ARO - Terrestrial Research Program, Methodologies and Protocols for Characterization of Geomaterials

DTIC Science & Technology

2015-05-14

of ice involves melting, digestion, and analysis using inductively coupled plasma – mass spectrometry (ICPMS). ICP-MS analysis established elemental...4] have distinct chemical compositions. Knowledge of the chemical composition of the mineral assemblage present in a rock is critical to...activation analysis (INAA), to inductively-coupled plasma analysis and mass spectrometry (ICP & ICP-MS), mass spectrometry (MS), and laser-ablation

Compositional studies of Mare Moscoviense: New perspectives from Chandrayaan-1 VIS-NIR data

NASA Astrophysics Data System (ADS)

Bhatt, Megha; Wöhler, Christian; Dhingra, Deepak; Thangjam, Guneshwar; Rommel, Daniela; Mall, Urs; Bhardwaj, Anil; Grumpe, Arne

2018-03-01

Moscoviense is one of the prominent mare-filled basin on the lunar far side holding key insights about volcanic activity on the far side. Here, we present spectral and elemental maps of mare Moscoviense, using the Moon Mineralogy Mapper (M3) and Infrared Spectrometer-2 (SIR-2) data-sets. The different mare units are mapped based on their spectral properties analyzing both quantitatively (band center, band depth) and qualitatively (Integrated Band Depth composite images), and also using their elemental compositions. We find a total of five distinct spectral units from the basin floor based on the spectral properties. Our analysis suggests that the northern part which was mapped as Iltm unit (Imbrian low Ti, low Fe) by earlier researchers is actually a distinct unit, which is different in composition and age, named as Ivltm unit (Imbrian very low Ti and very low Fe). We obtain the absolute model age of 3.2 Ga with uncertainties of +0.2/ -0.5 Ga for the unit Ivltm. The newly identified basalt unit Ivltm is compositionally intermediate to the units Im and Iltm in FeO and TiO2 abundances. We find a total of five distinct spectral units from the basin floor based on the spectral properties. The units Im (Imbrian very low Ti) from southern and northern regions of the basin floor are spectrally distinct in terms of band center position and corresponding band depths but considered a single unit based on the elemental abundance analysis. The units Ivltm and Im are consistent with a high-Al basalt composition. Our detailed analysis of the entire Moscoviense basin indicates that the concentrations of orthopyroxene, olivine, and Mg-rich spinel, named as OOS rock family are widespread and dominant at the western and southern side of the middle ring of the basin with one isolated area found on the northern side of the peak ring.

Benthic foraminifera as bio-indicators of trace element pollution in the heavily contaminated Santa Gilla lagoon (Cagliari, Italy).

PubMed

Frontalini, Fabrizio; Buosi, Carla; Da Pelo, Stefania; Coccioni, Rodolfo; Cherchi, Antonietta; Bucci, Carla

2009-06-01

In order to assess the response of benthic foraminifera to trace element pollution, a study of benthic foraminiferal assemblages was carried out into sediment samples collected from the Santa Gilla lagoon (Sardinia, Italy). The lagoon has been contaminated by industrial waste, mainly trace elements, as well as by agricultural and domestic effluent. The analysis of surficial sediment shows enrichment in trace elements, including Cr, Cu, Hg, Ni, Pb and Zn. Biotic and abiotic data, analyzed with multivariate techniques of statistical analysis, reveal a distinct separation of both the highly polluted and less polluted sampling sites. The innermost part of the lagoon, comprising the industrial complex at Macchiareddu, is exposed to a high load of trace elements which are probably enhanced by their accumulation in the finer sediment fraction. This area reveals lower diversity and higher percentages of abnormalities when compared to the outermost part of the lagoon.

Repeatability and reproducibility of intracellular molar concentration assessed by synchrotron-based x-ray fluorescence microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merolle, L., E-mail: lucia.merolle@elettra.eu; Gianoncelli, A.; Malucelli, E., E-mail: emil.malucelli@unibo.it

2016-01-28

Elemental analysis of biological sample can give information about content and distribution of elements essential for human life or trace elements whose absence is the cause of abnormal biological function or development. However, biological systems contain an ensemble of cells with heterogeneous chemistry and elemental content; therefore, accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. Powerful methods in molecular biology are abundant, among them X-Ray microscopy based on synchrotron light source has gaining increasing attention thanks to its extremely sensitivity. However, reproducibility and repeatability of these measurements is one of the majormore » obstacles in achieving a statistical significance in single cells population analysis. In this study, we compared the elemental content of human colon adenocarcinoma cells obtained by three distinct accesses to synchrotron radiation light.« less

Methods of Analysis by the U.S. Geological Survey National Water Quality Laboratory - Determination of Elements in Whole-Water Digests Using Inductively Coupled Plasma-Optical Emission Spectrometry and Inductively Coupled Plasma-Mass Spectrometry

USGS Publications Warehouse

Garbarino, John R.; Struzeski, Tedmund M.

1998-01-01

Inductively coupled plasma-optical emission spectrometry (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) can be used to determine 26 elements in whole-water digests. Both methods have distinct advantages and disadvantages--ICP-OES is capable of analyzing samples with higher elemental concentrations without dilution, however, ICP-MS is more sensitive and capable of determining much lower elemental concentrations. Both techniques gave accurate results for spike recoveries, digested standard reference-water samples, and whole-water digests. Average spike recoveries in whole-water digests were 100 plus/minus 10 percent, although recoveries for digests with high dissolved-solid concentrations were lower for selected elements by ICP-MS. Results for standard reference-water samples were generally within 1 standard deviation of hte most probable values. Statistical analysis of the results from 43 whole-water digest indicated that there was no significant difference among ICP-OES, ICP-MS, and former official methods of analysis for 24 of the 26 elements evaluated.

BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.

PubMed

Zhang, Xiaoyu; Wessler, Susan R

2005-05-01

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.

Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils

PubMed Central

Gueriau, Pierre; Mocuta, Cristian; Dutheil, Didier B.; Cohen, Serge X.; Thiaudière, Dominique; Charbonnier, Sylvain; Clément, Gaël; Bertrand, Loïc

2014-01-01

The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies. PMID:24489809

Trace elemental imaging of rare earth elements discriminates tissues at microscale in flat fossils.

PubMed

Gueriau, Pierre; Mocuta, Cristian; Dutheil, Didier B; Cohen, Serge X; Thiaudière, Dominique; Charbonnier, Sylvain; Clément, Gaël; Bertrand, Loïc

2014-01-01

The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies.

ATMOSPHERIC MERCURY SIMULATION USING THE CMAQ MODEL: FORMULATION DESCRIPTION AND ANALYSIS OF WET DEPOSITION RESULTS

EPA Science Inventory

The Community Multiscale Air Quality (CMAQ) modeling system has recently been adapted to simulate the emission, transport, transformation and deposition of atmospheric mercury in three distinct forms; elemental mercury gas, reactive gaseous mercury, and particulate mercury. Emis...

Identification of cis-acting regulatory elements in the human oxytocin gene promoter.

PubMed

Richard, S; Zingg, H H

1991-12-01

The expression of hormone-inducible genes is determined by the interaction of trans-acting factors with hormone-inducible elements and elements mediating basal and cell-specific expression. We have shown earlier that the gene encoding the hypothalamic nonapeptide oxytocin (OT) is under the control of an estrogen response element (ERE). The present study was aimed at identifying cis-acting elements mediating basal expression of the OT gene. A construct containing sequences -381 to +36 of the human OT gene was linked to a reporter gene and transiently transfected into a series of neuronal and nonneuronal cell lines. Expression of this construct was cell specific: it was highest in the neuroblastoma-derived cell line, Neuro-2a, and lowest in NIH 3T3 and JEG-3 cells. By 5' deletion analysis, we determined that a segment from -49 to +36 was capable of mediating cells-pecific promoter activity. Within this segment, we identified three proximal promoter elements (PPE-1, PPE-2, and PPE-3) that are each required for promoter activity. Most notably, mutation of a conserved purine-rich element (GAGAGA) contained within PPE-2 leads to a 10-fold decrease in promoter strength. Gel mobility shift analysis with three different double-stranded oligonucleotides demonstrated that each proximal promoter element binds distinct nuclear factors. In each case, only the homologous oligonucleotide, but neither of the oligonucleotides corresponding to adjacent elements, was able to act as a competitor. Thus, a different set of factors appears to bind independently to each element. By reinserting the homologous ERE or a heterologous glucocorticoid response element upstream of intact or altered proximal promoter segments we determined that removal or mutation of proximal promoter elements decreases basal expression, but does not abrogate the hormone responsiveness of the promoter. In conclusion, these results indicate that an important component of the transcriptional activity of the OT promoter resides in a small region extending only 50 bases upstream of the cap site and that this activity is the result of a cooperative interaction of at least three distinct proximal promoter elements.

Description of textures by a structural analysis.

PubMed

Tomita, F; Shirai, Y; Tsuji, S

1982-02-01

A structural analysis system for describing natural textures is introduced. The analyzer automatically extracts the texture elements in an input image, measures their properties, classifies them into some distinctive classes (one ``ground'' class and some ``figure'' classes), and computes the distributions of the gray level, the shape, and the placement of the texture elements in each class. These descriptions are used for classification of texture images. An analysis-by-synthesis method for evaluating texture analyzers is also presented. We propose a synthesizer which generates a texture image based on the descriptions. By comparing the reconstructed image with the original one, we can see what information is preserved and what is lost in the descriptions.

Selfish genetic elements favor the evolution of a distinction between soma and germline.

PubMed

Johnson, Louise J

2008-08-01

Many multicellular organisms have evolved a dedicated germline. This can benefit the whole organism, but its advantages to genetic parasites have not been explored. Here I model the evolutionary success of a selfish element, such as a transposable element or endosymbiont, which is capable of creating or strengthening a germline-soma distinction in a primitively multicellular host, and find that it will always benefit the element to do so. Genes causing germline sequestration can therefore spread in a population even if germline sequestration is maladaptive for the host organism. Costly selfish elements are expected to survive only in sexual populations, so sexual species may experience an additional push toward germline-soma distinction, and hence toward cell differentiation and multicellularity.

Color pattern analysis of nymphalid butterfly wings: revision of the nymphalid groundplan.

PubMed

Otaki, Joji M

2012-09-01

To better understand the developmental mechanisms of color pattern variation in butterfly wings, it is important to construct an accurate representation of pattern elements, known as the "nymphalid groundplan". However, some aspects of the current groundplan remain elusive. Here, I examined wing-wide elemental patterns of various nymphalid butterflies and confirmed that wing-wide color patterns are composed of the border, central, and basal symmetry systems. The central and basal symmetry systems can express circular patterns resembling eyespots, indicating that these systems have developmental mechanisms similar to those of the border symmetry system. The wing root band commonly occurs as a distinct symmetry system independent from the basal symmetry system. In addition, the marginal and submarginal bands are likely generated as a single system, referred to as the "marginal band system". Background spaces between two symmetry systems are sometimes light in coloration and can produce white bands, contributing significantly to color pattern diversity. When an element is enlarged with a pale central area, a visually similar (yet developmentally distinct) white band is produced. Based on the symmetric relationships of elements, I propose that both the central and border symmetry systems are comprised of "core elements" (the discal spot and the border ocelli, respectively) and a pair of "paracore elements" (the distal and proximal bands and the parafocal elements, respectively). Both core and paracore elements can be doubled, or outlined. Developmentally, this system configuration is consistent with the induction model, but not with the concentration gradient model for positional information.

PLANS: A finite element program for nonlinear analysis of structures. Volume 1: Theoretical manual

NASA Technical Reports Server (NTRS)

Pifko, A.; Levine, H. S.; Armen, H., Jr.

1975-01-01

The PLANS system is described which is a finite element program for nonlinear analysis. The system represents a collection of special purpose computer programs each associated with a distinct physical problem class. Modules of PLANS specifically referenced and described in detail include: (1) REVBY, for the plastic analysis of bodies of revolution; (2) OUT-OF-PLANE, for the plastic analysis of 3-D built-up structures where membrane effects are predominant; (3) BEND, for the plastic analysis of built-up structures where bending and membrane effects are significant; (4) HEX, for the 3-D elastic-plastic analysis of general solids; and (5) OUT-OF-PLANE-MG, for material and geometrically nonlinear analysis of built-up structures. The SATELLITE program for data debugging and plotting of input geometries is also described. The theoretical foundations upon which the analysis is based are presented. Discussed are the form of the governing equations, the methods of solution, plasticity theories available, a general system description and flow of the programs, and the elements available for use.

Analysis of Microstrip Line Fed Patch Antenna for Wireless Communications

NASA Astrophysics Data System (ADS)

Singh, Ashish; Aneesh, Mohammad; Kamakshi; Ansari, J. A.

2017-11-01

In this paper, theoretical analysis of microstrip line fed rectangular patch antenna loaded with parasitic element and split-ring resonator is presented. The proposed antenna shows that the dualband operation depends on gap between parasitic element, split-ring resonator, length and width of microstrip line. It is found that antenna resonates at two distinct resonating modes i.e., 0.9 GHz and 1.8 GHz for lower and upper resonance frequencies respectively. The antenna shows dual frequency nature with frequency ratio 2.0. The characteristics of microstrip line fed rectangular patch antenna loaded with parasitic element and split-ring resonator antenna is compared with other prototype microstrip line fed antennas. Further, the theoretical results are compared with simulated and reported experimental results, they are in close agreement.

Structure and Strength in Causal Induction

ERIC Educational Resources Information Center

Griffiths, Thomas L.; Tenenbaum, Joshua B.

2005-01-01

We present a framework for the rational analysis of elemental causal induction--learning about the existence of a relationship between a single cause and effect--based upon causal graphical models. This framework makes precise the distinction between causal structure and causal strength: the difference between asking whether a causal relationship…

Multivariate statistical analysis to characterize/discriminate between anthropogenic and geogenic trace elements occurrence in the Campania Plain, Southern Italy.

PubMed

Busico, Gianluigi; Cuoco, Emilio; Kazakis, Nerantzis; Colombani, Nicolò; Mastrocicco, Micòl; Tedesco, Dario; Voudouris, Konstantinos

2018-03-01

Shallow aquifers are the most accessible reservoirs of potable groundwater; nevertheless, they are also prone to various sources of pollution and it is usually difficult to distinguish between human and natural sources at the watershed scale. The area chosen for this study (the Campania Plain) is characterized by high spatial heterogeneities both in geochemical features and in hydraulic properties. Groundwater mineralization is driven by many processes such as, geothermal activity, weathering of volcanic products and intense human activities. In such a landscape, multivariate statistical analysis has been used to differentiate among the main hydrochemical processes occurring in the area, using three different approaches of factor analysis: (i) major elements, (ii) trace elements, (iii) both major and trace elements. The elaboration of the factor analysis approaches has revealed seven distinct hydrogeochemical processes: i) Salinization (Cl - , Na + ); ii) Carbonate rocks dissolution; iii) Anthropogenic inputs (NO 3 - , SO 4 2- , U, V); iv) Reducing conditions (Fe 2+ , Mn 2+ ); v) Heavy metals contamination (Cr and Ni); vi) Geothermal fluids influence (Li + ); and vii) Volcanic products contribution (As, Rb). Results from this study highlight the need to separately apply factor analysis when a large data set of trace elements is available. In fact, the impact of geothermal fluids in the shallow aquifer was identified from the application of the factor analysis using only trace elements. This study also reveals that the factor analysis of major and trace elements can differentiate between anthropogenic and geogenic sources of pollution in intensively exploited aquifers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Orbital construction support equipment

NASA Technical Reports Server (NTRS)

1977-01-01

Approximately 200 separate construction steps were defined for the three solar power satellite (SPS) concepts. Detailed construction scenarios were developed which describe the specific tasks to be accomplished, and identify general equipment requirements. The scenarios were used to perform a functional analysis, which resulted in the definition of 100 distinct SPS elements. These elements are the components, parts, subsystems, or assemblies upon which construction activities take place. The major SPS elements for each configuration are shown. For those elements, 300 functional requirements were identified in seven generic processes. Cumulatively, these processes encompass all functions required during SPS construction/assembly. Individually each process is defined such that it includes a specific type of activity. Each SPS element may involve activities relating to any or all of the generic processes. The processes are listed, and examples of the requirements defined for a typical element are given.

Application of finite element substructuring to composite micromechanics. M.S. Thesis - Akron Univ., May 1984

NASA Technical Reports Server (NTRS)

Caruso, J. J.

1984-01-01

Finite element substructuring is used to predict unidirectional fiber composite hygral (moisture), thermal, and mechanical properties. COSMIC NASTRAN and MSC/NASTRAN are used to perform the finite element analysis. The results obtained from the finite element model are compared with those obtained from the simplified composite micromechanics equations. A unidirectional composite structure made of boron/HM-epoxy, S-glass/IMHS-epoxy and AS/IMHS-epoxy are studied. The finite element analysis is performed using three dimensional isoparametric brick elements and two distinct models. The first model consists of a single cell (one fiber surrounded by matrix) to form a square. The second model uses the single cell and substructuring to form a nine cell square array. To compare computer time and results with the nine cell superelement model, another nine cell model is constructed using conventional mesh generation techniques. An independent computer program consisting of the simplified micromechanics equation is developed to predict the hygral, thermal, and mechanical properties for this comparison. The results indicate that advanced techniques can be used advantageously for fiber composite micromechanics.

Elemental Characterization and Discrimination of Nontoxic Ammunition Using Scanning Electron Microscopy with Energy Dispersive X-Ray Analysis and Principal Components Analysis.

PubMed

Hogg, Seth R; Hunter, Brian C; Waddell Smith, Ruth

2016-01-01

Concerns over the toxic by-products produced by traditional ammunition have led to an increase in popularity of nontoxic ammunition. In this work, the chemical composition of six brands of nontoxic ammunition was investigated and compared to that of a road flare, which served as an environmental source with similar composition. Five rounds of each brand were fired while a further five were disassembled and the primer alone was fired. Particles collected from all samples, including the road flare, were analyzed by scanning electron microscopy with energy dispersive X-ray analysis. Common elements among the different ammunition brands included aluminum, potassium, silicon, calcium, and strontium. Spectra were then subjected to principal components analysis in which association of the primer to the intact ammunition sample was generally possible, with distinction among brands and from the road flare sample. Further, PCA loadings plots indicated the elements responsible for the association and discrimination observed. © 2015 American Academy of Forensic Sciences.

Laboratory and 3-D distinct element analysis of the failure mechanism of a slope under external surcharge

NASA Astrophysics Data System (ADS)

Li, N.; Cheng, Y. M.

2015-01-01

Landslide is a major disaster resulting in considerable loss of human lives and property damages in hilly terrain in Hong Kong, China and many other countries. The factor of safety and the critical slip surface for slope stabilization are the main considerations for slope stability analysis in the past, while the detailed post-failure conditions of the slopes have not been considered in sufficient detail. There is however increasing interest in the consequences after the initiation of failure that includes the development and propagation of the failure surfaces, the amount of failed mass and runoff and the affected region. To assess the development of slope failure in more detail and to consider the potential danger of slopes after failure has initiated, the slope stability problem under external surcharge is analyzed by the distinct element method (DEM) and a laboratory model test in the present research. A more refined study about the development of failure, microcosmic failure mechanisms and the post-failure mechanisms of slopes will be carried out. The numerical modeling method and the various findings from the present work can provide an alternate method of analysis of slope failure, which can give additional information not available from the classical methods of analysis.

Laboratory and 3-D-distinct element analysis of failure mechanism of slope under external surcharge

NASA Astrophysics Data System (ADS)

Li, N.; Cheng, Y. M.

2014-09-01

Landslide is a major disaster resulting in considerable loss of human lives and property damages in hilly terrain in Hong Kong, China and many other countries. The factor of safety and the critical slip surface for slope stabilization are the main considerations for slope stability analysis in the past, while the detailed post-failure conditions of the slopes have not been considered in sufficient details. There are however increasing interest on the consequences after the initiation of failure which includes the development and propagation of the failure surfaces, the amount of failed mass and runoff and the affected region. To assess the development of slope failure in more details and to consider the potential danger of slopes after failure has initiated, the slope stability problem under external surcharge is analyzed by the distinct element method (DEM) and laboratory model test in the present research. A more refined study about the development of failure, microcosmic failure mechanism and the post-failure mechanism of slope will be carried out. The numerical modeling method and the various findings from the present work can provide an alternate method of analysis of slope failure which can give additional information not available from the classical methods of analysis.

Assessment of trace elements levels in patients with Type 2 diabetes using multivariate statistical analysis.

PubMed

Badran, M; Morsy, R; Soliman, H; Elnimr, T

2016-01-01

The trace elements metabolism has been reported to possess specific roles in the pathogenesis and progress of diabetes mellitus. Due to the continuous increase in the population of patients with Type 2 diabetes (T2D), this study aims to assess the levels and inter-relationships of fast blood glucose (FBG) and serum trace elements in Type 2 diabetic patients. This study was conducted on 40 Egyptian Type 2 diabetic patients and 36 healthy volunteers (Hospital of Tanta University, Tanta, Egypt). The blood serum was digested and then used to determine the levels of 24 trace elements using an inductive coupled plasma mass spectroscopy (ICP-MS). Multivariate statistical analysis depended on correlation coefficient, cluster analysis (CA) and principal component analysis (PCA), were used to analysis the data. The results exhibited significant changes in FBG and eight of trace elements, Zn, Cu, Se, Fe, Mn, Cr, Mg, and As, levels in the blood serum of Type 2 diabetic patients relative to those of healthy controls. The statistical analyses using multivariate statistical techniques were obvious in the reduction of the experimental variables, and grouping the trace elements in patients into three clusters. The application of PCA revealed a distinct difference in associations of trace elements and their clustering patterns in control and patients group in particular for Mg, Fe, Cu, and Zn that appeared to be the most crucial factors which related with Type 2 diabetes. Therefore, on the basis of this study, the contributors of trace elements content in Type 2 diabetic patients can be determine and specify with correlation relationship and multivariate statistical analysis, which confirm that the alteration of some essential trace metals may play a role in the development of diabetes mellitus. Copyright © 2015 Elsevier GmbH. All rights reserved.

Explaining Academic Progress via Combining Concepts of Integration Theory and Rational Choice Theory.

ERIC Educational Resources Information Center

Beekhoven, S.; De Jong, U.; Van Hout, H.

2002-01-01

Compared elements of rational choice theory and integration theory on the basis of their power to explain variance in academic progress. Asserts that the concepts should be combined, and the distinction between social and academic integration abandoned. Empirical analysis showed that an extended model, comprising both integration and rational…

Analysis of an Assemblage of Discs Employing Interactive Graphics.

DTIC Science & Technology

1980-12-01

facilitate the program’s efficiency. Indeed, the ulsabilitv of tie distinct element method is pred icated on ef f ic ielt Irogramming techniques...paragraphs. Any subsequent user of DISC should not necessarily feel bound to this scheme. 33. At the outset of writing DISC, it was decided that a disc

Biomechanical Evaluation of Different Fixation Methods for Mandibular Anterior Segmental Osteotomy Using Finite Element Analysis, Part Two: Superior Repositioning Surgery With Bone Allograft.

PubMed

Kilinç, Yeliz; Erkmen, Erkan; Kurt, Ahmet

2016-01-01

In this study, the biomechanical behavior of different fixation methods used to fix the mandibular anterior segment following various amounts of superior repositioning was evaluated by using Finite Element Analysis (FEA). The three-dimensional finite element models representing 3 and 5 mm superior repositioning were generated. The gap in between segments was assumed to be filled by block bone allograft and resignated to be in perfect contact with the mandible and segmented bone. Six different finite element models with 2 distinct mobilization rate including 3 different fixation configurations, double right L (DRL), double left L (DLL), or double I (DI) miniplates with monocortical screws, correspondingly were created. A comparative evaluation has been made under vertical, horizontal and oblique loads. The von Mises and principal maximum stress (Pmax) values were calculated by finite element solver programme. The first part of our ongoing Finite Element Analysis research has been addressed to the mechanical behavior of the same fixation configurations in nongrafted models. In comparison with the findings of the first part of the study, it was concluded that bone graft offers superior mechanical stability without any limitation of mobilization and less stress on the fixative appliances as well as in the bone.

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra

PubMed Central

Shewaramani, Sonal; Finn, Thomas J.; Kassen, Rees; Rainey, Paul B.

2017-01-01

Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements. The anaerobically grown populations displayed a mutation rate nearly twice that of the aerobic populations, showed distinct asymmetric mutational strand biases, and greater insertion element activity. Consistent with mutation rate and spectra observations, genes for transposition and recombination repair associated with SVs were up-regulated during anaerobic growth. Together, these results define differences in mutational spectra affecting the evolution of facultative anaerobes. PMID:28103245

Recurrence quantification analysis to characterize cyclical components of environmental elemental exposures during fetal and postnatal development

PubMed Central

Austin, Christine; Gennings, Chris; Tammimies, Kristiina; Bölte, Sven; Arora, Manish

2017-01-01

Environmental exposures to essential and toxic elements may alter health trajectories, depending on the timing, intensity, and mixture of exposures. In epidemiologic studies, these factors are typically analyzed as a function of elemental concentrations in biological matrices measured at one or more points in time. Such an approach, however, fails to account for the temporal cyclicity in the metabolism of environmental chemicals, which if perturbed may lead to adverse health outcomes. Here, we conceptualize and apply a non-linear method–recurrence quantification analysis (RQA)–to quantify cyclical components of prenatal and early postnatal exposure profiles for elements essential to normal development, including Zn, Mn, Mg, and Ca, and elements associated with deleterious health effects or narrow tolerance ranges, including Pb, As, and Cr. We found robust evidence of cyclical patterns in the metabolic profiles of nutrient elements, which we validated against randomized twin-surrogate time-series, and further found that nutrient dynamical properties differ from those of Cr, As, and Pb. Furthermore, we extended this approach to provide a novel method of quantifying dynamic interactions between two environmental exposures. To achieve this, we used cross-recurrence quantification analysis (CRQA), and found that elemental nutrient-nutrient interactions differed from those involving toxicants. These rhythmic regulatory interactions, which we characterize in two geographically distinct cohorts, have not previously been uncovered using traditional regression-based approaches, and may provide a critical unit of analysis for environmental and dietary exposures in epidemiological studies. PMID:29112980

Determination of essential and toxic elements in Cordyceps kyushuensis Kawam by inductively coupled plasma mass spectrometry.

PubMed

Zhang, Guoying; Zhao, Yanxin; Liu, Fengjun; Ling, Jianya; Lin, Jianqiang; Zhang, Changkai

2013-01-01

In this study, a total of 20 elements (essential, non-essential and toxic): lithium (Li), sodium (Na), potassium (K), gallium (Ga), magnesium (Mg), zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), vanadium (V), chromium (Cr), nickel (Ni), cobalt (Co), molybdenum (Mo), selenium (Se), barium (Ba), tin (Sn), arsenic (As), lead (Pb) cadmium (Cd) and mercury (Hg) in natural and cultured Cordyceps kyushuensis have been determined by means of inductively coupled plasma mass spectrometry (ICP-MS). Cultured stroma, natural stroma and natural worm were digested by microwave-assisted method before analysis. The proposed ICP-MS method was validated by analyzing a certified reference material (CRM) GBW10015 (spinach). The results of one-way analysis of variance (ANOVA) revealed that the element concentrations in the three kinds of samples were significantly different (p<0.05). Except for Mg, Zn, Cu, the values of other elemental contents were the highest in the stroma of natural C. kyushuensis. In comparison with the worm, the concentrations of determined elements in wild stroma were higher. The remarkable difference of elemental contents between cultured and natural stroma may be caused by distinct growing environment. This finding highlighted the usefulness of ICP-MS elemental analysis and enhanced the value of C. kyushuensis as a candidate for nourishing food based on its composition. Copyright © 2012 Elsevier B.V. All rights reserved.

Adaptive Bloom Filter: A Space-Efficient Counting Algorithm for Unpredictable Network Traffic

NASA Astrophysics Data System (ADS)

Matsumoto, Yoshihide; Hazeyama, Hiroaki; Kadobayashi, Youki

The Bloom Filter (BF), a space-and-time-efficient hashcoding method, is used as one of the fundamental modules in several network processing algorithms and applications such as route lookups, cache hits, packet classification, per-flow state management or network monitoring. BF is a simple space-efficient randomized data structure used to represent a data set in order to support membership queries. However, BF generates false positives, and cannot count the number of distinct elements. A counting Bloom Filter (CBF) can count the number of distinct elements, but CBF needs more space than BF. We propose an alternative data structure of CBF, and we called this structure an Adaptive Bloom Filter (ABF). Although ABF uses the same-sized bit-vector used in BF, the number of hash functions employed by ABF is dynamically changed to record the number of appearances of a each key element. Considering the hash collisions, the multiplicity of a each key element on ABF can be estimated from the number of hash functions used to decode the membership of the each key element. Although ABF can realize the same functionality as CBF, ABF requires the same memory size as BF. We describe the construction of ABF and IABF (Improved ABF), and provide a mathematical analysis and simulation using Zipf's distribution. Finally, we show that ABF can be used for an unpredictable data set such as real network traffic.

Plasticity - Theory and finite element applications.

NASA Technical Reports Server (NTRS)

Armen, H., Jr.; Levine, H. S.

1972-01-01

A unified presentation is given of the development and distinctions associated with various incremental solution procedures used to solve the equations governing the nonlinear behavior of structures, and this is discussed within the framework of the finite-element method. Although the primary emphasis here is on material nonlinearities, consideration is also given to geometric nonlinearities acting separately or in combination with nonlinear material behavior. The methods discussed here are applicable to a broad spectrum of structures, ranging from simple beams to general three-dimensional bodies. The finite-element analysis methods for material nonlinearity are general in the sense that any of the available plasticity theories can be incorporated to treat strain hardening or ideally plastic behavior.

The profile of repeat-associated histone lysine methylation states in the mouse epigenome

PubMed Central

Martens, Joost H A; O'Sullivan, Roderick J; Braunschweig, Ulrich; Opravil, Susanne; Radolf, Martin; Steinlein, Peter; Jenuwein, Thomas

2005-01-01

Histone lysine methylation has been shown to index silenced chromatin regions at, for example, pericentric heterochromatin or of the inactive X chromosome. Here, we examined the distribution of repressive histone lysine methylation states over the entire family of DNA repeats in the mouse genome. Using chromatin immunoprecipitation in a cluster analysis representing repetitive elements, our data demonstrate the selective enrichment of distinct H3-K9, H3-K27 and H4-K20 methylation marks across tandem repeats (e.g. major and minor satellites), DNA transposons, retrotransposons, long interspersed nucleotide elements and short interspersed nucleotide elements. Tandem repeats, but not the other repetitive elements, give rise to double-stranded (ds) RNAs that are further elevated in embryonic stem (ES) cells lacking the H3-K9-specific Suv39h histone methyltransferases. Importantly, although H3-K9 tri- and H4-K20 trimethylation appear stable at the satellite repeats, many of the other repeat-associated repressive marks vary in chromatin of differentiated ES cells or of embryonic trophoblasts and fibroblasts. Our data define a profile of repressive histone lysine methylation states for the repetitive complement of four distinct mouse epigenomes and suggest tandem repeats and dsRNA as primary triggers for more stable chromatin imprints. PMID:15678104

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

PubMed

Baillie, J Kenneth; Bretherick, Andrew; Haley, Christopher S; Clohisey, Sara; Gray, Alan; Neyton, Lucile P A; Barrett, Jeffrey; Stahl, Eli A; Tenesa, Albert; Andersson, Robin; Brown, J Ben; Faulkner, Geoffrey J; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Itoh, Masayoshi; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Mole, Damian; Bajic, Vladimir B; Heutink, Peter; Rehli, Michael; Kawaji, Hideya; Sandelin, Albin; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A; Hacohen, Nir; Freeman, Thomas C; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Hume, David A

2018-03-01

Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

PubMed Central

Gray, Alan; Neyton, Lucile P. A.; Barrett, Jeffrey; Stahl, Eli A.; Tenesa, Albert; Andersson, Robin; Brown, J. Ben; Faulkner, Geoffrey J.; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Kawaji, Hideya; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A.; Hacohen, Nir; Freeman, Thomas C.; Hayashizaki, Yoshihide; Forrest, Alistair R. R.; Hume, David A.

2018-01-01

Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn’s disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits. PMID:29494619

Analysis of a Waveguide-Fed Metasurface Antenna

NASA Astrophysics Data System (ADS)

Smith, David R.; Yurduseven, Okan; Mancera, Laura Pulido; Bowen, Patrick; Kundtz, Nathan B.

2017-11-01

The metasurface concept has emerged as an advantageous reconfigurable antenna architecture for beam forming and wave-front shaping, with applications that include satellite and terrestrial communications, radar, imaging, and wireless power transfer. The metasurface antenna consists of an array of metamaterial elements distributed over an electrically large structure, each subwavelength in dimension and with subwavelength separation between elements. In the antenna configuration we consider, the metasurface is excited by the fields from an attached waveguide. Each metamaterial element can be modeled as a polarizable dipole that couples the waveguide mode to radiation modes. Distinct from the phased array and electronically-scanned-antenna architectures, a dynamic metasurface antenna does not require active phase shifters and amplifiers but rather achieves reconfigurability by shifting the resonance frequency of each individual metamaterial element. We derive the basic properties of a one-dimensional waveguide-fed metasurface antenna in the approximation in which the metamaterial elements do not perturb the waveguide mode and are noninteracting. We derive analytical approximations for the array factors of the one-dimensional antenna, including the effective polarizabilities needed for amplitude-only, phase-only, and binary constraints. Using full-wave numerical simulations, we confirm the analysis, modeling waveguides with slots or complementary metamaterial elements patterned into one of the surfaces.

Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage.

PubMed

Chidambaranathan, Parameswaran; Jagannadham, Prasanth Tej Kumar; Satheesh, Viswanathan; Kohli, Deshika; Basavarajappa, Santosh Halasabala; Chellapilla, Bharadwaj; Kumar, Jitendra; Jain, Pradeep Kumar; Srinivasan, R

2018-05-01

The heat stress transcription factors (Hsfs) play a prominent role in thermotolerance and eliciting the heat stress response in plants. Identification and expression analysis of Hsfs gene family members in chickpea would provide valuable information on heat stress responsive Hsfs. A genome-wide analysis of Hsfs gene family resulted in the identification of 22 Hsf genes in chickpea in both desi and kabuli genome. Phylogenetic analysis distinctly separated 12 A, 9 B, and 1 C class Hsfs, respectively. An analysis of cis-regulatory elements in the upstream region of the genes identified many stress responsive elements such as heat stress elements (HSE), abscisic acid responsive element (ABRE) etc. In silico expression analysis showed nine and three Hsfs were also expressed in drought and salinity stresses, respectively. Q-PCR expression analysis of Hsfs under heat stress at pod development and at 15 days old seedling stage showed that CarHsfA2, A6, and B2 were significantly upregulated in both the stages of crop growth and other four Hsfs (CarHsfA2, A6a, A6c, B2a) showed early transcriptional upregulation for heat stress at seedling stage of chickpea. These subclasses of Hsfs identified in this study can be further evaluated as candidate genes in the characterization of heat stress response in chickpea.

