gebhart/patrepeval huggingface dataset:
Agglomerates of aberrant DNA methylation are associated with toxicant-induced malignant transformation (2012)

Epigenetic dysfunction is a known contributor in carcinogenesis, and is emerging as a mechanism involved in toxicant-induced malignant transformation for environmental carcinogens such as arsenicals or cadmium. In addition to aberrant DNA methylation of single genes, another manifestation of epigenetic dysfunction in cancer is agglomerative DNA methylation, which can participate in long-range epigenetic silencing that targets many neighboring genes and has been shown to occur in several types of clinical cancers. Using in vitro model systems of toxicant-induced malignant transformation, we found hundreds of aberrant DNA methylation events that emerge during malignant transformation, some of which occur in an agglomerative fashion. In an arsenite-transformed prostate epithelial cell line, the protocadherin (PCDH), HOXC and HOXD gene family clusters are targeted for agglomerative DNA methylation. The agglomerative DNA methylation changes induced by arsenicals appear to be common and clinically relevant events, since they occur in other human cancer cell lines and models of malignant transformation, as well as clinical cancer specimens. Aberrant DNA methylation in general occurred more often within histone H3 lysine-27 trimethylation stem cell domains. We found a striking association between enrichment of histone H3 lysine-9 trimethylation stem cell domains and toxicant-induced agglomerative DNA methylation, suggesting these epigenetic modifications may become aberrantly linked during malignant transformation. In summary, we found an association between toxicant-induced malignant transformation and agglomerative DNA methylation, which lends further support to the hypothesis that epigenetic dysfunction plays an important role in toxicant-induced malignant transformation.
Ectopia cordis with single ventricle and a diverticulum. Exsanguination from septic necrosis of the ductus arteriosus. (1975)

Following Birkhoff and von Neumann, quantum logic has traditionally been based\non the lattice of closed linear subspaces of some Hilbert space, or, more generally,\non the lattice of projections in a von Neumann algebra A. Unfortunately, the logical\ninterpretation of these lattices is impaired by their nondistributivity and by various\nother problems. We show that a possible resolution of these difficulties, suggested by\nthe ideas of Bohr, emerges if instead of single projections one considers elementary\npropositions to be families of projections indexed by a partially ordered set C(A) of\nappropriate commutative subalgebras of A. In fact, to achieve both maximal generality\nand ease of use within topos theory, we assume that A is a so-called Rickart C*-algebra\nand that C(A) consists of all unital commutative Rickart C*-subalgebras of A. Such\nfamilies of projections form a Heyting algebra in a natural way, so that the associated\npropositional logic is intuitionistic: distributivity is recovered at the expense of the\nlaw of the excluded middle.\nSubsequently, generalizing an earlier computation for n×n matrices, we prove that\nthe Heyting algebra thus associated to A arises as a basis for the internal Gelfand\nspectrum (in the sense of Banaschewski–Mulvey) of the "Bohrification" A of A, which\nis a commutative Rickart C*-algebra in the topos of functors from C(A) to the category\nof sets. We explain the relationship of this construction to partial Boolean algebras\nand Bruns–Lakser completions. Finally, we establish a connection between probability\nmeasure on the lattice of projections on a Hilbert space H and probability valuations\non the internal Gelfand spectrum of A for A = B(H).
Drugs affecting the cell cycle via actions on the polyamine metabolic pathway. (2003)

Polyamines (putrescine, spermidine, and spermine) are ubiquitous cellular components that have multiple functions, including actions affecting the cell cycle. Polyamine biosynthesis and content is altered during the course of cell cycling via changes in two key biosynthetic enzymes, ornithine decarboxylase and S-adenosyl-methionine decarboxylase. Decreases in polyamine content and/or alterations in the relative amounts of polyamines can be achieved by treatment with inhibitors of these enzymes or by application of polyamine analogues, which subvert mechanisms for polyamine homeostasis and may interfere directly with polyamine-dependent processes. Such changes cause G1 and G2-M cell cycle blocks that can be brought about via induction of p21WAF1/CIP1.
ChemInform Abstract: Combining Spontaneous Molecular Assembly with Microfabrication to Pattern Surfaces: Selective Binding of Isonitriles to Platinum Microwires and Characterization by Electrochemistry and Surface Spectroscopy. (1989)

