gebhart/patrepeval huggingface dataset:
Structure and expression of the rice class‐I type histone deacetylase genes OsHDAC1–3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture (2003)

Histone deacetylases (HDACs) modulate chromatin structure and transcription. HDACs have been studied as negative regulators in eukaryotic transcription. We isolated the rice OsHDAC1-3 genes for class I-type histone deacetylases, which are related to the RPD3 family. The OsHDAC1 gene encoded a protein of approximately 57 kDa that shared 73.5, 72.7, 79.9, and 57.1% amino acid sequence identity with the OsHDAC2, OsHDAC3, maize RPD3, and human HDAC1 proteins, respectively. Genomic structures and Southern blot analyses revealed that OsHDAC1-3 contained seven, six, and seven exons, respectively, and constituted a class I-type family in the rice genome. OsHDAC1 was expressed at similar levels in the leaves, roots, and callus cells, whereas OsHDAC2 and 3 were expressed in the roots and callus cells, but not in the leaves, exhibiting distinct tissue specificity. To explore the role of histone deacetylases in transgenic plants, we inserted the OsHDAC1 cDNA fragment into the expression vector Ai::OsHDAC1 under the control of the ABA-inducible promoter Ai, and transformed the construct into rice. Levels of mRNA, protein, and HDAC activity were significantly increased in Ai::OsHDAC1 callus cells. The amount of tetra-acetylated H4 in the transgenic cells was greatly reduced, and the reduction was abolished upon treatment with trichostatin A. These results demonstrate that OsHDAC1 overexpression in transgenic cells both yields enzymatically active HDAC complexes and induces changes in histone acetylation in vivo. The overexpression leads to a range of novel phenotypes, involving increased growth rate and altered plant architecture, suggesting that OsHDAC1 functions in the genome-wide programming of gene expression.
Structure–activity relationships of dinucleotides: Potent and selective agonists of P2Y receptors (2005)

Dinucleoside polyphosphates act as agonists on purinergic P2Y receptors to mediate a variety of cellular processes. Symmetrical, naturally occurring purine dinucleotides are found in most living cells and their actions are generally known. Unsymmetrical purine dinucleotides and all pyrimidine containing dinucleotides, however, are not as common and therefore their actions are not well understood. To carry out a thorough examination of the activities and specificities of these dinucleotides, a robust method of synthesis was developed to allow manipulation of either nucleoside of the dinucleotide as well as the phosphate chain lengths. Adenosine containing dinucleotides exhibit some level of activity on P2Y(1) while uridine containing dinucleotides have some level of agonist response on P2Y(2) and P2Y(6). The length of the linking phosphate chain determines a different specificity; diphosphates are most accurately mimicked by dinucleoside triphosphates and triphosphates most resemble dinucleoside tetraphosphates. The pharmacological activities and relative metabolic stabilities of these dinucleotides are reported with their potential therapeutic applications being discussed.
The Rationale, Feasibility, and Optimal Training of the Non-Physician Medical Nutrition Scientist (2015)

Dietary components have potential to arrest or modify chronic disease processes including obesity, cancer, and comorbidities. However, clinical research to translate mechanistic nutrition data into clinical interventions is needed. We have developed a one-year transitional postdoctoral curriculum to prepare nutrition scientists in the language and practice of medicine and in clinical research methodology before undertaking independent research. Candidates with an earned doctorate in nutrition science receive intensive, didactic training at the interface of nutrition and medicine, participate in supervised medical observerships, and join ongoing clinical research. To date, we have trained four postdoctoral fellows. Formative evaluation revealed several learning barriers to this training, including deficits in prior medical science knowledge and diverse perceptions of the role of the translational nutrition scientist. Several innovative techniques to address these barriers are discussed. We propose the fact that this “train the trainer” approach has potential to create a new translational nutrition researcher competent to identify clinical problems, collaborate with clinicians and researchers, and incorporate nutrition science across disciplines from “bench to bedside.” We also expect the translational nutrition scientist to serve as an expert resource to the medical team in use of nutrition as adjuvant therapy for the prevention and management of chronic disease.
Fusion Method Combining Ground-Level Observations with Chemical Transport Model Predictions Using an Ensemble Deep Learning Framework: Application in China to Estimate Spatiotemporally-Resolved PM2.5 Exposure Fields in 2014–2017 (2019)

