gebhart/patrepeval huggingface dataset:
Ultrahigh-resolution full-field optical coherence tomography (2004)

We have developed a white-light interference microscope for ultrahigh-resolution full-field optical coherence tomography of biological media. The experimental setup is based on a Linnik-type interferometer illuminated by a tungsten halogen lamp. En face tomographic images are calculated by a combination of interferometric images recorded by a high-speed CCD camera. Spatial resolution of 1.8 microm x 0.9 microm (transverse x axial) is achieved owing to the extremely short coherence length of the source, the compensation of dispersion mismatch in the interferometer arms, and the use of relatively high-numerical-aperture microscope objectives. A shot-noise-limited detection sensitivity of 90 dB is obtained in an acquisition time per image of 4 s. Subcellular-level images of plant, animal, and human tissues are presented.
Researches on Pyrimidines. CXLIX. The Synthesis of Aryl Substituted Dihydrouracils and their Conversion to Uracil Derivatives1 (1936)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTResearches on Pyrimidines. CXLIX. The Synthesis of Aryl Substituted Dihydrouracils and their Conversion to Uracil Derivatives1Treat B. Johnson and John E. LivakCite this: J. Am. Chem. Soc. 1936, 58, 2, 299–303Publication Date (Print):February 1, 1936Publication History Published online1 May 2002Published inissue 1 February 1936https://pubs.acs.org/doi/10.1021/ja01293a033https://doi.org/10.1021/ja01293a033research-articleACS PublicationsRequest reuse permissionsArticle Views383Altmetric-Citations51LEARN 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
Update on Dental Nanocomposites (2010)

Dental resin-composites are comprised of a photo-polymerizable organic resin matrix and mixed with silane-treated reinforcing inorganic fillers. In the development of the composites, the three main components can be modified: the inorganic fillers, the organic resin matrix, and the silane coupling agents. The aim of this article is to review recent studies of the development of dental nanocomposites and their clinical applications. In nanocomposites, nanofillers are added and distributed in a dispersed form or as clusters. For increasing the mineral content of the tooth, calcium and phosphate ion-releasing composites and fluoride-releasing nanocomposites were developed by the addition of DCPA-whiskers or TTCP-whiskers or by the use of calcium fluoride or kaolinite. For enhancing mechanical properties, nanocomposites reinforced with nanofibers or nanoparticles were investigated. For reducing polymerization shrinkage, investigators modified the resin matrix by using methacrylate and epoxy functionalized nanocomposites based on silsesquioxane cores or epoxy-resin-based nanocomposites. The effects of silanization were also studied. Clinical consideration of light-curing modes and mechanical properties of nanocomposites, especially strength durability after immersion, was also addressed.
Hydrolysis of Acyloxy Nitroso Compounds Yields Nitroxyl (HNO) (2006)

Nitroxyl (HNO/NO(-)), the reduced form of nitric oxide, has gained attention based on its separate chemistry and biology from nitric oxide. The inherent reactivity of HNO requires new and mechanistically unique donors for the detailed study of HNO chemistry and biology. Oxidation of cyclohexanone oxime with lead tetraacetate yields 1-nitrosocyclohexyl acetate, whereas oxidation of oximes in the presence of excess carboxylic acid gives various acyloxy nitroso compounds. These bright blue compounds exist as monomers as indicated by their infrared, proton, and carbon NMR spectra, and X-ray crystallographic analysis reveals the nitroso groups possess a "nitroxyl-like" bent configuration. Hydrolysis of these compounds produces nitrous oxide, the dimerization and dehydration product of HNO, and provides evidence for the intermediacy of HNO. Both thiols and oxidative metal complexes inhibit nitrous oxide formation. Hydrolysis of these compounds in the presence of ferric heme complexes forms ferrous nitrosyl complexes providing further evidence for the intermediacy of HNO. Kinetic analysis shows that the rate of hydrolysis depends on pH and the structure of the acyl group of the acyloxy nitroso compound. These compounds relax pre-constricted rat aortic rings similar to known HNO donors. Together, these results identify acyloxy nitroso compounds as a new class of HNO donors.
A New Type of Asymmetric Tridentate Pyrrolyl-Linked Pincer Ligand and Its Aluminum Dihydride Complexes (2009)