Abstract The selective modification of the Pt microelectrodes of a microfabricated array by using the redox reagents (I) having an isonitrile functional group is reported.
“Super Hydrocarbon Reformer Trap” for the Complete Oxidation of Toluene Using Iron‐Exchanged β‐Zeolite with a Low Silicon/Aluminum Ratio (2016)

Abstract This study examines the effects of the Si/Al ratio and metal cation exchange of a zeolite on the ability to adsorb and reform unburned hydrocarbons (HCs) in emissions from gasoline vehicles. Iron ion‐exchanged β‐zeolites with a low Si/Al ratio not only trap but also oxidize HCs efficiently, which spurred on the development of a “super HC reformer trap”. Toluene temperature‐programmed desorption experiments in an O 2 ‐containing stream revealed that >90 % of the adsorbed toluene was converted into CO 2 , and other oxygenates were not observed. This material could be reused and it retained its performance. The strong adsorption of toluene on the zeolites was derived from two synergistic effects: (1) electrostatic interactions between the π orbital of the aromatic ring and the p orbital of the metal cation and (2) interactions between the positively polarized methyl group of toluene and a basic oxygen atom in the zeolite framework. This new material will pave the way for low‐emission, Pt‐free vehicles.
Dynamic Monitoring Approach for Multi-poin Multimedia Systems. (1999)

Bien qu'il existe a ce jour de nombreux systemes de monitoring developpes dans le milieu academique et industriel, peu d'entre eux peuvent clamer qu'ils sont dynamiques. Cet article decrit une nouvelle architecture de monitoring, appelee HiFi, qui autorise la programmation des tâches de monitoring, la reconfiguration des services d'inscription, une plus grande flexibilite d'interaction pour les utilisateurs, et une meilleure adaptation aux changements de l'environnement et des besoins des applications. L'article presente egalement un exemple de monitoring pour illustrer l'efficacite de HiFi dans sa capacite a controler et a ameliorer les performances des systemes multimedia multipoints.
Warming of Global Abyssal and Deep Southern Ocean Waters between the 1990s and 2000s: Contributions to Global Heat and Sea Level Rise Budgets* (2010)

Abstract Abyssal global and deep Southern Ocean temperature trends are quantified between the 1990s and 2000s to assess the role of recent warming of these regions in global heat and sea level budgets. The authors 1) compute warming rates with uncertainties along 28 full-depth, high-quality hydrographic sections that have been occupied two or more times between 1980 and 2010; 2) divide the global ocean into 32 basins, defined by the topography and climatological ocean bottom temperatures; and then 3) estimate temperature trends in the 24 sampled basins. The three southernmost basins show a strong statistically significant abyssal warming trend, with that warming signal weakening to the north in the central Pacific, western Atlantic, and eastern Indian Oceans. Eastern Atlantic and western Indian Ocean basins show statistically insignificant abyssal cooling trends. Excepting the Arctic Ocean and Nordic seas, the rate of abyssal (below 4000 m) global ocean heat content change in the 1990s and 2000s is equivalent to a heat flux of 0.027 (±0.009) W m−2 applied over the entire surface of the earth. Deep (1000–4000 m) warming south of the Subantarctic Front of the Antarctic Circumpolar Current adds 0.068 (±0.062) W m−2. The abyssal warming produces a 0.053 (±0.017) mm yr−1 increase in global average sea level and the deep warming south of the Subantarctic Front adds another 0.093 (±0.081) mm yr−1. Thus, warming in these regions, ventilated primarily by Antarctic Bottom Water, accounts for a statistically significant fraction of the present global energy and sea level budgets.
PROCESS ISSUES FOR A MULTI-LAYER MICROELECTROFLUIDIC PLATFORM (2008)