The New Element Berkelium (Atomic Number 97)

DOE R&D Accomplishments Database

Seaborg, G. T.; Thompson, S. G.; Ghiorso, A.

1950-04-26

An isotope of the element with atomic number 97 has been discovered as a product of the helium-ion bombardment of americium. The name berkelium, symbol Bk, is proposed for element 97. The chemical separation of element 97 from the target material and other reaction products was made by combinations of precipitation and ion exchange adsorption methods making use of its anticipated (III) and (IV) oxidation states and its position as a member of the actinide transition series. The distinctive chemical properties made use of in its separation and the equally distinctive decay properties of the particular isotope constitute the principal evidence for the new element.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens

PubMed Central

Glinsky, Gennadi V.

2016-01-01

Abstract Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8–10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. PMID:27503290

Correlation of soil and sediment organic matter polarity to aqueous sorption of nonionic compounds

USGS Publications Warehouse

Kile, D.E.; Wershaw, R. L.; Chiou, C.T.

1999-01-01

Polarities of the soiL/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment sam pies were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (K(oc)) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxylamide-ester carbons. A plot of the measured partition coefficients (K(oc)) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of K(oc) values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in K(oc) between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with K(oc) illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.Polarities of the soil/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment samples were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (Koc) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxyl-amide-ester carbons. A plot of the measured partition coefficients (Koc) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of Koc values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in Koc between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with Koc illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.

Characterization of ancient glass excavated in Enez (Ancient Ainos) Turkey by combined Instrumental Neutron Activation Analysis and Fourier Transform Infrared spectrometry techniques

NASA Astrophysics Data System (ADS)

Akyuz, Sevim; Akyuz, Tanil; Mukhamedshina, Nuranya M.; Mirsagatova, A. Adiba; Basaran, Sait; Cakan, Banu

2012-05-01

Ancient glass fragments excavated in the archaeological district Enez (Ancient Ainos)-Turkey were investigated by combined Instrumental Neutron Activation Analysis (INAA) and Fourier Transform Infrared (FTIR) spectrometry techniques. Multi-elemental contents of 15 glass fragments that belong to Hellenistic, Roman, Byzantine, and Ottoman Periods, were determined by INAA. The concentrations of twenty six elements (Na, K, Ca, Sc, Cr, Mn, Fe, Co, Cu, Zn, As, Rb, Sr, Sb, Cs, Ba, Ce, Sm, Eu, Tb, Yb, Lu, Hf, Ta, Au and Th), which might be present in the samples as flux, stabilizers, colorants or opacifiers, and impurities, were examined. Chemometric treatment of the INAA data was performed and principle component analysis revealed presence of 3 distinct groups. The thermal history of the glass samples was determined by FTIR spectrometry.

The finite element method in low speed aerodynamics

NASA Technical Reports Server (NTRS)

Baker, A. J.; Manhardt, P. D.

1975-01-01

The finite element procedure is shown to be of significant impact in design of the 'computational wind tunnel' for low speed aerodynamics. The uniformity of the mathematical differential equation description, for viscous and/or inviscid, multi-dimensional subsonic flows about practical aerodynamic system configurations, is utilized to establish the general form of the finite element algorithm. Numerical results for inviscid flow analysis, as well as viscous boundary layer, parabolic, and full Navier Stokes flow descriptions verify the capabilities and overall versatility of the fundamental algorithm for aerodynamics. The proven mathematical basis, coupled with the distinct user-orientation features of the computer program embodiment, indicate near-term evolution of a highly useful analytical design tool to support computational configuration studies in low speed aerodynamics.

Structural mode significance using INCA. [Interactive Controls Analysis computer program

NASA Technical Reports Server (NTRS)

Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

1990-01-01

Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

Multi-elemental imaging of paraffin-embedded human samples by laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Moncayo, S.; Trichard, F.; Busser, B.; Sabatier-Vincent, M.; Pelascini, F.; Pinel, N.; Templier, I.; Charles, J.; Sancey, L.; Motto-Ros, V.

2017-07-01

Chemical elements play central roles for physiological homeostasis in human cells, and their dysregulation might lead to a certain number of pathologies. Novel imaging techniques that improve the work of pathologists for tissue analysis and diagnostics are continuously sought. We report the use of Laser-Induced Breakdown Spectroscopy (LIBS) to perform multi-elemental images of human paraffin-embedded skin samples on the entire biopsy scale in a complementary and compatible way with microscope histopathological examination. A specific instrumental configuration is proposed in order to detect most of the elements of medical interest (i.e. P, Al, Mg, Na, Zn, Si, Fe, and Cu). As an example of medical application, we selected and analysed skin biopsies, including healthy skin tissue, cutaneous metastasis of melanoma, Merkel-cell carcinoma and squamous cell carcinoma. Clear distinctions in the distribution of chemical elements are observed from the different samples investigated. This study demonstrates the high complementarity of LIBS elemental imaging with conventional histopathology, opening new opportunities for any medical application involving metals.

The influence of distinct types of aquatic vegetation on the flow field

NASA Astrophysics Data System (ADS)

Valyrakis, Manousos; Barcroft, Stephen; Yagci, Oral

2014-05-01

The Sustainable management of fluvial systems dealing with flood prevention, erosion protection and restoration of rivers and estuaries requires implementation of soft/green-engineering methods. In-stream aquatic vegetation can be regarded as one of these as it plays an important role for both river ecology (function) and geomorphology (form). The goal of this research is to offer insight gained from pilot experimental studies on the effects of a number of different elements modeling instream, aquatic vegetation on the local flow field. It is hypothesized that elements of the same effective "blockage" area but of distinct characteristics (structure, porosity and flexibility), will affect both the mean and fluctuating levels of the turbulent flow to a different degree. The above hypothesis is investigated through a set of rigorous set of experimental runs which are appropriately designed to assess the variability between the interaction of aquatic elements and flow, both quantitatively and qualitatively. In this investigation three elements are employed to model aquatic vegetation, namely a rigid cylinder, a porous but rigid structure and a flexible live plant (Cupressus Macrocarpa). Firstly, the flow field downstream each of the mentioned elements was measured under steady uniform flow conditions employing acoustic Doppler velocimetry. Three-dimensional flow velocities downstream the vegetation element are acquired along a measurement grid extending about five-fold the element's diameter. These measurements are analyzed to develop mean velocity and turbulent intensity profiles for all velocity components. A detailed comparison between the obtained results is demonstrative of the validity of the above hypothesis as each of the employed elements affects in a different manner and degree the flow field. Then a flow visualization technique, during which fluorescent dye is injected upstream of the element and images are captured for further analysis and comparison, was employed to visualize the flow structures shed downstream the aquatic elements. This method allows to further observe qualitatively and visually identify the different characteristics of the eddies advected downstream, conclusively confirming the results of the aforementioned experimental campaign.

Risk assessment of trace metals in an extreme environment sediment: shallow, hypersaline, alkaline, and industrial Lake Acıgöl, Denizli, Turkey.

PubMed

Budakoglu, Murat; Karaman, Muhittin; Kumral, Mustafa; Zeytuncu, Bihter; Doner, Zeynep; Yildirim, Demet Kiran; Taşdelen, Suat; Bülbül, Ali; Gumus, Lokman

2018-02-23

The major and trace element component of 48 recent sediment samples in three distinct intervals (0-10, 10-20, and 20-30 cm) from Lake Acıgöl is described to present the current contamination levels and grift structure of detrital and evaporate mineral patterns of these sediments in this extreme saline environment. The spatial and vertical concentrations of major oxides were not uniform in the each subsurface interval. However, similar spatial distribution patterns were observed for some major element couples, due mainly to the detrital and evaporate origin of these elements. A sequential extraction procedure including five distinct steps was also performed to determine the different bonds of trace elements in the < 60-μ particulate size of recent sediments. Eleven trace elements (Ni, Fe, Cd, Pb, Cu, Zn, As, Co, Cr, Al and Mn) in nine surface and subsurface sediment samples were analyzed with chemical partitioning procedures to determine the trace element percentage loads in these different sequential extraction phases. The obtained accuracy values via comparison of the bulk trace metal loads with the total loads of five extraction steps were satisfying for the Ni, Fe, Cd, Zn, and Co. While, bulk analysis results of the Cu, Ni, and V elements have good correlation with total organic matter, organic fraction of sequential extraction characterized by Cu, As, Cd, and Pb. Shallow Lake Acıgöl sediment is characteristic with two different redox layer a) oxic upper level sediments, where trace metals are mobilized, b) reduced subsurface level, where the trace metals are precipitated.

Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kass, D.H.; Batzer, M.A.; Deininger, P.L.

The Alu repetitive family of short interspersed elements (SINEs) in primates can be subdivided into distinct subfamilies by specific diagnostic nucleotide changes. The older subfamilies are generally very abundant, while the younger subfamilies have fewer copies. Some of the youngest Alu elements are absent in the orthologous loci of nonhuman primates, indicative of recent retroposition events, the primary mode of SINE evolutions. PCR analysis of one young Alu subfamily (Sb2) member found in the low-density lipoprotein receptor gene apparently revealed the presence of this element in the green monkey, orangutan, gorilla, and chimpanzee genomes, as well as the human genome.more » However, sequence analysis of these genomes revealed a highly mutated, older, primate-specific Alu element was present at this position in the nonhuman primates. Comparison of the flanking DNA sequences upstream of this Alu insertion corresponded to evolution expected for standard primate phylogeny, but comparison of the Alu repeat sequences revealed that the human element departed from this phylogeny. The change in the human sequence apparently occurred by a gene conversion event only within the Alu element itself, converting it from one of the oldest to one of the youngest Alu subfamilies. Although gene conversions of Alu elements are clearly very rare, this finding shows that such events can occur and contribute to specific cases of SINE subfamily evolution.« less

Apollo 15 green glass - Compositional distribution and petrogenesis

NASA Technical Reports Server (NTRS)

Steele, Alison M.; Colson, Russell O.; Korotev, Randy L.; Haskin, Larry A.

1992-01-01

We have characterized a comprehensive suite of individual green-glass beads from Apollo 15 soil to determine interelement behavior and to constrain petrogenetic relationships. We analyzed 365 particles for trace elements by instrumental neutron activation analysis and analyzed 52 of them, selected to cover the compositional ranges observed for trace elements, for major elements by electron microprobe analysis. We confirm the observation of Delano (1979) that the beads comprise discrete compositional groups, although two of the groups he defined are further split on the basis of trace-element compositions. Each of the resulting seven groups has distinct average rare-earth abundances. The coherence between major- and trace-element data was masked in previous studies by imprecision, correlated error, and nonrepresentative sampling of the different groups. Most of the compositional characteristics of the green glasses can be explained by a model for batch equilibrium melting of a nearly homogeneous, ultramafic source region, when the complicating effects of high pressure and low oxygen fugacity are taken into account. The previously puzzling behavior of Ni and Co as apparently incompatible elements may arise from partial reduction of those elements to the zero oxidation state, resulting in low mineral/melt partition coefficients. The model also offers explanations for why the green glasses form boomerang-shaped trends on many two-element variation diagrams and why certain compositions (Groups A and D) are more abundant than glasses with other compositions.

Multiple intensity distributions from a single optical element

NASA Astrophysics Data System (ADS)

Berens, Michael; Bruneton, Adrien; Bäuerle, Axel; Traub, Martin; Wester, Rolf; Stollenwerk, Jochen; Loosen, Peter

2013-09-01

We report on an extension of the previously published two-step freeform optics tailoring algorithm using a Monge-Kantorovich mass transportation framework. The algorithm's ability to design multiple freeform surfaces allows for the inclusion of multiple distinct light paths and hence the implementation of multiple lighting functions in a single optical element. We demonstrate the procedure in the context of automotive lighting, in which a fog lamp and a daytime running lamp are integrated in a single optical element illuminated by two distinct groups of LEDs.

Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.

PubMed

Bekiaris, Pavlos Stephanos; Tekath, Tobias; Staiger, Dorothee; Danisman, Selahattin

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.

Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs

PubMed Central

Staiger, Dorothee

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, “Exploration of Distinctive CREs and CRMs” (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, “CRM Network Generator” (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression. PMID:29298348

Coil-to-coil physiological noise correlations and their impact on fMRI time-series SNR

PubMed Central

Triantafyllou, C.; Polimeni, J. R.; Keil, B.; Wald, L. L.

2017-01-01

Purpose Physiological nuisance fluctuations (“physiological noise”) are a major contribution to the time-series Signal to Noise Ratio (tSNR) of functional imaging. While thermal noise correlations between array coil elements have a well-characterized effect on the image Signal to Noise Ratio (SNR0), the element-to-element covariance matrix of the time-series fluctuations has not yet been analyzed. We examine this effect with a goal of ultimately improving the combination of multichannel array data. Theory and Methods We extend the theoretical relationship between tSNR and SNR0 to include a time-series noise covariance matrix Ψt, distinct from the thermal noise covariance matrix Ψ0, and compare its structure to Ψ0 and the signal coupling matrix SSH formed from the signal intensity vectors S. Results Inclusion of the measured time-series noise covariance matrix into the model relating tSNR and SNR0 improves the fit of experimental multichannel data and is shown to be distinct from Ψ0 or SSH. Conclusion Time-series noise covariances in array coils are found to differ from Ψ0 and more surprisingly, from the signal coupling matrix SSH. Correct characterization of the time-series noise has implications for the analysis of time-series data and for improving the coil element combination process. PMID:26756964

Experimental and analytical analysis of stress-strain behavior in a (90/0 deg)2s, SiC/Ti-15-3 laminate

NASA Technical Reports Server (NTRS)

Lerch, Bradley A.; Melis, Matthew E.; Tong, Mike

1991-01-01

The nonlinear stress strain behavior of 90 degree/0 degree sub 2s, SiC/Ti-15-3 composite laminate was numerically investigated with a finite element, unit cell approach. Tensile stress-strain curves from room temperature experiments depicted three distinct regions of deformation, and these regions were predicted by finite element analysis. The first region of behavior, which was linear elastic, occurred at low applied stresses. As applied stresses increased, fiber/matrix debonding in the 90 degree plies caused a break in the stress-strain curve and initiated a second linear region. In this second region, matrix plasticity in the 90 degree plies developed. The third region, which was typified by nonlinear, stress-strain behavior occr red at high stresses. In this region, the onset of matrix plasticity in the 0 degree plies stiffened the laminate in the direction transverse to the applied load. Metallographic sections confirmed the existence of matrix plasticity in specific areas of the structure. Finite element analysis also predicted these locations of matrix slip.

Contact stresses in gear teeth: A new method of analysis

NASA Technical Reports Server (NTRS)

Somprakit, Paisan; Huston, Ronald L.; Oswald, Fred B.

1991-01-01

A new, innovative procedure called point load superposition for determining the contact stresses in mating gear teeth. It is believed that this procedure will greatly extend both the range of applicability and the accuracy of gear contact stress analysis. Point load superposition is based upon fundamental solutions from the theory of elasticity. It is an iterative numerical procedure which has distinct advantages over the classical Hertz method, the finite element method, and over existing applications with the boundary element method. Specifically, friction and sliding effects, which are either excluded from or difficult to study with the classical methods, are routinely handled with the new procedure. Presented here are the basic theory and the algorithms. Several examples are given. Results are consistent with those of the classical theories. Applications to spur gears are discussed.

Differentiation of commercial vermiculite based on statistical analysis of bulk chemical data: Fingerprinting vermiculite from Libby, Montana U.S.A

USGS Publications Warehouse

Gunter, M.E.; Singleton, E.; Bandli, B.R.; Lowers, H.A.; Meeker, G.P.

2005-01-01

Major-, minor-, and trace-element compositions, as determined by X-ray fluorescence (XRF) analysis, were obtained on 34 samples of vermiculite to ascertain whether chemical differences exist to the extent of determining the source of commercial products. The sample set included ores from four deposits, seven commercially available garden products, and insulation from four attics. The trace-element distributions of Ba, Cr, and V can be used to distinguish the Libby vermiculite samples from the garden products. In general, the overall composition of the Libby and South Carolina deposits appeared similar, but differed from the South Africa and China deposits based on simple statistical methods. Cluster analysis provided a good distinction of the four ore types, grouped the four attic samples with the Libby ore, and, with less certainty, grouped the garden samples with the South Africa ore.

Cyberbullying: the challenge to define.

PubMed

Langos, Colette

2012-06-01

Cyberbullying is a reality of the digital age. To address this phenomenon, it becomes imperative to understand exactly what cyberbullying is. Thus, establishing a workable and theoretically sound definition is essential. This article contributes to the existing literature in relation to the definition of cyberbullying. The specific elements of repetition, power imbalance, intention, and aggression, regarded as essential criteria of traditional face-to-face bullying, are considered in the cyber context. It is posited that the core bullying elements retain their importance and applicability in relation to cyberbullying. The element of repetition is in need of redefining, given the public nature of material in the online environment. In this article, a clear distinction between direct and indirect cyberbullying is made and a model definition of cyberbullying is offered. Overall, the analysis provided lends insight into how the essential bullying elements have evolved and should apply in our parallel cyber universe.

Coupled tomography and distinct-element-method approach to exploring the granular media microstructure in a jamming hourglass

NASA Astrophysics Data System (ADS)

Tsukahara, M.; Mitrovic, S.; Gajdosik, V.; Margaritondo, G.; Pournin, L.; Ramaioli, M.; Sage, D.; Hwu, Y.; Unser, M.; Liebling, Th. M.

2008-06-01

We describe an approach for exploring microscopic properties of granular media that couples x-ray microtomography and distinct-element-method (DEM) simulations through image analysis. We illustrate it via the study of the intriguing phenomenon of instant arching in an hourglass (in our case a cylinder filled with a polydisperse mixture of glass beads that has a small circular shutter in the bottom). X-ray tomography provides three-dimensional snapshots of the microscopic conditions of the system both prior to opening the shutter, and thereafter, once jamming is completed. The process time in between is bridged using DEM simulation, which settles to positions in remarkably good agreement with the x-ray images. Specifically designed image analysis procedures accurately extract the geometrical information, i.e., the positions and sizes of the beads, from the raw x-ray tomographs, and compress the data representation from initially 5 gigabytes to a few tens of kilobytes per tomograph. The scope of the approach is explored through a sensitivity analysis to input data perturbations in both bead sizes and positions. We establish that accuracy of size—much more than position—estimates is critical, thus explaining the difficulty in considering a mixture of beads of different sizes. We further point to limits in the replication ability of granular flows away from equilibrium; i.e., the difficulty of numerically reproducing chaotic motion.

Two-Dimensional Nonlinear Finite Element Analysis of CMC Microstructures

NASA Technical Reports Server (NTRS)

Mital, Subodh K.; Goldberg, Robert K.; Bonacuse, Peter J.

2011-01-01

Detailed two-dimensional finite element analyses of the cross-sections of a model CVI (chemical vapor infiltrated) SiC/SiC (silicon carbide fiber in a silicon carbide matrix) ceramic matrix composites are performed. High resolution images of the cross-section of this composite material are generated using serial sectioning of the test specimens. These images are then used to develop very detailed finite element models of the cross-sections using the public domain software OOF2 (Object Oriented Analysis of Material Microstructures). Examination of these images shows that these microstructures have significant variability and irregularity. How these variabilities manifest themselves in the variability in effective properties as well as the stress distribution, damage initiation and damage progression is the overall objective of this work. Results indicate that even though the macroscopic stress-strain behavior of various sections analyzed is very similar, each section has a very distinct damage pattern when subjected to in-plane tensile loads and this damage pattern seems to follow the unique architectural and microstructural details of the analyzed sections.

Broadband diffractive lens or imaging element

DOEpatents

Ceglio, Natale M.; Hawryluk, Andrew M.; London, Richard A.; Seppala, Lynn G.

1991-01-01

A broadband diffractive lens or imaging element produces a sharp focus and/or a high resolution image with broad bandwidth illuminating radiation. The diffractive lens is sectored or segmented into regions, each of which focuses or images a distinct narrowband of radiation but all of which have a common focal length. Alternatively, a serial stack of minus filters, each with a diffraction pattern which focuses or images a distinct narrowband of radiation but all of which have a common focal length, is used. The two approaches can be combined. Multifocal broadband diffractive elements can also be formed.

Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate

PubMed Central

Kimura-Yoshida, Chiharu; Yan, Kuo; Bormuth, Olga; Ding, Qiong; Nakanishi, Akiko; Sasaki, Takeshi; Hirakawa, Mika; Sumiyama, Kenta; Furuta, Yasuhide; Tarabykin, Victor; Matsuo, Isao; Okada, Norihiro

2016-01-01

Acquisition of cis-regulatory elements is a major driving force of evolution, and there are several examples of developmental enhancers derived from transposable elements (TEs). However, it remains unclear whether one enhancer element could have been produced via cooperation among multiple, yet distinct, TEs during evolution. Here we show that an evolutionarily conserved genomic region named AS3_9 comprises three TEs (AmnSINE1, X6b_DNA and MER117), inserted side-by-side, and functions as a distal enhancer for wnt5a expression during morphogenesis of the mammalian secondary palate. Functional analysis of each TE revealed step-by-step retroposition/transposition and co-option together with acquisition of a binding site for Msx1 for its full enhancer function during mammalian evolution. The present study provides a new perspective suggesting that a huge variety of TEs, in combination, could have accelerated the diversity of cis-regulatory elements involved in morphological evolution. PMID:27741242

Organic matrix-related mineralization of sea urchin spicules, spines, test and teeth.

PubMed

Veis, Arthur

2011-06-01

The camarodont echinoderms have five distinct mineralized skeletal elements: embryonic spicules, mature test, spines, lantern stereom and teeth. The spicules are transient structural elements whereas the spines, and test plates are permanent. The teeth grow continuously. The mineral is a high magnesium calcite, but the magnesium content is different in each type of skeletal element, varying from 5 to 40 mole% Mg. The organic matrix creates the spaces and environments for crystal initiation and growth. The detailed mechanisms of crystal regulation are not known, but acidic and phosphorylated matrix proteins may be of special importance. Biochemical studies, sequencing of the complete genome, and high-throughput proteomic analysis have not yet provided insight into the mechanisms of crystallization, calcite composition, and orientation applicable to all skeletal elements. The embryonic spicules are not representative of the mature skeletal elements. The next phase of research will have to focus on the specific localization of the proteins and individual biochemistries of each system with regard to mineral content and placement.

Characterization and distribution of repetitive elements in association with genes in the human genome.

PubMed

Liang, Kai-Chiang; Tseng, Joseph T; Tsai, Shaw-Jenq; Sun, H Sunny

2015-08-01

Repetitive elements constitute more than 50% of the human genome. Recent studies implied that the complexity of living organisms is not just a direct outcome of a number of coding sequences; the repetitive elements, which do not encode proteins, may also play a significant role. Though scattered studies showed that repetitive elements in the regulatory regions of a gene control gene expression, no systematic survey has been done to report the characterization and distribution of various types of these repetitive elements in the human genome. Sequences from 5' and 3' untranslated regions and upstream and downstream of a gene were downloaded from the Ensembl database. The repetitive elements in the neighboring of each gene were identified and classified using cross-matching implemented in the RepeatMasker. The annotation and distribution of distinct classes of repetitive elements associated with individual gene were collected to characterize genes in association with different types of repetitive elements using systems biology program. We identified a total of 1,068,400 repetitive elements which belong to 37-class families and 1235 subclasses that are associated with 33,761 genes and 57,365 transcripts. In addition, we found that the tandem repeats preferentially locate proximal to the transcription start site (TSS) of genes and the major function of these genes are involved in developmental processes. On the other hand, interspersed repetitive elements showed a tendency to be accumulated at distal region from the TSS and the function of interspersed repeat-containing genes took part in the catabolic/metabolic processes. Results from the distribution analysis were collected and used to construct a gene-based repetitive element database (GBRED; http://www.binfo.ncku.edu.tw/GBRED/index.html). A user-friendly web interface was designed to provide the information of repetitive elements associated with any particular gene(s). This is the first study focusing on the gene-associated repetitive elements in the human genome. Our data showed distinct genes associated with different kinds of repetitive element and implied such combination may shape the function of these genes. Aside from the conventional view of these elements in genome evolution, results from this study offer a systemic review to facilitate exploitation of these elements in genome function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Trace elements in lake sediments measured by the PIXE technique

NASA Astrophysics Data System (ADS)

Gatti, Luciana V.; Mozeto, Antônio A.; Artaxo, Paulo

1999-04-01

Lakes are ecosystems where there is a great potential of metal accumulation in sediments due to their depositional characteristics. Total concentration of trace elements was measured on a 50 cm long sediment core from the Infernão Lake, that is an oxbow lake of the Moji-Guaçu River basin, in the state of São Paulo, Brazil. Dating of the core shows up to 180 yrs old sediment layers. The use of the PIXE technique for elemental analysis avoids the traditional acid digestion procedure common in other techniques. The multielemental characteristic of PIXE allows a simultaneous determination of about 20 elements in the sediment samples, such as, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Rb, Sr, Zr, Ba, and Pb. Average values for the elemental composition were found to be similar to the bulk crustal composition. The lake flooding pattern strongly influences the time series of the elemental profiles. Factor analysis of the elemental variability shows five factors. Two of the factors represent the mineralogical matrix, and others represent the organic component, a factor with lead, and another loaded with chromium. The mineralogical component consists of elements such as, Fe, Al, V, Ti, Mn, Ni, K, Zr, Sr, Cu and Zn. The variability of Si is explained by two distinct factors, because it is influenced by two different sources, aluminum-silicates and quartz, and the effect of inundation are different for each other. The organic matter is strongly associated with calcium, and also bounded with S, Zn, Cu and P. Lead and chromium appears as separated factors, although it is not clear the evidences for their anthropogenic origin. The techniques developed for sample preparation and PIXE analysis was proven as advantageous and provided very good reproducibility and accuracy.

System and method for authentication of goods

DOEpatents

Kaish, Norman; Fraser, Jay; Durst, David I.

1999-01-01

An authentication system comprising a medium having a plurality of elements, the elements being distinctive, detectable and disposed in an irregular pattern or having an intrinsic irregularity. Each element is characterized by a determinable attribute distinct from a two-dimensional coordinate representation of simple optical absorption or simple optical reflection intensity. An attribute and position of the plurality of elements, with respect to a positional reference is detected. A processor generates an encrypted message including at least a portion of the attribute and position of the plurality of elements. The encrypted message is recorded in physical association with the medium. The elements are preferably dichroic fibers, and the attribute is preferably a polarization or dichroic axis, which may vary over the length of a fiber. An authentication of the medium based on the encrypted message may be authenticated with a statistical tolerance, based on a vector mapping of the elements of the medium, without requiring a complete image of the medium and elements to be recorded.

Comet composition and density analyzer

NASA Technical Reports Server (NTRS)

Clark, B. C.

1982-01-01

Distinctions between cometary material and other extraterrestrial materials (meteorite suites and stratospherically-captured cosmic dust) are addressed. The technique of X-ray fluorescence (XRF) for analysis of elemental composition is involved. Concomitant with these investigations, the problem of collecting representative samples of comet dust (for rendezvous missions) was solved, and several related techniques such as mineralogic analysis (X-ray diffraction), direct analysis of the nucleus without docking (electron macroprobe), dust flux rate measurement, and test sample preparation were evaluated. An explicit experiment concept based upon X-ray fluorescence analysis of biased and unbiased sample collections was scoped and proposed for a future rendezvous mission with a short-period comet.

Major factors influencing the elemental composition of surface estuarine sediments: the case of 15 estuaries in Portugal.

PubMed

Mil-Homens, M; Vale, C; Raimundo, J; Pereira, P; Brito, P; Caetano, M

2014-07-15

Upper sediments (0-5 cm) were sampled in 94 sites of water bodies of the fifteen Portuguese estuaries characterized by distinct settings of climate, topography and lithology, and marked by diverse anthropogenic pressures. Confined areas recognized as highly anthropogenic impacted, as well as areas dominated by erosion or frequently dredged were not sampled. Grain size, organic carbon (Corg), Al and trace elements (As, Cd, Co, Cr, Cu, Hg, Ni, Pb and Zn) were determined. Normalisation of trace element concentrations to Al and Corg, correlations between elements and Principal Component Analysis (PCA) allowed identifying elemental associations and the relevance of grain-size, lithology and anthropogenic inputs on sediment chemical composition. Whereas grain-size is the dominant effect for the majority of the studied estuaries, the southern estuaries Mira, Arade and Guadiana are dominated by specific lithologies of their river basins, and anthropogenic effects are identified in Ave, Leça, Tagus and Sado. This study emphasizes how baseline values of trace elements in sediments may vary within and among estuarine systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

PubMed

Glinsky, Gennadi V

2016-09-19

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A discourse on sensitivity analysis for discretely-modeled structures

NASA Technical Reports Server (NTRS)

Adelman, Howard M.; Haftka, Raphael T.

1991-01-01

A descriptive review is presented of the most recent methods for performing sensitivity analysis of the structural behavior of discretely-modeled systems. The methods are generally but not exclusively aimed at finite element modeled structures. Topics included are: selections of finite difference step sizes; special consideration for finite difference sensitivity of iteratively-solved response problems; first and second derivatives of static structural response; sensitivity of stresses; nonlinear static response sensitivity; eigenvalue and eigenvector sensitivities for both distinct and repeated eigenvalues; and sensitivity of transient response for both linear and nonlinear structural response.

Evidence for holistic episodic recollection via hippocampal pattern completion.

PubMed

Horner, Aidan J; Bisby, James A; Bush, Daniel; Lin, Wen-Jing; Burgess, Neil

2015-07-02

Recollection is thought to be the hallmark of episodic memory. Here we provide evidence that the hippocampus binds together the diverse elements forming an event, allowing holistic recollection via pattern completion of all elements. Participants learn complex 'events' from multiple overlapping pairs of elements, and are tested on all pairwise associations. At encoding, element 'types' (locations, people and objects/animals) produce activation in distinct neocortical regions, while hippocampal activity predicts memory performance for all within-event pairs. When retrieving a pairwise association, neocortical activity corresponding to all event elements is reinstated, including those incidental to the task. Participant's degree of incidental reinstatement correlates with their hippocampal activity. Our results suggest that event elements, represented in distinct neocortical regions, are bound into coherent 'event engrams' in the hippocampus that enable episodic recollection--the re-experiencing or holistic retrieval of all aspects of an event--via a process of hippocampal pattern completion and neocortical reinstatement.

Seasonal differences in trace element concentrations and distribution in Spartina alterniflora root tissue

DOE PAGES

Feng, Huan; Qian, Yu; Cochran, J. Kirk; ...

2018-04-13

This study uses nanometer-scale synchrotron X-ray nanofluorescence to investigate season differences in concentrations and distributions of major (Ca, K, S and P) and trace elements (As, Cr, Cu, Fe and Zn) in the root system of Spartina alterniflora collected from Jamaica Bay, New York, in April and September 2015. The root samples were cross-sectioned at a thickness of 10 μm. Selected areas in the root epidermis and endodermis were mapped with a sampling resolution of 100 and 200 nm, varying with the mapping areas. The results indicate that trace element concentrations in the epidermis and endodermis vary among the elementsmore » measured, possibly because of their different chemical properties or their ability to act as micronutrients for the plants. Elemental concentrations (As, Ca, Cr, Cu, Fe, K, P, S and Zn) within each individual root sample and between the root samples collected during two different seasons are both significantly different (p < 0.01). Furthermore, this study indicates that the nonessential elements (As and Cr) are significantly correlated (p < 0.01) with Fe, with high concentrations in the root epidermis, while others are not, implying that Fe may be a barrier to nonessential element transport in the root system. Hierarchy cluster analysis shows two distinct groups, one including As, Cr and Fe and the other the rest of the elements measured. Factor analysis also indicates that the processes and mechanisms controlling element transport in the root system can be different between the nutrient and nonessential elements.« less

Seasonal differences in trace element concentrations and distribution in Spartina alterniflora root tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Huan; Qian, Yu; Cochran, J. Kirk

This study uses nanometer-scale synchrotron X-ray nanofluorescence to investigate season differences in concentrations and distributions of major (Ca, K, S and P) and trace elements (As, Cr, Cu, Fe and Zn) in the root system of Spartina alterniflora collected from Jamaica Bay, New York, in April and September 2015. The root samples were cross-sectioned at a thickness of 10 μm. Selected areas in the root epidermis and endodermis were mapped with a sampling resolution of 100 and 200 nm, varying with the mapping areas. The results indicate that trace element concentrations in the epidermis and endodermis vary among the elementsmore » measured, possibly because of their different chemical properties or their ability to act as micronutrients for the plants. Elemental concentrations (As, Ca, Cr, Cu, Fe, K, P, S and Zn) within each individual root sample and between the root samples collected during two different seasons are both significantly different (p < 0.01). Furthermore, this study indicates that the nonessential elements (As and Cr) are significantly correlated (p < 0.01) with Fe, with high concentrations in the root epidermis, while others are not, implying that Fe may be a barrier to nonessential element transport in the root system. Hierarchy cluster analysis shows two distinct groups, one including As, Cr and Fe and the other the rest of the elements measured. Factor analysis also indicates that the processes and mechanisms controlling element transport in the root system can be different between the nutrient and nonessential elements.« less

Autoshaping with common and distinctive stimulus elements, compact and dispersed arrays.

PubMed

Sperling, S E; Perkins, M E

1979-05-01

Four groups of pigeons were trained with a standard autoshaping procedure in which a brief fixed-duration interval always followed by a grain delivery alternated with a longer variable-duration interval never associated with grain delivery. One of two stimuli was always presented during each interval. One of them contained three black dots and a black star on a green background; the other contained four black dots on a green background. The four elements of each stimulus were arranged in a more compact array for two groups and in a more dispersed array for the other two groups. Which of the two stimuli preceded grain delivery was counterbalanced within each pair of groups. The speed of occurrence of the first autoshaped peck was not affected by whether the stimulus containing the distinctive star element preceded grain delivery, but autoshaping was faster when the stimulus arrays were compact than when they were dispersed. During 560 response-independent training trials that followed the first autoshaped peck, this pattern reversed; both discriminative control over responding and the relative frequency of pecking the stimulus that preceded grain delivery were greater for the two groups where this stimulus contained the discriminative element than for the two groups where it contained only common elements. During subsequent testing with stimuli containing only a single element each, the distinctive feature was responded to proportionately more often by the two groups for which it had been an element of the stimulus preceding grain delivery than by the two groups for which it had been an element of the stimulus complex that never was associated with grain delivery. These data add further support to the hypothesis that the initial occurrence of autoshaped responding and its subsequent maintenance are not affected by the same variables. They also suggest that automaintenance is as sensitive as response-dependent training to the presence or absence of a distinctive stimulus element among several common elements and that this sensitivity appears to be independent of the specific method used for presenting the stimuli during automaintenance.

Autoshaping with common and distinctive stimulus elements, compact and dispersed arrays1

PubMed Central

Sperling, Sally E.; Perkins, Mark E.