The new pyrrolyl-linked pincer-type ligand, [C(4)H(2)NH(2-CH(2)NH(t)Bu)(5-CH(2)NMe(2))] (1), that has been employed conveniently in high yield by treatment of (2-t-butylaminomethyl)pyrrole with 1 equiv of formaldehyde and dimethylamine hydrochloride each in diethylether and its corresponding aluminum derivative, [C(4)H(2)N(2-CH(2)NH(t)Bu)(5-CH(2)NMe(2))]AlH(2) (2), that has been generated from Me(3)N.AlH(3) using diethylether as a solvent are described. Furthermore, reactions of 2 with 2 equiv of either 1,3-diphenylpropane-1,3-dione in diethylether or phenyl thioisocyanate in dichloromethane interestingly formed [C(4)H(2)N(2-CH(2)NH(t)Bu)(5-CH(2)NMe(2))]Al(PhCOCHCOPh)(2) (3) and [C(4)H(2)N(2-CH(2)NH(t)Bu)(5-CH(2)NMe(2))]Al(SCHNPh)(2) (4), respectively, following deprotonation or hydroalumination reaction kinetics under a dry nitrogen environment. All of the compounds have been subjected to the X-ray diffraction technique in the solid state as well as characterized by NMR spectra.
On the detection of dispersion in the head-related transfer function (2003)

Because of dispersion in head-related transfer functions (HRTFs), the interaural time difference (ITD) varies with frequency. This physical effect ought to have consequences for the size or shape of the auditory image of broadband noise because different frequency regions of the noise have different ITDs. However, virtual reality experiments suggest that human listeners are insensitive to head-related dispersion. The experiments of this article test that suggestion by experiments that isolate dispersion from amplitude effects in the HRTF and attempt to optimize the opportunity for detecting it. Nevertheless, the experiments find that the only effect of dispersion is to shift the lateralization of the auditory image. This negative result is explained in terms of the cross-correlation function for head-dispersed noise. Although the broad-band cross-correlation function differs considerably from 1.0, the cross-correlation functions within bands characteristic of auditory filters do not. A detailed study of the lateralization shifts show that the experimental shifts can be successfully calculated as an average of stimulus ITDs as weighted by Raatgever's frequency-weighting function (Thesis, Delft, The Netherlands, 1980).
Adhesion Molecules in the Lung: An Overview (1993)

Several distinct cell adhesion molecule families have recently been identified and found to be important in the inflammatory response and for epithelial and endothelial homeostasis. The integrin family of adhesion molecules functions in both cell-matrix and cell-cell interactions, whereas the cadherins serve as important cell-cell receptors for maintenance of epithelial integrity. The leukocyte integrins, selectins, members of the immunoglobulin supergene family, and specific carbohydrates mediate adhesive interactions between leukocytes and endothelial cells. The mechanisms of leukocyte-epithelial adhesion are less well understood, but integrins and members of the immunoglobulin supergene family are also involved. The role of these molecules in pulmonary structure and inflammation is currently being actively explored. Further knowledge of these interactions, and the interplay of adhesion molecules, cytokines, and chemoattractants is likely to lead to novel therapeutic modalities in inflammatory diseases of the airway and lung parenchyma. In this overview, the families of adhesion molecules will be summarized, and their relevance for pulmonary structure and inflammation will be discussed.
Development of CD8α-Positive Dendritic Cells from a Common Myeloid Progenitor (2000)

Dendritic cells (DCs) are critical in both initiating adaptive immune responses and maintaining tolerance to self antigens. These apparently contradictory roles have been suggested to depend on different subsets of DCs that arise from either myeloid or lymphoid hematopoietic origins, respectively. Although DC expression of CD8alpha is attributed to a lymphoid origin, here we show that both CD8alpha+ and CD8alpha- DCs can arise from clonogenic common myeloid progenitors in both thymus and spleen. Thus, expression of CD8alpha is not indicative of a lymphoid origin, and phenotypic and functional differences among DC subsets are likely to reflect maturation status rather than ontogeny.
The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass (2009)

Lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. However, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic pH. The extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challenges. Rapid, efficient cellulase screening techniques, using cellulase assays and metagenomic libraries, are a must. Rare cellulases with activities on soluble and crystalline cellulose have been isolated from strains of Paenibacillus and Bacillus and shown to have high thermostability and/or activity over a wide pH spectrum. While novel cellulases from strains like Cellulomonas flavigena and Terendinibacter turnerae, produce multifunctional cellulases with broader substrate utilization. These enzymes offer a framework for enhancement of cellulases including: specific activity, thermalstability, or end-product inhibition. In addition, anaerobic bacteria like the clostridia offer potential due to species capable of producing compound multienzyme complexes called cellulosomes. Cellulosomes provide synergy and close proximity of enzymes to substrate, increasing activity towards crystalline cellulose. This has lead to the construction of designer cellulosomes enhanced for specific substrate activity. Furthermore, cellulosome-producing Clostridium thermocellum and its ability to ferment sugars to ethanol; its amenability to co-culture and, recent advances in genetic engineering, offer a promising future in biofuels. The exploitation of bacteria in the search for improved enzymes or strategies provides a means to upgrade feasibility for lignocellulosic biomass conversion, ultimately providing means to a 'greener' technology.
Dynamic visual attention: searching for coding length increments (2008)