Atmospheric chemical transport models (CTMs) have been widely used to simulate spatiotemporally resolved PM<sub>2.5</sub> concentrations. However, CTM results are usually prone to bias and errors. In this study, we improved the accuracy of PM<sub>2.5</sub> predictions by developing an ensemble deep learning framework to fuse model simulations with ground-level observations. The framework encompasses four machine-learning models, i.e., general linear model, fully connected neural network, random forest, and gradient boosting machine, and combines them by stacking approach. This framework is applied to PM<sub>2.5</sub> concentrations simulated by the Community Multiscale Air Quality (CMAQ) model for China from 2014 to 2017, which has complete spatial coverage over the entirety of China at a 12-km resolution, with no sampling biases. The fused PM<sub>2.5</sub> concentration fields were evaluated by comparing with an independent network of observations. The R<sup>2</sup> values increased from 0.39 to 0.64, and the RMSE values decreased from 33.7 μg/m<sup>3</sup> to 24.8 μg/m<sup>3</sup>. According to the fused data, the percentage of Chinese population residing under the level II National Ambient Air Quality Standards of 35 μg/m<sup>3</sup> for PM<sub>2.5</sub> has increased from 46.5% in 2014 to 61.7% in 2017. The method is readily adapted to utilize near-real-time observations for operational analyses and forecasting of pollutant concentrations and can be extended to provide source apportionment forecasts as well.
Accelerating frequency-domain diffuse optical tomographic image reconstruction using graphics processing units (2010)

Diffuse optical tomographic image reconstruction uses advanced numerical models that are computationally costly to be implemented in the real time. The graphics processing units (GPUs) offer desktop massive parallelization that can accelerate these computations. An open-source GPU-accelerated linear algebra library package is used to compute the most intensive matrix-matrix calculations and matrix decompositions that are used in solving the system of linear equations. These open-source functions were integrated into the existing frequency-domain diffuse optical image reconstruction algorithms to evaluate the acceleration capability of the GPUs (NVIDIA Tesla C 1060) with increasing reconstruction problem sizes. These studies indicate that single precision computations are sufficient for diffuse optical tomographic image reconstruction. The acceleration per iteration can be up to 40, using GPUs compared to traditional CPUs in case of three-dimensional reconstruction, where the reconstruction problem is more underdetermined, making the GPUs more attractive in the clinical settings. The current limitation of these GPUs in the available onboard memory (4 GB) that restricts the reconstruction of a large set of optical parameters, more than 13,377.
Corn Silage Preservation with Anhydrous Ammonia, Live Culture Microbial, or Organic Acid-Based Additives (1984)

Chopped whole corn plants were ensiled with anhydrous ammonia or one of two commercial additives in ten 2.4 x 6.1 m upright concrete silos at the Virginia Forage Research Station at Middleburg. The five treatments were: two silages harvested at full and late maturity with no additives, full maturity silage with Silabac 3 (a live lactobacillus culture) added at .05%, full maturity silage with anhydrous ammonia (Cold-Flo Process) added at approximately .28%, and a late maturity silage with Silosyn II 4 (an organic acidbased additive) at .1%. Additions were based on wet forage weights. Feeding comparisons were obtained from silages as prepared and fed without further supplementation. Digestion of dry matter (yearling steers) was reduced in the microbial-treated silage. Digestibility of fibrous components was reduced in the late harvested silages (more mature corn). Enrichment with ammonia increased apparent digestibility of nitrogen. Mean dry matter intakes were 2.50, 2.45, 2.35, 2.30, and 2.27% of body weight (230 to 270 kg crossbred heifers) for ammoniatreated, acid-treated, full maturity, late
Bulky Achiral Triarylphosphines Mimic BINAP in Ru(II)‐ Catalyzed Asymmetric Hydrogenation of Ketones (2005)