1979-01-01

Four groups of pigeons were trained with a standard autoshaping procedure in which a brief fixed-duration interval always followed by a grain delivery alternated with a longer variable-duration interval never associated with grain delivery. One of two stimuli was always presented during each interval. One of them contained three black dots and a black star on a green background; the other contained four black dots on a green background. The four elements of each stimulus were arranged in a more compact array for two groups and in a more dispersed array for the other two groups. Which of the two stimuli preceded grain delivery was counterbalanced within each pair of groups. The speed of occurrence of the first autoshaped peck was not affected by whether the stimulus containing the distinctive star element preceded grain delivery, but autoshaping was faster when the stimulus arrays were compact than when they were dispersed. During 560 response-independent training trials that followed the first autoshaped peck, this pattern reversed; both discriminative control over responding and the relative frequency of pecking the stimulus that preceded grain delivery were greater for the two groups where this stimulus contained the discriminative element than for the two groups where it contained only common elements. During subsequent testing with stimuli containing only a single element each, the distinctive feature was responded to proportionately more often by the two groups for which it had been an element of the stimulus preceding grain delivery than by the two groups for which it had been an element of the stimulus complex that never was associated with grain delivery. These data add further support to the hypothesis that the initial occurrence of autoshaped responding and its subsequent maintenance are not affected by the same variables. They also suggest that automaintenance is as sensitive as response-dependent training to the presence or absence of a distinctive stimulus element among several common elements and that this sensitivity appears to be independent of the specific method used for presenting the stimuli during automaintenance. PMID:16812139

Dissection of cis-regulatory element architecture of the rice oleosin gene promoters to assess abscisic acid responsiveness in suspension-cultured rice cells.

PubMed

Kim, Sol; Lee, Soo-Bin; Han, Chae-Seong; Lim, Mi-Na; Lee, Sung-Eun; Yoon, In Sun; Hwang, Yong-Sic

2017-08-01

Oleosins are the most abundant proteins in the monolipid layer surrounding neutral storage lipids that form oil bodies in plants. Several lines of evidence indicate that they are physiologically important for the maintenance of oil body structure and for mobilization of the lipids stored inside. Rice has six oleosin genes in its genome, the expression of all of which was found to be responsive to abscisic acid (ABA) in our examination of mature embryo and aleurone tissues. The 5'-flanking region of OsOle5 was initially characterized for its responsiveness to ABA through a transient expression assay system using the protoplasts from suspension-cultured rice cells. A series of successive deletions and site-directed mutations identified five regions critical for the hormonal induction of its promoter activity. A search for cis-acting elements in these regions deposited in a public database revealed that they contain various promoter elements previously reported to be involved in the ABA response of various genes. A gain-of-function experiment indicated that multiple copies of all five regions were sufficient to provide the minimal promoter with a distinct ABA responsiveness. Comparative sequence analysis of the short, but still ABA-responsive, promoters of OsOle genes revealed no common modular architecture shared by them, indicating that various distinct promoter elements and independent trans-acting factors are involved in the ABA responsiveness of rice oleosin multigenes. Copyright © 2017 Elsevier GmbH. All rights reserved.

Coil-to-coil physiological noise correlations and their impact on functional MRI time-series signal-to-noise ratio.

PubMed

Triantafyllou, Christina; Polimeni, Jonathan R; Keil, Boris; Wald, Lawrence L

2016-12-01

Physiological nuisance fluctuations ("physiological noise") are a major contribution to the time-series signal-to-noise ratio (tSNR) of functional imaging. While thermal noise correlations between array coil elements have a well-characterized effect on the image Signal to Noise Ratio (SNR 0 ), the element-to-element covariance matrix of the time-series fluctuations has not yet been analyzed. We examine this effect with a goal of ultimately improving the combination of multichannel array data. We extend the theoretical relationship between tSNR and SNR 0 to include a time-series noise covariance matrix Ψ t , distinct from the thermal noise covariance matrix Ψ 0 , and compare its structure to Ψ 0 and the signal coupling matrix SS H formed from the signal intensity vectors S. Inclusion of the measured time-series noise covariance matrix into the model relating tSNR and SNR 0 improves the fit of experimental multichannel data and is shown to be distinct from Ψ 0 or SS H . Time-series noise covariances in array coils are found to differ from Ψ 0 and more surprisingly, from the signal coupling matrix SS H . Correct characterization of the time-series noise has implications for the analysis of time-series data and for improving the coil element combination process. Magn Reson Med 76:1708-1719, 2016. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Nutrient Intake Is Associated with Longevity Characterization by Metabolites and Element Profiles of Healthy Centenarians

PubMed Central

Cai, Da; Zhao, Shancang; Li, Danlei; Chang, Fang; Tian, Xiangxu; Huang, Guohong; Zhu, Zhenjun; Liu, Dong; Dou, Xiaowei; Li, Shubo; Zhao, Mouming; Li, Quanyang

2016-01-01

The relationships between diet and metabolites as well as element profiles in healthy centenarians are important but remain inconclusive. Therefore, to test the interesting hypothesis that there would be distinctive features of metabolites and element profiles in healthy centenarians, and that these would be associated with nutrient intake; the short chain fatty acids (SCFAs), total bile acids and ammonia in feces, phenol, p-cresol, uric acid, urea, creatinine and ammonia in urine, and element profiles in fingernails were determined in 90 healthy elderly people, including centenarians from Bama county (China)—a famous longevous region—and elderly people aged 80–99 from the longevous region and a non-longevous region. The partial least squares-discriminant analysis was used for pattern recognition. As a result, the centenarians showed a distinct metabolic pattern. Seven characteristic components closely related to the centenarians were identified, including acetic acid, total SCFA, Mn, Co, propionic acid, butyric acid and valeric acid. Their concentrations were significantly higher in the centenarians group (p < 0.05). Additionally, the dietary fiber intake was positively associated with butyric acid contents in feces (r = 0.896, p < 0.01), and negatively associated with phenol in urine (r = −0.326, p < 0.01). The results suggest that the specific metabolic pattern of centenarians may have an important and positive influence on the formation of the longevity phenomenon. Elevated dietary fiber intake should be a path toward health and longevity. PMID:27657115

Broadband diffractive lens or imaging element

DOEpatents

Ceglio, Natale M.; Hawryluk, Andrew M.; London, Richard A.; Seppala, Lynn G.

1993-01-01

A broadband diffractive lens or imaging element produces a sharp focus and/or a high resolution image with broad bandwidth illuminating radiation. The diffractive lens is sectored or segmented into regions, each of which focuses or images a distinct narrowband of radiation but all of which have a common focal length. Alternatively, a serial stack of minus filters, each with a diffraction pattern which focuses or images a distinct narrowband of radiation but all of which have a common focal length, is used. The two approaches can be combined. Multifocal broadband diffractive elements can also be formed. Thin film embodiments are described.

Broadband diffractive lens or imaging element

DOEpatents

Ceglio, N.M.; Hawryluk, A.M.; London, R.A.; Seppala, L.G.

1993-10-26

A broadband diffractive lens or imaging element produces a sharp focus and/or a high resolution image with broad bandwidth illuminating radiation. The diffractive lens is sectored or segmented into regions, each of which focuses or images a distinct narrowband of radiation but all of which have a common focal length. Alternatively, a serial stack of minus filters, each with a diffraction pattern which focuses or images a distinct narrowband of radiation but all of which have a common focal length, is used. The two approaches can be combined. Multifocal broadband diffractive elements can also be formed. Thin film embodiments are described. 21 figures.

Local Structure and Short-Range Order in a NiCoCr Solid Solution Alloy

DOE PAGES

Zhang, F. X.; Zhao, Shijun; Jin, Ke; ...

2017-05-19

Multi-element solid solution alloys are intrinsically disordered on the atomic scale, and many of their advanced properties originate from the unique local structural characteristics. We measured the local structure of a NiCoCr solid solution alloy with X-ray/neutron total scattering and extended X-ray absorption fine structure (EXAFS) techniques. The atomic pair distribution function analysis (PDF) did not exhibit distinct structural distortion. But, EXAFS analysis suggested that the Cr atoms are favorably bonded with Ni and Co in the solid solution alloys. This short-range order (SRO) plays a role in the distinct low values of electrical and thermal conductivities in Ni-based solidmore » solution alloys when Cr is incorporated. Both the long-range and local structures of the NiCoCr alloy upon Ni ion irradiation were studied and an irradiation-induced enhancement of SRO was found.« less

Element Interactivity and Intrinsic, Extraneous, and Germane Cognitive Load

ERIC Educational Resources Information Center

Sweller, John

2010-01-01

In cognitive load theory, element interactivity has been used as the basic, defining mechanism of intrinsic cognitive load for many years. In this article, it is suggested that element interactivity underlies extraneous cognitive load as well. By defining extraneous cognitive load in terms of element interactivity, a distinct relation between…

Whole body-element composition of Atlantic salmon Salmo salar influenced by migration direction and life stage in three distinct populations.

PubMed

Ebel, J D; Leroux, S J; Robertson, M J; Dempson, J B

2016-11-01

Body-element content was measured for three life stages of wild Atlantic salmon Salmo salar from three distinct Newfoundland populations as individuals crossed between freshwater and marine ecosystems. Life stage explained most of the variation in observed body-element concentration whereas river of capture explained very little variation. Element composition of downstream migrating post-spawn adults (i.e. kelts) and juvenile smolts were similar and the composition of these two life stages strongly differed from adults migrating upstream to spawn. Low variation within life stages and across populations suggests that S. salar may exert rheostatic control of their body-element composition. Additionally, observed differences in trace element concentration between adults and other life stages were probably driven by the high carbon concentration in adults because abundant elements, such as carbon, can strongly influence the observed concentrations of less abundant elements. Thus, understanding variation among individuals in trace elements composition requires the measurement of more abundant elements. Changes in element concentration with ontogeny have important consequences the role of fishes in ecosystem nutrient cycling and should receive further attention. © 2016 The Fisheries Society of the British Isles.

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

PubMed Central

Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

2007-01-01

Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks. PMID:17672917

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

PubMed

Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

2007-08-01

In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.

Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

PubMed Central

Prazak, Lisa; Fujioka, Miki; Gergen, J. Peter

2010-01-01

The relatively simple combinatorial rules responsible for establishing the initial metameric expression of sloppy-paired-1 (slp1) in the Drosophila blastoderm embryo make this system an attractive model for investigating the mechanism of regulation by pair rule transcription factors. This investigation of slp1 cis-regulatory architecture identifies two distinct elements, a proximal early stripe element (PESE) and a distal early stripe element (DESE) located from −3.1 kb to −2.5 kb and from −8.1 kb to −7.1 kb upstream of the slp1 promoter, respectively, that mediate this early regulation. The proximal element expresses only even-numbered stripes and mediates repression by Even-skipped (Eve) as well as by the combination of Runt and Fushi-tarazu (Ftz). A 272 basepair sub-element of PESE retains Eve-dependent repression, but is expressed throughout the even-numbered parasegments due to the loss of repression by Runt and Ftz. In contrast, the distal element expresses both odd and even-numbered stripes and also drives inappropriate expression in the anterior half of the odd-numbered parasegments due to an inability to respond to repression by Eve. Importantly, a composite reporter gene containing both early stripe elements recapitulates pair-rule gene-dependent regulation in a manner beyond what is expected from combining their individual patterns. These results indicate interactions involving distinct cis-elements contribute to the proper integration of pair-rule regulatory information. A model fully accounting for these results proposes that metameric slp1 expression is achieved through the Runt-dependent regulation of interactions between these two pair-rule response elements and the slp1 promoter. PMID:20435028

Using NASTRAN to solve symmetric structures with nonsymmetric loads

NASA Technical Reports Server (NTRS)

Butler, T. G.

1982-01-01

A method for computation of reflective dihedral symmetry in symmetrical structures under nonsymmetric loads is described. The method makes it possible to confine the analysis to a half, a quarter, or an octagonal segment. The symmetry of elastic deformation is discussed, and antisymmetrical deformation is distinguished from nonsymmetrical deformation. Modes of deformation considered are axial, bending, membrane, and torsional deformation. Examples of one and two dimensional elements are presented and extended to three dimensional elements. The method of setting up a problem within NASTRAN is discussed. The technique is applied to a thick structure having quarter symmetry which was modeled with polyhedra and subjected to five distinct loads having varying degrees of symmetry.

Inorganic profile of some Brazilian medicinal plants obtained from ethanolic extract and ''in natura'' samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferreira, M.O.M.; de Sousa, P.T.; Salvador, V.L.R.

The Anadenathera macrocarpa, Schinus molle, Hymenaea courbaril, Cariniana legalis, Solidago microglossa and Stryphnodendron barbatiman, were collected ''in natura'' samples (leaves, flowers, barks and seeds) from different commercial suppliers. The pharmaco-active compounds in ethanolic extracts had been made by the Mato Grosso Federal University (UFMT). The energy-dispersive x-ray fluorescence (ED-XRF) spectrometry was used for the elemental analysis in different parts of the plants and respective ethanolic extracts. The Ca, Cl, Cu, Fe, K, Mg, Mn, Na, Ni, P, Rb, S, Sr and Zn concentrations were determined by the fundamental parameters method. Some specimens showed a similar inorganic profile for ''in natura''more » and ethanolic extract samples and some ones showed a distinct inorganic profile. For example, the Anadenathera macrocarpa showed a similar concentration in Mg, P, Cu, Zn and Rb elements in ''in natura'' and ethanolic extract samples; however very different concentration in Na, S, Cl, K , Ca, Mn, Fe and Sr was observed in distinctive samples. The Solidago microglossa showed the K, Ca, Cl, S, Mg, P and Fe elements as major constituents in both samples, suggesting that the extraction process did not affect in a considerable way the ''in natura'' inorganic composition. The elemental composition of the different parts of the plants (leaves, flowers, barks and seeds) has been also determined. For example, the Schinus molle specimen showed P, K, Cl and Ca elements as major constituents in the seeds, Mg, K and Sr in the barks and Mg, S, Cl and Mn in the leaves, demonstrating a differentiated elementary distribution. These inorganic profiles will contribute to evaluate the quality control of the Brazilian herbaceous trade and also will assist to identify which parts of the medicinal plants has greater therapeutic effect.« less

The Variscan calc-alkalic plutonism of western Corsica: mineralogy and major and trace element geochemistry

NASA Astrophysics Data System (ADS)

Cocherie, A.; Rossi, Ph.; Le Bel, L.

1984-10-01

Petrographic and structural observations on the calc-alkalic plutonism of western Corsica revealed the existence of several successively emplaced units associated with large basic bodies. The present mineralogical and geochemical study deals with the genesis, evolution and relationships of these different units. Basic plutonism is represented by three genetically linked types of rock: norites and troctolites with cumulate textures characterized by low REE contents and either no Eu anomaly or a positive Eu anomaly; gabbros with enriched LREE relatively to HREE patterns, probably close to an initial basaltic liquid; and diorites ranging up to charnockites which represent liquids evolved to varying degrees, mainly by fractional crystallization. Trace element data and studies on the evolution of pyroxene pairs demonstrate the consanguinity of these calc-alkaline basic rocks which are derived from a high alumina basaltic melt. The various granitoids (granodiorites, monzogranites and leucocratic monzogranites, i.e., adamellites) have distinct evolution trends as shown by the composition of their mafic minerals and by trace element distributions. They cannot be considered as being derivatives of the basic suite and they cannot be related by a common fractionation sequence. Rather, they represent distinctive batches of crustal anatexis. In addition, hybridization phenomena with the basic melt are noticed in granodiorites. The particular problem of the low La/Yb, Eu/Eu∗ and the high U, Th, Cs leucocratic monzogranites is discussed in detail. In addition to more conventional trace element diagrams, the simultaneous statistical treatment of all the geochemical data by correspondence factor analysis is shown to be a very use tool in distinguishing between the different units and to classify the elements according to their geochemical properties.

Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements.

PubMed

Nunes, Luiz R; Rosato, Yoko B; Muto, Nair H; Yanai, Giane M; da Silva, Vivian S; Leite, Daniela B; Gonçalves, Edmilson R; de Souza, Alessandra A; Coletta-Filho, Helvécio D; Machado, Marcos A; Lopes, Silvio A; de Oliveira, Regina Costa

2003-04-01

Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species.

Integration and segregation in auditory scene analysis

NASA Astrophysics Data System (ADS)

Sussman, Elyse S.

2005-03-01

Assessment of the neural correlates of auditory scene analysis, using an index of sound change detection that does not require the listener to attend to the sounds [a component of event-related brain potentials called the mismatch negativity (MMN)], has previously demonstrated that segregation processes can occur without attention focused on the sounds and that within-stream contextual factors influence how sound elements are integrated and represented in auditory memory. The current study investigated the relationship between the segregation and integration processes when they were called upon to function together. The pattern of MMN results showed that the integration of sound elements within a sound stream occurred after the segregation of sounds into independent streams and, further, that the individual streams were subject to contextual effects. These results are consistent with a view of auditory processing that suggests that the auditory scene is rapidly organized into distinct streams and the integration of sequential elements to perceptual units takes place on the already formed streams. This would allow for the flexibility required to identify changing within-stream sound patterns, needed to appreciate music or comprehend speech..

Optimising LAN access to grid enabled storage elements

NASA Astrophysics Data System (ADS)

Stewart, G. A.; Cowan, G. A.; Dunne, B.; Elwell, A.; Millar, A. P.

2008-07-01

When operational, the Large Hadron Collider experiments at CERN will collect tens of petabytes of physics data per year. The worldwide LHC computing grid (WLCG) will distribute this data to over two hundred Tier-1 and Tier-2 computing centres, enabling particle physicists around the globe to access the data for analysis. Although different middleware solutions exist for effective management of storage systems at collaborating institutes, the patterns of access envisaged for Tier-2s fall into two distinct categories. The first involves bulk transfer of data between different Grid storage elements using protocols such as GridFTP. This data movement will principally involve writing ESD and AOD files into Tier-2 storage. Secondly, once datasets are stored at a Tier-2, physics analysis jobs will read the data from the local SE. Such jobs require a POSIX-like interface to the storage so that individual physics events can be extracted. In this paper we consider the performance of POSIX-like access to files held in Disk Pool Manager (DPM) storage elements, a popular lightweight SRM storage manager from EGEE.

Fallon, Nevada FORGE Distinct Element Reservoir Modeling

DOE Data Explorer

Blankenship, Doug; Pettitt, Will; Riahi, Azadeh; Hazzard, Jim; Blanksma, Derrick

2018-03-12

Archive containing input/output data for distinct element reservoir modeling for Fallon FORGE. Models created using 3DEC, InSite, and in-house Python algorithms (ITASCA). List of archived files follows; please see 'Modeling Metadata.pdf' (included as a resource below) for additional file descriptions. Data sources include regional geochemical model, well positions and geometry, principal stress field, capability for hydraulic fractures, capability for hydro-shearing, reservoir geomechanical model-stimulation into multiple zones, modeled thermal behavior during circulation, and microseismicity.

Soluble trace elements and total mercury in Arctic Alaskan snow

USGS Publications Warehouse

Snyder-Conn, E.; Garbarino, J.R.; Hoffman, G.L.; Oelkers, A.

1997-01-01

Ultraclean field and laboratory procedures were used to examine trace element concentrations in northern Alaskan snow. Sixteen soluble trace elements and total mercury were determined in snow core samples representing the annual snowfall deposited during the 1993-94 season at two sites in the Prudhoe Bay oil field and nine sites in the Arctic National Wildlife Refuge (Arctic NWR). Results indicate there were two distinct point sources for trace elements in the Prudhoe Bay oil field - a source associated with oil and gas production and a source associated with municipal solid-waste incineration. Soluble trace element concentrations measured in snow from the Arctic NWR resembled concentrations of trace elements measured elsewhere in the Arctic using clean sample-collection and processing techniques and were consistent with deposition resulting from widespread arctic atmospheric contamination. With the exception of elements associated with sea salts, there were no orographic or east-west trends observed in the Arctic NWR data, nor were there any detectable influences from the Prudhoe Bay oil field, probably because of the predominant easterly and northeasterly winds on the North Slope of Alaska. However, regression analysis on latitude suggested significant south-to-north increases in selected trace element concentrations, many of which appear unrelated to the sea salt contribution.

Distinctive Pattern of Serum Elements During the Progression of Alzheimer’s Disease

PubMed Central

Paglia, Giuseppe; Miedico, Oto; Cristofano, Adriana; Vitale, Michela; Angiolillo, Antonella; Chiaravalle, Antonio Eugenio; Corso, Gaetano; Di Costanzo, Alfonso

2016-01-01

Element profiling is an interesting approach for understanding neurodegenerative processes, considering that compelling evidences show that element toxicity might play a crucial role in the onset and progression of Alzheimer’s disease (AD). Aim of this study was to profile 22 serum elements in subjects with or at risk of AD. Thirtyfour patients with probable AD, 20 with mild cognitive impairment (MCI), 24 with subjective memory complaint (SMC) and 40 healthy subjects (HS) were included in the study. Manganese, iron, copper, zinc, selenium, thallium, antimony, mercury, vanadium and molybdenum changed significantly among the 4 groups. Several essential elements, such as manganese, selenium, zinc and iron tended to increase in SMC and then progressively to decrease in MCI and AD. Toxic elements show a variable behavior, since some elements tended to increase, while others tended to decrease in AD. A multivariate model, built using a panel of six essential elements (manganese, iron, copper, zinc, selenium and calcium) and their ratios, discriminated AD patients from HS with over 90% accuracy. These findings suggest that essential and toxic elements contribute to generate a distinctive signature during the progression of AD, and their monitoring in elderly might help to detect preclinical stages of AD. PMID:26957294

Distinctive Pattern of Serum Elements During the Progression of Alzheimer's Disease.

PubMed

Paglia, Giuseppe; Miedico, Oto; Cristofano, Adriana; Vitale, Michela; Angiolillo, Antonella; Chiaravalle, Antonio Eugenio; Corso, Gaetano; Di Costanzo, Alfonso

2016-03-09

Element profiling is an interesting approach for understanding neurodegenerative processes, considering that compelling evidences show that element toxicity might play a crucial role in the onset and progression of Alzheimer's disease (AD). Aim of this study was to profile 22 serum elements in subjects with or at risk of AD. Thirtyfour patients with probable AD, 20 with mild cognitive impairment (MCI), 24 with subjective memory complaint (SMC) and 40 healthy subjects (HS) were included in the study. Manganese, iron, copper, zinc, selenium, thallium, antimony, mercury, vanadium and molybdenum changed significantly among the 4 groups. Several essential elements, such as manganese, selenium, zinc and iron tended to increase in SMC and then progressively to decrease in MCI and AD. Toxic elements show a variable behavior, since some elements tended to increase, while others tended to decrease in AD. A multivariate model, built using a panel of six essential elements (manganese, iron, copper, zinc, selenium and calcium) and their ratios, discriminated AD patients from HS with over 90% accuracy. These findings suggest that essential and toxic elements contribute to generate a distinctive signature during the progression of AD, and their monitoring in elderly might help to detect preclinical stages of AD.

Genetic and epigenetic variation in the lineage specification of regulatory T cells

PubMed Central

Arvey, Aaron; van der Veeken, Joris; Plitas, George; Rich, Stephen S; Concannon, Patrick; Rudensky, Alexander Y

2015-01-01

Regulatory T (Treg) cells, which suppress autoimmunity and other inflammatory states, are characterized by a distinct set of genetic elements controlling their gene expression. However, the extent of genetic and associated epigenetic variation in the Treg cell lineage and its possible relation to disease states in humans remain unknown. We explored evolutionary conservation of regulatory elements and natural human inter-individual epigenetic variation in Treg cells to identify the core transcriptional control program of lineage specification. Analysis of single nucleotide polymorphisms in core lineage-specific enhancers revealed disease associations, which were further corroborated by high-resolution genotyping to fine map causal polymorphisms in lineage-specific enhancers. Our findings suggest that a small set of regulatory elements specify the Treg lineage and that genetic variation in Treg cell-specific enhancers may alter Treg cell function contributing to polygenic disease. DOI: http://dx.doi.org/10.7554/eLife.07571.001 PMID:26510014

Investigation of the differentiation of ex vivo nerve and fat tissues using laser-induced breakdown spectroscopy (LIBS): Prospects for tissue-specific laser surgery.

PubMed

Mehari, Fanuel; Rohde, Maximillian; Kanawade, Rajesh; Knipfer, Christian; Adler, Werner; Klämpfl, Florian; Stelzle, Florian; Schmidt, Michael

2016-10-01

In the present study, the elemental compositions of fat and nerve tissue during their plasma mediated laser ablation are studied in the context of tissue differentiation for laser surgery applications by using Laser-Induced Breakdown Spectroscopy (LIBS). Tissue samples of porcine fat and nerve were prepared as ex vivo experimental objects. Plasma mediated laser ablation is performed using an Nd : YAG laser in open air and under normal stray light conditions. The performed measurements suggest that the two tissue types show a high similarity in terms of qualitative elemental composition while at the same time revealing a distinct difference in the concentration of the constituent elements. Different analysis approaches are evaluated and discussed to optimize the tissue-differentiation performance of the LIBS approach. Plasma mediated laser tissue ablation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-guided statistical textural distinctiveness for salient region detection in natural images.

PubMed

Scharfenberger, Christian; Wong, Alexander; Clausi, David A

2015-01-01

We propose a simple yet effective structure-guided statistical textural distinctiveness approach to salient region detection. Our method uses a multilayer approach to analyze the structural and textural characteristics of natural images as important features for salient region detection from a scale point of view. To represent the structural characteristics, we abstract the image using structured image elements and extract rotational-invariant neighborhood-based textural representations to characterize each element by an individual texture pattern. We then learn a set of representative texture atoms for sparse texture modeling and construct a statistical textural distinctiveness matrix to determine the distinctiveness between all representative texture atom pairs in each layer. Finally, we determine saliency maps for each layer based on the occurrence probability of the texture atoms and their respective statistical textural distinctiveness and fuse them to compute a final saliency map. Experimental results using four public data sets and a variety of performance evaluation metrics show that our approach provides promising results when compared with existing salient region detection approaches.

Elemental micro-PIXE mapping of hypersensitive lesions in Lagenaria sphaerica (Cucurbitaceae) resistant to Sphaerotheca fuliginea (powdery mildew)

NASA Astrophysics Data System (ADS)

Weiersbye-Witkowski, I. M.; Przybylowicz, W. J.; Straker, C. J.; Mesjasz-Przybylowicz, J.

1997-07-01

Genotypes of the Southern African cucurbit, Lagenaria sphaerica, that are resistant to powdery-mildew ( Sphaerotheca fuliginea) exhibit foliar hypersensitive (HS) lesions on inoculation with this fungal pathogen. Elemental distributions across radially symmetrical HS lesions, surrounding unlesioned leaf tissue and uninoculated leaf tissue, were obtained using the true elemental imaging system (Dynamic Analysis) of the NAC Van de Graaff nuclear microprobe. Raster scans of 3 MeV protons were complemented by simultaneous PIXE and BS point analyses. The composition of cellulose (C 6H 10O 5) was used as constant matrix composition for scans, and the sample thickness was found from BS spectra. Si and elements heavier than Ca contributed to matrix composition within HS lesions and the locally elevated Ca raised the limits of detection for some trace metals of interest. In comparison to uninoculated tissue, inoculated tissue was characterised by higher overall concentrations of all measured elements except Cu. Fully developed, 6 day-old HS lesions and the surrounding tissue could be divided into five zones, centred on the fungal infection site. Each zone was characterized by distinct local elemental distributions (either depletion, or accumulation to potentially phytotoxic levels).

Analytical validation of an explicit finite element model of a rolling element bearing with a localised line spall

NASA Astrophysics Data System (ADS)

Singh, Sarabjeet; Howard, Carl Q.; Hansen, Colin H.; Köpke, Uwe G.

2018-03-01

In this paper, numerically modelled vibration response of a rolling element bearing with a localised outer raceway line spall is presented. The results were obtained from a finite element (FE) model of the defective bearing solved using an explicit dynamics FE software package, LS-DYNA. Time domain vibration signals of the bearing obtained directly from the FE modelling were processed further to estimate time-frequency and frequency domain results, such as spectrogram and power spectrum, using standard signal processing techniques pertinent to the vibration-based monitoring of rolling element bearings. A logical approach to analyses of the numerically modelled results was developed with an aim to presenting the analytical validation of the modelled results. While the time and frequency domain analyses of the results show that the FE model generates accurate bearing kinematics and defect frequencies, the time-frequency analysis highlights the simulation of distinct low- and high-frequency characteristic vibration signals associated with the unloading and reloading of the rolling elements as they move in and out of the defect, respectively. Favourable agreement of the numerical and analytical results demonstrates the validation of the results from the explicit FE modelling of the bearing.

A Combined Remote Sensing-Numerical Modelling Approach to the Stability Analysis of Delabole Slate Quarry, Cornwall, UK

NASA Astrophysics Data System (ADS)

Havaej, Mohsen; Coggan, John; Stead, Doug; Elmo, Davide

2016-04-01

Rock slope geometry and discontinuity properties are among the most important factors in realistic rock slope analysis yet they are often oversimplified in numerical simulations. This is primarily due to the difficulties in obtaining accurate structural and geometrical data as well as the stochastic representation of discontinuities. Recent improvements in both digital data acquisition and incorporation of discrete fracture network data into numerical modelling software have provided better tools to capture rock mass characteristics, slope geometries and digital terrain models allowing more effective modelling of rock slopes. Advantages of using improved data acquisition technology include safer and faster data collection, greater areal coverage, and accurate data geo-referencing far exceed limitations due to orientation bias and occlusion. A key benefit of a detailed point cloud dataset is the ability to measure and evaluate discontinuity characteristics such as orientation, spacing/intensity and persistence. This data can be used to develop a discrete fracture network which can be imported into the numerical simulations to study the influence of the stochastic nature of the discontinuities on the failure mechanism. We demonstrate the application of digital terrestrial photogrammetry in discontinuity characterization and distinct element simulations within a slate quarry. An accurately geo-referenced photogrammetry model is used to derive the slope geometry and to characterize geological structures. We first show how a discontinuity dataset, obtained from a photogrammetry model can be used to characterize discontinuities and to develop discrete fracture networks. A deterministic three-dimensional distinct element model is then used to investigate the effect of some key input parameters (friction angle, spacing and persistence) on the stability of the quarry slope model. Finally, adopting a stochastic approach, discrete fracture networks are used as input for 3D distinct element simulations to better understand the stochastic nature of the geological structure and its effect on the quarry slope failure mechanism. The numerical modelling results highlight the influence of discontinuity characteristics and kinematics on the slope failure mechanism and the variability in the size and shape of the failed blocks.

Skeletal trauma reflects hunting behaviour in extinct sabre-tooth cats and dire wolves.

PubMed

Brown, Caitlin; Balisi, Mairin; Shaw, Christopher A; Van Valkenburgh, Blaire

2017-04-10

Skeletal-injury frequency and distribution are likely to reflect hunting behaviour in predatory vertebrates and might therefore differ between species with distinct hunting modes. Two Pleistocene predators from the Rancho La Brea asphalt seeps, the sabre-tooth cat, Smilodon fatalis, and dire wolf, Canis dirus, represent ambush and pursuit predators, respectively. On the basis of a collection of over 1,900 pathological elements, the frequency of traumatic injury across skeletal elements in these two species was calculated. Here we show that the frequency of trauma in the sabre-tooth cat exceeds that of the dire wolf (4.3% compared to 2.8%), implying that the killing behaviour of S. fatalis entailed greater risk of injury. The distribution of traumatic injuries also differed between the two species. S. fatalis, an ambush predator, was injured more often than expected across the lumbar vertebrae and shoulders whereas C. dirus, a pursuit predator, had higher than expected levels of injury in the limbs and cervical vertebrae. Spatial analysis was used to quantify differences in the distribution of putative hunting injuries. Analysis of injury locations discriminated true hotspots from injury-dense areas and facilitated interpretation of predatory behaviour, demonstrating the use of spatial analyses in the study of vertebrate behaviour and evolution. These results suggest that differences in trauma distribution reflect distinct hazards of each species' hunting mode.

Provirophages and transpovirons as the diverse mobilome of giant viruses.

PubMed

Desnues, Christelle; La Scola, Bernard; Yutin, Natalya; Fournous, Ghislain; Robert, Catherine; Azza, Saïd; Jardot, Priscilla; Monteil, Sonia; Campocasso, Angélique; Koonin, Eugene V; Raoult, Didier

2012-10-30

A distinct class of infectious agents, the virophages that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements, the transpovirons. The transpovirons are linear DNA elements of ~7 kb that encompass six to eight protein-coding genes, two of which are homologous to virophage genes. Fluorescence in situ hybridization showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns and inteins constitute the complex, interconnected mobilome of the giant viruses and are likely to substantially contribute to interviral gene transfer.

Provirophages and transpovirons as the diverse mobilome of giant viruses

PubMed Central

Desnues, Christelle; La Scola, Bernard; Yutin, Natalya; Fournous, Ghislain; Robert, Catherine; Azza, Saïd; Jardot, Priscilla; Monteil, Sonia; Campocasso, Angélique; Koonin, Eugene V.; Raoult, Didier

2012-01-01

A distinct class of infectious agents, the virophages that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements, the transpovirons. The transpovirons are linear DNA elements of ∼7 kb that encompass six to eight protein-coding genes, two of which are homologous to virophage genes. Fluorescence in situ hybridization showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns and inteins constitute the complex, interconnected mobilome of the giant viruses and are likely to substantially contribute to interviral gene transfer. PMID:23071316

Copper, zinc, gallium and germanium distributions in taenite lamellae of iron meteorites and their importance for cooling rate estimations

NASA Astrophysics Data System (ADS)

Braun-Dullaeus, Karl-Ulrich; Traxel, Kurt

1995-02-01

One method forestimating cooling rates of meteorite parent bodies is to model measured nickel distributions in taenite lamellae of iron meteorites. Goldstein and Ogilvie ( Geochim. Cosmochim. Acta29, 893, 1965) and Rasmussen ( Icarus45, 564, 1981) developed techniques based on this idea to examine the cooling history in the temperature range between ˜700 and ˜400°C. As a result of Instrumental Neutron Activation Analysis (INAA) Rasmussen et al. ( Meteoritics23, 105, 1988) postulated that some trace elements would also be good cooling rate indicators. They argued that elements with distinct diffusion behavior are sensitive to different temperature ranges. The new Heidelberg proton microprobe uses the method of Proton Induced X-ray Emission (PIXE) for elemental analysis. This microprobe is an appropriate instrument to measure distributions of trace elements with a spatial resolution of 2 μm. We demonstrated on the iron meteorites Cape York (Agpalilik), Toluca and Odessa that the elements copper, zinc, gallium and germanium imitate the profiles of nickel in taenite lamella. The interpretation of the Zn, Ga and Ge profiles leads to the conclusion that these elements undergo diffusion mechanisms comparable to those of Ni. The numerical simulation of Cu distributions with a simplified model points out that little new information can be obtained about the cooling history of the meteorites by modelling Cu profiles. To simulate Zn, Ga or Ge distributions, the use of ternary phase diagrams is necessary.

