gebhart/patrepeval huggingface dataset:
Toward an Analogue of the Transition State of PreD<sub>3</sub>−D<sub>3</sub> Isomerization: Stereoselective Synthesis of Linearly Fused 6-8-6 Carbocyclic Systems<sup>1</sup> (2002)

[reaction: see text] A stereoselective synthesis of 6-8-6 fused carbocyclic systems based on enol alkylation, ketone allylation, RCM, and Heck cyclization was developed to obtain compounds with a carbon framework that mimics the putative transition structure of the isomerization of previtamin D3 to vitamin D3.
Exploitation of a new flagellatropic phage of<i>Erwinia</i>for positive selection of bacterial mutants attenuated in plant virulence: towards phage therapy (2009)

To isolate and characterize novel bacteriophages for the phytopathogen, Erwinia carotovora ssp. atroseptica (Eca), and to isolate phage-resistant mutants attenuated in virulence.A novel flagellatropic phage was isolated on the potato-rotting bacterial species, Eca, and characterized using electron microscopy and restriction analysis. The phage, named PhiAT1, has an icosahedral head and a long, contractile tail; it belongs to the Myoviridae family. Partial sequencing revealed the presence of genes with homology to those of coliphages T4, T7 and Mu. Phage-resistant transposon mutants of Eca were isolated and studied in vitro for a number of virulence-related phenotypes; only motility was found to be affected. In vivo tuber rotting assays showed that these mutants were attenuated in virulence, presumably because the infection is unable to spread from the initial site of inoculation.The Eca flagellum can act as a receptor for PhiAT1 infection, and resistant mutants are enriched for motility and virulence defects.PhiAT1 is the first reported flagellatropic phage found to infect Eca and has enabled further study of the virulence of this economically important phytopathogen.
A biomimetic system for localization and separation of multiple sound sources (1995)

This paper presents a system for sound source localization and separation inspired by the auditory mechanisms of biological systems. The system consists of three omni-directional microphones, banks of band-pass filters, and a personal computer with a digital signal processor. Sound sources are localized using arrival temporal disparities. The zero-crossing method is used to quickly detect the arrival temporal disparities at signal onset to cope with echo. Arrival temporal disparity histograms remove ambiguity and improve accuracy. The Histogram Mapping Method is introduced to localize multiple sound sources. The system separates multiple sound sources by obtaining their direction information from the localization process. Localization and separation experiments were conducted in an anechoic chamber and an empty room. Two sound sources, human voices, were used. Directions of the sound sources were localized within a few degrees. Sound sources were separated by 25 dB attenuation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Power in Modal Radiation Fields: Limitations of the Complex Poynting Theorem and the Potential for Electrically Small Antennas (1997)

Analyses of power in radiation fields are nearly universally based upon the complex Poynting theorem, CPT, yet the scientific basis for its use is not well established. The time dependent Poynting theorem, TDPT, is seldom used yet its scientific basis is well established. We use Hansen's method to obtain a generalized modal expansion for all possible electromagnetic fields that can originate within a confined volume and travel infinitely outward, combine the modal expansions and both Poynting theorems to determine the power expressions, and contrast results. The TDPT shows that the characterization of power in a sinusoidal field requires three numbers. Therefore it cannot be fully described by only real and reactive values. We conclude that the CPT is intrinsically an insufficient basis for a full description of power in a radiation field. We compare TDPT and CPT solutions for several idealized antenna designs. Comparative analyses show that the TDPT provides solutions that correspond to reality in all cases and the CPT does not. Proofs that electrically small antennas cannot be efficient are based upon the CPT; we re-examine these proofs using the TDPT and find that certain mixed modal configurations may surpass the generally accepted small antenna rules.
Long-Lasting Changes in DNA Methylation Following Short-Term Hypoxic Exposure in Primary Hippocampal Neuronal Cultures (2013)

While the effects of hypoxia on gene expression have been investigated in the CNS to some extent, we currently do not know what role epigenetics plays in the transcription of many genes during such hypoxic stress. To start understanding the role of epigenetic changes during hypoxia, we investigated the long-term effect of hypoxia on gene expression and DNA methylation in hippocampal neuronal cells. Primary murine hippocampal neuronal cells were cultured for 7 days. Hypoxic stress of 1% O2, 5% CO2 for 24 hours was applied on Day 3, conditions we found to maximize cellular hypoxic stress response without inducing cell death. Cells were returned to normoxia for 4 days following the period of hypoxic stress. On Day 7, Methyl-Sensitive Cut Counting (MSCC) was used to identify a genome-wide methylation profile of the hippocampal cell lines to assess methylation changes resulting from hypoxia. RNA-Seq was also done on Day 7 to analyze changes in gene transcription. Phenotypic analysis showed that neuronal processes were significantly shorter after 1 day of hypoxia, but there was a catch-up growth of these processes after return to normoxia. Transcriptome profiling using RNA-Seq revealed 369 differentially expressed genes with 225 being upregulated, many of which form networks shown to affect CNS development and function. Importantly, the expression level of 59 genes could be correlated to the changes in DNA methylation in their promoter regions. CpG islands, in particular, had a strong tendency to remain hypomethylated long after hypoxic stress was removed. From this study, we conclude that short-term, sub-lethal hypoxia results in long-lasting changes to genome wide DNA methylation status and that some of these changes can be highly correlated with transcriptional modulation in a number of genes involved in functional pathways that have been previously implicated in neural growth and development.
Nuclear Translocation of Cardiac G Protein-Coupled Receptor Kinase 5 Downstream of Select Gq-Activating Hypertrophic Ligands Is a Calmodulin-Dependent Process (2013)