A visual attention system should respond placidly when common stimuli are presented, while at the same time keep alert to anomalous visual inputs. In this paper,&#13;\na dynamic visual attention model based on the rarity of features is proposed. We introduce the Incremental Coding Length (ICL) to measure the perspective entropy&#13;\ngain of each feature. The objective of our model is to maximize the entropy of the sampled visual features. In order to optimize energy consumption, the limit amount of energy of the system is re-distributed amongst features according to their Incremental Coding Length. By selecting features with large coding length increments, the computational system can achieve attention selectivity in&#13;\nboth static and dynamic scenes. We demonstrate that the proposed model achieves superior accuracy in comparison to mainstream approaches in static saliency map&#13;\ngeneration. Moreover, we also show that our model captures several less-reported dynamic visual search behaviors, such as attentional swing and inhibition of return.
Isolation and Characterization of Residual Lignins from Hardwood Pulps: Method Improvements (2005)

A modified procedure for isolation of enzymatic residual lignin from Eucalyptus globules kraft pulps consisting in extraction of the residual lignins with aqueous dioxane after enzymatic hydrolysis (ERL) followed by ball milling of the insoluble residues and another dioxane extraction provides additional 20-35% amounts of lignin (MRL). The modified procedure produces residual lignins with the total yields of 70 - 95 % and with rather low protein contaminations. Significant efforts have been made to modify the analysis of the technical lignins with quantitative 13C NMR spectroscopy to increase the amount of information obtained and its reliability. Kraft residual and dissolved lignin isolated after pulping of Eucalyptus globules-EGL, Eucalyptus grandis-ERG and birch were characterized using the modified NMR approach, and differences in their structure were discussed. Appreciable differences between the ERL and MRL fractions have been observed. The latter has significantly lower amounts of carboxyl and aliphatic hydroxyl groups, lower S/G ratio, higher degree of condensation. In contrast to wood and pulp, the EGL residual lignin preparations contain rather high amounts of galactose and arabinose indicating their importance in kraft pulp LCC. The differences between the fractions of the residual lignin indicate its heterogeneous character. Among the technical lignins investigated, EGL residual lignins were much less degraded than the other lignin preparations, whereas degradation of the birch residual and kraft lignins was very high, especially in the side chain.
Highly efficient solid-state neutron scintillators based on hybrid sol-gel nanocomposite materials (2006)

This research highlights opportunities in the formulation of neutron scintillators that not only have high scintillation efficiencies but also can be readily cast into two-dimensional detectors. Series of transparent, crack-free monoliths were prepared from hybrid polystyrene-silica nanocomposites in the presence of arene-containing alkoxide precursor through room temperature sol-gel processing. The monoliths also contain lithium-6 salicylate as a target material for neutron-capture reactions and amphiphilic scintillator solution as a fluorescent sensitizer. Polystyrene was functionalized by trimethoxysilyl group in order to enable the covalent incorporation of aromatic functional groups into the inorganic sol-gel matrices for minimizing macroscopic phase segregation and facilitating lithium-6 doping in the sol-gel samples. Neutron and alpha responses of these hybrid polystyrene-silica monoliths were explored.
Low-Dose Estrogen Therapy Ameliorates Experimental Autoimmune Encephalomyelitis in Two Different Inbred Mouse Strains (2001)

It has been proposed that homeostatic levels of estrogen can enhance female susceptibility to autoimmunity, whereas the heightened levels of estrogen associated with pregnancy are protective. This hypothesis was tested using the mouse model of experimental autoimmune encephalomyelitis (EAE). Diestrus (<100 pg/ml in serum) levels of 17beta-estradiol were found to significantly reduce the clinical manifestations of active EAE in both male and female mice. Estriol was also effective but at doses below those previously established for pregnancy. The reduction in disease severity was accompanied by a coincident reduction in the number and size of inflammatory foci in the CNS of estrogen (17beta-estradiol or estriol)-treated mice. Recipients of encephalitogenic T cells from low-dose estrogen-treated mice developed less severe paralysis than mice receiving T cells from placebo-treated mice. A modest shift in Th1/Th2 balance suggested that low dose estrogen therapy could bias the immune reaction toward a protective anti-inflammatory cytokine response. However, estrogen treatment at the onset of active EAE failed to reduce disease severity, a result that is consistent with the hypothesis that naive cells are more sensitive to sex hormones than differentiated effector cells. These data suggest that treatment with low doses of estrogen can reduce the capacity of developing myelin-reactive T cells to initiate disease and challenges the idea that increased susceptibility to autoimmunity in females is dependent on homeostatic levels of estrogen.
Frequency and Damping Estimation Methods - An Overview (2011)