Quantifying Diffuse Contamination: Method and Application to Pb in Soil.

PubMed

Fabian, Karl; Reimann, Clemens; de Caritat, Patrice

2017-06-20

A new method for detecting and quantifying diffuse contamination at the continental to regional scale is based on the analysis of cumulative distribution functions (CDFs). It uses cumulative probability (CP) plots for spatially representative data sets, preferably containing >1000 determinations. Simulations demonstrate how different types of contamination influence elemental CDFs of different sample media. It is found that diffuse contamination is characterized by a distinctive shift of the low-concentration end of the distribution of the studied element in its CP plot. Diffuse contamination can be detected and quantified via either (1) comparing the distribution of the contaminating element to that of an element with a geochemically comparable behavior but no contamination source (e.g., Pb vs Rb), or (2) comparing the top soil distribution of an element to the distribution of the same element in subsoil samples from the same area, taking soil forming processes into consideration. Both procedures are demonstrated for geochemical soil data sets from Europe, Australia, and the U.S.A. Several different data sets from Europe deliver comparable results at different scales. Diffuse Pb contamination in surface soil is estimated to be <0.5 mg/kg for Australia, 1-3 mg/kg for Europe, and 1-2 mg/kg, or at least <5 mg/kg, for the U.S.A. The analysis presented here also allows recognition of local contamination sources and can be used to efficiently monitor diffuse contamination at the continental to regional scale.

Discrete elements for 3D microfluidics.

PubMed

Bhargava, Krisna C; Thompson, Bryant; Malmstadt, Noah

2014-10-21

Microfluidic systems are rapidly becoming commonplace tools for high-precision materials synthesis, biochemical sample preparation, and biophysical analysis. Typically, microfluidic systems are constructed in monolithic form by means of microfabrication and, increasingly, by additive techniques. These methods restrict the design and assembly of truly complex systems by placing unnecessary emphasis on complete functional integration of operational elements in a planar environment. Here, we present a solution based on discrete elements that liberates designers to build large-scale microfluidic systems in three dimensions that are modular, diverse, and predictable by simple network analysis techniques. We develop a sample library of standardized components and connectors manufactured using stereolithography. We predict and validate the flow characteristics of these individual components to design and construct a tunable concentration gradient generator with a scalable number of parallel outputs. We show that these systems are rapidly reconfigurable by constructing three variations of a device for generating monodisperse microdroplets in two distinct size regimes and in a high-throughput mode by simple replacement of emulsifier subcircuits. Finally, we demonstrate the capability for active process monitoring by constructing an optical sensing element for detecting water droplets in a fluorocarbon stream and quantifying their size and frequency. By moving away from large-scale integration toward standardized discrete elements, we demonstrate the potential to reduce the practice of designing and assembling complex 3D microfluidic circuits to a methodology comparable to that found in the electronics industry.

Determining distinct circuit in complete graphs using permutation

NASA Astrophysics Data System (ADS)

Karim, Sharmila; Ibrahim, Haslinda; Darus, Maizon Mohd

2017-11-01

A Half Butterfly Method (HBM) is a method introduced to construct the distinct circuits in complete graphs where used the concept of isomorphism. The Half Butterfly Method was applied in the field of combinatorics such as in listing permutations of n elements. However the method of determining distinct circuit using HBM for n > 4 is become tedious. Thus, in this paper, we present the method of generating distinct circuit using permutation.

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster.

PubMed

Liu, Xiaochuan; Freitas, Jaime; Zheng, Dinghai; Oliveira, Marta S; Hoque, Mainul; Martins, Torcato; Henriques, Telmo; Tian, Bin; Moreira, Alexandra

2017-12-01

Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster , expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis -element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate. © 2017 Liu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Geochemical and Isotopic Estimates of Eolian Dust in Soils of the San Juan Mountains, USA.

NASA Astrophysics Data System (ADS)

Lawrence, C. R.; Neff, J. C.; Farmer, L.; Painter, T. H.; Landry, C.

2007-12-01

Eolian dust deposition in the San Juan Mountain Range in southern Colorado has increased 5-7 fold in the past two centuries. This dust deposition contributes an exogenous supply of biologically relevant elements such as Ca, K, Mg, and P to these alpine ecosystems in the form of fine textured mineral particulates. The deposition of eolian dust may be an underestimated factor of soil formation and soil chemistry in these alpine settings. The importance of eolian dust relative to the weathering of local bedrock likely varies across bedrock types. The San Juan Range is geologically diverse with distinct regions of Meso-proterozic crystalline granites in the Weminuche Wilderness, Mesozoic sedimentary layers near Molas Pass in the San Juan National Forest, and Tertiary volcanic geology found on Red Mountain Pass in the Uncompahgre National Forest. Principle component analysis of element chemistry shows that bedrock and soils from these sites cluster by geology. In addition, these groups are chemically distinct from eolian dust collected from snow in the San Juan Range. Several elements seem to drive the difference of dust from soils and bedrock including Ca, Sr, Cu and Cd. The purpose of this research was to estimate the relative contribution of eolian dust to alpine soil element pools in the San Juan Mountains across a range of local geologic parent material. A calculation of element mass- balance shows that Cu and Cd are enriched in the surface soils of both volcanic and sedimentary soils relative to concentrations in local bedrock. However, Ca is enriched only in volcanic soils. These observations support the notion that eolian dust contributes to soil formation and that the relative contribution of dust across the landscape varies with geology. In addition to element mass-balance estimates we utilize Sr and Nd isotope measurements of soil, bedrock, and dust to further constrain the importance of eolian dust to these alpine soils.

And lead us (not) into persuasion…? Persuasive technology and the ethics of communication.

PubMed

Spahn, Andreas

2012-12-01

The paper develops ethical guidelines for the development and usage of persuasive technologies (PT) that can be derived from applying discourse ethics to this type of technologies. The application of discourse ethics is of particular interest for PT, since 'persuasion' refers to an act of communication that might be interpreted as holding the middle between 'manipulation' and 'convincing'. One can distinguish two elements of discourse ethics that prove fruitful when applied to PT: the analysis of the inherent normativity of acts of communication ('speech acts') and the Habermasian distinction between 'communicative' and 'strategic rationality' and their broader societal interpretation. This essay investigates what consequences can be drawn if one applies these two elements of discourse ethics to PT.

A new procedure for calculating contact stresses in gear teeth

NASA Technical Reports Server (NTRS)

Somprakit, Paisan; Huston, Ronald L.

1991-01-01

A numerical procedure for evaluating and monitoring contact stresses in meshing gear teeth is discussed. The procedure is intended to extend the range of applicability and to improve the accuracy of gear contact stress analysis. The procedure is based upon fundamental solution from the theory of elasticity. It is an iterative numerical procedure. The method is believed to have distinct advantages over the classical Hertz method, the finite-element method, and over existing approaches with the boundary element method. Unlike many classical contact stress analyses, friction effects and sliding are included. Slipping and sticking in the contact region are studied. Several examples are discussed. The results are in agreement with classical results. Applications are presented for spur gears.

Trace-metal concentrations, waters from selected sky lakes, streams and springs, northern Shawangunk Mountains, New York: geologic and ecologic implications

USGS Publications Warehouse

Friedman, J.D.; Huth, P.C.; Smiley, D.

1990-01-01

Reconnaissance sampling and chemical analysis of water from selected lakes, streams and springs of the northern Shawangunk Mountains in 1987 to 1988 to determine the influence of lithology on trace-metal concentrations in surface water, and to establish a base level of concentration of 27 selected metals by ICP-AES and Hg by cold-vapor AAS methods, for geochemical exploration, ecologic, acid-rain, and climatic-change studies, have yielded trace-metal concentrations greater than detection limits for 10 metallic elements. Eighteen additional metallic elements were also present in trace quantities below the quantitative detection limit. Two distinct geochemical populations are related to source lithology and pH. -from Authors

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

PubMed Central

2013-01-01

Background Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group. PMID:24088337

Indentation creep behaviors of amorphous Cu-based composite alloys

NASA Astrophysics Data System (ADS)

Song, Defeng; Ma, Xiangdong; Qian, Linfang

2018-04-01

This work reports the indentation creep behaviors of two Si2Zr3/amorphous Cu-based composite alloys utilizing nanoindentation technique. By analysis with Kelvin model, the retardation spectra of alloys at different positions, detached and attached regions to the intermetallics, were deduced. For the indentation of detached regions to Si2Zr3 intermetallics in both alloys, very similarity in creep displacement can be observed and retardation spectra show a distinct disparity in the second retardation peak. For the indentation of detached regions, the second retardation spectra also display distinct disparity. At both positions, the retardation spectra suggest that Si elements may lead to the relatively dense structure in the amorphous matrix and to form excessive Si2Zr3 intermetallics which may deteriorate the plastic deformation of current Cu-based composite alloys.

Discontinuum-Equivalent Continuum Analysis of the Stability of Tunnels in a Deep Coal Mine Using the Distinct Element Method

NASA Astrophysics Data System (ADS)

Shreedharan, Srisharan; Kulatilake, Pinnaduwa H. S. W.

2016-05-01

An imperative task for successful underground mining is to ensure the stability of underground structures. This is more so for deep excavations which may be under significantly high stresses. In this manuscript, we present stability studies on two tunnels, a horseshoe-shaped and an inverted arch-shaped tunnel, in a deep coal mine in China, performed using the 3DEC distinct element code. The rock mass mechanical property values for the tunnel shapes have been estimated through a back-analysis procedure using available field deformation data. The back-analysis has been carried out through a pseudo-time dependent support installation routine which incorporates the effect of time through a stress-relaxation mechanism. The back-analysis indicates that the rock mass cohesion, tensile strength, uniaxial compressive strength, and elastic modulus values are about 35-45 % of the corresponding intact rock property values. Additionally, the importance of incorporating stress relaxation before support installation has been illustrated through the increased support factor of safety and reduced grout failures. The calibrated models have been analyzed for different supported and unsupported cases to estimate the significance and adequacy of the current supports being used in the mine and to suggest a possible optimization. The effects of supports have been demonstrated using deformations and yield zones around the tunnels, and average factors of safety and grout failures of the supports. The use of longer supports and floor bolting has provided greater stability for the rock masses around the tunnels. Finally, a comparison between the two differently shaped tunnels establishes that the inverted arch tunnel may be more efficient in reducing roof sag and floor heave for the existing geo-mining conditions.

Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning.

PubMed

Davies, T Jonathan; Urban, Mark C; Rayfield, Bronwyn; Cadotte, Marc W; Peres-Neto, Pedro R

2016-09-01

Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity-ecosystem-function literature. © 2016 by the Ecological Society of America.

Imperial College near infrared spectroscopy neuroimaging analysis framework.

PubMed

Orihuela-Espina, Felipe; Leff, Daniel R; James, David R C; Darzi, Ara W; Yang, Guang-Zhong

2018-01-01

This paper describes the Imperial College near infrared spectroscopy neuroimaging analysis (ICNNA) software tool for functional near infrared spectroscopy neuroimaging data. ICNNA is a MATLAB-based object-oriented framework encompassing an application programming interface and a graphical user interface. ICNNA incorporates reconstruction based on the modified Beer-Lambert law and basic processing and data validation capabilities. Emphasis is placed on the full experiment rather than individual neuroimages as the central element of analysis. The software offers three types of analyses including classical statistical methods based on comparison of changes in relative concentrations of hemoglobin between the task and baseline periods, graph theory-based metrics of connectivity and, distinctively, an analysis approach based on manifold embedding. This paper presents the different capabilities of ICNNA in its current version.

Intrapopulation variation in stature and body proportions: social status and sex differences in an Italian medieval population (Trino Vercellese, VC).

PubMed

Vercellotti, Giuseppe; Stout, Sam D; Boano, Rosa; Sciulli, Paul W

2011-06-01

The phenotypic expression of adult body size and shape results from synergistic interactions between hereditary factors and environmental conditions experienced during growth. Variation in body size and shape occurs even in genetically relatively homogeneous groups, due to different occurrence, duration, and timing of growth insults. Understanding the causes and patterns of intrapopulation variation can foster meaningful information on early life conditions in living and past populations. This study assesses the pattern of biological variation in body size and shape attributable to sex and social status in a medieval Italian population. The sample includes 52 (20 female, 32 male) adult individuals from the medieval population of Trino Vercellese, Italy. Differences in element size and overall body size (skeletal height and body mass) were assessed through Monte Carlo methods, while univariate non-parametric tests and Principal Component Analysis (PCA) were employed to examine segmental and overall body proportions. Discriminant Analysis was employed to determine the predictive value of individual skeletal elements for social status in the population. Our results highlight a distinct pattern in body size and shape variation in relation to status and sex. Male subsamples exhibit significant postcranial variation in body size, while female subsamples express smaller, nonsignificant differences. The analysis of segmental proportions highlighted differences in trunk/lower limb proportions between different status samples, and PCA indicated that in terms of purely morphological variation high status males were distinct from all other groups. The pattern observed likely resulted from a combination of biological factors and cultural practices. Copyright © 2011 Wiley-Liss, Inc.

Binary rare earth element-Ni/Co metallic glasses with distinct β-relaxation behaviors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Z. G.; Wang, Z.; Wang, W. H., E-mail: whw@iphy.ac.cn

2015-10-21

We report the formation of a series of rare earth element (RE)-Ni/Co binary metallic glasses (MGs) with unusual distinct β-relaxation peak compared with that of most of the reported MGs which usually exhibit as an excess wing or a shoulder. The β-relaxation behavior of RE-Ni/Co MGs is sensitive to the composition and the atomic radii of the RE and can be tuned through changing the fraction of RE-Ni (or Co) atomic pairs. The novel RE-Ni/Co MGs with distinct β-relaxation can serve as model system to investigate the nature of the β-relaxation as well as its relations with other physical andmore » mechanical properties of MGs.« less

Determination of minor and trace elements concentration in kidney stones using elemental analysis techniques

NASA Astrophysics Data System (ADS)

Srivastava, Anjali

The determination of accurate material composition of a kidney stone is crucial for understanding the formation of the kidney stone as well as for preventive therapeutic strategies. Radiations probing instrumental activation analysis techniques are excellent tools for identification of involved materials present in the kidney stone. The X-ray fluorescence (XRF) and neutron activation analysis (NAA) experiments were performed and different kidney stones were analyzed. The interactions of X-ray photons and neutrons with matter are complementary in nature, resulting in distinctly different materials detection. This is the first approach to utilize combined X-ray fluorescence and neutron activation analysis for a comprehensive analysis of the kideny stones. Presently, experimental studies in conjunction with analytical techniques were used to determine the exact composition of the kidney stone. The use of open source program Python Multi-Channel Analyzer was utilized to unfold the XRF spectrum. A new type of experimental set-up was developed and utilized for XRF and NAA analysis of the kidney stone. To verify the experimental results with analytical calculation, several sets of kidney stones were analyzed using XRF and NAA technique. The elements which were identified from XRF technique are Br, Cu, Ga, Ge, Mo, Nb, Ni, Rb, Se, Sr, Y, Zr. And, by using Neutron Activation Analysis (NAA) are Au, Br, Ca, Er, Hg, I, K, Na, Pm, Sb, Sc, Sm, Tb, Yb, Zn. This thesis presents a new approach for exact detection of accurate material composition of kidney stone materials using XRF and NAA instrumental activation analysis techniques.

Ablation behaviors of carbon reinforced polymer composites by laser of different operation modes

NASA Astrophysics Data System (ADS)

Wu, Chen-Wu; Wu, Xian-Qian; Huang, Chen-Guang

2015-10-01

Laser ablation mechanism of Carbon Fiber Reinforced Polymer (CFRP) composite is of critical meaning for the laser machining process. The ablation behaviors are investigated on the CFRP laminates subject to continuous wave, long duration pulsed wave and short duration pulsed wave lasers. Distinctive ablation phenomena have been observed and the effects of laser operation modes are discussed. The typical temperature patterns resulted from laser irradiation are computed by finite element analysis and thereby the different ablation mechanisms are interpreted.

Accurate interlaminar stress recovery from finite element analysis

NASA Technical Reports Server (NTRS)

Tessler, Alexander; Riggs, H. Ronald

1994-01-01

The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

Quality, Social Justice and Accountability--Crucial Determinants of Excellence in Education

ERIC Educational Resources Information Center

Rossouw, J. P.

2015-01-01

Internationally, the quality of education, social justice and accountability can be regarded as key elements of successful school systems and societies. Separately or jointly, these elements can be analysed and debated as distinct fields of study, and linked to an education system to determine the success thereof. Being a pivotal element of…

Forensic analysis of printing inks using tandem Laser Induced Breakdown Spectroscopy and Laser Ablation Inductively Coupled Plasma Mass Spectrometry

NASA Astrophysics Data System (ADS)

Subedi, Kiran; Trejos, Tatiana; Almirall, José

2015-01-01

Elemental analysis, using either LA-ICP-MS or LIBS, can be used for the chemical characterization of materials of forensic interest to discriminate between source materials originating from different sources and also for the association of materials known to originate from the same source. In this study, a tandem LIBS/LA-ICP-MS system that combines the benefits of both LIBS and LA-ICP-MS was evaluated for the characterization of samples of printing inks (toners, inkjets, intaglio and offset.). The performance of both laser sampling methods is presented. A subset of 9 black laser toners, 10 colored (CMYK) inkjet samples, 12 colored (CMYK) offset samples and 12 intaglio inks originating from different manufacturing sources were analyzed to evaluate the discrimination capability of the tandem method. These samples were selected because they presented a very similar elemental profile by LA-ICP-MS. Although typical discrimination between different ink sources is found to be > 99% for a variety of inks when only LA-ICP-MS was used for the analysis, additional discrimination was achieved by combining the elemental results from the LIBS analysis to the LA-ICP-MS analysis in the tandem technique, enhancing the overall discrimination capability of the individual laser ablation methods. The LIBS measurements of the Ca, Fe, K and Si signals, in particular, improved the discrimination for this specific set of different ink samples previously shown to exhibit very similar LA-ICP-MS elemental profiles. The combination of these two techniques in a single setup resulted in better discrimination of the printing inks with two distinct fingerprint spectra, providing information from atomic/ionic emissions and isotopic composition (m/z) for each ink sample.

Filament condition-specific response elements control the expression of NRG1 and UME6, key transcriptional regulators of morphology and virulence in Candida albicans.

PubMed

Childers, Delma S; Kadosh, David

2015-01-01

Candida albicans is the most frequently isolated human fungal pathogen and can cause a range of mucosal and systemic infections in immunocompromised individuals. Morphogenesis, the ability to undergo a reversible transition from budding yeast to elongated filaments, is an essential virulence trait. The yeast-to-filament transition is associated with expression of genes specifically important for filamentation as well as other virulence-related processes, and is controlled, in part, by the key transcriptional regulators Nrg1 and Ume6. Both of these regulators are themselves controlled at the transcriptional level by filament-inducing environmental cues, although little is known about how this process occurs. In order to address this question and determine whether environmental signals regulate transcription of UME6 and NRG1 via distinct and/or common promoter elements, we performed promoter deletion analyses. Strains bearing promoter deletion constructs were induced to form filaments in YEPD plus 10% serum at 37°C, Spider medium (nitrogen and carbon starvation) and/or Lee's medium pH 6.8 (neutral pH) and reporter gene expression was measured. In the NRG1 promoter we identified several distinct condition-specific response elements for YEPD plus 10% serum at 37°C and Spider medium. In the UME6 promoter we also identified response elements for YEPD plus 10% serum at 37°C. While a few of these elements are distinct, others overlap with those which respond to Lee's pH 6.8 medium. Consistent with UME6 possessing a very long 5' UTR, many response elements in the UME6 promoter are located significantly upstream from the coding sequence. Our data indicate that certain distinct condition-specific elements can control expression of C. albicans UME6 and NRG1 in response to key filament-inducing environmental cues. Because C. albicans encounters a variety of host microenvironments during infection, our results suggest that UME6 and NRG1 expression can be differentially modulated by multiple signaling pathways to control filamentation and virulence in vivo.

FEM Analysis of Glass/Epoxy Composite Based Industrial Safety Helmet

NASA Astrophysics Data System (ADS)

Ram, Khushi; Bajpai, Pramendra Kumar

2017-08-01

Recently, the use of fiber reinforced polymer in every field of engineering (automobile, industry and aerospace) and medical has increased due to its distinctive mechanical properties. The fiber based polymer composites are more popular because these have high strength, light in weight, low cost and easily available. In the present work, the finite element analysis (FEA) of glass/epoxy composite based industrial safety helmet has been performed using solid-works simulation software. The modeling results show that glass fiber reinforced epoxy composite can be used as a material for fabrication of industrial safety helmet which has good mechanical properties than the existing helmet material.

An exploration of inter-organisational partnership assessment tools in the context of Australian Aboriginal-mainstream partnerships: a scoping review of the literature.

PubMed

Tsou, Christina; Haynes, Emma; Warner, Wayne D; Gray, Gordon; Thompson, Sandra C

2015-04-23

The need for better partnerships between Aboriginal organisations and mainstream agencies demands attention on process and relational elements of these partnerships, and improving partnership functioning through transformative or iterative evaluation procedures. This paper presents the findings of a literature review which examines the usefulness of existing partnership tools to the Australian Aboriginal-mainstream partnership (AMP) context. Three sets of best practice principles for successful AMP were selected based on authors' knowledge and experience. Items in each set of principles were separated into process and relational elements and used to guide the analysis of partnership assessment tools. The review and analysis of partnership assessment tools were conducted in three distinct but related parts. Part 1- identify and select reviews of partnership tools; part 2 - identify and select partnership self-assessment tool; part 3 - analysis of selected tools using AMP principles. The focus on relational and process elements in the partnership tools reviewed is consistent with the focus of Australian AMP principles by reconciliation advocates; however, historical context, lived experience, cultural context and approaches of Australian Aboriginal people represent key deficiencies in the tools reviewed. The overall assessment indicated that the New York Partnership Self-Assessment Tool and the VicHealth Partnership Analysis Tools reflect the greatest number of AMP principles followed by the Nuffield Partnership Assessment Tool. The New York PSAT has the strongest alignment with the relational elements while VicHealth and Nuffield tools showed greatest alignment with the process elements in the chosen AMP principles. Partnership tools offer opportunities for providing evidence based support to partnership development. The multiplicity of tools in existence and the reported uniqueness of each partnership, mean the development of a generic partnership analysis for AMP may not be a viable option for future effort.

The influence of the mechanical behaviour of the middle ear ligaments: a finite element analysis.

PubMed

Gentil, F; Parente, M; Martins, P; Garbe, C; Jorge, R N; Ferreira, A; Tavares, João Manuel R S

2011-01-01

The interest in computer modelling of biomechanical systems, mainly by using the finite element method (FEM), has been increasing, in particular for analysis of the mechanical behaviour of the human ear. In this work, a finite element model of the middle ear was developed to study the dynamic structural response to harmonic vibrations for distinct sound pressure levels applied on the eardrum. The model includes different ligaments and muscle tendons with elastic and hyperelastic behaviour for these supportive structures. Additionally, the nonlinear behaviour of the ligaments and muscle tendons was investigated, as they are the connection between ossicles by contact formulation. Harmonic responses of the umbo and stapes footplate displacements, between 100 Hz and 10 kHz, were obtained and compared with previously published work. The stress state of ligaments (superior, lateral, and anterior of malleus and superior and posterior of incus) was analysed, with the focus on balance of the supportive structures of the middle ear, as ligaments make the link between the ossicular chain and the walls of the tympanic cavity. The results obtained in this work highlight the importance of using hyperelastic models to simulate the mechanical behaviour for the ligaments and tendons.

Advancing the science of forensic data management

NASA Astrophysics Data System (ADS)

Naughton, Timothy S.

2002-07-01

Many individual elements comprise a typical forensics process. Collecting evidence, analyzing it, and using results to draw conclusions are all mutually distinct endeavors. Different physical locations and personnel are involved, juxtaposed against an acute need for security and data integrity. Using digital technologies and the Internet's ubiquity, these diverse elements can be conjoined using digital data as the common element. This result is a new data management process that can be applied to serve all elements of the community. The first step is recognition of a forensics lifecycle. Evidence gathering, analysis, storage, and use in legal proceedings are actually just distinct parts of a single end-to-end process, and thus, it is hypothesized that a single data system that can also accommodate each constituent phase using common network and security protocols. This paper introduces the idea of web-based Central Data Repository. Its cornerstone is anywhere, anytime Internet upload, viewing, and report distribution. Archives exist indefinitely after being created, and high-strength security and encryption protect data and ensure subsequent case file additions do not violate chain-of-custody or other handling provisions. Several legal precedents have been established for using digital information in courts of law, and in fact, effective prosecution of cyber crimes absolutely relies on its use. An example is a US Department of Agriculture division's use of digital images to back up its inspection process, with pictures and information retained on secure servers to enforce the Perishable Agricultural Commodities Act. Forensics is a cumulative process. Secure, web-based data management solutions, such as the Central Data Repository postulated here, can support each process step. Logically marrying digital technologies with Internet accessibility should help nurture a thought process to explore alternatives that make forensics data accessible to authorized individuals, whenever and wherever they need it.

Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts

PubMed Central

HATAKEYAMA, YOSHINORI; SHIBUYA, NORIHIRO; NISHIYAMA, TAKASHI; NAKASHIMA, NOBUHIKO

2004-01-01

The intergenic region (IGR) located upstream of the capsid protein gene in dicistroviruses contains an internal ribosome entry site (IRES). Translation initiation mediated by the IRES does not require initiator methionine tRNA. Comparison of the IGRs among dicistroviruses suggested that Taura syndrome virus (TSV) and acute bee paralysis virus have an extra side stem loop in the predicted IRES. We examined whether the side stem is responsible for translation activity mediated by the IGR using constructs with compensatory mutations. In vitro translation analysis showed that TSV has an IGR-IRES that is structurally distinct from those previously described. Because IGR-IRES elements determine the translation initiation site by virtue of their own tertiary structure formation, the discovery of this initiation mechanism suggests the possibility that eukaryotic mRNAs might have more extensive coding regions than previously predicted. To test this hypothesis, we searched full-length cDNA databases and whole genome sequences of eukaryotes using the pattern matching program, Scan For Matches, with parameters that can extract sequences containing secondary structure elements resembling those of IGR-IRES. Our search yielded several sequences, but their predicted secondary structures were suggested to be unstable in comparison to those of dicistroviruses. These results suggest that RNAs structurally similar to dicistroviruses are not common. If some eukaryotic mRNAs are translated independently of an initiator methionine tRNA, their structures are likely to be significantly distinct from those of dicistroviruses. PMID:15100433

Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity

PubMed Central

Thakurela, Sudhir; Sahu, Sanjeeb Kumar; Garding, Angela; Tiwari, Vijay K.

2015-01-01

Gene regulation in mammals involves a complex interplay between promoters and distal regulatory elements that function in concert to drive precise spatiotemporal gene expression programs. However, the dynamics of the distal gene regulatory landscape and its function in the transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here, we performed a combinatorial analysis of genome-wide data sets for chromatin accessibility (FAIRE-seq) and the enhancer mark H3K27ac, revealing the highly dynamic nature of distal gene regulation during neurogenesis, which gets progressively restricted to distinct genomic regions as neurons acquire a post-mitotic, terminally differentiated state. We further find that the distal accessible and active regions serve as target sites for distinct transcription factors that function in a stage-specific manner to contribute to the transcriptional program underlying neuronal commitment and maturation. Mature neurons respond to a sustained activity of NMDA receptors by epigenetic reprogramming at a large number of distal regulatory regions as well as dramatic reorganization of super-enhancers. Such massive remodeling of the distal regulatory landscape in turn results in a transcriptome that confers a transient loss of neuronal identity and gain of cellular plasticity. Furthermore, NMDA receptor activity also induces many novel prosurvival genes that function in neuroprotective pathways. Taken together, these findings reveal the dynamics of the distal regulatory landscape during neurogenesis and uncover novel regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate the transcriptome underlying neuronal development and activity. PMID:26170447

Genetic exchange between endogenous and exogenous LINE-1 repetitive elements in mouse cells.

PubMed Central

Belmaaza, A; Wallenburg, J C; Brouillette, S; Gusew, N; Chartrand, P

1990-01-01

The repetitive LINE (L1) elements of the mouse, which are present at about 10(5) copies per genome and share over 80% of sequence homology, were examined for their ability to undergo genetic exchange with exogenous L1 sequences. The exogenous L1 sequences, carried by a shuttle vector, consisted of an internal fragment from L1Md-A2, a previously described member of the L1 family of the mouse. Using an assay that does not require the reconstitution of a selectable marker we found that this vector, in either circular or linear form, acquired DNA sequences from endogenous L1 elements at a frequency of 10(-3) to 10(-4) per rescued vector. Physical analysis of the acquired L1 sequences revealed that distinct endogenous L1 elements acted as donors and that different subfamilies participated. These results demonstrate that L1 elements are readily capable of genetic exchange. Apart from gene conversion events, the acquisition of L1 sequences outside the region of homology suggested that a second mechanism was also involved in the genetic exchange. A model which accounts for this mechanism is presented and its potential implication on the rearrangement of L1 elements is discussed. Images PMID:1978749

Electret Acoustic Transducer Array For Computerized Ultrasound Risk Evaluation System

DOEpatents

Moore, Thomas L.; Fisher, Karl A.

2005-08-09

An electret-based acoustic transducer array is provided and may be used in a system for examining tissue. The acoustic transducer array is formed with a substrate that has a multiple distinct cells formed therein. Within each of the distinct cells is positioned an acoustic transducing element formed of an electret material. A conductive membrane is formed over the distinct cells and may be flexible.

Two-dimensional nonlinear finite element analysis of well damage due to reservoir compaction, well-to-well interactions, and localization on weak layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hilbert, L.B. Jr.; Fredrich, J.T.; Bruno, M.S.