G protein-Coupled Receptors (GPCRs) kinases (GRKs) play a crucial role in regulating cardiac hypertrophy. Recent data from our lab has shown that, following ventricular pressure overload, GRK5, a primary cardiac GRK, facilitates maladaptive myocyte growth via novel nuclear localization. In the nucleus, GRK5's newly discovered kinase activity on histone deacetylase 5 induces hypertrophic gene transcription. The mechanisms governing the nuclear targeting of GRK5 are unknown. We report here that GRK5 nuclear accumulation is dependent on Ca(2+)/calmodulin (CaM) binding to a specific site within the amino terminus of GRK5 and this interaction occurs after selective activation of hypertrophic Gq-coupled receptors. Stimulation of myocytes with phenylephrine or angiotensinII causes GRK5 to leave the sarcolemmal membrane and accumulate in the nucleus, while the endothelin-1 does not cause nuclear GRK5 localization. A mutation within the amino-terminus of GRK5 negating CaM binding attenuates GRK5 movement from the sarcolemma to the nucleus and, importantly, overexpression of this mutant does not facilitate cardiac hypertrophy and related gene transcription in vitro and in vivo. Our data reveal that CaM binding to GRK5 is a physiologically relevant event that is absolutely required for nuclear GRK5 localization downstream of hypertrophic stimuli, thus facilitating GRK5-dependent regulation of maladaptive hypertrophy.
Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community (2012)

Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private 'Workbench' spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.
University Professor Josef Stingl, MD, PhD, JUBILEE (2010)

Dear Professor Stingl, These days, here in the middle of the Congress you have organised, you will celebrate your 70th birthday. Having the privilege to be your friend, I take the honour to comment on this event and present your portrait to this scientific community. You started your medical education at the Medical Faculty of the Charles University in Plzeň where you were soon recognised as one of the most talented students. All our young community admired your acute sense of duty, respect for a serious work, and warm idealism crystallising in a humble and deeply empathic attitude towards the human suffering. Your fun-loving and unselfish character made of you our beloved companion.
THE RELATIONS BETWEEN THE CHEMICAL STRUCTURES OF CARBONYL DERIVATIVES AND THEIR REACTIVITIES TOWARD SALTS OF SEMICARBAZIDE. (1919)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE RELATIONS BETWEEN THE CHEMICAL STRUCTURES OF CARBONYL DERIVATIVES AND THEIR REACTIVITIES TOWARD SALTS OF SEMICARBAZIDE.Arthur MichaelCite this: J. Am. Chem. Soc. 1919, 41, 3, 393–424Publication Date (Print):March 1, 1919Publication History Published online1 May 2002Published inissue 1 March 1919https://pubs.acs.org/doi/10.1021/ja01460a015https://doi.org/10.1021/ja01460a015research-articleACS PublicationsRequest reuse permissionsArticle Views107Altmetric-Citations15LEARN 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
Multimedia interface design (1992)

Examines the use of audio, video, graphics, and animation in computer systems, specifically in the design and construction of the computer-human interface. Multimedia extensions to current computer systems allow us to employ our senses in new ways when interacting with the computer.
Fundamentals of Environmental Chemistry (2008)

Introduction to Chemistry and Green Chemistry Matter and Materials Atoms and Elements Chemical Bonds, Molecules, and Compounds Chemical Reactions, Equations, and Stoichiometry Acids, Bases, and Salts Solutions and Solvents Chemistry and Electricity Organic Chemistry Biological Chemistry Water and the Hydrosphere Environmental Chemistry and Pollution of the Hydrosphere Sustaining the Hydrosphere: Keeping Water Green The Atmosphere: A Protective Blanket Around Us Atmospheric Chemistry Blue Skies for a Green Earth The Geosphere and Geochemistry Soil, Agriculture, and Food Production Sustaining the Geosphere The Biosphere and Biospeheric Resource Toxicological Chemistry The Anthrosphere and Technology Green Chemistry and Industrial Ecology The Anthrosphere and Wastes Green Chemistry and Industrial Ecology in Waste Management Sustainable Energy: The Key to Everything Fundamentals of Analytical Chemistry Environmental and Xenobiotics Analysis Literature Cited Supplementary References Questions and Problems Index
lnterleukin-8 Induces HLA-DR Expression on Cultured Human Keratinocytes via Specific Receptors (1995)