Frequency and Damping Estimation Methods - An Overview This overview paper presents and compares different methods traditionally used for estimating damped sinusoid parameters. Firstly, direct nonlinear least squares fitting the signal model in the time and frequency domains are described. Next, possible applications of the Hilbert transform for signal demodulation are presented. Then, a wide range of autoregressive modelling methods, valid for damped sinusoids, are discussed, in which frequency and damping are estimated from calculated signal linear self-prediction coefficients. These methods aim at solving, directly or using least squares, a matrix linear equation in which signal or its autocorrelation function samples are used. The Prony, Steiglitz-McBride, Kumaresan-Tufts, Total Least Squares, Matrix Pencil, Yule-Walker and Pisarenko methods are taken into account. Finally, the interpolated discrete Fourier transform is presented with examples of Bertocco, Yoshida, and Agrež algorithms. The Matlab codes of all the discussed methods are given. The second part of the paper presents simulation results, compared with the Cramér-Rao lower bound and commented. All tested methods are compared with respect to their accuracy (systematic errors), noise robustness, required signal length, and computational complexity.
The Ensembl gene annotation system (2016)

The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.
Regulation of Daily Locomotor Activity and Sleep by Hypothalamic EGF Receptor Signaling (2001)

The circadian clock in the suprachiasmatic nucleus (SCN) is thought to drive daily rhythms of behavior by secreting factors that act locally within the hypothalamus. In a systematic screen, we identified transforming growth factor-alpha (TGF-alpha) as a likely SCN inhibitor of locomotion. TGF-alpha is expressed rhythmically in the SCN, and when infused into the third ventricle it reversibly inhibited locomotor activity and disrupted circadian sleep-wake cycles. These actions are mediated by epidermal growth factor (EGF) receptors on neurons in the hypothalamic subparaventricular zone. Mice with a hypomorphic EGF receptor mutation exhibited excessive daytime locomotor activity and failed to suppress activity when exposed to light. These results implicate EGF receptor signaling in the daily control of locomotor activity, and identify a neural circuit in the hypothalamus that likely mediates the regulation of behavior both by the SCN and the retina.
ErbB2 Activation Upregulates Glutaminase 1 Expression Which Promotes Breast Cancer Cell Proliferation (2013)

Active glutamine utilization is critical for tumor cell proliferation. Glutaminolysis represents the first and rate-limiting step of glutamine utilization and is catalyzed by glutaminase (GLS). Activation of ErbB2 is one of the major causes of breast cancers, the second most common cause of death for women in many countries. However, it remains unclear whether ErbB2 signaling affects glutaminase expression in breast cancer cells. In this study, we show that MCF10A-NeuT cell line has higher GLS1 expression at both mRNA and protein levels than its parental line MCF10A, and knockdown of ErbB2 decreases GLS1 expression in MCF10A-NeuT cells. We further show that in these cells, ErbB2-mediated upregulation of GLS1 is not correlated to c-Myc expression. Moreover, activation of neither PI3K-Akt nor MAPK pathway is sufficient to upregulate GLS1 expression. Interestingly, inhibition of NF-κB blocks ErbB2-stimulated GLS1 expression, whereas stimulation of NF-κB is sufficient to enhance GLS1 levels in MCF10A cells, suggesting a PI3K-Akt-independent activation of NF-κB upregulates GLS1 in ErbB2-positive breast cancer cells. Finally, knockdown or inhibition of GLS1 significantly decreased the proliferation of breast cancer cells with high GLS1 levels. Taken together, our data indicate that ErbB2 activation promotes GLS1 expression via a PI3K-Akt-independent NF-κB pathway in breast cancer cells, identifying another oncogenic signaling pathway which stimulates GLS1 expression, and thus promoting glutamine utilization in cancer cells. These findings, if validated by in vivo model, may facilitate the identification of novel biochemical targets for cancer prevention and therapy.
The Genetics of RNA Silencing (2002)

Although initially recognized as a handy tool to reduce gene expression, RNA silencing, triggered by double-stranded RNA molecules, is now recognized as a mechanism for cellular protection and cleansing: It defends the genome against molecular parasites such as viruses and transposons, while removing abundant but aberrant nonfunctional messenger RNAs. The underlying mechanisms in distinct gene silencing phenomena in different genetic systems, such as cosuppression in plants and RNAi in animals, are very similar. There are common RNA intermediates, and similar genes are required in RNA silencing pathways in protozoa, plants, fungi, and animals, thus indicating an ancient pathway. This chapter gives an overview of both biochemical and genetic approaches leading to the current understanding of the molecular mechanism of RNA silencing and its probable biological function.