Abstract In the present work, we report on catalysis of the enantioselective hydrogenation of ketones with Ru(II) complexes composed of cheap achiral monodentate phosphine ligands in combination with an enantiopure 1,2‐diamine, affording a variety of optically active secondary alcohols with high efficiency and enantioselectivity. The steric impact of achiral monophosphine ligands in Ru complexes was found to be a critical factor for the high enantioselectivity of the reaction. This finding throws some light on a long‐standing challenge, the high cost of chiral bisphosphine ligands, associated with an industrial application of the asymmetric hydrogenation of ketones.
Motions of Water in Biological Systems (1976)

While much has been written about the hydration of biomacromolecules, most measurements cannot be reduced to simple molecular pictures (1). The most successful approach to (static) structural questions has been diffraction experiments (e.g. x-ray and neutron studies of protein single crystals,2,3). Kinetic information is increasingly available.The most informative kinetic experiments seem to be the various dispersive techniques - especially dielectric relaxation and NMR relaxation investigations (4,5). To summarize a number of experiments for a simple system such as a dilute aqueous solution of a globular protein (1,6): 1) most of the water molecules, at any instant, tumble and diffuse as freely as in a nonproteinaceous solution of equivalent viscosity 2) The motions of a small number of water molecules, at any instant are coupled to the relatively slow rotation of the protein molecules (5). 3) A small number of water molecules have intermediate rotational correlation times between the value of
Expansion of the tetragonal magnetic phase with pressure in the iron arsenide superconductorBa1−xKxFe2As2 (2016)

In the temperature-concentration phase diagram of most iron-based superconductors, antiferromagnetic order is gradually suppressed to zero at a critical point, and a dome of superconductivity forms around that point. The nature of the magnetic phase and its fluctuations is of fundamental importance for elucidating the pairing mechanism. In ${\mathrm{Ba}}_{1\ensuremath{-}x}{\mathrm{K}}_{x}{\mathrm{Fe}}_{2}{\mathrm{As}}_{2}$ and ${\text{Ba}}_{1\ensuremath{-}x}{\text{Na}}_{x}{\text{Fe}}_{2}{\text{As}}_{2}$, it has recently become clear that the usual stripelike magnetic phase, of orthorhombic symmetry, gives way to a second magnetic phase, of tetragonal symmetry, near the critical point, in the range from $x=0.24$ to $x=0.28$ for ${\mathrm{Ba}}_{1\ensuremath{-}x}{\mathrm{K}}_{x}{\mathrm{Fe}}_{2}{\mathrm{As}}_{2}$. In a prior study, an unidentified phase was discovered for $x&lt;0.24$ but under applied pressure, whose onset was detected as a sharp anomaly in the resistivity. Here we report measurements of the electrical resistivity of ${\mathrm{Ba}}_{1\ensuremath{-}x}{\mathrm{K}}_{x}{\mathrm{Fe}}_{2}{\mathrm{As}}_{2}$ under applied hydrostatic pressures up to 2.75 GPa, for $x=0.22$, 0.24, and 0.28. The critical pressure above which the unidentified phase appears is seen to decrease with increasing $x$ and vanish at $x=0.24$, thereby linking the pressure-induced phase to the tetragonal magnetic phase observed at ambient pressure. In the temperature-concentration phase diagram of ${\mathrm{Ba}}_{1\ensuremath{-}x}{\mathrm{K}}_{x}{\mathrm{Fe}}_{2}{\mathrm{As}}_{2}$, we find that pressure greatly expands the tetragonal magnetic phase, while the stripelike phase shrinks. This reveals that pressure may be a powerful tuning parameter with which to explore the interplay between magnetism and superconductivity in this material.
APS‐sulfotransferase activity is identical to higher plant APS‐kinase (EC 2.7.1.25) (1994)