1996-05-01

In this paper the authors present the results of a coupled nonlinear finite element geomechanics model for reservoir compaction and well-to-well interactions for the high-porosity, low strength diatomite reservoirs of the Belridge field near Bakersfield, California. They show that well damage and failures can occur under the action of two distinct mechanisms: shear deformations induced by pore compaction, and subsidence, and shear deformations due to well-to-well interactions during production or water injection. They show such casting damage or failure can be localized to weak layers that slide or slip under shear due to subsidence. The magnitude of shear displacements andmore » surface subsidence agree with field observations.« less

Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

PubMed

Leung, Wilson; Shaffer, Christopher D; Reed, Laura K; Smith, Sheryl T; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E J; Machone, Joshua F; Patterson, Seantay D; Price, Amber L; Turner, Bryce A; Robic, Srebrenka; Luippold, Erin K; McCartha, Shannon R; Walji, Tezin A; Walker, Chelsea A; Saville, Kenneth; Abrams, Marita K; Armstrong, Andrew R; Armstrong, William; Bailey, Robert J; Barberi, Chelsea R; Beck, Lauren R; Blaker, Amanda L; Blunden, Christopher E; Brand, Jordan P; Brock, Ethan J; Brooks, Dana W; Brown, Marie; Butzler, Sarah C; Clark, Eric M; Clark, Nicole B; Collins, Ashley A; Cotteleer, Rebecca J; Cullimore, Peterson R; Dawson, Seth G; Docking, Carter T; Dorsett, Sasha L; Dougherty, Grace A; Downey, Kaitlyn A; Drake, Andrew P; Earl, Erica K; Floyd, Trevor G; Forsyth, Joshua D; Foust, Jonathan D; Franchi, Spencer L; Geary, James F; Hanson, Cynthia K; Harding, Taylor S; Harris, Cameron B; Heckman, Jonathan M; Holderness, Heather L; Howey, Nicole A; Jacobs, Dontae A; Jewell, Elizabeth S; Kaisler, Maria; Karaska, Elizabeth A; Kehoe, James L; Koaches, Hannah C; Koehler, Jessica; Koenig, Dana; Kujawski, Alexander J; Kus, Jordan E; Lammers, Jennifer A; Leads, Rachel R; Leatherman, Emily C; Lippert, Rachel N; Messenger, Gregory S; Morrow, Adam T; Newcomb, Victoria; Plasman, Haley J; Potocny, Stephanie J; Powers, Michelle K; Reem, Rachel M; Rennhack, Jonathan P; Reynolds, Katherine R; Reynolds, Lyndsey A; Rhee, Dong K; Rivard, Allyson B; Ronk, Adam J; Rooney, Meghan B; Rubin, Lainey S; Salbert, Luke R; Saluja, Rasleen K; Schauder, Taylor; Schneiter, Allison R; Schulz, Robert W; Smith, Karl E; Spencer, Sarah; Swanson, Bryant R; Tache, Melissa A; Tewilliager, Ashley A; Tilot, Amanda K; VanEck, Eve; Villerot, Matthew M; Vylonis, Megan B; Watson, David T; Wurzler, Juliana A; Wysocki, Lauren M; Yalamanchili, Monica; Zaborowicz, Matthew A; Emerson, Julia A; Ortiz, Carlos; Deuschle, Frederic J; DiLorenzo, Lauren A; Goeller, Katie L; Macchi, Christopher R; Muller, Sarah E; Pasierb, Brittany D; Sable, Joseph E; Tucci, Jessica M; Tynon, Marykathryn; Dunbar, David A; Beken, Levent H; Conturso, Alaina C; Danner, Benjamin L; DeMichele, Gabriella A; Gonzales, Justin A; Hammond, Maureen S; Kelley, Colleen V; Kelly, Elisabeth A; Kulich, Danielle; Mageeney, Catherine M; McCabe, Nikie L; Newman, Alyssa M; Spaeder, Lindsay A; Tumminello, Richard A; Revie, Dennis; Benson, Jonathon M; Cristostomo, Michael C; DaSilva, Paolo A; Harker, Katherine S; Jarrell, Jenifer N; Jimenez, Luis A; Katz, Brandon M; Kennedy, William R; Kolibas, Kimberly S; LeBlanc, Mark T; Nguyen, Trung T; Nicolas, Daniel S; Patao, Melissa D; Patao, Shane M; Rupley, Bryan J; Sessions, Bridget J; Weaver, Jennifer A; Goodman, Anya L; Alvendia, Erica L; Baldassari, Shana M; Brown, Ashley S; Chase, Ian O; Chen, Maida; Chiang, Scott; Cromwell, Avery B; Custer, Ashley F; DiTommaso, Tia M; El-Adaimi, Jad; Goscinski, Nora C; Grove, Ryan A; Gutierrez, Nestor; Harnoto, Raechel S; Hedeen, Heather; Hong, Emily L; Hopkins, Barbara L; Huerta, Vilma F; Khoshabian, Colin; LaForge, Kristin M; Lee, Cassidy T; Lewis, Benjamin M; Lydon, Anniken M; Maniaci, Brian J; Mitchell, Ryan D; Morlock, Elaine V; Morris, William M; Naik, Priyanka; Olson, Nicole C; Osterloh, Jeannette M; Perez, Marcos A; Presley, Jonathan D; Randazzo, Matt J; Regan, Melanie K; Rossi, Franca G; Smith, Melanie A; Soliterman, Eugenia A; Sparks, Ciani J; Tran, Danny L; Wan, Tiffany; Welker, Anne A; Wong, Jeremy N; Sreenivasan, Aparna; Youngblom, Jim; Adams, Andrew; Alldredge, Justin; Bryant, Ashley; Carranza, David; Cifelli, Alyssa; Coulson, Kevin; Debow, Calise; Delacruz, Noelle; Emerson, Charlene; Farrar, Cassandra; Foret, Don; Garibay, Edgar; Gooch, John; Heslop, Michelle; Kaur, Sukhjit; Khan, Ambreen; Kim, Van; Lamb, Travis; Lindbeck, Peter; Lucas, Gabi; Macias, Elizabeth; Martiniuc, Daniela; Mayorga, Lissett; Medina, Joseph; Membreno, Nelson; Messiah, Shady; Neufeld, Lacey; Nguyen, San Francisco; Nichols, Zachary; Odisho, George; Peterson, Daymon; Rodela, Laura; Rodriguez, Priscilla; Rodriguez, Vanessa; Ruiz, Jorge; Sherrill, Will; Silva, Valeria; Sparks, Jeri; Statton, Geeta; Townsend, Ashley; Valdez, Isabel; Waters, Mary; Westphal, Kyle; Winkler, Stacey; Zumkehr, Joannee; DeJong, Randall J; Hoogewerf, Arlene J; Ackerman, Cheri M; Armistead, Isaac O; Baatenburg, Lara; Borr, Matthew J; Brouwer, Lindsay K; Burkhart, Brandon J; Bushhouse, Kelsey T; Cesko, Lejla; Choi, Tiffany Y Y; Cohen, Heather; Damsteegt, Amanda M; Darusz, Jess M; Dauphin, Cory M; Davis, Yelena P; Diekema, Emily J; Drewry, Melissa; Eisen, Michelle E M; Faber, Hayley M; Faber, Katherine J; Feenstra, Elizabeth; Felzer-Kim, Isabella T; Hammond, Brandy L; Hendriksma, Jesse; Herrold, Milton R; Hilbrands, Julia A; Howell, Emily J; Jelgerhuis, Sarah A; Jelsema, Timothy R; Johnson, Benjamin K; Jones, Kelly K; Kim, Anna; Kooienga, Ross D; Menyes, Erika E; Nollet, Eric A; Plescher, Brittany E; Rios, Lindsay; Rose, Jenny L; Schepers, Allison J; Scott, Geoff; Smith, Joshua R; Sterling, Allison M; Tenney, Jenna C; Uitvlugt, Chris; VanDyken, Rachel E; VanderVennen, Marielle; Vue, Samantha; Kokan, Nighat P; Agbley, Kwabea; Boham, Sampson K; Broomfield, Daniel; Chapman, Kayla; Dobbe, Ali; Dobbe, Ian; Harrington, William; Ibrahem, Marwan; Kennedy, Andre; Koplinsky, Chad A; Kubricky, Cassandra; Ladzekpo, Danielle; Pattison, Claire; Ramirez, Roman E; Wande, Lucia; Woehlke, Sarah; Wawersik, Matthew; Kiernan, Elizabeth; Thompson, Jeffrey S; Banker, Roxanne; Bartling, Justina R; Bhatiya, Chinmoy I; Boudoures, Anna L; Christiansen, Lena; Fosselman, Daniel S; French, Kristin M; Gill, Ishwar S; Havill, Jessen T; Johnson, Jaelyn L; Keny, Lauren J; Kerber, John M; Klett, Bethany M; Kufel, Christina N; May, Francis J; Mecoli, Jonathan P; Merry, Callie R; Meyer, Lauren R; Miller, Emily G; Mullen, Gregory J; Palozola, Katherine C; Pfeil, Jacob J; Thomas, Jessica G; Verbofsky, Evan M; Spana, Eric P; Agarwalla, Anant; Chapman, Julia; Chlebina, Ben; Chong, Insun; Falk, I N; Fitzgibbons, John D; Friedman, Harrison; Ighile, Osagie; Kim, Andrew J; Knouse, Kristin A; Kung, Faith; Mammo, Danny; Ng, Chun Leung; Nikam, Vinayak S; Norton, Diana; Pham, Philip; Polk, Jessica W; Prasad, Shreya; Rankin, Helen; Ratliff, Camille D; Scala, Victoria; Schwartz, Nicholas U; Shuen, Jessica A; Xu, Amy; Xu, Thomas Q; Zhang, Yi; Rosenwald, Anne G; Burg, Martin G; Adams, Stephanie J; Baker, Morgan; Botsford, Bobbi; Brinkley, Briana; Brown, Carter; Emiah, Shadie; Enoch, Erica; Gier, Chad; Greenwell, Alyson; Hoogenboom, Lindsay; Matthews, Jordan E; McDonald, Mitchell; Mercer, Amanda; Monsma, Nicholaus; Ostby, Kristine; Ramic, Alen; Shallman, Devon; Simon, Matthew; Spencer, Eric; Tomkins, Trisha; Wendland, Pete; Wylie, Anna; Wolyniak, Michael J; Robertson, Gregory M; Smith, Samuel I; DiAngelo, Justin R; Sassu, Eric D; Bhalla, Satish C; Sharif, Karim A; Choeying, Tenzin; Macias, Jason S; Sanusi, Fareed; Torchon, Karvyn; Bednarski, April E; Alvarez, Consuelo J; Davis, Kristen C; Dunham, Carrie A; Grantham, Alaina J; Hare, Amber N; Schottler, Jennifer; Scott, Zackary W; Kuleck, Gary A; Yu, Nicole S; Kaehler, Marian M; Jipp, Jacob; Overvoorde, Paul J; Shoop, Elizabeth; Cyrankowski, Olivia; Hoover, Betsy; Kusner, Matt; Lin, Devry; Martinov, Tijana; Misch, Jonathan; Salzman, Garrett; Schiedermayer, Holly; Snavely, Michael; Zarrasola, Stephanie; Parrish, Susan; Baker, Atlee; Beckett, Alissa; Belella, Carissa; Bryant, Julie; Conrad, Turner; Fearnow, Adam; Gomez, Carolina; Herbstsomer, Robert A; Hirsch, Sarah; Johnson, Christen; Jones, Melissa; Kabaso, Rita; Lemmon, Eric; Vieira, Carolina Marques Dos Santos; McFarland, Darryl; McLaughlin, Christopher; Morgan, Abbie; Musokotwane, Sepo; Neutzling, William; Nietmann, Jana; Paluskievicz, Christina; Penn, Jessica; Peoples, Emily; Pozmanter, Caitlin; Reed, Emily; Rigby, Nichole; Schmidt, Lasse; Shelton, Micah; Shuford, Rebecca; Tirasawasdichai, Tiara; Undem, Blair; Urick, Damian; Vondy, Kayla; Yarrington, Bryan; Eckdahl, Todd T; Poet, Jeffrey L; Allen, Alica B; Anderson, John E; Barnett, Jason M; Baumgardner, Jordan S; Brown, Adam D; Carney, Jordan E; Chavez, Ramiro A; Christgen, Shelbi L; Christie, Jordan S; Clary, Andrea N; Conn, Michel A; Cooper, Kristen M; Crowley, Matt J; Crowley, Samuel T; Doty, Jennifer S; Dow, Brian A; Edwards, Curtis R; Elder, Darcie D; Fanning, John P; Janssen, Bridget M; Lambright, Anthony K; Lane, Curtiss E; Limle, Austin B; Mazur, Tammy; McCracken, Marly R; McDonough, Alexa M; Melton, Amy D; Minnick, Phillip J; Musick, Adam E; Newhart, William H; Noynaert, Joseph W; Ogden, Bradley J; Sandusky, Michael W; Schmuecker, Samantha M; Shipman, Anna L; Smith, Anna L; Thomsen, Kristen M; Unzicker, Matthew R; Vernon, William B; Winn, Wesley W; Woyski, Dustin S; Zhu, Xiao; Du, Chunguang; Ament, Caitlin; Aso, Soham; Bisogno, Laura Simone; Caronna, Jason; Fefelova, Nadezhda; Lopez, Lenin; Malkowitz, Lorraine; Marra, Jonathan; Menillo, Daniella; Obiorah, Ifeanyi; Onsarigo, Eric Nyabeta; Primus, Shekerah; Soos, Mahdi; Tare, Archana; Zidan, Ameer; Jones, Christopher J; Aronhalt, Todd; Bellush, James M; Burke, Christa; DeFazio, Steve; Does, Benjamin R; Johnson, Todd D; Keysock, Nicholas; Knudsen, Nelson H; Messler, James; Myirski, Kevin; Rekai, Jade Lea; Rempe, Ryan Michael; Salgado, Michael S; Stagaard, Erica; Starcher, Justin R; Waggoner, Andrew W; Yemelyanova, Anastasia K; Hark, Amy T; Bertolet, Anne; Kuschner, Cyrus E; Parry, Kesley; Quach, Michael; Shantzer, Lindsey; Shaw, Mary E; Smith, Mary A; Glenn, Omolara; Mason, Portia; Williams, Charlotte; Key, S Catherine Silver; Henry, Tyneshia C P; Johnson, Ashlee G; White, Jackie X; Haberman, Adam; Asinof, Sam; Drumm, Kelly; Freeburg, Trip; Safa, Nadia; Schultz, Darrin; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Wellinghoff, Jules; Hoopes, Laura L M; Chau, Kim M; Ward, Alyssa; Regisford, E Gloria C; Augustine, LaJerald; Davis-Reyes, Brionna; Echendu, Vivienne; Hales, Jasmine; Ibarra, Sharon; Johnson, Lauriaun; Ovu, Steven; Braverman, John M; Bahr, Thomas J; Caesar, Nicole M; Campana, Christopher; Cassidy, Daniel W; Cognetti, Peter A; English, Johnathan D; Fadus, Matthew C; Fick, Cameron N; Freda, Philip J; Hennessy, Bryan M; Hockenberger, Kelsey; Jones, Jennifer K; King, Jessica E; Knob, Christopher R; Kraftmann, Karen J; Li, Linghui; Lupey, Lena N; Minniti, Carl J; Minton, Thomas F; Moran, Joseph V; Mudumbi, Krishna; Nordman, Elizabeth C; Puetz, William J; Robinson, Lauren M; Rose, Thomas J; Sweeney, Edward P; Timko, Ashley S; Paetkau, Don W; Eisler, Heather L; Aldrup, Megan E; Bodenberg, Jessica M; Cole, Mara G; Deranek, Kelly M; DeShetler, Megan; Dowd, Rose M; Eckardt, Alexandra K; Ehret, Sharon C; Fese, Jessica; Garrett, Amanda D; Kammrath, Anna; Kappes, Michelle L; Light, Morgan R; Meier, Anne C; O'Rouke, Allison; Perella, Mallory; Ramsey, Kimberley; Ramthun, Jennifer R; Reilly, Mary T; Robinett, Deirdre; Rossi, Nadine L; Schueler, Mary Grace; Shoemaker, Emma; Starkey, Kristin M; Vetor, Ashley; Vrable, Abby; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R; Herrick, Douglas A; Khoury, Christopher B; Lea, Charlotte; Louie, Christopher A; Lowell, Shannon M; Reynolds, Thomas J; Schibler, Jeanine; Scoma, Alexandra H; Smith-Gee, Maxwell T; Tuberty, Sarah; Smith, Christopher D; Lopilato, Jane E; Hauke, Jeanette; Roecklein-Canfield, Jennifer A; Corrielus, Maureen; Gilman, Hannah; Intriago, Stephanie; Maffa, Amanda; Rauf, Sabya A; Thistle, Katrina; Trieu, Melissa; Winters, Jenifer; Yang, Bib; Hauser, Charles R; Abusheikh, Tariq; Ashrawi, Yara; Benitez, Pedro; Boudreaux, Lauren R; Bourland, Megan; Chavez, Miranda; Cruz, Samantha; Elliott, GiNell; Farek, Jesse R; Flohr, Sarah; Flores, Amanda H; Friedrichs, Chelsey; Fusco, Zach; Goodwin, Zane; Helmreich, Eric; Kiley, John; Knepper, John Mark; Langner, Christine; Martinez, Megan; Mendoza, Carlos; Naik, Monal; Ochoa, Andrea; Ragland, Nicolas; Raimey, England; Rathore, Sunil; Reza, Evangelina; Sadovsky, Griffin; Seydoux, Marie-Isabelle B; Smith, Jonathan E; Unruh, Anna K; Velasquez, Vicente; Wolski, Matthew W; Gosser, Yuying; Govind, Shubha; Clarke-Medley, Nicole; Guadron, Leslie; Lau, Dawn; Lu, Alvin; Mazzeo, Cheryl; Meghdari, Mariam; Ng, Simon; Pamnani, Brad; Plante, Olivia; Shum, Yuki Kwan Wa; Song, Roy; Johnson, Diana E; Abdelnabi, Mai; Archambault, Alexi; Chamma, Norma; Gaur, Shailly; Hammett, Deborah; Kandahari, Adrese; Khayrullina, Guzal; Kumar, Sonali; Lawrence, Samantha; Madden, Nigel; Mandelbaum, Max; Milnthorp, Heather; Mohini, Shiv; Patel, Roshni; Peacock, Sarah J; Perling, Emily; Quintana, Amber; Rahimi, Michael; Ramirez, Kristen; Singhal, Rishi; Weeks, Corinne; Wong, Tiffany; Gillis, Aubree T; Moore, Zachary D; Savell, Christopher D; Watson, Reece; Mel, Stephanie F; Anilkumar, Arjun A; Bilinski, Paul; Castillo, Rostislav; Closser, Michael; Cruz, Nathalia M; Dai, Tiffany; Garbagnati, Giancarlo F; Horton, Lanor S; Kim, Dongyeon; Lau, Joyce H; Liu, James Z; Mach, Sandy D; Phan, Thu A; Ren, Yi; Stapleton, Kenneth E; Strelitz, Jean M; Sunjed, Ray; Stamm, Joyce; Anderson, Morgan C; Bonifield, Bethany Grace; Coomes, Daniel; Dillman, Adam; Durchholz, Elaine J; Fafara-Thompson, Antoinette E; Gross, Meleah J; Gygi, Amber M; Jackson, Lesley E; Johnson, Amy; Kocsisova, Zuzana; Manghelli, Joshua L; McNeil, Kylie; Murillo, Michael; Naylor, Kierstin L; Neely, Jessica; Ogawa, Emmy E; Rich, Ashley; Rogers, Anna; Spencer, J Devin; Stemler, Kristina M; Throm, Allison A; Van Camp, Matt; Weihbrecht, Katie; Wiles, T Aaron; Williams, Mallory A; Williams, Matthew; Zoll, Kyle; Bailey, Cheryl; Zhou, Leming; Balthaser, Darla M; Bashiri, Azita; Bower, Mindy E; Florian, Kayla A; Ghavam, Nazanin; Greiner-Sosanko, Elizabeth S; Karim, Helmet; Mullen, Victor W; Pelchen, Carly E; Yenerall, Paul M; Zhang, Jiayu; Rubin, Michael R; Arias-Mejias, Suzette M; Bermudez-Capo, Armando G; Bernal-Vega, Gabriela V; Colon-Vazquez, Mariela; Flores-Vazquez, Arelys; Gines-Rosario, Mariela; Llavona-Cartagena, Ivan G; Martinez-Rodriguez, Javier O; Ortiz-Fuentes, Lionel; Perez-Colomba, Eliezer O; Perez-Otero, Joseph; Rivera, Elisandra; Rodriguez-Giron, Luke J; Santiago-Sanabria, Arnaldo J; Senquiz-Gonzalez, Andrea M; delValle, Frank R Soto; Vargas-Franco, Dorianmarie; Velázquez-Soto, Karla I; Zambrana-Burgos, Joan D; Martinez-Cruzado, Juan Carlos; Asencio-Zayas, Lillyann; Babilonia-Figueroa, Kevin; Beauchamp-Pérez, Francis D; Belén-Rodríguez, Juliana; Bracero-Quiñones, Luciann; Burgos-Bula, Andrea P; Collado-Méndez, Xavier A; Colón-Cruz, Luis R; Correa-Muller, Ana I; Crooke-Rosado, Jonathan L; Cruz-García, José M; Defendini-Ávila, Marianna; Delgado-Peraza, Francheska M; Feliciano-Cancela, Alex J; Gónzalez-Pérez, Valerie M; Guiblet, Wilfried; Heredia-Negrón, Aldo; Hernández-Muñiz, Jennifer; Irizarry-González, Lourdes N; Laboy-Corales, Ángel L; Llaurador-Caraballo, Gabriela A; Marín-Maldonado, Frances; Marrero-Llerena, Ulises; Martell-Martínez, Héctor A; Martínez-Traverso, Idaliz M; Medina-Ortega, Kiara N; Méndez-Castellanos, Sonya G; Menéndez-Serrano, Krizia C; Morales-Caraballo, Carol I; Ortiz-DeChoudens, Saryleine; Ortiz-Ortiz, Patricia; Pagán-Torres, Hendrick; Pérez-Afanador, Diana; Quintana-Torres, Enid M; Ramírez-Aponte, Edwin G; Riascos-Cuero, Carolina; Rivera-Llovet, Michelle S; Rivera-Pagán, Ingrid T; Rivera-Vicéns, Ramón E; Robles-Juarbe, Fabiola; Rodríguez-Bonilla, Lorraine; Rodríguez-Echevarría, Brian O; Rodríguez-García, Priscila M; Rodríguez-Laboy, Abneris E; Rodríguez-Santiago, Susana; Rojas-Vargas, Michael L; Rubio-Marrero, Eva N; Santiago-Colón, Albeliz; Santiago-Ortiz, Jorge L; Santos-Ramos, Carlos E; Serrano-González, Joseline; Tamayo-Figueroa, Alina M; Tascón-Peñaranda, Edna P; Torres-Castillo, José L; Valentín-Feliciano, Nelson A; Valentín-Feliciano, Yashira M; Vargas-Barreto, Nadyan M; Vélez-Vázquez, Miguel; Vilanova-Vélez, Luis R; Zambrana-Echevarría, Cristina; MacKinnon, Christy; Chung, Hui-Min; Kay, Chris; Pinto, Anthony; Kopp, Olga R; Burkhardt, Joshua; Harward, Chris; Allen, Robert; Bhat, Pavan; Chang, Jimmy Hsiang-Chun; Chen, York; Chesley, Christopher; Cohn, Dara; DuPuis, David; Fasano, Michael; Fazzio, Nicholas; Gavinski, Katherine; Gebreyesus, Heran; Giarla, Thomas; Gostelow, Marcus; Greenstein, Rachel; Gunasinghe, Hashini; Hanson, Casey; Hay, Amanda; He, Tao Jian; Homa, Katie; Howe, Ruth; Howenstein, Jeff; Huang, Henry; Khatri, Aaditya; Kim, Young Lu; Knowles, Olivia; Kong, Sarah; Krock, Rebecca; Kroll, Matt; Kuhn, Julia; Kwong, Matthew; Lee, Brandon; Lee, Ryan; Levine, Kevin; Li, Yedda; Liu, Bo; Liu, Lucy; Liu, Max; Lousararian, Adam; Ma, Jimmy; Mallya, Allyson; Manchee, Charlie; Marcus, Joseph; McDaniel, Stephen; Miller, Michelle L; Molleston, Jerome M; Diez, Cristina Montero; Ng, Patrick; Ngai, Natalie; Nguyen, Hien; Nylander, Andrew; Pollack, Jason; Rastogi, Suchita; Reddy, Himabindu; Regenold, Nathaniel; Sarezky, Jon; Schultz, Michael; Shim, Jien; Skorupa, Tara; Smith, Kenneth; Spencer, Sarah J; Srikanth, Priya; Stancu, Gabriel; Stein, Andrew P; Strother, Marshall; Sudmeier, Lisa; Sun, Mengyang; Sundaram, Varun; Tazudeen, Noor; Tseng, Alan; Tzeng, Albert; Venkat, Rohit; Venkataram, Sandeep; Waldman, Leah; Wang, Tracy; Yang, Hao; Yu, Jack Y; Zheng, Yin; Preuss, Mary L; Garcia, Angelica; Juergens, Matt; Morris, Robert W; Nagengast, Alexis A; Azarewicz, Julie; Carr, Thomas J; Chichearo, Nicole; Colgan, Mike; Donegan, Megan; Gardner, Bob; Kolba, Nik; Krumm, Janice L; Lytle, Stacey; MacMillian, Laurell; Miller, Mary; Montgomery, Andrew; Moretti, Alysha; Offenbacker, Brittney; Polen, Mike; Toth, John; Woytanowski, John; Kadlec, Lisa; Crawford, Justin; Spratt, Mary L; Adams, Ashley L; Barnard, Brianna K; Cheramie, Martin N; Eime, Anne M; Golden, Kathryn L; Hawkins, Allyson P; Hill, Jessica E; Kampmeier, Jessica A; Kern, Cody D; Magnuson, Emily E; Miller, Ashley R; Morrow, Cody M; Peairs, Julia C; Pickett, Gentry L; Popelka, Sarah A; Scott, Alexis J; Teepe, Emily J; TerMeer, Katie A; Watchinski, Carmen A; Watson, Lucas A; Weber, Rachel E; Woodard, Kate A; Barnard, Daron C; Appiah, Isaac; Giddens, Michelle M; McNeil, Gerard P; Adebayo, Adeola; Bagaeva, Kate; Chinwong, Justina; Dol, Chrystel; George, Eunice; Haltaufderhyde, Kirk; Haye, Joanna; Kaur, Manpreet; Semon, Max; Serjanov, Dmitri; Toorie, Anika; Wilson, Christopher; Riddle, Nicole C; Buhler, Jeremy; Mardis, Elaine R; Elgin, Sarah C R

2015-03-04

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. Copyright © 2015 Leung et al.

Market Basket Analysis: a new tool in ecology to describe chemical relations in the environment--a case study of the fern Athyrium distentifolium in the Tatra National Park in Poland.

PubMed

Samecka-Cymerman, Aleksandra; Stankiewicz, Andrzej; Kolon, Krzysztof; Kempers, Alexander J; Leuven, Rob S E W

2010-09-01

In this study, the novel data mining technique Market Basket Analysis (MBA) was applied for the first time in biogeochemical and ecological investigations. The method was tested on the fern Athyrium distentifolium, in which we measured concentrations of the elements Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, and Zn. Plants were sampled from sites with different types of bedrock in the Tatra National Park in Poland. MBA was used to investigate whether specimens of Athyrium distentifolium that contain elevated levels of certain elements occur more frequently on a specific type of bedrock and to identify relationships between the type of bedrock and the concentrations of the elements in this fern. The results were compared with those of the commonly used principal component and classification analysis (PCCA) technique. MBA and PCCA ordination both yielded distinct groups of ferns growing on different types of bedrock. Although the results of MBA and PCCA were similar, MBA has the advantage of being independent of the size of the data set. In addition, MBA revealed not only dominant elements but, in the case of limestone bedrock, also showed very low concentrations of Cd, Fe, Mn, and Pb in ferns growing on this type of parent material. MBA, thus, appeared to be a promising data mining method to reveal chemical relations in the environment as well as the accumulation of chemical elements in bioindicators. This technique can be used to reveal associations and correlations among items in large data sets collected on a national or even larger scale.

Band-gap analysis of a novel lattice with a hierarchical periodicity using the spectral element method

NASA Astrophysics Data System (ADS)

Wu, Zhijing; Li, Fengming; Zhang, Chuanzeng

2018-05-01

Inspired by the hierarchical structures of butterfly wing surfaces, a new kind of lattice structures with a two-order hierarchical periodicity is proposed and designed, and the band-gap properties are investigated by the spectral element method (SEM). The equations of motion of the whole structure are established considering the macro and micro periodicities of the system. The efficiency of the SEM is exploited in the modeling process and validated by comparing the results with that of the finite element method (FEM). Based on the highly accurate results in the frequency domain, the dynamic behaviors of the proposed two-order hierarchical structures are analyzed. An original and interesting finding is the existence of the distinct macro and micro stop-bands in the given frequency domain. The mechanisms for these two types of band-gaps are also explored. Finally, the relations between the hierarchical periodicities and the different types of the stop-bands are investigated by analyzing the parametrical influences.

Identifying elemental genomic track types and representing them uniformly

PubMed Central

2011-01-01

Background With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated. Results We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0. Conclusions The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience. PMID:22208806

Unraveling Appalachian tectonics: domain analysis of topographic lineaments in Pennsylvania

NASA Astrophysics Data System (ADS)

Karimi, B.; Schon, K.; Nussbaum, G. W.; Storer, N. D.; McGuire, J. L.; Hardcastle, K.

2016-12-01

Litho-tectonic provinces provide different components of a regions' tectonic history, and are identified as spatial entities with common structural elements, or a number of contiguous related elements. The province boundaries are easily identified when geomorphic expressions are distinct, or significant rock exposure allows for little uncertainty. When exposures are limited, locations of boundaries between provinces are uncertain. In such instances, satellite imagery can be quite advantageous, as tectonically sourced features (faults, folds, fractures, and joints) may exert a strong control on topographic patterns by creating pathways for weathering and erosion. Lineament analyses of topography often focus on well-pronounced tectonic features to interpret regional tectonics. We suggest that lineament analyses including all topographic features may include more subtle tectonic features, resulting in the identification of minor heterogeneities within litho-tectonic provinces. Our study focuses on Appalachian tectonics, specifically in Pennsylvania (PA), home to the Appalachian Orocline and 5 distinct tectonic provinces. Using hillshades from a digital elevation model (DEM) of PA, we manually pick all topographic lineaments 1 km or greater, discriminating only against man-made structures. The final lineament coverage of the state is subdivided into smaller areas for which rose diagrams were prepared. The dominant lineament trends were compared and associated with known structural features. Peaks with no known source are marked as possible tectonic features requiring further research. A domain analysis is performed on the lineament data to identify the extent and interplay of swarms, followed by an investigation of their azimuthal compatibility. We present the results of our domain analysis of all topographic lineaments in the context of identifying litho-tectonic provinces associated with Appalachian tectonics in Pennsylvania, and possible heterogeneities within them.

Rare earth elements in Angra dos Reis and Lewis Cliff 86010, two meteorites with similar but distinct magma evolutions

NASA Technical Reports Server (NTRS)

Crozaz, Ghislaine; Mckay, Gordon

1990-01-01

Data are presented on ion microprobe measurements of REE and selected trace element abundances in individual grains of merrillite, fassaite, olivine, kirschsteinite, and plagioclase of Lewis Cliff 86010 (LEW 86010) meteorite and in merrillite and fassaite grains of Angra dos Reis (ADOR). Results show a close relationship between the two meteorites and support a magmatic origin for LEW 86010. However, the measurements indicate that, despite numerous common characteristics, the two meteorites must have been produced in separate magmatic events involving similar but distinct processes and parent melts.

Single kernel ionomic profiles are highly heritable indicators of genetic and environmental influences on elemental accumulation in maize grain (Zea mays)

USDA-ARS?s Scientific Manuscript database

The ionome, or elemental profile, of a maize kernel represents at least two distinct ideas. First, the collection of elements within the kernel are food, feed and feedstocks for people, animals and industrial processes. Second, the ionome of the kernel represents a developmental end point that can s...

Comparisons of Elemental Profiles of the Western Spruce Budworm Reared on Three host Foilages and Artificial Medium

Treesearch

John A. McLean; P. Laks; T.L. Shore

1983-01-01

Western spruce budworm were reared on three host foliages and artificial medium. Trace element analyses showed large differences in elemental concentrations between food sources and only minor differences between insect life stages. Discriminant analyses were carried out to test the distinctiveness of adult chemoprints from each rearing regime. Fe, Cu, and Zn were...

Mapping Potassium

NASA Image and Video Library

2015-04-16

During the first year of NASA MESSENGER orbital mission, the spacecraft GRS instrument measured the elemental composition of Mercury surface materials. mong the most important discoveries from the GRS was the observation of higher abundances of the moderately volatile elements potassium, sodium, and chlorine than expected from previous scientific models and theories. Particularly high concentrations of these elements were observed at high northern latitudes, as illustrated in this potassium abundance map, which provides a view of the surface centered at 60° N latitude and 120° E longitude. This map was the first elemental map ever made of Mercury's surface and is to-date the only map to report absolute elemental concentrations, in comparison to element ratios. Prior to MESSENGER's arrival at Mercury, scientists expected that the planet would be depleted in moderately volatile elements, as is the case for our Moon. The unexpectedly high abundances observed with the GRS have forced a reevaluation of our understanding of the formation and evolution of Mercury. In addition, the K map provided the first evidence for distinct geochemical terranes on Mercury, as the high-potassium region was later found to also be distinct in its low Mg/Si, Ca/Si, S/Si, and high Na/Si and Cl/Si abundances. Instrument: Gamma-Ray Spectrometer (GRS) http://photojournal.jpl.nasa.gov/catalog/PIA19414

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

PubMed Central

Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

2016-01-01

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent. PMID:26779141

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

PubMed

Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

2015-01-01

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.

Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

PubMed Central

Leung, Wilson; Shaffer, Christopher D.; Reed, Laura K.; Smith, Sheryl T.; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E. J.; Machone, Joshua F.; Patterson, Seantay D.; Price, Amber L.; Turner, Bryce A.; Robic, Srebrenka; Luippold, Erin K.; McCartha, Shannon R.; Walji, Tezin A.; Walker, Chelsea A.; Saville, Kenneth; Abrams, Marita K.; Armstrong, Andrew R.; Armstrong, William; Bailey, Robert J.; Barberi, Chelsea R.; Beck, Lauren R.; Blaker, Amanda L.; Blunden, Christopher E.; Brand, Jordan P.; Brock, Ethan J.; Brooks, Dana W.; Brown, Marie; Butzler, Sarah C.; Clark, Eric M.; Clark, Nicole B.; Collins, Ashley A.; Cotteleer, Rebecca J.; Cullimore, Peterson R.; Dawson, Seth G.; Docking, Carter T.; Dorsett, Sasha L.; Dougherty, Grace A.; Downey, Kaitlyn A.; Drake, Andrew P.; Earl, Erica K.; Floyd, Trevor G.; Forsyth, Joshua D.; Foust, Jonathan D.; Franchi, Spencer L.; Geary, James F.; Hanson, Cynthia K.; Harding, Taylor S.; Harris, Cameron B.; Heckman, Jonathan M.; Holderness, Heather L.; Howey, Nicole A.; Jacobs, Dontae A.; Jewell, Elizabeth S.; Kaisler, Maria; Karaska, Elizabeth A.; Kehoe, James L.; Koaches, Hannah C.; Koehler, Jessica; Koenig, Dana; Kujawski, Alexander J.; Kus, Jordan E.; Lammers, Jennifer A.; Leads, Rachel R.; Leatherman, Emily C.; Lippert, Rachel N.; Messenger, Gregory S.; Morrow, Adam T.; Newcomb, Victoria; Plasman, Haley J.; Potocny, Stephanie J.; Powers, Michelle K.; Reem, Rachel M.; Rennhack, Jonathan P.; Reynolds, Katherine R.; Reynolds, Lyndsey A.; Rhee, Dong K.; Rivard, Allyson B.; Ronk, Adam J.; Rooney, Meghan B.; Rubin, Lainey S.; Salbert, Luke R.; Saluja, Rasleen K.; Schauder, Taylor; Schneiter, Allison R.; Schulz, Robert W.; Smith, Karl E.; Spencer, Sarah; Swanson, Bryant R.; Tache, Melissa A.; Tewilliager, Ashley A.; Tilot, Amanda K.; VanEck, Eve; Villerot, Matthew M.; Vylonis, Megan B.; Watson, David T.; Wurzler, Juliana A.; Wysocki, Lauren M.; Yalamanchili, Monica; Zaborowicz, Matthew A.; Emerson, Julia A.; Ortiz, Carlos; Deuschle, Frederic J.; DiLorenzo, Lauren A.; Goeller, Katie L.; Macchi, Christopher R.; Muller, Sarah E.; Pasierb, Brittany D.; Sable, Joseph E.; Tucci, Jessica M.; Tynon, Marykathryn; Dunbar, David A.; Beken, Levent H.; Conturso, Alaina C.; Danner, Benjamin L.; DeMichele, Gabriella A.; Gonzales, Justin A.; Hammond, Maureen S.; Kelley, Colleen V.; Kelly, Elisabeth A.; Kulich, Danielle; Mageeney, Catherine M.; McCabe, Nikie L.; Newman, Alyssa M.; Spaeder, Lindsay A.; Tumminello, Richard A.; Revie, Dennis; Benson, Jonathon M.; Cristostomo, Michael C.; DaSilva, Paolo A.; Harker, Katherine S.; Jarrell, Jenifer N.; Jimenez, Luis A.; Katz, Brandon M.; Kennedy, William R.; Kolibas, Kimberly S.; LeBlanc, Mark T.; Nguyen, Trung T.; Nicolas, Daniel S.; Patao, Melissa D.; Patao, Shane M.; Rupley, Bryan J.; Sessions, Bridget J.; Weaver, Jennifer A.; Goodman, Anya L.; Alvendia, Erica L.; Baldassari, Shana M.; Brown, Ashley S.; Chase, Ian O.; Chen, Maida; Chiang, Scott; Cromwell, Avery B.; Custer, Ashley F.; DiTommaso, Tia M.; El-Adaimi, Jad; Goscinski, Nora C.; Grove, Ryan A.; Gutierrez, Nestor; Harnoto, Raechel S.; Hedeen, Heather; Hong, Emily L.; Hopkins, Barbara L.; Huerta, Vilma F.; Khoshabian, Colin; LaForge, Kristin M.; Lee, Cassidy T.; Lewis, Benjamin M.; Lydon, Anniken M.; Maniaci, Brian J.; Mitchell, Ryan D.; Morlock, Elaine V.; Morris, William M.; Naik, Priyanka; Olson, Nicole C.; Osterloh, Jeannette M.; Perez, Marcos A.; Presley, Jonathan D.; Randazzo, Matt J.; Regan, Melanie K.; Rossi, Franca G.; Smith, Melanie A.; Soliterman, Eugenia A.; Sparks, Ciani J.; Tran, Danny L.; Wan, Tiffany; Welker, Anne A.; Wong, Jeremy N.; Sreenivasan, Aparna; Youngblom, Jim; Adams, Andrew; Alldredge, Justin; Bryant, Ashley; Carranza, David; Cifelli, Alyssa; Coulson, Kevin; Debow, Calise; Delacruz, Noelle; Emerson, Charlene; Farrar, Cassandra; Foret, Don; Garibay, Edgar; Gooch, John; Heslop, Michelle; Kaur, Sukhjit; Khan, Ambreen; Kim, Van; Lamb, Travis; Lindbeck, Peter; Lucas, Gabi; Macias, Elizabeth; Martiniuc, Daniela; Mayorga, Lissett; Medina, Joseph; Membreno, Nelson; Messiah, Shady; Neufeld, Lacey; Nguyen, San Francisco; Nichols, Zachary; Odisho, George; Peterson, Daymon; Rodela, Laura; Rodriguez, Priscilla; Rodriguez, Vanessa; Ruiz, Jorge; Sherrill, Will; Silva, Valeria; Sparks, Jeri; Statton, Geeta; Townsend, Ashley; Valdez, Isabel; Waters, Mary; Westphal, Kyle; Winkler, Stacey; Zumkehr, Joannee; DeJong, Randall J.; Hoogewerf, Arlene J.; Ackerman, Cheri M.; Armistead, Isaac O.; Baatenburg, Lara; Borr, Matthew J.; Brouwer, Lindsay K.; Burkhart, Brandon J.; Bushhouse, Kelsey T.; Cesko, Lejla; Choi, Tiffany Y. Y.; Cohen, Heather; Damsteegt, Amanda M.; Darusz, Jess M.; Dauphin, Cory M.; Davis, Yelena P.; Diekema, Emily J.; Drewry, Melissa; Eisen, Michelle E. M.; Faber, Hayley M.; Faber, Katherine J.; Feenstra, Elizabeth; Felzer-Kim, Isabella T.; Hammond, Brandy L.; Hendriksma, Jesse; Herrold, Milton R.; Hilbrands, Julia A.; Howell, Emily J.; Jelgerhuis, Sarah A.; Jelsema, Timothy R.; Johnson, Benjamin K.; Jones, Kelly K.; Kim, Anna; Kooienga, Ross D.; Menyes, Erika E.; Nollet, Eric A.; Plescher, Brittany E.; Rios, Lindsay; Rose, Jenny L.; Schepers, Allison J.; Scott, Geoff; Smith, Joshua R.; Sterling, Allison M.; Tenney, Jenna C.; Uitvlugt, Chris; VanDyken, Rachel E.; VanderVennen, Marielle; Vue, Samantha; Kokan, Nighat P.; Agbley, Kwabea; Boham, Sampson K.; Broomfield, Daniel; Chapman, Kayla; Dobbe, Ali; Dobbe, Ian; Harrington, William; Ibrahem, Marwan; Kennedy, Andre; Koplinsky, Chad A.; Kubricky, Cassandra; Ladzekpo, Danielle; Pattison, Claire; Ramirez, Roman E.; Wande, Lucia; Woehlke, Sarah; Wawersik, Matthew; Kiernan, Elizabeth; Thompson, Jeffrey S.; Banker, Roxanne; Bartling, Justina R.; Bhatiya, Chinmoy I.; Boudoures, Anna L.; Christiansen, Lena; Fosselman, Daniel S.; French, Kristin M.; Gill, Ishwar S.; Havill, Jessen T.; Johnson, Jaelyn L.; Keny, Lauren J.; Kerber, John M.; Klett, Bethany M.; Kufel, Christina N.; May, Francis J.; Mecoli, Jonathan P.; Merry, Callie R.; Meyer, Lauren R.; Miller, Emily G.; Mullen, Gregory J.; Palozola, Katherine C.; Pfeil, Jacob J.; Thomas, Jessica G.; Verbofsky, Evan M.; Spana, Eric P.; Agarwalla, Anant; Chapman, Julia; Chlebina, Ben; Chong, Insun; Falk, I.N.; Fitzgibbons, John D.; Friedman, Harrison; Ighile, Osagie; Kim, Andrew J.; Knouse, Kristin A.; Kung, Faith; Mammo, Danny; Ng, Chun Leung; Nikam, Vinayak S.; Norton, Diana; Pham, Philip; Polk, Jessica W.; Prasad, Shreya; Rankin, Helen; Ratliff, Camille D.; Scala, Victoria; Schwartz, Nicholas U.; Shuen, Jessica A.; Xu, Amy; Xu, Thomas Q.; Zhang, Yi; Rosenwald, Anne G.; Burg, Martin G.; Adams, Stephanie J.; Baker, Morgan; Botsford, Bobbi; Brinkley, Briana; Brown, Carter; Emiah, Shadie; Enoch, Erica; Gier, Chad; Greenwell, Alyson; Hoogenboom, Lindsay; Matthews, Jordan E.; McDonald, Mitchell; Mercer, Amanda; Monsma, Nicholaus; Ostby, Kristine; Ramic, Alen; Shallman, Devon; Simon, Matthew; Spencer, Eric; Tomkins, Trisha; Wendland, Pete; Wylie, Anna; Wolyniak, Michael J.; Robertson, Gregory M.; Smith, Samuel I.; DiAngelo, Justin R.; Sassu, Eric D.; Bhalla, Satish C.; Sharif, Karim A.; Choeying, Tenzin; Macias, Jason S.; Sanusi, Fareed; Torchon, Karvyn; Bednarski, April E.; Alvarez, Consuelo J.; Davis, Kristen C.; Dunham, Carrie A.; Grantham, Alaina J.; Hare, Amber N.; Schottler, Jennifer; Scott, Zackary W.; Kuleck, Gary A.; Yu, Nicole S.; Kaehler, Marian M.; Jipp, Jacob; Overvoorde, Paul J.; Shoop, Elizabeth; Cyrankowski, Olivia; Hoover, Betsy; Kusner, Matt; Lin, Devry; Martinov, Tijana; Misch, Jonathan; Salzman, Garrett; Schiedermayer, Holly; Snavely, Michael; Zarrasola, Stephanie; Parrish, Susan; Baker, Atlee; Beckett, Alissa; Belella, Carissa; Bryant, Julie; Conrad, Turner; Fearnow, Adam; Gomez, Carolina; Herbstsomer, Robert A.; Hirsch, Sarah; Johnson, Christen; Jones, Melissa; Kabaso, Rita; Lemmon, Eric; Vieira, Carolina Marques dos Santos; McFarland, Darryl; McLaughlin, Christopher; Morgan, Abbie; Musokotwane, Sepo; Neutzling, William; Nietmann, Jana; Paluskievicz, Christina; Penn, Jessica; Peoples, Emily; Pozmanter, Caitlin; Reed, Emily; Rigby, Nichole; Schmidt, Lasse; Shelton, Micah; Shuford, Rebecca; Tirasawasdichai, Tiara; Undem, Blair; Urick, Damian; Vondy, Kayla; Yarrington, Bryan; Eckdahl, Todd T.; Poet, Jeffrey L.; Allen, Alica B.; Anderson, John E.; Barnett, Jason M.; Baumgardner, Jordan S.; Brown, Adam D.; Carney, Jordan E.; Chavez, Ramiro A.; Christgen, Shelbi L.; Christie, Jordan S.; Clary, Andrea N.; Conn, Michel A.; Cooper, Kristen M.; Crowley, Matt J.; Crowley, Samuel T.; Doty, Jennifer S.; Dow, Brian A.; Edwards, Curtis R.; Elder, Darcie D.; Fanning, John P.; Janssen, Bridget M.; Lambright, Anthony K.; Lane, Curtiss E.; Limle, Austin B.; Mazur, Tammy; McCracken, Marly R.; McDonough, Alexa M.; Melton, Amy D.; Minnick, Phillip J.; Musick, Adam E.; Newhart, William H.; Noynaert, Joseph W.; Ogden, Bradley J.; Sandusky, Michael W.; Schmuecker, Samantha M.; Shipman, Anna L.; Smith, Anna L.; Thomsen, Kristen M.; Unzicker, Matthew R.; Vernon, William B.; Winn, Wesley W.; Woyski, Dustin S.; Zhu, Xiao; Du, Chunguang; Ament, Caitlin; Aso, Soham; Bisogno, Laura Simone; Caronna, Jason; Fefelova, Nadezhda; Lopez, Lenin; Malkowitz, Lorraine; Marra, Jonathan; Menillo, Daniella; Obiorah, Ifeanyi; Onsarigo, Eric Nyabeta; Primus, Shekerah; Soos, Mahdi; Tare, Archana; Zidan, Ameer; Jones, Christopher J.; Aronhalt, Todd; Bellush, James M.; Burke, Christa; DeFazio, Steve; Does, Benjamin R.; Johnson, Todd D.; Keysock, Nicholas; Knudsen, Nelson H.; Messler, James; Myirski, Kevin; Rekai, Jade Lea; Rempe, Ryan Michael; Salgado, Michael S.; Stagaard, Erica; Starcher, Justin R.; Waggoner, Andrew W.; Yemelyanova, Anastasia K.; Hark, Amy T.; Bertolet, Anne; Kuschner, Cyrus E.; Parry, Kesley; Quach, Michael; Shantzer, Lindsey; Shaw, Mary E.; Smith, Mary A.; Glenn, Omolara; Mason, Portia; Williams, Charlotte; Key, S. Catherine Silver; Henry, Tyneshia C. P.; Johnson, Ashlee G.; White, Jackie X.; Haberman, Adam; Asinof, Sam; Drumm, Kelly; Freeburg, Trip; Safa, Nadia; Schultz, Darrin; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Wellinghoff, Jules; Hoopes, Laura L. M.; Chau, Kim M.; Ward, Alyssa; Regisford, E. Gloria C.; Augustine, LaJerald; Davis-Reyes, Brionna; Echendu, Vivienne; Hales, Jasmine; Ibarra, Sharon; Johnson, Lauriaun; Ovu, Steven; Braverman, John M.; Bahr, Thomas J.; Caesar, Nicole M.; Campana, Christopher; Cassidy, Daniel W.; Cognetti, Peter A.; English, Johnathan D.; Fadus, Matthew C.; Fick, Cameron N.; Freda, Philip J.; Hennessy, Bryan M.; Hockenberger, Kelsey; Jones, Jennifer K.; King, Jessica E.; Knob, Christopher R.; Kraftmann, Karen J.; Li, Linghui; Lupey, Lena N.; Minniti, Carl J.; Minton, Thomas F.; Moran, Joseph V.; Mudumbi, Krishna; Nordman, Elizabeth C.; Puetz, William J.; Robinson, Lauren M.; Rose, Thomas J.; Sweeney, Edward P.; Timko, Ashley S.; Paetkau, Don W.; Eisler, Heather L.; Aldrup, Megan E.; Bodenberg, Jessica M.; Cole, Mara G.; Deranek, Kelly M.; DeShetler, Megan; Dowd, Rose M.; Eckardt, Alexandra K.; Ehret, Sharon C.; Fese, Jessica; Garrett, Amanda D.; Kammrath, Anna; Kappes, Michelle L.; Light, Morgan R.; Meier, Anne C.; O’Rouke, Allison; Perella, Mallory; Ramsey, Kimberley; Ramthun, Jennifer R.; Reilly, Mary T.; Robinett, Deirdre; Rossi, Nadine L.; Schueler, Mary Grace; Shoemaker, Emma; Starkey, Kristin M.; Vetor, Ashley; Vrable, Abby; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R.; Herrick, Douglas A.; Khoury, Christopher B.; Lea, Charlotte; Louie, Christopher A.; Lowell, Shannon M.; Reynolds, Thomas J.; Schibler, Jeanine; Scoma, Alexandra H.; Smith-Gee, Maxwell T.; Tuberty, Sarah; Smith, Christopher D.; Lopilato, Jane E.; Hauke, Jeanette; Roecklein-Canfield, Jennifer A.; Corrielus, Maureen; Gilman, Hannah; Intriago, Stephanie; Maffa, Amanda; Rauf, Sabya A.; Thistle, Katrina; Trieu, Melissa; Winters, Jenifer; Yang, Bib; Hauser, Charles R.; Abusheikh, Tariq; Ashrawi, Yara; Benitez, Pedro; Boudreaux, Lauren R.; Bourland, Megan; Chavez, Miranda; Cruz, Samantha; Elliott, GiNell; Farek, Jesse R.; Flohr, Sarah; Flores, Amanda H.; Friedrichs, Chelsey; Fusco, Zach; Goodwin, Zane; Helmreich, Eric; Kiley, John; Knepper, John Mark; Langner, Christine; Martinez, Megan; Mendoza, Carlos; Naik, Monal; Ochoa, Andrea; Ragland, Nicolas; Raimey, England; Rathore, Sunil; Reza, Evangelina; Sadovsky, Griffin; Seydoux, Marie-Isabelle B.; Smith, Jonathan E.; Unruh, Anna K.; Velasquez, Vicente; Wolski, Matthew W.; Gosser, Yuying; Govind, Shubha; Clarke-Medley, Nicole; Guadron, Leslie; Lau, Dawn; Lu, Alvin; Mazzeo, Cheryl; Meghdari, Mariam; Ng, Simon; Pamnani, Brad; Plante, Olivia; Shum, Yuki Kwan Wa; Song, Roy; Johnson, Diana E.; Abdelnabi, Mai; Archambault, Alexi; Chamma, Norma; Gaur, Shailly; Hammett, Deborah; Kandahari, Adrese; Khayrullina, Guzal; Kumar, Sonali; Lawrence, Samantha; Madden, Nigel; Mandelbaum, Max; Milnthorp, Heather; Mohini, Shiv; Patel, Roshni; Peacock, Sarah J.; Perling, Emily; Quintana, Amber; Rahimi, Michael; Ramirez, Kristen; Singhal, Rishi; Weeks, Corinne; Wong, Tiffany; Gillis, Aubree T.; Moore, Zachary D.; Savell, Christopher D.; Watson, Reece; Mel, Stephanie F.; Anilkumar, Arjun A.; Bilinski, Paul; Castillo, Rostislav; Closser, Michael; Cruz, Nathalia M.; Dai, Tiffany; Garbagnati, Giancarlo F.; Horton, Lanor S.; Kim, Dongyeon; Lau, Joyce H.; Liu, James Z.; Mach, Sandy D.; Phan, Thu A.; Ren, Yi; Stapleton, Kenneth E.; Strelitz, Jean M.; Sunjed, Ray; Stamm, Joyce; Anderson, Morgan C.; Bonifield, Bethany Grace; Coomes, Daniel; Dillman, Adam; Durchholz, Elaine J.; Fafara-Thompson, Antoinette E.; Gross, Meleah J.; Gygi, Amber M.; Jackson, Lesley E.; Johnson, Amy; Kocsisova, Zuzana; Manghelli, Joshua L.; McNeil, Kylie; Murillo, Michael; Naylor, Kierstin L.; Neely, Jessica; Ogawa, Emmy E.; Rich, Ashley; Rogers, Anna; Spencer, J. Devin; Stemler, Kristina M.; Throm, Allison A.; Van Camp, Matt; Weihbrecht, Katie; Wiles, T. Aaron; Williams, Mallory A.; Williams, Matthew; Zoll, Kyle; Bailey, Cheryl; Zhou, Leming; Balthaser, Darla M.; Bashiri, Azita; Bower, Mindy E.; Florian, Kayla A.; Ghavam, Nazanin; Greiner-Sosanko, Elizabeth S.; Karim, Helmet; Mullen, Victor W.; Pelchen, Carly E.; Yenerall, Paul M.; Zhang, Jiayu; Rubin, Michael R.; Arias-Mejias, Suzette M.; Bermudez-Capo, Armando G.; Bernal-Vega, Gabriela V.; Colon-Vazquez, Mariela; Flores-Vazquez, Arelys; Gines-Rosario, Mariela; Llavona-Cartagena, Ivan G.; Martinez-Rodriguez, Javier O.; Ortiz-Fuentes, Lionel; Perez-Colomba, Eliezer O.; Perez-Otero, Joseph; Rivera, Elisandra; Rodriguez-Giron, Luke J.; Santiago-Sanabria, Arnaldo J.; Senquiz-Gonzalez, Andrea M.; delValle, Frank R. Soto; Vargas-Franco, Dorianmarie; Velázquez-Soto, Karla I.; Zambrana-Burgos, Joan D.; Martinez-Cruzado, Juan Carlos; Asencio-Zayas, Lillyann; Babilonia-Figueroa, Kevin; Beauchamp-Pérez, Francis D.; Belén-Rodríguez, Juliana; Bracero-Quiñones, Luciann; Burgos-Bula, Andrea P.; Collado-Méndez, Xavier A.; Colón-Cruz, Luis R.; Correa-Muller, Ana I.; Crooke-Rosado, Jonathan L.; Cruz-García, José M.; Defendini-Ávila, Marianna; Delgado-Peraza, Francheska M.; Feliciano-Cancela, Alex J.; Gónzalez-Pérez, Valerie M.; Guiblet, Wilfried; Heredia-Negrón, Aldo; Hernández-Muñiz, Jennifer; Irizarry-González, Lourdes N.; Laboy-Corales, Ángel L.; Llaurador-Caraballo, Gabriela A.; Marín-Maldonado, Frances; Marrero-Llerena, Ulises; Martell-Martínez, Héctor A.; Martínez-Traverso, Idaliz M.; Medina-Ortega, Kiara N.; Méndez-Castellanos, Sonya G.; Menéndez-Serrano, Krizia C.; Morales-Caraballo, Carol I.; Ortiz-DeChoudens, Saryleine; Ortiz-Ortiz, Patricia; Pagán-Torres, Hendrick; Pérez-Afanador, Diana; Quintana-Torres, Enid M.; Ramírez-Aponte, Edwin G.; Riascos-Cuero, Carolina; Rivera-Llovet, Michelle S.; Rivera-Pagán, Ingrid T.; Rivera-Vicéns, Ramón E.; Robles-Juarbe, Fabiola; Rodríguez-Bonilla, Lorraine; Rodríguez-Echevarría, Brian O.; Rodríguez-García, Priscila M.; Rodríguez-Laboy, Abneris E.; Rodríguez-Santiago, Susana; Rojas-Vargas, Michael L.; Rubio-Marrero, Eva N.; Santiago-Colón, Albeliz; Santiago-Ortiz, Jorge L.; Santos-Ramos, Carlos E.; Serrano-González, Joseline; Tamayo-Figueroa, Alina M.; Tascón-Peñaranda, Edna P.; Torres-Castillo, José L.; Valentín-Feliciano, Nelson A.; Valentín-Feliciano, Yashira M.; Vargas-Barreto, Nadyan M.; Vélez-Vázquez, Miguel; Vilanova-Vélez, Luis R.; Zambrana-Echevarría, Cristina; MacKinnon, Christy; Chung, Hui-Min; Kay, Chris; Pinto, Anthony; Kopp, Olga R.; Burkhardt, Joshua; Harward, Chris; Allen, Robert; Bhat, Pavan; Chang, Jimmy Hsiang-Chun; Chen, York; Chesley, Christopher; Cohn, Dara; DuPuis, David; Fasano, Michael; Fazzio, Nicholas; Gavinski, Katherine; Gebreyesus, Heran; Giarla, Thomas; Gostelow, Marcus; Greenstein, Rachel; Gunasinghe, Hashini; Hanson, Casey; Hay, Amanda; He, Tao Jian; Homa, Katie; Howe, Ruth; Howenstein, Jeff; Huang, Henry; Khatri, Aaditya; Kim, Young Lu; Knowles, Olivia; Kong, Sarah; Krock, Rebecca; Kroll, Matt; Kuhn, Julia; Kwong, Matthew; Lee, Brandon; Lee, Ryan; Levine, Kevin; Li, Yedda; Liu, Bo; Liu, Lucy; Liu, Max; Lousararian, Adam; Ma, Jimmy; Mallya, Allyson; Manchee, Charlie; Marcus, Joseph; McDaniel, Stephen; Miller, Michelle L.; Molleston, Jerome M.; Diez, Cristina Montero; Ng, Patrick; Ngai, Natalie; Nguyen, Hien; Nylander, Andrew; Pollack, Jason; Rastogi, Suchita; Reddy, Himabindu; Regenold, Nathaniel; Sarezky, Jon; Schultz, Michael; Shim, Jien; Skorupa, Tara; Smith, Kenneth; Spencer, Sarah J.; Srikanth, Priya; Stancu, Gabriel; Stein, Andrew P.; Strother, Marshall; Sudmeier, Lisa; Sun, Mengyang; Sundaram, Varun; Tazudeen, Noor; Tseng, Alan; Tzeng, Albert; Venkat, Rohit; Venkataram, Sandeep; Waldman, Leah; Wang, Tracy; Yang, Hao; Yu, Jack Y.; Zheng, Yin; Preuss, Mary L.; Garcia, Angelica; Juergens, Matt; Morris, Robert W.; Nagengast, Alexis A.; Azarewicz, Julie; Carr, Thomas J.; Chichearo, Nicole; Colgan, Mike; Donegan, Megan; Gardner, Bob; Kolba, Nik; Krumm, Janice L.; Lytle, Stacey; MacMillian, Laurell; Miller, Mary; Montgomery, Andrew; Moretti, Alysha; Offenbacker, Brittney; Polen, Mike; Toth, John; Woytanowski, John; Kadlec, Lisa; Crawford, Justin; Spratt, Mary L.; Adams, Ashley L.; Barnard, Brianna K.; Cheramie, Martin N.; Eime, Anne M.; Golden, Kathryn L.; Hawkins, Allyson P.; Hill, Jessica E.; Kampmeier, Jessica A.; Kern, Cody D.; Magnuson, Emily E.; Miller, Ashley R.; Morrow, Cody M.; Peairs, Julia C.; Pickett, Gentry L.; Popelka, Sarah A.; Scott, Alexis J.; Teepe, Emily J.; TerMeer, Katie A.; Watchinski, Carmen A.; Watson, Lucas A.; Weber, Rachel E.; Woodard, Kate A.; Barnard, Daron C.; Appiah, Isaac; Giddens, Michelle M.; McNeil, Gerard P.; Adebayo, Adeola; Bagaeva, Kate; Chinwong, Justina; Dol, Chrystel; George, Eunice; Haltaufderhyde, Kirk; Haye, Joanna; Kaur, Manpreet; Semon, Max; Serjanov, Dmitri; Toorie, Anika; Wilson, Christopher; Riddle, Nicole C.; Buhler, Jeremy; Mardis, Elaine R.

2015-01-01

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. PMID:25740935

Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea Fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)

PubMed Central

Dunlap, Paul V.; Ast, Jennifer C.

2005-01-01

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040T, and the type strain of Photobacterium iliopiscarium, ATCC 51760T. Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040T. These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes. PMID:15691950

Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae).

PubMed

Dunlap, Paul V; Ast, Jennifer C

2005-02-01

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040(T), and the type strain of Photobacterium iliopiscarium, ATCC 51760(T). Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040(T). These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.

Homogenisation of sulphide inclusions within diamonds: A new approach to diamond inclusion geochemistry

NASA Astrophysics Data System (ADS)

McDonald, Iain; Hughes, Hannah S. R.; Butler, Ian B.; Harris, Jeffrey W.; Muir, Duncan

2017-11-01

Base metal sulphide (BMS) inclusions in diamonds provide a unique insight into the chalcophile and highly siderophile element composition of the mantle. Entombed within their diamond hosts, these provide a more robust (closed system) sample, from which to determine the trace element, Re-Os and S-isotopic compositions of the mantle than mantle xenoliths or orogenic peridotites, as they are shielded from alteration during ascent to the Earth's crust and subsequent surface weathering. However, at temperatures below 1100 °C some BMS inclusions undergo subsolidus re-equilibration from an original monosulphide solid solution (Mss) and this causes fractionation of the major and trace elements within the inclusions. Thus to study the subjects noted above, current techniques require the entire BMS inclusion to be extracted for analyses. Unfortunately, 'flaking' of inclusions during break-out is a frequent occurrence and hence the risk of accidentally under-sampling a portion of the BMS inclusion is inherent in current practices. This loss may have significant implications for Re-Os isotope analyses where incomplete sampling of a Re-rich phase, such as chalcopyrite that typically occurs at the outer margins of BMS inclusions, may induce significant bias in the Re-Os and 187Os/188Os measurements and resulting model and isochron ages. We have developed a method for the homogenisation of BMS inclusions in diamond prior to their break-out from the host stone. Diamonds are heated to 1100 °C and then quenched to chemically homogenise any sulphide inclusions for both major and trace elements. Using X-ray Computed Microtomography (μCT) we determine the shape and spatial setting of multiple inclusions within a host stone and crucially show that the volume of a BMS inclusion is the same both before and after homogenisation. We show that the homogenisation process significantly reduces the inherent variability of in situ analysis when compared with unhomogenised BMS, thereby widening the scope for multiple methods for quantitative analysis, even on 'flakes' of single BMS inclusions. Finally we show that the trace elements present in peridotite (P-type) and eclogitic (E-type) BMS are distinct, with P-type diamonds having systematically higher total platinum-group element (particularly Os, Ir, Ru) and Te and As concentrations. These distinctions suggest that the PGE and semi-metal budgets of mantle-derived partial melts will be significantly dependent upon the type(s) and proportions of sulphides present in the mantle source.

Dual element ((15)N/(14)N, (13)C/(12)C) isotope analysis of glyphosate and AMPA by derivatization-gas chromatography isotope ratio mass spectrometry (GC/IRMS) combined with LC/IRMS.

PubMed

Mogusu, Emmanuel O; Wolbert, J Benjamin; Kujawinski, Dorothea M; Jochmann, Maik A; Elsner, Martin

2015-07-01

To assess sources and degradation of the herbicide glyphosate [N-(phosphonomethyl) glycine] and its metabolite AMPA (aminomethylphosphonic acid), concentration measurements are often inconclusive and even (13)C/(12)C analysis alone may give limited information. To advance isotope ratio analysis of an additional element, we present compound-specific (15)N/(14)N analysis of glyphosate and AMPA by a two step derivatization in combination with gas chromatography/isotope ratio mass spectrometry (GC/IRMS). The N-H group was derivatized with isopropyl chloroformate (iso-PCF), and remaining acidic groups were subsequently methylated with trimethylsilyldiazomethane (TMSD). Iso-PCF treatment at pH <10 gave too low (15)N/(14)N ratios indicating an incomplete derivatization; in contrast, too high (15)N/(14)N ratios at pH >10 indicated decomposition of the derivative. At pH 10, and with an excess of iso-PCF by 10-24, greatest yields and accurate (15)N/(14)N ratios were obtained (deviation from elemental analyzer-IRMS: -0.2 ± 0.9% for glyphosate; -0.4 ± 0.7% for AMPA). Limits for accurate δ(15)N analysis of glyphosate and AMPA were 150 and 250 ng injected, respectively. A combination of δ(15)N and δ(13)C analysis by liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) (1) enabled an improved distinction of commercial glyphosate products and (2) showed that glyphosate isotope values during degradation by MnO2 clearly fell outside the commercial product range. This highlights the potential of combined carbon and nitrogen isotopes analysis to trace sources and degradation of glyphosate.

Composition and microstructure of MTA and Aureoseal Plus: XRF, EDS, XRD and FESEM evaluation.

PubMed

Cianconi, L; Palopoli, P; Campanella, V; Mancini, M

2016-12-01

The aim of this study was to determine the chemical composition and the phases' microstructure of Aureoseal Plus (OGNA, Italy) and ProRoot MTA (Dentsply Tulsa Dental, USA) and to compare their characteristics. Study Design: Comparing Aureoseal Plus and ProRoot MTA microstructure by means of several analyses type. The chemical analysis of the two cements was assessed following the UNI EN ISO 196-2 norm. X-Ray fluorescence (XRF) was used to determine the element composition. The crystalline structure was analysed quantitatively using x-ray diffraction (XRD). Powders morphology was evaluated using a scanning electron microscope (SEM) with backscattering detectors, and a field emission scanning electron microscope (FESEM). Elemental analysis was performed by energy dispersive x-ray analysis (EDS). The semi-quantitative XRF analysis showed the presence of heavy metal oxides in both cements. The XRD spectra of the two cements reported the presence of dicalcium silicate, tricalcium silicate, tricalcium aluminate, tetracalcium aluminoferrite, bismuth oxide and gypsum. SEM analysis showed that ProRoot MTA powder is less coarse and more homogeneous than Aureoseal. Both powders are formed by particles of different shapes: round, prismatic and oblong. The EDS analysis showed that some ProRoot MTA particles, differently from Aureoseal, contain Ca, Si, Al and Fe. Oblong particles in ProRoot and Aureoseal are rich of bismuth. The strong interest in developing new Portland cement-based endodontic sealers will create materials with increased handling characteristics and physicochemical properties. A thorough investigation on two cement powders was carried out by using XRF, XRD, SEM and EDS analysis. To date there was a lack of studies on Aureoseal Plus. This cement is similar in composition to ProRoot MTA. Despite that it has distinctive elements that could improve its characteristics, resulting in a good alternative to MTA.

Organic Matrix-related mineralization of sea urchin spicules, spines, test and teeth

PubMed Central

Veis, Arthur

2012-01-01

The camarodont echinoderms have five distinct mineralized skeletal elements: the embryonic spicules and mature test; spines, lantern stereom and teeth. The embryonic spicules are transient structural elements of the larval skeleton whereas the spines and test plates are permanent structural elements. The teeth are continuously growing structures, matching wear at the incisal adoral end to the rate of new production at the aboral plumula. The mineral in all cases is a high magnesium calcite, but the magnesium content, crystal shape and growth pattern is different in each type of skeletal element. The crystal shape and organization into macro structures depends on the presence of an organic matrix which creates the spaces and controls the environments for crystal initiation and growth. The detailed mechanisms of crystal regulation are not known, but much work has been done on defining the proteins which appear to be involved. Phosphorylated matrix proteins may be of special importance. Biochemical isolation of proteins, construction and analysis of cDNA libraries, and most recently high-throughput proteomic analysis in conjunction with the sequencing of the complete genome have yielded a detailed list of protein components likely to be involved in the mineralization processes. However, the proteome-genome analyses have not yet provided insight into the mechanisms of crystallization, calcite composition, and orientation applicable to all skeletal elements. Although the embryonic pluteus and their spicules are the best studied system, it appears that spicule is not representative of the mature skeletal elements. Now armed with the compositions of most of the proteins involved, the next phase of research will have to focus on the specific localization of the proteins and individual biochemistries of each system with regard to mineral content and placement. PMID:21622194

Mineralogy and petrogenesis of lunar magnesian granulitic meteorite Northwest Africa 5744

NASA Astrophysics Data System (ADS)

Kent, Jeremy J.; Brandon, Alan D.; Joy, Katherine H.; Peslier, Anne H.; Lapen, Thomas J.; Irving, Anthony J.; Coleff, Daniel M.

2017-09-01

Lunar meteorite Northwest Africa (NWA) 5744 is a granulitic breccia with an anorthositic troctolite composition that may represent a distinct crustal lithology not previously described. This meteorite is the namesake and first-discovered stone of its pairing group. Bulk rock major element abundances show the greatest affinity to Mg-suite rocks, yet trace element abundances are more consistent with those of ferroan anorthosites. The relatively low abundances of incompatible trace elements (including K, P, Th, U, and rare earth elements) in NWA 5744 could indicate derivation from a highlands crustal lithology or mixture of lithologies that are distinct from the Procellarum KREEP terrane on the lunar nearside. Impact-related thermal and shock metamorphism of NWA 5744 was intense enough to recrystallize mafic minerals in the matrix, but not intense enough to chemically equilibrate the constituent minerals. Thus, we infer that NWA 5744 was likely metamorphosed near the lunar surface, either as a lithic component within an impact melt sheet or from impact-induced shock.

Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

PubMed

Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

2015-03-03

Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data.

Finite element analysis and genetic algorithm optimization design for the actuator placement on a large adaptive structure

NASA Astrophysics Data System (ADS)

Sheng, Lizeng

The dissertation focuses on one of the major research needs in the area of adaptive/intelligent/smart structures, the development and application of finite element analysis and genetic algorithms for optimal design of large-scale adaptive structures. We first review some basic concepts in finite element method and genetic algorithms, along with the research on smart structures. Then we propose a solution methodology for solving a critical problem in the design of a next generation of large-scale adaptive structures---optimal placements of a large number of actuators to control thermal deformations. After briefly reviewing the three most frequently used general approaches to derive a finite element formulation, the dissertation presents techniques associated with general shell finite element analysis using flat triangular laminated composite elements. The element used here has three nodes and eighteen degrees of freedom and is obtained by combining a triangular membrane element and a triangular plate bending element. The element includes the coupling effect between membrane deformation and bending deformation. The membrane element is derived from the linear strain triangular element using Cook's transformation. The discrete Kirchhoff triangular (DKT) element is used as the plate bending element. For completeness, a complete derivation of the DKT is presented. Geometrically nonlinear finite element formulation is derived for the analysis of adaptive structures under the combined thermal and electrical loads. Next, we solve the optimization problems of placing a large number of piezoelectric actuators to control thermal distortions in a large mirror in the presence of four different thermal loads. We then extend this to a multi-objective optimization problem of determining only one set of piezoelectric actuator locations that can be used to control the deformation in the same mirror under the action of any one of the four thermal loads. A series of genetic algorithms, GA Version 1, 2 and 3, were developed to find the optimal locations of piezoelectric actuators from the order of 1021 ˜ 1056 candidate placements. Introducing a variable population approach, we improve the flexibility of selection operation in genetic algorithms. Incorporating mutation and hill climbing into micro-genetic algorithms, we are able to develop a more efficient genetic algorithm. Through extensive numerical experiments, we find that the design search space for the optimal placements of a large number of actuators is highly multi-modal and that the most distinct nature of genetic algorithms is their robustness. They give results that are random but with only a slight variability. The genetic algorithms can be used to get adequate solution using a limited number of evaluations. To get the highest quality solution, multiple runs including different random seed generators are necessary. The investigation time can be significantly reduced using a very coarse grain parallel computing. Overall, the methodology of using finite element analysis and genetic algorithm optimization provides a robust solution approach for the challenging problem of optimal placements of a large number of actuators in the design of next generation of adaptive structures.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.

PubMed

Smyth, Redmond P; Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe; von Kleist, Max; Marquet, Roland

2018-05-18

Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

PubMed Central

Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe

2018-01-01

Abstract Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5′ region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5′ PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production. PMID:29514260

The Role of Triads in the Evolution of the Periodic Table: Past and Present

ERIC Educational Resources Information Center

Scerri, Eric

2008-01-01

The purpose of this article is to propose a new design for the presentation of the periodic system of the elements. It is a system that highlights the fundamental importance of elements as basic substances rather than elements as simple substances, a distinction that is explained in the article. The proposed table is a variant of the Janet or…

Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease

PubMed Central

Kleinjan, Dirk A.; van Heyningen, Veronica

2005-01-01

Transcriptional control is a major mechanism for regulating gene expression. The complex machinery required to effect this control is still emerging from functional and evolutionary analysis of genomic architecture. In addition to the promoter, many other regulatory elements are required for spatiotemporally and quantitatively correct gene expression. Enhancer and repressor elements may reside in introns or up- and downstream of the transcription unit. For some genes with highly complex expression patterns—often those that function as key developmental control genes—the cis-regulatory domain can extend long distances outside the transcription unit. Some of the earliest hints of this came from disease-associated chromosomal breaks positioned well outside the relevant gene. With the availability of wide-ranging genome sequence comparisons, strong conservation of many noncoding regions became obvious. Functional studies have shown many of these conserved sites to be transcriptional regulatory elements that sometimes reside inside unrelated neighboring genes. Such sequence-conserved elements generally harbor sites for tissue-specific DNA-binding proteins. Developmentally variable chromatin conformation can control protein access to these sites and can regulate transcription. Disruption of these finely tuned mechanisms can cause disease. Some regulatory element mutations will be associated with phenotypes distinct from any identified for coding-region mutations. PMID:15549674

Trace elements and heavy metals in hair of stage III breast cancer patients.