We report on the development of some process capabilities for a polymer-based, multi-layer microelectrofluidic platform, namely: the hot embossing process, metallization on polymer and polymer bonding. Hot embossing experiments were conducted to look at the effects of load applied, embossing temperature and embossing time on the fidelity of line arrays representing micro channels. The results revealed that the embossing temperature is a more sensitive parameter than the others due to its large effect on the polymer material’s viscoelastic properties. Dynamic mechanical analysis (DMA) on polymethyl methacrylate (PMMA) revealed a steep glass transition over a 20 o C range, with the material losing more than 95 % of its storage modulus. The data explained the hot embossing results which showed large change in the embossed channel dimensions when the temperature is within the glass transition range. It was demonstrated that the micro-printing of silver epoxy is a possible low-cost technique in the mass production of disposable lab chips. An interconnecting network of electrical traces was fabricated in the form of a four-layer PMMA-based device. A four PMMA layer device with interconnecting microfluidic channels was also fabricated and tested. 1.
Condensation/evaporation of insoluble organic vapor as functions of source rate and saturation vapor pressure (2002)

Condensation growth of atmospheric particles by insoluble organic vapors was studied by a monodisperse aerosol dynamics model MONO32 including atmospheric chemistry mechanism. The source rate of the vapor and its saturation vapor density at a particle surface were varied. The initial particle number size distribution was assumed to be bimodal, and aerosol was initially an internal mixture of particles consisting of soluble sulphuric acid and insoluble organic material in a ratio of 1:1. Model simulations predicted that if the ratio of the vapor source rate and the condensation sink of particles, Q /CS, exceeded 10 8 cm −3 and the vapor was nonvolatile or low volatile, the 10 nm nuclei grew with the growth rates of 2.5–3 nm h −1 and could act as cloud condensation nuclei in supersaturations of 1.6% or lower after 24 h simulation. Then the vapors must have saturation vapor pressures less than 7 × 10 6 cm −3 . However, the higher the ratio of Q /CS, the higher the saturation vapor pressure could be. When the vapor was highly volatile, i.e., the saturation vapor density was high enough, in our simulations greater than 6 × 10 7 cm −3 the Ostwald ripening was observed. Then the nucleation mode particles were not able to grow but coagulated with larger particles without causing any significant impact on climate. An analytical expression for the saturation vapor density for the Ostwald ripening ( c Ost ) was derived as a function of the ratio of Q /CS. Sensitivity tests for the accommodation coefficient and thermodynamic parameters as well as their effects on c Ost were investigated.
The impact of electronic medical records data sources on an adverse drug event quality measure (2010)

More detailed clinical information may result in quality measures that are not comparable across institutions due institution-specific workflow, differences that are exposed using EMR-derived data.
Gradient‐based parameter optimization for systems containing discrete‐valued functions (2002)

Abstract Gradient‐based parameter optimization is commonly used for training neural networks and optimizing the performance of other complex systems that only contain continuously differentiable functions. However, there is a large class of important parameter optimization problems involving systems containing discrete‐valued functions that do not permit the direct use of gradient‐based methods. Examples include optimization of control systems containing discrete‐level actuators such as on/off devices, systems with discrete‐valued inputs and outputs, discrete‐decision‐making systems (accept/reject), and neural networks built with signums (also known as hard‐limiters or Heaviside step functions) rather than sigmoids. Even if most of the system is continuously differentiable, the presence of one or more discrete‐valued functions will not allow gradient‐based optimization to be used directly. A new algorithm, ‘noisy backpropagation,’ is developed here, as an extension of backpropagation, which solves this problem and extends gradient‐based parameter optimization to permit application to systems containing discrete‐valued functions. Moreover, the modification to backpropagation is small, requiring only (1) replacement of the discrete‐valued functions with continuously differentiable approximations, and (2) injection of noise into the smooth approximating function on the forward sweep during training. Noise injection is the key to reducing the round‐off error created when the discrete‐valued functions are replaced after training. This generic approach is applicable whenever gradient‐based parameter optimization is used with systems containing discrete‐valued functions; it is not limited to training neural networks. The examples in this paper demonstrate the use of noisy backpropagation in training two different multi‐layer signum networks and in training a neural network for a control problem involving on‐off actuators. This final example includes implementation on a laboratory model of a ‘free‐flying space robot’ to validate the realizability and practical utility of the method. Copyright © 2002 John Wiley & Sons, Ltd.
Defoliation, waterlogging and dung influences allocation patterns of Deschampsia caespitosa (2003)