Recent studies suggest that interleukin (IL)-8 exerts a direct influence on several functions such as the chemotaxis or proliferation of human keratinocytes (HK). Since the effects of IL-8 in skin are mediated through specific receptors, we have studied the characteristics of the keratinocyte IL-8 receptor. We could identify specific binding sites for IL-8 in cultured HKs by flow cytometry. Pretreatment of the cells with tumor necrosis factor (TNF)-alpha or IL-1 alpha resulted in a significant increase in IL-8 binding. IL-8 selectively induced expression of HLA-DR antigen, but had no effect on the expression of other cell surface antigens (CD11a, CD18, CD36 and CD54).
Intracavernous Sodium Nitroprusside: Inappropriate Impotence Treatment (1993)

On the basis of reports describing nitric oxide as a form of endothelium-derived relaxing factor and on our own experience with intracavernous use of nitric oxide-releasing substances in animal models, we undertook an approved human study of intracavernous sodium nitroprusside as a treatment for impotence. We report our early experience in which severe hypotension and only mild tumescence in our first 3 patients caused us to discontinue the trial.
Structure of the Borosilicate Zeolite Catalyst SSZ-82 Solved Using 2D-XPD Charge Flipping (2011)

The structure of the calcined borosilicate zeolite catalyst SSZ-82 ([Si(61.3)B(4.7)O(132)], Pmmn, a = 24.2783(4), b = 11.4665(2), and c = 14.1127(3) Å) has been solved from X-ray powder diffraction (XPD) data using the recently developed 2D-XPD charge flipping approach. The electron density maps generated with the more conventional powder charge flipping (pCF) algorithm could not be interpreted easily, so this new method, which begins by phasing low-resolution, 2D subsets of the data, was applied. Crystallographic phases were derived for the three main projections ([100], [010], and [001]) by using just the corresponding subsets of reflections (0kl, h0l, and hk0, respectively) from the full set of 3039 extracted intensities. These phases were then imposed on the (otherwise random) starting phases in the application of the pCF algorithm to the full data set. The framework structure, with 11 Si/B atoms in the asymmetric unit and a novel 12-/10-ring 2D channel system, could be seen clearly in the resulting electron density map. This is the first application of the 2D-XPD method to data collected on a material of unknown structure. Rietveld refinement of the structure revealed the positions of the B atoms in the framework and indicated that some water had been readsorbed in the pores.
Stability-Indicating High-Performance Liquid Chromatographic Determination of Apixaban in Presence of Degradation Products (2014)

A simple, robust, and stability-indicating reversed-phase high-performance liquid chromatographic (HPLC) method for the analysis of apixaban and its related substances has been successfully developed. Chromatography was performed on a 250 mm × 4.6 mm, 5 μm C18 column with a gradient mixture of a phosphate buffer-methanol 60:40 (v/v) at 1.0 mL min(-1). Ultraviolet detection of apixaban was at 220 nm. The method was validated for linearity, precision, repeatability, sensitivity, and selectivity. Selectivity was validated by subjecting apixaban solution to photolytic, acidic, basic, oxidative, and thermal degradation. The peaks from the degradation products did not interfere with that from apixaban. The method was used to quantify the related substances in apixaban in the bulk drug and can be used for routine quality control purposes.
Data-Driven Modeling of Control Valve Stiction Using Revised Binary-Tree Structure (2014)

An accurate stiction model enables the detection, quantification, and compensation of this nonlinear phenomenon in a control valve. Compared with stiction models obtained from physical laws, data-driven models are more popular because of their simplicity in terms of the number of parameters required. In this work, the previously proposed two-layer binary tree data-driven stiction model is revised to overcome its limitations in handling instantaneous input commands on reverse motion. Then, the accuracy of the revised model is validated using the full set of ISA control valve standard tests. From these results, its advantages over other major existing data-driven models are indicated in terms of simplicity and accuracy.
Transcriptional profiling reveals a critical role for tyrosine phosphatase VE‐PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis (2009)