PubMed

Benderli Cihan, Yasemin; Sözen, Selim; Oztürk Yıldırım, Sema

2011-12-01

This prospective study was designed to compare the hair levels of 36 elements in 52 patients with stage III breast cancer to those of an equal number of healthy individuals. Principal component and cluster analysis were used for source of identification and apportionment of heavy metals and trace elements in these two groups. A higher average level of iron was found in samples from patients while controls had higher levels of calcium. Both patients and controls had elevated levels of tin, magnesium, zinc, and sodium. Almost all element values in cancer patients showed higher dispersion and asymmetry than in healthy controls. Between the two groups, there were statistically significant differences in the concentrations of silver, arsenic, gold, boron, barium, beryllium, calcium, cadmium, cerium, cobalt, cesium, gadolinium, manganese, nickel, lead, antimony, scandium, selenium, and zinc (p < 0.05). Strong positive correlations were found between lead and gold (r = 0.785) in the cancer group and between palladium and cobalt (r = 0.945) in the healthy individuals. Our results show that there are distinct patterns of heavy metals and trace elements in the hair of breast cancer patients in comparison to healthy controls. These results could be of significance in the diagnosis of breast cancer.

Dynamic simulations of geologic materials using combined FEM/DEM/SPH analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, J P; Johnson, S M

2008-03-26

An overview of the Lawrence Discrete Element Code (LDEC) is presented, and results from a study investigating the effect of explosive and impact loading on geologic materials using the Livermore Distinct Element Code (LDEC) are detailed. LDEC was initially developed to simulate tunnels and other structures in jointed rock masses using large numbers of polyhedral blocks. Many geophysical applications, such as projectile penetration into rock, concrete targets, and boulder fields, require a combination of continuum and discrete methods in order to predict the formation and interaction of the fragments produced. In an effort to model this class of problems, LDECmore » now includes implementations of Cosserat point theory and cohesive elements. This approach directly simulates the transition from continuum to discontinuum behavior, thereby allowing for dynamic fracture within a combined finite element/discrete element framework. In addition, there are many application involving geologic materials where fluid-structure interaction is important. To facilitate solution of this class of problems a Smooth Particle Hydrodynamics (SPH) capability has been incorporated into LDEC to simulate fully coupled systems involving geologic materials and a saturating fluid. We will present results from a study of a broad range of geomechanical problems that exercise the various components of LDEC in isolation and in tandem.« less

Spatial computation of intratumoral T cells correlates with survival of patients with pancreatic cancer.

PubMed

Carstens, Julienne L; Correa de Sampaio, Pedro; Yang, Dalu; Barua, Souptik; Wang, Huamin; Rao, Arvind; Allison, James P; LeBleu, Valerie S; Kalluri, Raghu

2017-04-27

The exact nature and dynamics of pancreatic ductal adenocarcinoma (PDAC) immune composition remains largely unknown. Desmoplasia is suggested to polarize PDAC immunity. Therefore, a comprehensive evaluation of the composition and distribution of desmoplastic elements and T-cell infiltration is necessary to delineate their roles. Here we develop a novel computational imaging technology for the simultaneous evaluation of eight distinct markers, allowing for spatial analysis of distinct populations within the same section. We report a heterogeneous population of infiltrating T lymphocytes. Spatial distribution of cytotoxic T cells in proximity to cancer cells correlates with increased overall patient survival. Collagen-I and αSMA + fibroblasts do not correlate with paucity in T-cell accumulation, suggesting that PDAC desmoplasia may not be a simple physical barrier. Further exploration of this technology may improve our understanding of how specific stromal composition could impact T-cell activity, with potential impact on the optimization of immune-modulatory therapies.

Chemo-stratigraphy in the Murray Formation Using ChemCam

NASA Astrophysics Data System (ADS)

Blaney, D. L.; Anderson, R. B.; Bridges, N.; Bridges, J.; Calef, F. J., III; Clegg, S. M.; Le Deit, L.; Fisk, M. R.; Forni, O.; Gasnault, O.; Kah, L. C.; Kronyak, R. E.; Lanza, N.; Lasue, J.; Mangold, N.; Maurice, S.; Milliken, R.; Ming, D. W.; Nachon, M.; Newsom, H. E.; Rapin, W.; Stack, K.; Sumner, D. Y.; Wiens, R. C.

2015-12-01

Curiosity has completed a detailed chemo-stratigraphy analysis at the Pahrump exposure of the Murray formation. In total >570 chemical measurements and supporting remote micro images to classify texturally were collected. Chemical trends with both stratigraphic position and with texture were evaluated. From these data emerges a complex aqueous history where sediments have interacted with fluids with variable chemistry in distinct episodes. The ChemCam data collected at the nearby "Garden City" (GC) vein complex provides constraints on the chemical evolution of the Pahrump. GC is thought be stratigraphically above the Pahrump outcrop. Fluids producing the veins likely also migrated through the Pahrump sediments. Multiple episodes of fluids are evident at GC, forming distinct Ca sulfate, F-rich, enhanced MgO, and FeO-rich veins. These different fluid chemistries could be the result of distinct fluids migrating through the section from a distance with a pre-established chemical signature, fluids locally evolved from water rock interactions, or both. Texturally rocks have been classified into two distinct categories: fine grained or as cross-bedded sandstones. The sandstones have significantly lower SiO2, Al2O3, and K2O and higher FeO, and CaO. Fine grained rocks have further been sub-classified as resistant and recessive with other textural features such as laminations and pits noted.The strongest chemical trend in the fine-grained sandstones shows enhancements in MgO and FeO in erosion-resistant materials compared to fine grained recessive units, suggesting that increased abundance of Mg- and/or iron-rich cements may provide additional strength. The MgO and FeO variations with texture are independent of stratigraphic locations (e.g resistant material at both the bottom and top of the outcrop both are enhanced in MgO and FeO). The presence of the GC MgO and FeO rich veins provides additional evidence for fluids rich in these elements were present in the outcrop. Other elemental trends results including SiO2, Al2O3, K2O and Na2O will be explored in addition to key trace element signatures such as Li, Cr and F to understand the chemical evolution of the outcrop.

Epigenetic Differentiation of Natural Populations of Lilium bosniacum Associated with Contrasting Habitat Conditions.

PubMed

Zoldoš, Vlatka; Biruš, Ivan; Muratovic, Edina; Šatovic, Zlatko; Vojta, Aleksandar; Robin, Odile; Pustahija, Fatima; Bogunic, Faruk; Vicic Bockor, Vedrana; Siljak-Yakovlev, Sonja

2018-01-01

Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses revealed that the three populations did not differentiate genetically, but were clearly separated in three distinct clusters according to DNA methylation profiles. Principal coordinate analysis showed that overall epigenetic variation was closely related to habitat conditions. A new methylation-sensitive amplification polymorphism scoring approach allowed identification of mainly unmethylated (φST = 0.190) and fully CpG methylated (φST = 0.118) subepiloci playing a role in overall population differentiation, in comparison with hemimethylated sites (φST = 0.073). In addition, unusual rDNA repatterning and the presence of B chromosomes bearing 5S rDNA loci were recorded in the population growing on serpentine soil, suggesting dynamic chromosome rearrangements probably linked to global genome demethylation, which might have reactivated some mobile elements. We discuss our results considering our earlier data on morphology and leaf anatomy of several L. bosniacum populations, and suggest a possible role of epigenetics as a key element in population differentiation associated with environmental stress in these particular lily populations. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

NanoSIMS Reveals New Structural and Elemental Signatures of Early Life

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; Mostefaoui, Smail; Meibom, Anders; Selo, Madeleine; Robert, Francois; McKay, David S.

2006-01-01

The young technology of NanoSIMS is unlocking new information from organic matter in ancient sediments. We have used this technique to characterize sub-micron scale element composition of Proterozoic organics that are clearly biogenic as a guide for interpreting problematic structures in terrestrial or extraterrestrial samples. We used the NanoSIMS 50 of the National Museum of Natural History in Paris to map carbon, nitrogen (as CN), and sulfur in organic structures from the approximately 0.8 Ga Bitter Springs Formation. We analyzed spheroidal and filamentous microfossils as well as organic laminae that appeared amorphous by optical and scanning electron microscopy. In clear-cut microfossils, a coincidence between optical images and NanoSIMS element maps suggests a biological origin for the mapped carbon, sulfur, and nitrogen; this conclusion is supported by high resolution NanoSIMS maps showing identical spatial distributions of C, CN and S. High resolution images also demonstrate distinctive nano structure of the filaments and spheroids. In the amorphous laminae, NanoSIMS reveals morphologies reminiscent of compressed microfossils. Distinct CN/C ratios of the spheroids, filaments, and laminae may reflect their biological precursors (cell walls, cyanobacterial sheaths, and microbial communities/biofilms, respectively). Similar amorphous laminae comprise a preponderance of the organic matter in many Precambrian deposits. Thus it is possible that NanoSIMS will provide fresh insight into a large body of previously uninterpretable material. Additionally, NanoSIMS analysis may establish new biosignatures that will be helpful for assessing the origin and biogenicity of controversial Archean structures and any organic materials that may occur in Martian or other extraterrestrial samples.

What Do We Mean by 'Community Resilience'? A Systematic Literature Review of How It Is Defined in the Literature.

PubMed

Patel, Sonny S; Rogers, M Brooke; Amlôt, Richard; Rubin, G James

2017-02-01

Government, industry and charitable organisations have an increasing focus on programs intended to support community resilience to disasters. But has consensus been reached as to what defines 'community resilience' and what its core characteristics are? We undertook a systematic literature review of definitions of community resilience related to disasters. We conducted an inductive thematic analysis of the definitions and descriptions that we identified, in order to determine the proposed characteristics of community resilience prior to, during and after a disaster. We identified 80 relevant papers. There was no evidence of a common, agreed definition of community resilience. In spite of this, evidence was found of nine core elements of community resilience that were common among the definitions. The core elements were: local knowledge, community networks and relationships, communication, health, governance and leadership, resources, economic investment, preparedness, and mental outlook. Within these core elements, we identified 19 sub-elements linked to community resilience. Our findings show that community resilience remains an amorphous concept that is understood and applied differently by different research groups. Yet in spite of the differences in conception and application, there are well-understood elements that are widely proposed as important for a resilient community. A focus on these individual elements may be more productive than attempting to define and study community resilience as a distinct concept.

What Do We Mean by 'Community Resilience'? A Systematic Literature Review of How It Is Defined in the Literature

PubMed Central

Patel, Sonny S.; Rogers, M. Brooke; Amlôt, Richard; Rubin, G. James

2017-01-01

Background: Government, industry and charitable organisations have an increasing focus on programs intended to support community resilience to disasters. But has consensus been reached as to what defines 'community resilience' and what its core characteristics are? Methods: We undertook a systematic literature review of definitions of community resilience related to disasters. We conducted an inductive thematic analysis of the definitions and descriptions that we identified, in order to determine the proposed characteristics of community resilience prior to, during and after a disaster. Results: We identified 80 relevant papers. There was no evidence of a common, agreed definition of community resilience. In spite of this, evidence was found of nine core elements of community resilience that were common among the definitions. The core elements were: local knowledge, community networks and relationships, communication, health, governance and leadership, resources, economic investment, preparedness, and mental outlook. Within these core elements, we identified 19 sub-elements linked to community resilience. Conclusion: Our findings show that community resilience remains an amorphous concept that is understood and applied differently by different research groups. Yet in spite of the differences in conception and application, there are well-understood elements that are widely proposed as important for a resilient community. A focus on these individual elements may be more productive than attempting to define and study community resilience as a distinct concept. PMID:29188132

Hilbert's Hotel in polarization singularities.

PubMed

Wang, Yangyundou; Gbur, Greg

2017-12-15

We demonstrate theoretically how the creation of polarization singularities by the evolution of a fractional nonuniform polarization optical element involves the peculiar mathematics of countably infinite sets in the form of "Hilbert's Hotel." Two distinct topological processes can be observed, depending on the structure of the fractional optical element.

ARE ELEMENTAL FINGERPRINTS OF FISH OTOLITHS DISTINCT AMONG GREAT LAKES COASTAL NURSERY AREAS?

EPA Science Inventory

Elemental composition of an otolith reflects a fish's rearing environment,
so otolith geochemistry can record differences in ambient water conditions
specific to habitats used during a fish's life history. Although few studies
have been conducted in freshwater, trace ...

Comparison of the DiversiLab Repetitive Element PCR System with spa Typing and Pulsed-Field Gel Electrophoresis for Clonal Characterization of Methicillin-Resistant Staphylococcus aureus▿

PubMed Central

Babouee, B.; Frei, R.; Schultheiss, E.; Widmer, A. F.; Goldenberger, D.

2011-01-01

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with spa typing, spa clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into spa clonal complexes resulted in 3 clusters: spa-CC 067/548, spa-CC 008, and spa-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE, spa typing, DL typing, and spa clonal clustering, respectively. DL typing and spa clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to spa type t008 and spa-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and spa typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns. PMID:21307215

DNA methylation analysis reveals distinct methylation signatures in pediatric germ cell tumors.

PubMed

Amatruda, James F; Ross, Julie A; Christensen, Brock; Fustino, Nicholas J; Chen, Kenneth S; Hooten, Anthony J; Nelson, Heather; Kuriger, Jacquelyn K; Rakheja, Dinesh; Frazier, A Lindsay; Poynter, Jenny N

2013-06-27

Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q < 0.05), including a number of CpGs in stem cell and pluripotency-related pathways. Both YST and germinoma showed significantly lower methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy.

Electronegativity and the Bond Triangle

ERIC Educational Resources Information Center

Meek, Terry L.; Garner, Leah D.

2005-01-01

The usefulness of the bond triangle for categorizing compounds of the main-group elements may be extended by the use of weighted average electronegativities to allow distinction between compounds of the same elements with different stoichiometries. In such cases a higher valency for the central atom leads to greater covalent character and the…

Ruthenium in komatiitic chromite

NASA Astrophysics Data System (ADS)

Locmelis, Marek; Pearson, Norman J.; Barnes, Stephen J.; Fiorentini, Marco L.

2011-07-01

The distinction between Ru in solid solution and Ru-bearing inclusions is essential for the predictive modeling of platinum-group element (PGE) geochemistry in applications such as the lithogeochemical exploration for magmatic sulfide deposits in komatiites. This study investigates the role of chromite in the fractionation of Ru in ultramafic melts by analyzing chromite grains from sulfide-undersaturated komatiites and a komatiitic basalt from the Yilgarn Craton in Western Australia. In situ analysis using laser ablation ICP-MS yields uniform Ru concentrations in chromites both within-grain and on a sample scale, with concentrations between 220 and 540 ppb. All other platinum-group elements are below the detection limit of the laser ablation ICP-MS analysis. Carius tube digestion isotope dilution ICP-MS analysis of chromite concentrates confirms the accuracy of the in-situ method. Time resolved laser ablation ICP-MS analyses have identified the presence of sub-micron Ir-bearing inclusions in some chromite grains from the komatiitic basalt. However, Ru-bearing inclusions have not been recognized in the analyzed chromites and this combined with the in situ data suggests that Ru exists in solid solution in the crystal lattice of chromite. These results show that chromite can control the fractionation and concentration of Ru in ultramafic systems.

Co-citation Network Analysis of Religious Texts

NASA Astrophysics Data System (ADS)

Murai, Hajime; Tokosumi, Akifumi

This paper introduces a method of representing in a network the thoughts of individual authors of dogmatic texts numerically and objectively by means of co-citation analysis and a method of distinguishing between the thoughts of various authors by clustering and analysis of clustered elements, generated by the clustering process. Using these methods, this paper creates and analyzes the co-citation networks for five authoritative Christian theologians through history (Augustine, Thomas Aquinas, Jean Calvin, Karl Barth, John Paul II). These analyses were able to extract the core element of Christian thought (Jn 1:14, Ph 2:6, Ph 2:7, Ph 2:8, Ga 4:4), as well as distinctions between the individual theologians in terms of their sect (Catholic or Protestant) and era (thinking about the importance of God's creation and the necessity of spreading the Gospel). By supplementing conventional literary methods in areas such as philosophy and theology, with these numerical and objective methods, it should be possible to compare the characteristics of various doctrines. The ability to numerically and objectively represent the characteristics of various thoughts opens up the possibilities of utilizing new information technology, such as web ontology and the Artificial Intelligence, in order to process information about ideological thoughts in the future.

Nonlinear modelling in time domain numerical analysis of stringed instrument dynamics

NASA Astrophysics Data System (ADS)

Bielski, Paweł; Kujawa, Marcin

2017-03-01

Musical instruments are very various in terms of sound quality with their timbre shaped by materials and geometry. Materials' impact is commonly treated as dominant one by musicians, while it is unclear whether it is true or not. The research proposed in the study focuses on determining influence of both these factors on sound quality based on their impact on harmonic composition. Numerical approach has been chosen to allowed independent manipulation of geometrical and material parameters as opposed to experimental study subjected to natural randomness of instrument construction. Distinctive element of this research is precise modelling of whole instrument and treating it as one big vibrating system instead of performing modal analysis on an isolated part. Finite elements model of a stringed instrument has been built and a series of nonlinear time-domain dynamic analyses were executed to obtain displacement signals and perform subsequent spectral analysis. Precision of computations seems sufficient to determine the influence of instrument's macroscopic mechanical parameters on timbre. Further research should focus on implementation of acoustic medium in attempt to include dissipation and synchronization mechanisms. Outside the musical field this kind of research could be potentially useful in noise reduction problems.

Origin of the heavy elements in binary neutron-star mergers from a gravitational-wave event.

PubMed

Kasen, Daniel; Metzger, Brian; Barnes, Jennifer; Quataert, Eliot; Ramirez-Ruiz, Enrico

2017-11-02

The cosmic origin of elements heavier than iron has long been uncertain. Theoretical modelling shows that the matter that is expelled in the violent merger of two neutron stars can assemble into heavy elements such as gold and platinum in a process known as rapid neutron capture (r-process) nucleosynthesis. The radioactive decay of isotopes of the heavy elements is predicted to power a distinctive thermal glow (a 'kilonova'). The discovery of an electromagnetic counterpart to the gravitational-wave source GW170817 represents the first opportunity to detect and scrutinize a sample of freshly synthesized r-process elements. Here we report models that predict the electromagnetic emission of kilonovae in detail and enable the mass, velocity and composition of ejecta to be derived from observations. We compare the models to the optical and infrared radiation associated with the GW170817 event to argue that the observed source is a kilonova. We infer the presence of two distinct components of ejecta, one composed primarily of light (atomic mass number less than 140) and one of heavy (atomic mass number greater than 140) r-process elements. The ejected mass and a merger rate inferred from GW170817 imply that such mergers are a dominant mode of r-process production in the Universe.

A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

PubMed

Churakov, Gennady; Smit, Arian F A; Brosius, Jürgen; Schmitz, Jürgen

2005-04-01

About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high-copy-number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed, and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided them into six distinct subfamilies. We extracted tRNA(Ala)-derived monomers, two types of dimers, and three subfamilies of chimeric fusion products of a tRNA(Ala) domain and an approximately 180-nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA-like D-arm structure in the respective founder RNAs, as shown by compensatory mutations. By analysis of subfamily-specific genetic variability, comparison of the proportion of direct repeats, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

A useful and non-invasive microanalysis method for dental restoration materials

NASA Astrophysics Data System (ADS)

Hosoki, M.; Satsuma, T.; Nishigawa, K.; Takeuchi, H.; Asaoka, K.

2012-12-01

The elemental analysis of intraoral dental restorations provides considerable information for the treatment of dental metal allergy. Elemental analyses require specific instruments and complicated procedures, so this examination is not commonly carried out in private dental clinics. We describe a novel, simple and useful micro-analytical method for dental metal restorations. Micro metal dust was obtained by polishing the surface of restorative metal material with an unused silicone point (SUPER-SNAP). The metal dust on the silicone point was then rubbed onto adhesive tape, and this tape was covered with polyethylene film. The amount of metal dust material was <20 μg. An energy dispersive X-ray fluorescence spectrometer was used to carry out the elementary analysis of the metal dust on the polyethylene film. Three types of dental metal alloy materials of known components were examined. The results of elementary analyses were compared with the specifications provided by the manufacturer. The same procedure was carried out for three dental metal restorations of an adult female volunteer in vivo. The results of elemental analyses for five alloy materials exactly matched the product specification. Three metal samples obtained from intraoral restoration were also available for elemental analyses. The distinct advantage of this method is that it enables sample extraction without an invasive effect for the restoration. The metal sample is in a polyethylene film, so it is easy to mail it for inspection at specialist institutes yet it can be also be used in general dental clinics.

Biosensor commercialization strategy - a theoretical approach.

PubMed

Lin, Chin-Tsai; Wang, Su-Man

2005-01-01

Biosensors are analytical devices, which use biological interactions to provide either qualitative or quantitative results. They are extensively employed in many fields such as clinical diagnosis and biomedicine, military applications, anti-terrorism, farm, garden and veterinary analysis, process control, fermentation control and analysis, pharmaceutical and drug analysis, food and drink production and analysis, pollution control and monitoring, microbiology, bacterial and viral analysis, mining, and industrial and toxic gases. The biosensor market has significantly increased and will be mushrooming in the next decade. The total biosensor market is estimated to be 10.8 billion dollars by 2007. The emerging biosensor market presents both opportunities and obstacles to start-up biosensor entrepreneurs. The major challenge and threat for these entrepreneurs is how to predict the biosensor market and how to convert promising biosensor technology into commercialized biosensors. By adopting a simple commercialization strategy framework, we identify two key elements of biosensor commercialization strategy: excludability and complementary asset. We further divide biosensor commercialization environments into four distinct sub-environments: the Attacker's Advantage, Reputation-Based Idea Trading, Greenfield Competition and Ideas Factories. This paper explains how the interaction between these two key elements shapes biosensor commercialization strategy and biosensor industry dynamics. This paper also discusses alternative commercialization strategies for each specific commercialization environment and how to choose from these alternatives. The analysis of this study further provides a good reference for start-up biosensor entrepreneurs to formulate effective biosensor commercialization strategy.

Tumor heterogeneity and progression: conceptual foundations for modeling.

PubMed

Greller, L D; Tobin, F L; Poste, G

1996-01-01

A conceptual foundation for modeling tumor progression, growth, and heterogeneity is presented. The purpose of such models is to aid understanding, test ideas, formulate experiments, and to model cancer 'in machina' to address the dynamic features of tumor cell heterogeneity, progression, and growth. The descriptive capabilities of such an approach provides a consistent language for qualitatively reasoning about tumor behavior. This approach provides a schema for building conceptual models that combine three key phenomenological driving elements: growth, progression, and genetic instability. The growth element encompasses processes contributing to changes in tumor bulk and is distinct from progression per se. The progression element subsumes a broad collection of processes underlying phenotypic progression. The genetics elements represents heritable changes which potentially affect tumor character and behavior. Models, conceptual and mathematical, can be built for different tumor situations by drawing upon the interaction of these three distinct driving elements. These models can be used as tools to explore a diversity of hypotheses concerning dynamic changes in cellular populations during tumor progression, including the generation of intratumor heterogeneity. Such models can also serve to guide experimentation and to gain insight into dynamic aspects of complex tumor behavior.

The development of individuation in autism

PubMed Central

O'Hearn, Kirsten; Franconeri, Steven; Wright, Catherine; Minshew, Nancy; Luna, Beatriz

2012-01-01

Evidence suggests that people with autism use holistic information differently than typical adults. The current studies examine this possibility by investigating how core visual processes that contribute to holistic processing – individuation and element grouping – develop in participants with autism and typically developing (TD) participants matched for age, IQ and gender. Individuation refers to the ability to `see' up to 4 elements simultaneously; grouping these elements can change the number of elements that are rapidly apprehended. We examined these core processes using two well-established paradigms, rapid enumeration and multiple object tracking (MOT). In both tasks, a performance limit of about 4 elements in adulthood is thought to reflect individuation capacity. Participants with autism has a smaller individuation capacity than TD controls, regardless of whether they were enumerating static elements or tracking moving ones. To manipulate holistic information and individuation performance, we grouped the elements into a design or had elements move together. Participants with autism were affected to a similar degree as TD participants by the holistic information, whether the manipulation helped or hurt performance, consistent with evidence that some types of gestalt/grouping information are processed typically in autism. There was substantial development in autism from childhood to adolescence, but not from adolescence to adulthood, a pattern distinct from TD participants. These results provide important information about core visual processes in autism, as well as insight into the architecture of vision (e.g., individuation appears distinct from visual strengths in autism, such as visual search, despite similarities). PMID:22963232

A dynamic melting model for the origin of Apollo 15 olivine-normative and quartz-normative mare basalts

NASA Technical Reports Server (NTRS)

Vetter, Scott K.; Shervais, John W.

1993-01-01

Early studies of mare basalts from the Apollo 15 site established that two distinct groups are represented: the olivine-normative basalts (ONB) and the quartz-normative basalts (QNB). The ONB and QNB suites are distinguished petrographically by their phenocryst assemblages (the ONB's are olivine-phyric, the QNB's are generally pyroxene-phyric) and chemically by their major element compositions: the QNB's are higher in SiO2 and MgO/FeO, and lower in FeO and TiO2 than ONB's with similar MgO contents. Experimental data show that the QNB suite is derived from a more magnesian, olivine-normative parent magma, a conclusion which is supported by the recent discovery of high-SiO2 olivine-normative basalt clasts in breccia 15498. The high-SiO2 ONB's fall on olivine control lines with primitive QNB's, and least-squares mixing calculations are consistent with the high-SiO2 ONB's being parental to the more evolved QNB suite. These high-SiO2 ONB's are included as part of the 'QNB suite'. Our major element modeling results also are consistent with the conclusions of earlier studies which showed that the ONB and QNB suites cannot be related to one another by low pressure crystal fractionation. The combination of high Mg#, high SiO2, and low TiO2 in the QNB suite precludes a relationship to the ONB suite by simple removal of liquidus minerals (olivine and pigeonite). Despite these significant differences in petrography and major element composition, both groups have nearly identical trace element concentrations and chondrite-normalized abundance patterns. The major question to be addressed by any petrogenetic model for Apollo 15 mare basalts is how to form mare basalt suites with distinctly different major element characteristics but nearly identical trace element compositions. The similarity in trace element concentrations imply compositionally similar source regions and similar percent melting, but these conclusions are not easily reconciled with the observed differences in major element compositions, which require sources with distinct mineralogies or large differences in percent melt.

A new method for detecting, quantifying and monitoring diffuse contamination

NASA Astrophysics Data System (ADS)

Fabian, Karl; Reimann, Clemens; de Caritat, Patrice

2017-04-01

A new method is presented for detecting and quantifying diffuse contamination at the regional to continental scale. It is based on the analysis of cumulative distribution functions (CDFs) in cumulative probability (CP) plots for spatially representative datasets, preferably containing >1000 samples. Simulations demonstrate how different types of contamination influence elemental CDFs of different sample media. Contrary to common belief, diffuse contamination does not result in exceedingly high element concentrations in regional- to continental-scale datasets. Instead it produces a distinctive shift of concentrations in the background distribution of the studied element resulting in a steeper data distribution in the CP plot. Via either (1) comparing the distribution of an element in top soil samples to the distribution of the same element in bottom soil samples from the same area, taking soil forming processes into consideration, or (2) comparing the distribution of the contaminating element (e.g., Pb) to that of an element with a geochemically comparable behaviour but no contamination source (e.g., Rb or Ba in case of Pb), the relative impact of diffuse contamination on the element concentration can be estimated either graphically in the CP plot via a best fit estimate or quantitatively via a Kolmogorov-Smirnov or Cramer vonMiese test. This is demonstrated using continental-scale geochemical soil datasets from Europe, Australia, and the USA, and a regional scale dataset from Norway. Several different datasets from Europe deliver comparable results at regional to continental scales. The method is also suitable for monitoring diffuse contamination based on the statistical distribution of repeat datasets at the continental scale in a cost-effective manner.

Chaperone expression profiles correlate with distinct physiological states of Plasmodium falciparum in malaria patients

PubMed Central

2010-01-01

Background Molecular chaperones have been shown to be important in the growth of the malaria parasite Plasmodium falciparum and inhibition of chaperone function by pharmacological agents has been shown to abrogate parasite growth. A recent study has demonstrated that clinical isolates of the parasite have distinct physiological states, one of which resembles environmental stress response showing up-regulation of specific molecular chaperones. Methods Chaperone networks operational in the distinct physiological clusters in clinical malaria parasites were constructed using cytoscape by utilizing their clinical expression profiles. Results Molecular chaperones show distinct profiles in the previously defined physiologically distinct states. Further, expression profiles of the chaperones from different cellular compartments correlate with specific patient clusters. While cluster 1 parasites, representing a starvation response, show up-regulation of organellar chaperones, cluster 2 parasites, which resemble active growth based on glycolysis, show up-regulation of cytoplasmic chaperones. Interestingly, cytoplasmic Hsp90 and its co-chaperones, previously implicated as drug targets in malaria, cluster in the same group. Detailed analysis of chaperone expression in the patient cluster 2 reveals up-regulation of the entire Hsp90-dependent pro-survival circuitries. In addition, cluster 2 also shows up-regulation of Plasmodium export element (PEXEL)-containing Hsp40s thought to have regulatory and host remodeling roles in the infected erythrocyte. Conclusion In all, this study demonstrates an intimate involvement of parasite-encoded chaperones, PfHsp90 in particular, in defining pathogenesis of malaria. PMID:20719001

Testing a laser-induced breakdown spectroscopy technique on the Arctic sediments

NASA Astrophysics Data System (ADS)

Han, D.; Nam, S. I.

2017-12-01

Physical and geochemical investigations coupled with the Laser-induced Breakdown Spectroscopy (LIBS) were performed on three surface sediment cores (ARA03B/24BOX, ARA02B/01(A)MUC, ARA02B/02MUC and ARA02B/03(A)MUC) recovered from the western Arctic Ocean (Chukchi Sea) during IBRV ARON expeditions in 2012. The LIBS technique was applied to carry out elemental chemical analysis of the Arctic sediments and compared with that measured by ITRAX X-ray fuorescence (XRF) core scanning. LIBS and XRF have shown similar elemental composition within each sediment core. In this study, mineral composition (XRD), grain size distribution and organic carbon content as well as elemental composition (LIBS) were all considered to understand paleoenvironmental changes (ocean circulation, sea-ice drift, iceberg discharge, and etc.) recorded in the Arctic Holocene sediment. Quantitative LIBS analysis shows a gradually varying distribution of the elements along the sampled core and clear separation between the cores. The cores are geochemically characterized by elevated Mn profile. The gradient of mineral composition and grain sizes among the cores shows regional distribution and variation in sedimentary condition due to geological distance between East Siberian and North America. The present study reveals that a LIBS technique can be employed for in-situ sediment analyses for the Arctic Ocean. Furthermore, LIBS does not require costly equipment, trained operators, and complicated sample pre-treatment processes compared to Atomic absorption spectroscopy (AAS) and inductively coupled plasma emission spectroscopy (ICP), and also known to show relatively high levels of sensitivity, precision, and distinction than XRF analysis, scanning electron microscopy-energy dispersive spectrometry (SEM-EDS), and electron probe X-ray microanalysis (EPMA).

Physiotherapy: a historical analysis of the transformation from an occupation to a profession in Brazil

PubMed Central

Oliveira, Ana L. O.; Nunes, Everardo D.

2015-01-01

ABSTRACT Background: Analyzing the historical and social path of an occupation using the sociology of professions and the perspective of scientific knowledge promotes an understanding of the origin of physical therapy in Brazil and of discussions of the profession in its contemporary context. Objective: The aim of this paper was to discuss the professionalization process of physical therapy in São Paulo. The authors tried to analyze bath therapy, massage therapy, and physical therapy as occupations involving distinct expertise and as part of the group of occupations that evolved into the profession of physiotherapy in the first half of the twentieth century. Method: The analysis undertaken was a qualitative study based on an analysis of historical documents. Eighty-six professional records from the Service of Inspection of Professional Practice in the state of São Paulo and healthcare legislation from the 1930s and 1940s were analyzed. Results: The distinction between physical therapy practitioner and profession of physiotherapy can be seen by examining registration requirements for rank-and-file nurses with expertise in interactions; this distinction suggests the emergence of specialized expertise that was clearly a part of neither medicine nor nursing and contributed to expertise in physical therapy since the 1950s. Conclusion: The regulation of physiotherapy practices, the recognition of expertise, the accreditation of practical nurses by the State, and the institutionalization of a course for physical therapy practitioners in 1951 are key elements of the professionalization process for the physical therapy profession in Brazil. PMID:26443976

The self adapting washer for lag screw fixation of mandibular fractures: finite element analysis and preclinical evaluation.

PubMed

Terheyden, H; Mühlendyck, C; Feldmann, H; Ludwig, K; Härle, F

1999-02-01

Besides rigid fixation, lag screws have distinct advantages compared with plates in appropriate indications in mandibular fractures. However, in current lag screw systems, the relatively small area of the screw head has to transfer the tensile force which can exceed 1000 N in the symphysis, to the thin cortical bone plate. Countersinking, which is obligatory in most systems, will weaken the cortical plate. Finite element analysis (FEA) revealed that load in this situation can exceed the normal tensile strength of metal and bone. Consequently, a new washer was constructed which both increased the supporting surface and did not require countersinking. The washer is self adapting (SAW) to the cortical plate in a defined position, forming a ball and socket joint with the screw head. Using the FEA model, a ten-fold reduction in load on bone and metal was observed with the new washer. In a miniature pig mandibular symphysis fracture model, the clinical applicability and a favourable histological reaction were demonstrated, compared with conventional lag screw designs.

A Chromatin Insulator-Like Element in the Herpes Simplex Virus Type 1 Latency-Associated Transcript Region Binds CCCTC-Binding Factor and Displays Enhancer-Blocking and Silencing Activities

PubMed Central

Amelio, Antonio L.; McAnany, Peterjon K.; Bloom, David C.

