was not pulled down with A11-immunoreactive oligomers. Stereological analyses revealed that Prnp ablation reduced dense-core and 6E10-immunoreactive plaque loads by 28% and 37%, respectively. Genetic ablation of PrPCalso affected levels of Aβ oligomers but did not alter levels of amyloid precursor protein (APP) or APP processing. We found that PrPC interacts with OC-immunoreactive Aβ oligomers, but not with A11-positive oligomers, and mediates plaque-associated cytopathology. Overall, these results suggest that PrPC-mediated neurotoxicity is specific for a given class of Aβ oligomers.
BioASQ-QA: A manually curated corpus for Biomedical Question Answering (2022)

ABSTRACT The BioASQ question answering (QA) benchmark dataset contains questions in English, along with golden standard (reference) answers and related material. The dataset has been designed to reflect real information needs of biomedical experts and is therefore more realistic and challenging than most existing datasets. Furthermore, unlike most previous QA benchmarks that contain only exact answers, the BioASQ-QA dataset also includes ideal answers (in effect summaries), which are particularly useful for research on multi-document summarization. The dataset combines structured and unstructured data. The material linked with each question comprise documents and snippets, which are useful for Information Retrieval and Passage Retrieval experiments, as well as concepts that are useful in concept-to-text Natural Language Generation. Researchers working on paraphrasing and textual entailment can also measure the degree to which their methods improve the performance of biomedical QA systems. Last but not least, the dataset is continuously extended, as the BioASQ challenge is running and new data are generated.
Editorial: Structural bioinformatics and biophysical approaches for understanding the plant responses to biotic and abiotic stresses (2022)

&lt;p&gt;Plants are exposed to a variety of environmental conditions that negatively impact&lt;/p&gt;\n&lt;p&gt;their physiology and yields (Rivero et al., 2022; Sharma et al., 2022; Zandalinas and&lt;/p&gt;\n&lt;p&gt;Mittler, 2022). Several studies identified mechanisms involving genes, proteins, and&lt;/p&gt;\n&lt;p&gt;metabolites that underlie plant responses to stress conditions (Chen et al., 2022; Hassan&lt;/p&gt;\n&lt;p&gt;et al., 2022; Huang et al., 2022; Mittler et al., 2022; Yang et al., 2022; Zhan et al.,&lt;/p&gt;\n&lt;p&gt;2022). Some of these molecules were used to improve plant responses to abiotic&lt;/p&gt;\n&lt;p&gt;and biotic stresses (Li et al., 2022; Mahto et al., 2022; Wang and Komatsu, 2022;&lt;/p&gt;\n&lt;p&gt;Zhao et al., 2022). However, the underlying structural and functional relationships of&lt;/p&gt;\n&lt;p&gt;these molecular mechanisms require more research. Computational and biophysical&lt;/p&gt;\n&lt;p&gt;approaches are viable options for analyses of target molecules to understand their&lt;/p&gt;\n&lt;p&gt;interactions and dynamics that initiate biochemical and physiological responses of&lt;/p&gt;\n&lt;p&gt;plants (Wan et al., 2015; Konda et al., 2018; Moffett and Shukla, 2018; Rayevsky et al.,&lt;/p&gt;\n&lt;p&gt;2019; Jha et al., 2022). These responses in turn control plant tolerance and resistance&lt;/p&gt;\n&lt;p&gt;to sub-optimal environmental conditions. Therefore, this Research Topic is aligned&lt;/p&gt;\n&lt;p&gt;with the current research trends and provides an update on the advances in structural&lt;/p&gt;\n&lt;p&gt;bioinformatics and biophysical approaches to understanding plant responses to biotic&lt;/p&gt;\n&lt;p&gt;and abiotic stresses at the molecular level. Here, we highlight some of the topics from the&lt;/p&gt;\n&lt;p&gt;following contributions.&lt;/p&gt;
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle (2015)

This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.