A cDNA from Arabidopsis thaliana L. Heynh encoding the APS-kinase (EC 2.7.1.25) was modified by deletion of a plastidic transit peptide to enable its expression in Escherichia coli. The resultant protein (MW 25,761) is enzymatically active as APS-kinase and restores prototrophic growth in an APS-kinase mutant. All transformants harbouring the modified plant DNA also acquired APS-sulfotransferase activity. In the absence of ATP but provided with DTT, a tetrameric form of recombinant APS-kinase exhibits APS-sulfotransferase activity. Monospecific polyclonal antibodies raised against the APS-kinase as immunogen also reacted against APS-sulfotransferase. We propose that APS-sulfotransferase activity is a nonphysiological side reaction of APS-kinase.
Biodistribution of mesenchymal stem cell-derived extracellular vesicles in a model of acute kidney injury monitored by optical imaging (2014)

Mesenchymal stem cells (MSCs) contribute to the recovery of tissue injury, providing a paracrine support. Cell-derived extracellular vesicles (EVs), carrying membrane and cytoplasmatic constituents of the cell of origin, have been described as a fundamental mechanism of intercellular communication. We previously demonstrated that EVs derived from human MSCs accelerated recovery following acute kidney injury (AKI) in vivo. The aim of the present study was to investigate the biodistribution and the renal localization of EVs in AKI. For this purpose, two methods for EV labeling suitable for in vivo tracking with optical imaging (OI), were employed using near infrared (NIR) dye (DiD): i) labeled EVs were generated by MSCs pre-incubated with NIR dye and collected from cell supernatants; ii) purified EVs were directly labeled with NIR dye. EVs obtained with these two procedures were injected intravenously (i.v.) into mice with glycerol-induced AKI and into healthy mice to compare the efficacy of the two labeling methods for in vivo detection of EVs at the site of damage. We found that the labeled EVs accumulated specifically in the kidneys of the mice with AKI compared with the healthy controls. After 5 h, the EVs were detectable in whole body images and in dissected kidneys by OI with both types of labeling procedures. The directly labeled EVs showed a higher and brighter fluorescence compared with the labeled EVs produced by cells. The signal generated by the directly labeled EVs was maintained in time, but provided a higher background than that of the labeled EVs produced by cells. The comparison of the two methods indicated that the latter displayed a greater specificity for the injured kidney.
Cloning of CDP‐Diacylglycerol Synthase from a Human Neuronal Cell Line (1996)

A critical step in the supply of substrate for the phosphoinositide signal transduction pathway is the formation of the liponucleotide intermediate, CDP-diacylglycerol, catalyzed by CDP-diacylglycerol synthase. Further insight into the regulation of phosphoinositide biosynthesis was sought by cloning of the gene for the vertebrate enzyme. Sequence of the corresponding gene from Drosophila was used to prepare a probe for screening of a human neuronal cell cDNA library. A cDNA was isolated with a predicted open reading frame of 1,332 bases, encoding a protein of 51 kDa. The amino acid sequence showed 50% identity (75% similarity) to that of Drosophila eye CDP-diacylglycerol synthase and substantial similarity to the Saccharomyces cerevisiae and Escherichia coli homologues. Northern blot analysis, with human cDNA riboprobes, suggested that the corresponding mRNA was expressed in all human tissues examined. Expression of the human cDNA in COS cells resulted in a more than fourfold increase in CDP-diacylglycerol synthase activity. Knowledge of the sequence of vertebrate CDP-diacylglycerol synthase should facilitate further investigations into its regulation and the possible existence of distinct isoforms.
Silica aerogel Cherenkov counter for the KEK B-factory experiment (1999)