To define molecular events accompanying formation of the 3-dimensional (3D) vascular tube, we have characterized gene expression during vascular endothelial growth factor (VEGF)-induced tubular morphogenesis of endothelial cells. Microarray analyses were performed comparing gene induction in growth-arrested, tube-forming endothelial cells harvested from 3D collagen cultures to that in proliferating endothelial cells cultured on fibronectin. Differentially expressed genes were clustered and analyzed for specific endothelial expression through publicly available datasets. We validated the contribution of one of the identified genes, vascular endothelial protein tyrosine phosphatase (VE-PTP), to endothelial morphogenesis. Silencing of VE-PTP expression was accompanied by increased VEGF receptor-2 (VEGFR2) tyrosine phosphorylation and activation of downstream signaling pathways. The increased VEGFR2 activity promoted endothelial cell cycle progression, overcoming the G(0)/G(1) arrest associated with organization into tubular structures in the 3D cultures. Proximity ligation showed close association between VEGFR2 and VE-PTP in resting cells. Activation of VEGFR2 by VEGF led to rapid loss of association, which was resumed with time in parallel with decreased receptor activity. In conclusion, we have identified genes, which may serve critical functions in formation of the vascular tube. One of these, VE-PTP, regulates VEGFR2 activity thereby modulating the VEGF-response during angiogenesis.
Standard methods for molecular research in<i>Apis mellifera</i> (2013)

SummaryFrom studies of behaviour, chemical communication, genomics and developmental biology, among many others, honey bees have long been a key organism for fundamental breakthroughs in biology. With a genome sequence in hand, and much improved genetic tools, honey bees are now an even more appealing target for answering the major questions of evolutionary biology, population structure, and social organization. At the same time, agricultural incentives to understand how honey bees fall prey to disease, or evade and survive their many pests and pathogens, have pushed for a genetic understanding of individual and social immunity in this species. Below we describe and reference tools for using modern molecular-biology techniques to understand bee behaviour, health, and other aspects of their biology. We focus on DNA and RNA techniques, largely because techniques for assessing bee proteins are covered in detail in Hartfelder et al. (2013). We cover practical needs for bee sampling, transport, and storage, and then discuss a range of current techniques for genetic analysis. We then provide a roadmap for genomic resources and methods for studying bees, followed by specific statistical protocols for population genetics, quantitative genetics, and phylogenetics. Finally, we end with three important tools for predicting gene regulation and function in honey bees: Fluorescence in situ hybridization (FISH), RNA interference (RNAi), and the estimation of chromosomal methylation and its role in epigenetic gene regulation.
Boosting unsupervised relation extraction by using NER (2006)

Web extraction systems attempt to use the immense amount of unlabeled text in the Web in order to create large lists of entities and relations. Unlike traditional IE methods, the Web extraction systems do not label every mention of the target entity or relation, instead focusing on extracting as many different instances as possible while keeping the precision of the resulting list reasonably high. URES is a Web relation extraction system that learns powerful extraction patterns from unlabeled text, using short descriptions of the target relations and their attributes. The performance of URES is further enhanced by classifying its output instances using the properties of the extracted patterns. The features we use for classification and the trained classification model are independent from the target relation, which we demonstrate in a series of experiments. In this paper we show how the introduction of a simple rule based NER can boost the performance of URES on a variety of relations. We also compare the performance of URES to the performance of the state-of-the-art KnowItAll system, and to the performance of its pattern learning component, which uses a simpler and less powerful pattern language than URES.
A Novel eIF5A Complex Functions As a Regulator of p53 and p53-dependent Apoptosis (2004)

Although eukaryotic translation initiation factor 5A (eIF5A) was originally designated as an "initiation factor," recent data have shown it to be also involved in apoptosis. However, the actual function of eIF5A in apoptosis is still unknown. In this study, we performed yeast two-hybrid screens to identify eIF5A-interacting proteins to help us understand the mechanisms of eIF5A. Our results demonstrated that eIF5A and syntenin could engage in a specific interaction both in vitro and in vivo and functioned collaboratively to regulate p53 activity. Our findings, for the first time, revealed a new biological activity for eIF5A as the regulator of p53. Overexpression of eIF5A or its EFP domain resulted in up-regulation of p53, and silencing eIF5A by small interfering RNA reduced the p53 protein level. Further analysis by reverse transcription PCR showed eIF5A-activated p53 transcription. The effect of eIF5A on p53 transcriptional activity was further demonstrated by the increasing expressions of p21 and Bax, well known target genes of p53. In contrast, a point mutant of eIF5A, hypusination being abolished, was revealed to be functionally defective in p53 up-regulation. Overexpression of eIF5A led to a p53-dependent apoptosis or sensitized cells to induction of apoptosis by chemotherapeutic agents. However, when eIF5A interacted with its novel partner, syntenin, the eIF5A-induced increase in p53 protein level was significantly inhibited. Therefore, eIF5A seems to be a previously unrecognized regulator of p53 that may define a new pathway for p53-dependent apoptosis, and syntenin might regulate p53 by balancing the regulation of eIF5A signaling to p53 for apoptosis.