Wet meadows are some of the most productive communities in the northern Rocky Mountains, USA but are also among the most sensitive to grazing by native ungulates and domestic livestock. These meadows typically are inundated with floodwater in spring and early summer but are relatively dry in summer. To determine the interactive effects of clipping and flooding on plant recovery after clipping, we subjected plants of tufted hairgrass (Deschampsia caespitosa (L.) Beauv) to 6-week and 10-week waterlogging treatments in combination with 1 and 2 clipping events, with and without dung amendment in a greenhouse experiment. The experiment was designed to mimic early and late growing-season patterns of herbivory by native and domestic herbivores on a dominant species of wet meadows of this region. Waterlogged plants produced a higher percentage of roots at the surface, elongated stems to the first axial leaf, increased the proportion of tillers that flowered, but increased aboveground yield and tiller height only with the addition of dung. Root biomass declined with waterlogging when dung was not added, and a second defoliation exacerbated the negative effects of waterlogging on roots. Defoliation with short-duration waterlogging increased shoot nitrogen (N) concentration and N yield/root biomass, while continuous waterlogging reduced shoot N concentration of aboveground biomass. Dung amendment did not reverse this effect. Although extended flooding in combination with moderate rates of defoliation did not reduce aboveground biomass of Deschampsia caespitosa, it aggravated total root loss, caused shifts to a shallower root distribution, and altered N concentration of aboveground biomass for herbivores.
On the Use of Stochastic Hessian Information in Optimization Methods for Machine Learning (2011)

This paper describes how to incorporate sampled curvature information in a Newton-CG method and in a limited memory quasi-Newton method for statistical learning. The motivation for this work stems from supervised machine learning applications involving a very large number of training points. We follow a batch approach, also known in the stochastic optimization literature as a sample average approximation approach. Curvature information is incorporated in two subsampled Hessian algorithms, one based on a matrix-free inexact Newton iteration and one on a preconditioned limited memory BFGS iteration. A crucial feature of our technique is that Hessian-vector multiplications are carried out with a significantly smaller sample size than is used for the function and gradient. The efficiency of the proposed methods is illustrated using a machine learning application involving speech recognition.
Real-time PCR detection and quantification of <i>Fusarium poae, F. graminearum, F. sporotrichioides</i> and <i>F. langsethiae</i> in cereal grains in Finland and Russia (2006)

Abstract TaqMan real-time quantitative PCR assays were developed for the accurate detection and quantification of DNA from Fusarium poae and F. graminearum species, which are able to produce trichothecenes. These and other PCR assays were used for the quantification of trichothecene-producing Fusarium fungi in cereal grains. A correlation was found between the levels of F. poae DNA and nivalenol and enniatins in barley and between the levels of F. graminearum DNA and deoxynivalenol in oats. The correlations between F. poae DNA and nivalenol and F. graminearum DNA and deoxynivalenol levels were higher than those between these mycotoxins and morphologically determined F. poae and F. graminearum/F. culmorum contamination levels. The use of F. poae specific primers and probe together with F. sporotrichioides/F. langsethiae specific primers and probe in a multiplex qPCR assay yielded results in accordance with those obtained using these primers and probes separately. Keywords: BarleydeoxynivalenolenniatinsnivalenoloatsTaqMan PCR Acknowledgements This study was supported by grants from the National Technology Agency of Finland (No. 40168/03), and the Academy of Finland (No. 52104) and the Nordic Research Board (No. 040291). The authors want to thank Nina Painilainen, Taina Lahtinen, Teija Koivula and Tarja Nordenstedt for their assistance with DNA extraction and qPCR analyses, Kati Lehti for skilful assistance with mycotoxin analyses, Dr Sonja Klemsdal for designing TMTRI and TMLAN primers and probe, Dr Jouni Ahlholm for help in statistical analyses and Dr Cees Waalwijk for critically reading the manuscript. The English was checked by Ellen Valle of the Department of English, University of Turku.
Preliminary results towards ciguatoxin immunodetection. (1992)