Low-refractive-index silica aerogel is a convenient radiator for threshold-type Cherenkov counters, which are used for particle identification in high-energy physics experiments. For the BELLE detector at the KEK B-Factory we have produced about 2 m3 of hydrophobic silica aerogels of n=1.01–1.03 using a new production method. The particle identification capability of the aerogel Cherenkov counters was tested and 3σ pion/proton separation has been achieved at 3.5 GeV/c. Radiation hardness of the aerogels was confirmed up to 9.8 Mrad. The Aerogel Cherenkov counter system (ACC) was successfully installed in the BELLE just before this conference.
Preparation of the 4-Iodo-1,2,3,4-tetramethylcyclobutenyl Cation. Ultraviolet and Nuclear Magnetic Resonance Spectra of Cyclobutenyl Cations in Methylene Chloride, Sulfuric Acid, and Liquid Sulfur Dioxide1 (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of the 4-Iodo-1,2,3,4-tetramethylcyclobutenyl Cation. Ultraviolet and Nuclear Magnetic Resonance Spectra of Cyclobutenyl Cations in Methylene Chloride, Sulfuric Acid, and Liquid Sulfur Dioxide1Elijah H. Gold and Thomas J. KatzCite this: J. Org. Chem. 1966, 31, 2, 372–374Publication Date (Print):February 1, 1966Publication History Published online1 May 2002Published inissue 1 February 1966https://pubs.acs.org/doi/10.1021/jo01340a006https://doi.org/10.1021/jo01340a006research-articleACS PublicationsRequest reuse permissionsArticle Views48Altmetric-Citations8LEARN 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
Blood BDNF Level Is Gender Specific in Severe Depression (2015)

Though the role of brain derived neurotrophic factor (BDNF) as a marker for major depressive disorder (MDD) and antidepressant efficacy has been widely studied, the role of BDNF in distinct groups of patients remains unclear. We evaluated the diagnostic value of BDNF as a marker of disease severity measured by HAM-D scores and antidepressants efficacy among MDD patients. Fifty-one patients who met DSM-IV criteria for MDD and were prescribed antidepressants and 38 controls participated in this study. BDNF in serum was measured at baseline, 1st, 2nd and 8th treatment weeks. Depression severity was evaluated using the Hamilton Rating Scale for Depression (HAM-D). BDNF polymorphism rs6265 (val66met) was genotyped. We found a positive correlation between blood BDNF levels and severity of depression only among untreated women with severe MDD (HAM-D>24). Serum BDNF levels were lower in untreated MDD patients compared to control group. Antidepressants increased serum BDNF levels and reduced between-group differences after two weeks of treatment. No correlations were observed between BDNF polymorphism, depression severity, duration of illness, age and BDNF serum levels. Further supporting the role of BDNF in the pathology and treatment of MDD, we suggest that it should not be used as a universal biomarker for diagnosis of MDD in the general population. However, it has diagnostic value for the assessment of disease progression and treatment efficacy in individual patients.
New Sphingolipids and a Sterol from a Lobophytum Species of the Indian Ocean (2005)

Chemical investigation of a soft coral species of the genus Lobophytum has resulted in the isolation of three new sphingolipids--(2S,3S,4R)-2-nonadecanoylamino-octadecane-1,3,4-triol (1), (2S,3R,4E,8E)-[(2'R)-2'-hydroxyheptadecanoylamino]-4,8-octadecadiene-1,3-diol (2), 1-O-(beta-D-glucopyranosyl)-(2S,3R,4E,8E)-2-[(2'R)-2'-hydroxynonadecanoylamino]-9-methyl-4,8-octadecadiene-1,3-diol (3) and a sterol--(24S)-ergost-5-en-3beta,7beta-diol (4) along with the known sphingolipid--(2S,3R,4E,8E)-2-hexadecanoylamino-4,8-octadecadien-1,3-diol (5) which showed cytotoxicity against human peripheral blood mononuclear cells (PBMC).