Due to the lack of purified ciguatoxin (CTX), monensin was used as a model for developing an enzyme immunoassay to detect CTX. Specific antibodies directed against monensin have been produced in rabbits and mice using a monensin-protein immunogen obtained in bulk quantities. Rabbit polyclonal and mouse monoclonal (MAb) antibodies of high specificity and affinity have been produced. Using MAb 2H8, in a competitive micro-ELISA performed in Terasaki plates, the detection limit for free monensin was 75 pg. No cross-reactivity was detected against CTX but a procedure requiring only 100 micrograms of hapten is under current investigation with a brevetoxin (PbTx-3), another marine toxin with a polyether backbone structure similar to CTX and recently commercially available.
Single-mode laser frequency modulation (1977)

This paper presents an analysis of the frequency response of single-mode laser frequency modulation. The method employed is based on the combined concepts of an active Fabry-Perot interferometer and of internal phase modulation, and is very transparent. The calculation of the sideband amplitudes and phases of the laser output reveals two main regions of the frequency response: for modulating frequencies lower than the cavity mode spacing the laser generates an ideally frequency-modulated signal. At higher frequencies the sideband amplitude versus modulating frequency shows an oscillatory behavior. Here, the response is mainly determined by the cavity mode spacing frequency and by the position of the modulator within the cavity. Comparing the theoretical results with previously reported experiments, very good agreement was found.
Biochemical and biophysical perspectives in marine biology. Volume 1 (Malins, D. C.; Sargent, J. R., eds.) (1976)

ADVERTISEMENT RETURN TO ISSUEPREVBook and Media Revie...Book and Media ReviewNEXTBiochemical and biophysical perspectives in marine biology. Volume 1 (Malins, D. C.; Sargent, J. R., eds.)Harry Zeitlin Cite this: J. Chem. Educ. 1976, 53, 7, A326Publication Date (Print):July 1, 1976Publication History Received3 August 2009Published online1 July 1976Published inissue 1 July 1976https://doi.org/10.1021/ed053pA326.3RIGHTS & PERMISSIONSArticle Views124Altmetric-Citations-LEARN 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 InReddit PDF (3 MB) Get e-Alerts Get e-Alerts
ChemInform Abstract: Indirect Electrochemical Oxidation of 4‐Picoline (I) and Its N‐Oxide ( IV) to Pyridine‐4‐aldehyde Diacetate (III) with Electrogenerated Cobalt(III) Acetate in an In‐Cell Process. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Very Stable Non-cyanide Electroless Gold Plating Bath Using Thiourea and hydroquinone as a Cooperating Double Reductant System. (1998)

The paper reports a new autocatalytic electroless gold plating bath that achieves almost neutral, low temperature bath conditions and excellent process stability without cyanide. The bath contains a thiosulfatesulfite mixed complex of Au (I) as the gold source and two reducing agents, thiourea and hydroquinone. The thiourea acts as the primary reductant for the gold complex, while the hydroquinone recycles thiourea by reducing the intermediate thiyl radical derived from thiourea oxidation. Therefore hydroquinone functions as a thiourea regenerator. This unique cooperative reductant system offers superb bath stability. The bath has been applied not only to the most advanced mainframe MLC boards but also to a variety of very fine pitch organic PWBs manufacturing process.