2006-01-01

A previous study demonstrated that the latency-associated transcript (LAT) promoter and the LAT enhancer/reactivation critical region (rcr) are enriched in acetyl histone H3 (K9, K14) during herpes simplex virus type 1 (HSV-1) latency, whereas all lytic genes analyzed (ICP0, UL54, ICP4, and DNA polymerase) are not (N. J. Kubat, R. K. Tran, P. McAnany, and D. C. Bloom, J. Virol. 78:1139-1149, 2004). This suggests that the HSV-1 latent genome is organized into histone H3 (K9, K14) hyperacetylated and hypoacetylated regions corresponding to transcriptionally permissive and transcriptionally repressed chromatin domains, respectively. Such an organization implies that chromatin insulators, similar to those of cellular chromosomes, may separate distinct transcriptional domains of the HSV-1 latent genome. In the present study, we sought to identify cis elements that could partition the HSV-1 genome into distinct chromatin domains. Sequence analysis coupled with chromatin immunoprecipitation and luciferase reporter assays revealed that (i) the long and short repeats and the unique-short region of the HSV-1 genome contain clustered CTCF (CCCTC-binding factor) motifs, (ii) CTCF motif clusters similar to those in HSV-1 are conserved in other alphaherpesviruses, (iii) CTCF binds to these motifs on latent HSV-1 genomes in vivo, and (iv) a 1.5-kb region containing the CTCF motif cluster in the LAT region possesses insulator activities, specifically, enhancer blocking and silencing. The finding that CTCF, a cellular protein associated with chromatin insulators, binds to motifs on the latent genome and insulates the LAT enhancer suggests that CTCF may facilitate the formation of distinct chromatin boundaries during herpesvirus latency. PMID:16474142

Basic Fibroblast Growth Factor Activates Serum Response Factor Gene Expression by Multiple Distinct Signaling Mechanisms

PubMed Central

Spencer, Jeffrey A.; Major, Michael L.; Misra, Ravi P.

1999-01-01

Serum response factor (SRF) plays a central role in the transcriptional response of mammalian cells to a variety of extracellular signals. It is a key regulator of many cellular early response genes which are believed to be involved in cell growth and differentiation. The mechanism by which SRF activates transcription in response to mitogenic agents has been extensively studied; however, significantly less is known about regulation of the SRF gene itself. Previously, we identified distinct regulatory elements in the SRF promoter that play a role in activation, including a consensus ETS domain binding site, a consensus overlapping Sp/Egr-1 binding site, and two SRF binding sites. We further showed that serum induces SRF by a mechanism that requires an intact SRF binding site, also termed a CArG box. In the present study we demonstrate that in response to stimulation of cells by a purified growth factor, basic fibroblast growth factor (bFGF), the SRF promoter is upregulated by a complex pathway that involves at least two independent mechanisms: a CArG box-independent mechanism that is mediated by an ETS binding site, and a novel CArG box-dependent mechanism that requires both an Sp factor binding site and the CArG motifs for maximal stimulation. Our analysis indicates that the CArG/Sp element activation mechanism is mediated by distinct signaling pathways. The CArG box-dependent component is targeted by a Rho-mediated pathway, and the Sp binding site-dependent component is targeted by a Ras-mediated pathway. Both SRF and bFGF have been implicated in playing an important role in mediating cardiogenesis during development. The implications of our findings for SRF expression during development are discussed. PMID:10330138

Spatial X-ray fluorescence micro-imaging of minerals in grain tissues of wheat and related genotypes.

PubMed

Singh, Sudhir P; Vogel-Mikuš, Katarina; Vavpetič, Primož; Jeromel, Luka; Pelicon, Primož; Kumar, Jitendra; Tuli, Rakesh

2014-08-01

Wheat and its related genotypes show distinct distribution patterns for mineral nutrients in maternal and filial tissues in grains. X-ray-based imaging techniques are very informative to identify genotypes with contrasting tissue-specific localization of different elements. This can help in the selection of suitable genotypes for nutritional improvement of food grain crops. Understanding mineral localization in cereal grains is important for their nutritional improvement. Spatial distribution of mineral nutrients (Mg, P, S, K, Ca, Fe, Zn, Mn and Cu) was investigated between and within the maternal and filial tissues in grains of two wheat cultivars (Triticum aestivum Cv. WH291 and WL711), a landrace (T. aestivum L. IITR26) and a related wild species Aegilops kotschyi, using micro-proton-induced X-ray emission (µ-PIXE) and micro-X-ray fluorescence (µ-XRF). Aleurone and scutellum were major storage tissues for macro (P, K, Ca and Mg) as well as micro (Fe, Zn, Cu and Mn) nutrients. Distinct elemental distribution patterns were observed in each of the four genotypes. A. kotschyi, the wild relative of wheat and the landrace, T. aestivum L. IITR26, accumulated more Zn and Fe in scutellum and aleurone than the cultivated wheat varieties, WH291 and WL711. The landrace IITR26, accumulated far more S in grains, Mn in scutellum, aleurone and embryo region, Ca and Cu in aleurone and scutellum, and Mg, K and P in scutellum than the other genotypes. Unlike wheat, lower Mn and higher Fe, Cu and Zn concentrations were noticed in the pigment strand of A. kotschyi. Multivariate statistical analysis, performed on mineral distribution in major grain tissues (aleurone, scutellum, endosperm and embryo region) resolved the four genotypes into distinct clusters.

Petroleomics: the next grand challenge for chemical analysis.

PubMed

Marshall, Alan G; Rodgers, Ryan P

2004-01-01

Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry has recently revealed that petroleum crude oil contains heteroatom-containing (N,O,S) organic components having more than 20,000 distinct elemental compositions (C(c)H(h)N(n)O(o)S(s)). It is therefore now possible to contemplate the ultimate characterization of all of the chemical constituents of petroleum, along with their interactions and reactivity, a concept we denote as "petroleomics". Such knowledge has already proved capable of distinguishing petroleum and its distillates according to their geochemical origin and maturity, distillation cut, extraction method, catalytic processing, etc. The key features that have opened up this new field have been (a) ultrahigh-resolution FT-ICR mass analysis, specifically, the capability to resolve species differing in elemental composition by C(3) vs SH(4) (i.e., 0.0034 Da); (b) higher magnetic field to cover the whole mass range at once; (c) dynamic range extension by external mass filtering; and (d) plots of Kendrick mass defect vs nominal Kendrick mass as a means for sorting different compound "classes" (i.e., numbers of N, O, and S atoms), "types" (rings plus double bonds), and alkylation ((-CH(2))(n)) distributions, thereby extending to >900 Da the upper limit for unique assignment of elemental composition based on accurate mass measurement. The same methods are also being applied successfully to analysis of humic and fulvic acids, coals, and other complex natural mixtures, often without prior or on-line chromatographic separation.

The role of recombination in the origin and evolution of Alu subfamilies.

PubMed

Teixeira-Silva, Ana; Silva, Raquel M; Carneiro, João; Amorim, António; Azevedo, Luísa

2013-01-01

Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.

3D Finite Element Modelling of Cutting Forces in Drilling Fibre Metal Laminates and Experimental Hole Quality Analysis

NASA Astrophysics Data System (ADS)

Giasin, Khaled; Ayvar-Soberanis, Sabino; French, Toby; Phadnis, Vaibhav

2017-02-01

Machining Glass fibre aluminium reinforced epoxy (GLARE) is cumbersome due to distinctively different mechanical and thermal properties of its constituents, which makes it challenging to achieve damage-free holes with the acceptable surface quality. The proposed work focuses on the study of the machinability of thin ( 2.5 mm) GLARE laminate. Drilling trials were conducted to analyse the effect of feed rate and spindle speed on the cutting forces and hole quality. The resulting hole quality metrics (surface roughness, hole size, circularity error, burr formation and delamination) were assessed using surface profilometry and optical scanning techniques. A three dimensional (3D) finite-element (FE) model of drilling GLARE laminate was also developed using ABAQUS/Explicit to help understand the mechanism of drilling GLARE. The homogenised ply-level response of GLARE laminate was considered in the FE model to predict cutting forces in the drilling process.

Auger electron spectroscopy for the determination of sex and age related Ca/P ratio at different bone sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balatsoukas, Ioannis; Kourkoumelis, Nikolaos; Tzaphlidou, Margaret

The Ca/P ratio of normal cortical and trabecular rat bone was measured by Auger electron spectroscopy (AES). Semiquantitative analysis was carried out using ratio techniques to draw conclusions on how age, sex and bone site affect the relative composition of calcium and phosphorus. Results show that Ca/P ratio is not sex dependent; quite the opposite, bone sites exhibit variations in elemental stoichiometry where femoral sections demonstrate higher Ca/P ratio than rear and front tibias. Age-related changes are more distinct for cortical bone in comparison with the trabecular bone. The latter's Ca/P ratio remains unaffected from all the parameters under study.more » This study confirms that AES is able to successfully quantify bone mineral main elements when certain critical points, related to the experimental conditions, are addressed effectively.« less

Potential of Sr isotopic analysis in ceramic provenance studies: Characterisation of Chinese stonewares

NASA Astrophysics Data System (ADS)

Li, Bao-Ping; Zhao, Jian-Xin; Greig, Alan; Collerson, Kenneth D.; Zhuo, Zhen-Xi; Feng, Yue-Xin

2005-11-01

We compare the trace element and Sr isotopic compositions of stoneware bodies made in Yaozhou and Jizhou to characterise these Chinese archaeological ceramics and examine the potential of Sr isotopes in provenance studies. Element concentrations determined by ICP-MS achieve distinct characterisation for Jizhou samples due to their restricted variation, yet had limited success with Yaozhou wares because of their large variability. In contrast, 87Sr/86Sr ratios in Yaozhou samples have a very small variation and are all significantly lower than those of Jizhou samples, which show a large variation and cannot be well characterised with Sr isotopes. Geochemical interpretation reveals that 87Sr/86Sr ratios will have greater potential to characterise ceramics made of low Rb/Sr materials such as kaolin clay, yet will show larger variations in ceramics made of high Rb/Sr materials such as porcelain stone.

Quantitative analysis and paleoecology of the Secor Coal and roof-shale floras (middle Pennsylvania, Oklahoma)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dimichele, W.A.; McBrinn, G.E.; Phillips, T.L.

1991-08-01

The Secor Coal of Oklahoma (Boggy Formation, lower Desmoinesian/Westphalian D equivalent) is one of the few coals discovered, to date, in which Anabathra pulcherrima (=Paralycopodites brevifolius) was a dominant element. Anabathra and Lepidophloios define the major assemblages in the coal, which also contains elements of medullosan pteridosperms and Cardiocarpus spinatus producing cordaites. The Lepidophloios to Medullosa gradient is not obscured by the numerous Anabathra-dominated zones, and a disturbance element is suggested in association with Anabathra abundance. Comparison of the coal-ball flora with a clastic-compression flora from the roof of the coal reveals widely divergent patterns of dominance and diversity. Themore » compression flora is strongly dominated by medullosan pteridosperms with subdominant marattialean tree ferns. As in most instances, the compression flora from the immediate roof of the coal is not an accurate representation of the peat-forming vegetation, at either the level of species composition or the relative abundance of major groups of plants. The swamp and surrounding clastic deltaic environments were edaphically distinct and supported separate floras between which there was limited species exchange.« less

[Diversity and distribution character of wood-rotting fungi in the secondary forest ecosystem of Liaodong areas, Northeast China].

PubMed

Zhang, Li Yan; Wei, Yu Lian; Li, Tong

2016-12-01

During July to September of 2013, field investigations and specimen collections on wood-rotting fungi were carried from three sites in the secondary forests (Qingyuan forest farm, Laotudingzi National Nature Reserve and Baishilaizi Nature Reserve) of eastern Liaoning Province. A total of 1062 specimens were collected and recorded, and 92 species were identified, belonging to48 genera. Among the three studying sites, Baishilaizi Nature Reserve had the most abundant polypore species and the Shannon diversity index was 4.04. The species biogeography of eastern Liaoning could be divided into 4 groups at genus level. The main elements were North temperate element and cosmopolitan element, and floristic analysis showed a distinct north temperate character. White rot species were the dominant decomposers here. Most species distributed in the fallen wood with decay stages 2 and 3. The wood dominant hosts of wood-rotting fungi were the Acer genus in the secondary forests of eastern Liaoning Province, and 243 specimens were collected from maples, occupying 23.2% of the total.

Numerical simulation of temperature field in K9 glass irradiated by ultraviolet pulse laser

NASA Astrophysics Data System (ADS)

Wang, Xi; Fang, Xiaodong

2015-10-01

The optical component of photoelectric system was easy to be damaged by irradiation of high power pulse laser, so the effect of high power pulse laser irradiation on K9 glass was researched. A thermodynamic model of K9 glass irradiated by ultraviolet pulse laser was established using the finite element software ANSYS. The article analyzed some key problems in simulation process of ultraviolet pulse laser damage of K9 glass based on ANSYS from the finite element models foundation, meshing, loading of pulse laser, setting initial conditions and boundary conditions and setting the thermal physical parameters of material. The finite element method (FEM) model was established and a numerical analysis was performed to calculate temperature field in K9 glass irradiated by ultraviolet pulse laser. The simulation results showed that the temperature of irradiation area exceeded the melting point of K9 glass, while the incident laser energy was low. The thermal damage dominated in the damage mechanism of K9 glass, the melting phenomenon should be much more distinct.

Nature and function of insulator protein binding sites in the Drosophila genome

PubMed Central

Schwartz, Yuri B.; Linder-Basso, Daniela; Kharchenko, Peter V.; Tolstorukov, Michael Y.; Kim, Maria; Li, Hua-Bing; Gorchakov, Andrey A.; Minoda, Aki; Shanower, Gregory; Alekseyenko, Artyom A.; Riddle, Nicole C.; Jung, Youngsook L.; Gu, Tingting; Plachetka, Annette; Elgin, Sarah C.R.; Kuroda, Mitzi I.; Park, Peter J.; Savitsky, Mikhail; Karpen, Gary H.; Pirrotta, Vincenzo

2012-01-01

Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes. PMID:22767387

Lemonade from lemons: the taphonomic effect of lawn mowers on skeletal remains.

PubMed

Martin, D C; Dabbs, Gretchen R; Roberts, Lindsey G

2013-09-01

This study provides a descriptive analysis of the taphonomic changes produced by passing over skeletonized remains (n = 4, Sus scrofa) with three common lawn mowers. Two skeletons were mowed over with a riding lawn mower set at multiple blade heights (10.16, 7.62, 5.08 cm) and one each with a rotary mower (9.53, 6.35 cm) and a mulching mower (6.35 cm). Results show that different types of common lawn mowers will produce different patterns of bone dispersal and fragmentation rates. Overall, skeletal elements projecting upward from the surface frequently exhibited a sheared morphology characterized by a smooth, flat, cut surface (7.0-7.6% of elements). The push mowers yielded a higher frequency of undamaged bone than the riding mower (54.8-61.2% vs. 17.7%), and the riding mower created more catastrophic damage to skeletal elements. Additionally, each mower produced a distinct dispersal pattern of skeletal fragments. The dispersal patterns have been identified as "bull's-eye" (riding), circular (mulching), and discontinuous rectangle (rotary). © 2013 American Academy of Forensic Sciences.

A 2D multi-term time and space fractional Bloch-Torrey model based on bilinear rectangular finite elements

NASA Astrophysics Data System (ADS)

Qin, Shanlin; Liu, Fawang; Turner, Ian W.

2018-03-01

The consideration of diffusion processes in magnetic resonance imaging (MRI) signal attenuation is classically described by the Bloch-Torrey equation. However, many recent works highlight the distinct deviation in MRI signal decay due to anomalous diffusion, which motivates the fractional order generalization of the Bloch-Torrey equation. In this work, we study the two-dimensional multi-term time and space fractional diffusion equation generalized from the time and space fractional Bloch-Torrey equation. By using the Galerkin finite element method with a structured mesh consisting of rectangular elements to discretize in space and the L1 approximation of the Caputo fractional derivative in time, a fully discrete numerical scheme is derived. A rigorous analysis of stability and error estimation is provided. Numerical experiments in the square and L-shaped domains are performed to give an insight into the efficiency and reliability of our method. Then the scheme is applied to solve the multi-term time and space fractional Bloch-Torrey equation, which shows that the extra time derivative terms impact the relaxation process.

Unpacking Clinical Supervision in Transitional and Permanent Supportive Housing: Scrutiny or Support?

PubMed

Choy-Brown, Mimi; Stanhope, Victoria; Tiderington, Emmy; Padgett, Deborah K

2016-07-01

Behavioral health organizations use clinical supervision to ensure professional development and practice quality. This qualitative study examined 35 service coordinators' perspectives on supervision in two distinct supportive housing program types (permanent and transitional). Thematic analysis of in-depth interviews yielded three contrast themes: support versus scrutiny, planned versus impromptu time, and housing first versus treatment first. Supervisory content and format resulted in differential perceptions of supervision, thereby influencing opportunities for learning. These findings suggest that unpacking discrete elements of supervision enactment in usual care settings can inform implementation of recovery-oriented practice.

Unpacking clinical supervision in transitional and permanent supportive housing: Scrutiny or support?

PubMed Central

Choy-Brown, Mimi; Stanhope, Victoria; Tiderington, Emmy; Padgett, Deborah K.

2015-01-01

Behavioral health organizations use clinical supervision to ensure professional development and practice quality. This qualitative study examined 35 service coordinators' perspectives on supervision in two distinct supportive housing program types (permanent and transitional). Thematic analysis of in-depth interviews yielded three contrast themes: support versus scrutiny, planned versus impromptu time, and Housing First versus Treatment First. Supervisory content and format resulted in differential perceptions of supervision, thereby influencing opportunities for learning. These findings suggest that unpacking discrete elements of supervision enactment in usual care settings can inform implementation of recovery-oriented practice. PMID:26066866

Limitations on analysis of small particles with an electron probe: pollution studies

USGS Publications Warehouse

Heidel, R.H.; Desborough, G.A.

1975-01-01

Recent literature concerning the size and composition of airborne lead particles in automobile exhaust emissions determined by electron microprobe analysis reports 14 distinct lead compounds. Particle sizes reported were from 0.2 ??m to 2 ??m in the diameter. The determination of chemical formulae for compounds requires quantitative elemental data for individual particles. It was also assumed that the lead bearing particles analysed were solid (specifically non porous or non fluffy) compounds which occurred as discrete (non aggregate) particles. Intensity data obtained in the laboratory from the excited volume in a 1 ??m diameter sphere of solid lead chloride indicate insufficient precision and sensitivity to obtain chemical formulae as reported in the literature for exhaust emission products.

Composite theory applied to elastomers

NASA Technical Reports Server (NTRS)

Clark, S. K.

1986-01-01

Reinforced elastomers form the basis for most of the structural or load carrying applications of rubber products. Computer based structural analysis in the form of finite element codes was highly successful in refining structural design in both isotropic materials and rigid composites. This has lead the rubber industry to attempt to make use of such techniques in the design of structural cord-rubber composites. While such efforts appear promising, they were not easy to achieve for several reasons. Among these is a distinct lack of a clearly defined set of material property descriptors suitable for computer analysis. There are substantial differences between conventional steel, aluminum, or even rigid composites such as graphite-epoxy, and textile-cord reinforced rubber. These differences which are both conceptual and practical are discussed.

Developmental Dyslexia: The Visual Attention Span Deficit Hypothesis

ERIC Educational Resources Information Center

Bosse, Marie-Line; Tainturier, Marie Josephe; Valdois, Sylviane

2007-01-01

The visual attention (VA) span is defined as the amount of distinct visual elements which can be processed in parallel in a multi-element array. Both recent empirical data and theoretical accounts suggest that a VA span deficit might contribute to developmental dyslexia, independently of a phonological disorder. In this study, this hypothesis was…

Three-Dimensional Constraints on Human Cognition as Expressed in Human Language

ERIC Educational Resources Information Center

Adam, Christopher C.

2015-01-01

Those advocating the existence of a distinct language instinct generally claim that human language is not reliant on general human cognition. However, limitations on recursive patterns in human language are universally attested, from the micro-level elements of phonology, throughout the mid-level elements of morphology and syntax, and up to the…

Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*

PubMed Central

Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel

2012-01-01

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499

Metal transport across biomembranes: emerging models for a distinct chemistry.

PubMed

Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

2012-04-20

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

Mesogondolella and Jinogondolella (Conodonta): Multielement definition of the taxa that bracket the basal Guadalupian (Middle Permian Series) GSSP

USGS Publications Warehouse

Lambert, L.L.; Wardlaw, B.R.; Henderson, C.M.

2007-01-01

Multielement definitions are presented here for Mesogondolella and Jinogondolella based on species that bracket the basal Guadalupian (Middle Permian Series) GSSP. Distinctive apparatus characters that appear with the first Jinogondolella include several details of P2 element dimorphism and process bifurcation in S3 elements. The sequential expression of these multielement characters is traced through M. idahoensis, M. lamberti, and J. nankingensis. The resulting multielement definition of Jinogondolella serves to distinguish it from all other closely related genera. Mesogondolella lamberti is recognized as a distinct species, and J. serrata is formally designated a junior synonym of J. nankingensis. ?? 2007 Nanjing Institute of Geology and Palaeontology, CAS.

Chemistry of Apollo 11 low-K mare basalts

NASA Technical Reports Server (NTRS)

Rhodes, J. M.; Blanchard, D. P.

1980-01-01

A reexamination of the bulk major and trace element geochemistry of Apollo 11 low-K mare basalts is presented. New analyses are given for seven previously unanalyzed samples (10003, 10020, 10044, 10047, 10050, 10058, and 10062) and for two low-K basalts (10029 and 10092) and one high-K basalt (10071) for which comprehensive compositional data were previously lacking. The data show that three distinct magma types have been sampled, as proposed by Beaty and Albee (1978), and that these magma types are unrelated by near-surface crystal fractionation. Each magma type is characterized by distinctive magmaphile element ratios, which enable previously unclassified samples (10050 and 10062) to be assigned to an appropriate magma type.

Reanalysis of a 15-year Archive of IMPROVE Samples

NASA Astrophysics Data System (ADS)

Hyslop, N. P.; White, W. H.; Trzepla, K.

2013-12-01

The IMPROVE (Interagency Monitoring of PROtected Visual Environments) network monitors aerosol concentrations at 170 remote sites throughout the United States. Twenty-four-hour filter samples of particulate matter are collected every third day and analyzed for chemical composition. About 30 of the sites have operated continuously since 1988, and the sustained data record (http://views.cira.colostate.edu/web/) offers a unique window on regional aerosol trends. All elemental analyses have been performed by Crocker Nuclear Laboratory at the University of California in Davis, and sample filters collected since 1995 are archived on campus. The suite of reported elements has remained constant, but the analytical methods employed for their determination have evolved. For example, the elements Na - Mn were determined by PIXE until November 2001, then by XRF analysis in a He-flushed atmosphere through 2004, and by XRF analysis in vacuum since January 2005. In addition to these fundamental changes, incompletely-documented operational factors such as detector performance and calibration details have introduced variations in the measurements. Because the past analytical methods were non-destructive, the archived filters can be re-analyzed with the current analytical systems and protocols. The 15-year sample archives from Great Smoky Mountains, Mount Rainier, and Point Reyes National Parks were selected for reanalysis. The agreement between the new analyses and original determinations varies with element and analytical era (Figure 1). Temporal trends for some elements are affected by these changes in measurement technique while others are not (Figure 2). Figure 1. Repeatability of analyses for sulfur and vanadium at Great Smoky Mountains National Park. Each point shows the ratio of mass loadings determined by the original analysis and recent reanalysis. Major method distinctions are indicated at the top. Figure 2. Trends, based on Thiel-Sen regression, in lead concentrations based on the original and reanalysis data.

Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis.

PubMed

Lang-Yona, Naama; Maier, Stefanie; Macholdt, Dorothea S; Müller-Germann, Isabell; Yordanova, Petya; Rodriguez-Caballero, Emilio; Jochum, Klaus P; Al-Amri, Abdullah; Andreae, Meinrat O; Fröhlich-Nowoisky, Janine; Weber, Bettina

2018-02-28

Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Multidrug-resistant Staphylococcus haemolyticus isolates from infected eyes and healthy conjunctivae in India.

PubMed

Panda, Sasmita; Kar, Sarita; Sharma, Savitri; Singh, Durg V

2016-09-01

This study aimed to determine the presence of antibiotic resistance genes (ARGs), SCCmec elements and genetic relatedness among Staphylococcus haemolyticus isolated from patients with a variety of eye infections (n=11) and from healthy conjunctiva (n=7). Minimum inhibitory concentrations were determined for 14 antimicrobials according to BSAC guidelines. PCR was used to identify the presence of mecA, mecC, SCCmec type and ARGs. Sequencing was used to determine mutations in gyrA, gyrB, topoisomerase IVA and IVB genes. Genetic relatedness was determined by PFGE. Of the 18 isolates, 17 showed resistance to at least one antibiotic, but none showed resistance to vancomycin or rifampicin. Ten isolates were oxacillin-resistant and carried the mecA gene, eight of which belonged to SCCmec type V. The presence of non-mec SCC elements in two meticillin-susceptible isolates and untypeable SCC elements in meticillin-resistant isolates suggests the involvement of S. haemolyticus in the diversification of SCC elements. Sequence analysis revealed point mutations in gyrA (Ser-84→Leu) and topoisomerase IVA genes (Ser-80→Leu) in 13 isolates, and additional variation in the QRDR (Asp-84→Asn) of two isolates, showing good correlation between mutations in gyrA and topoisomerase IV genes and the level of resistance to fluoroquinolones. PFGE analysis showed distinct pulsotypes forming two major clusters, indicating the existence of diversity among isolates, irrespective of the source of isolation. This study suggests that S. haemolyticus isolates from infected eyes and healthy conjunctivae invariably carried ARGs and SCCmec elements and showed diversity in their genomic content, irrespective of the source of isolation. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants

PubMed Central

Fukai, Eigo; Umehara, Yosuke; Sato, Shusei; Endo, Makoto; Kouchi, Hiroshi; Hayashi, Makoto; Stougaard, Jens; Hirochika, Hirohiko

2010-01-01

Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5′ LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool. PMID:20221264

[Spontaneous speech prosody and discourse analysis in schizophrenia and Fronto Temporal Dementia (FTD) patients].

PubMed

Martínez, Angela; Felizzola Donado, Carlos Alberto; Matallana Eslava, Diana Lucía

2015-01-01

Patients with schizophrenia and Frontotemporal Dementia (FTD) in their linguistic variants share some language characteristics such as the lexical access difficulties, disordered speech with disruptions, many pauses, interruptions and reformulations. For the schizophrenia patients it reflects a difficulty of affect expression, while for the FTD patients it reflects a linguistic issue. This study, through an analysis of a series of cases assessed Clinic both in memory and on the Mental Health Unit of HUSI-PUJ (Hospital Universitario San Ignacio), with additional language assessment (analysis speech and acoustic analysis), present distinctive features of the DFT in its linguistic variants and schizophrenia that will guide the specialist in finding early markers of a differential diagnosis. In patients with FTD language variants, in 100% of cases there is a difficulty understanding linguistic structure of complex type; and important speech fluency problems. In patients with schizophrenia, there are significant alterations in the expression of the suprasegmental elements of speech, as well as disruptions in discourse. We present how depth language assessment allows to reassess some of the rules for the speech and prosody analysis of patients with dementia and schizophrenia; we suggest how elements of speech are useful in guiding the diagnosis and correlate functional compromise in everyday psychiatrist's practice. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

PubMed

Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

2001-08-15

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.

PubMed

Reinharz, Vladimir; Soulé, Antoine; Westhof, Eric; Waldispühl, Jérôme; Denise, Alain

2018-05-04

The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.

Homo sapiens exhibit a distinct pattern of CNV genes regulation: an important role of miRNAs and SNPs in expression plasticity.

PubMed

Dweep, Harsh; Kubikova, Nada; Gretz, Norbert; Voskarides, Konstantinos; Felekkis, Kyriacos

2015-07-16

Gene expression regulation is a complex and highly organized process involving a variety of genomic factors. It is widely accepted that differences in gene expression can contribute to the phenotypic variability between species, and that their interpretation can aid in the understanding of the physiologic variability. CNVs and miRNAs are two major players in the regulation of expression plasticity and may be responsible for the unique phenotypic characteristics observed in different lineages. We have previously demonstrated that a close interaction between these two genomic elements may have contributed to the regulation of gene expression during evolution. This work presents the molecular interactions between CNV and non CNV genes with miRNAs and other genomic elements in eight different species. A comprehensive analysis of these interactions indicates a unique nature of human CNV genes regulation as compared to other species. By using genes with short 3' UTR that abolish the "canonical" miRNA-dependent regulation, as a model, we demonstrate a distinct and tight regulation of human genes that might explain some of the unique features of human physiology. In addition, comparison of gene expression regulation between species indicated that there is a significant difference between humans and mice possibly questioning the effectiveness of the latest as experimental models of human diseases.

Distinct regulators of Shh transcription in the floor plate and notochord indicate separate origins for these tissues in the mouse node.

PubMed

Jeong, Yongsu; Epstein, Douglas J

2003-08-01

The establishment of the floor plate at the ventral midline of the CNS is dependent on an inductive signaling process mediated by the secreted protein Sonic hedgehog (Shh). To understand molecularly how floor plate induction proceeds we identified a Shh-responsive regulatory element that directs transgene reporter expression to the ventral midline of the CNS and notochord in a Shh-like manner and characterized critical cis-acting sequences regulating this element. Cross-species comparisons narrowed the activity of the Shh floor plate enhancer to an 88-bp sequence within intron 2 of Shh that included highly conserved binding sites matching the consensus for homeodomain, Tbx and Foxa transcription factors. Mutational analysis revealed that the homeodomain and Foxa binding sites are each required for activation of the Shh floor plate enhancer, whereas the Tbx site was required for repression in regions of the CNS where Shh is not normally expressed. We further show that Shh enhancer activity was detected in the mouse node from where the floor plate and notochord precursors derive. Shh reporter expression was restricted to the ventral (mesodermal) layer of the node in a pattern similar to endogenous Shh. X-gal-positive cells emerging from the node were only detected in the notochord lineage, suggesting that the floor plate and notochord arise from distinct precursors in the mouse node.

Homo sapiens exhibit a distinct pattern of CNV genes regulation: an important role of miRNAs and SNPs in expression plasticity

PubMed Central

Dweep, Harsh; Kubikova, Nada; Gretz, Norbert; Voskarides, Konstantinos; Felekkis, Kyriacos

2015-01-01

Gene expression regulation is a complex and highly organized process involving a variety of genomic factors. It is widely accepted that differences in gene expression can contribute to the phenotypic variability between species, and that their interpretation can aid in the understanding of the physiologic variability. CNVs and miRNAs are two major players in the regulation of expression plasticity and may be responsible for the unique phenotypic characteristics observed in different lineages. We have previously demonstrated that a close interaction between these two genomic elements may have contributed to the regulation of gene expression during evolution. This work presents the molecular interactions between CNV and non CNV genes with miRNAs and other genomic elements in eight different species. A comprehensive analysis of these interactions indicates a unique nature of human CNV genes regulation as compared to other species. By using genes with short 3′ UTR that abolish the “canonical” miRNA-dependent regulation, as a model, we demonstrate a distinct and tight regulation of human genes that might explain some of the unique features of human physiology. In addition, comparison of gene expression regulation between species indicated that there is a significant difference between humans and mice possibly questioning the effectiveness of the latest as experimental models of human diseases. PMID:26178010

Multi-element otolith chemistry of juvenile sole ( Solea solea), whiting ( Merlangius merlangus) and European seabass ( Dicentrarchus labrax) in the Thames Estuary and adjacent coastal regions

NASA Astrophysics Data System (ADS)

Leakey, Chris D. B.; Attrill, Martin J.; Fitzsimons, Mark F.

2009-04-01

Estuaries are regarded as valuable nursery habitats for many commercially important marine fishes, potentially providing a thermal resource, refuge from predators and a source of abundant prey. To assess the extent of estuarine use by juvenile (0+) common sole ( Solea solea), whiting ( Merlangius merlangus) and European seabass ( Dicentrarchus labrax) we: (1) developed techniques to distinguish between estuarine and coastally-caught juveniles using otolith chemistry; and (2) examined the accuracy with which multi-elemental signatures could re-classify juveniles to their region of collection. High-resolution solution-based inductively coupled plasma mass spectrometry (HB-SB-ICPMS) was used to quantify 32 elements within the juvenile otoliths; 14 elements occurred above detection limits for all samples. Some elemental distributions demonstrated clear differences between estuarine and coastally-caught fish. Multivariate analysis of the otolith chemistry data resulted in 95-100% re-classification accuracy to the region of collection. Estuarine and coastal signatures were most clearly defined for sole which, compared to bass and whiting, have low mobility and are less likely to move from estuarine to coastal habitats between larval settlement and later migration to adult stocks. Sole were the only species to reveal an energetic benefit associated with an estuarine juvenile phase. The physiological ability of bass to access upper estuarine regions was consistent with some elemental data, while the high mobility and restricted range of whiting resulted in less distinct otolith chemistries.

Distinct families of cis-acting RNA replication elements epsilon from hepatitis B viruses

PubMed Central

Chen, Augustine; Brown, Chris

2012-01-01

The hepadnavirus encapsidation signal, epsilon (ε), is an RNA structure located at the 5′ end of the viral pregenomic RNA. It is essential for viral replication and functions in polymerase protein binding and priming. This structure could also have potential regulatory roles in controlling the expression of viral replicative proteins. In addition to its structure, the primary sequence of this RNA element has crucial functional roles in the viral lifecycle. Although the ε elements in hepadnaviruses share common critical functions, there are some significant differences in mammalian and avian hepadnaviruses, which include both sequence and structural variations.   Here we present several covariance models for ε elements from the Hepadnaviridae. The model building included experimentally determined data from previous studies using chemical probing and NMR analysis. These models have sufficient similarity to comprise a clan. The clan has in common a highly conserved overall structure consisting of a lower-stem, bulge, upper-stem and apical-loop. The models differ in functionally critical regions—notably the two types of avian ε elements have a tetra-loop (UGUU) including a non-canonical UU base pair, while the hepatitis B virus (HBV) epsilon has a tri-loop (UGU). The avian epsilon elements have a less stable dynamic structure in the upper stem. Comparisons between these models and all other Rfam models, and searches of genomes, showed these structures are specific to the Hepadnaviridae. Two family models and the clan are available from the Rfam database. PMID:22418844

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

PubMed Central

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M.; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P.; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M.; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org. PMID:21036865

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

PubMed

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

Pluripotent and Multipotent Stem Cells Display Distinct Hypoxic miRNA Expression Profiles

PubMed Central

Agrawal, Rahul; Dale, Tina P.; Al-Zubaidi, Mohammed A.; Benny Malgulwar, Prit; Forsyth, Nicholas R.; Kulshreshtha, Ritu

2016-01-01

MicroRNAs are reported to have a crucial role in the regulation of self-renewal and differentiation of stem cells. Hypoxia has been identified as a key biophysical element of the stem cell culture milieu however, the link between hypoxia and miRNA expression in stem cells remains poorly understood. We therefore explored miRNA expression in hypoxic human embryonic and mesenchymal stem cells (hESCs and hMSCs). A total of 50 and 76 miRNAs were differentially regulated by hypoxia (2% O2) in hESCs and hMSCs, respectively, with a negligible overlap of only three miRNAs. We found coordinate regulation of precursor and mature miRNAs under hypoxia suggesting their regulation mainly at transcriptional level. Hypoxia response elements were located upstream of 97% of upregulated hypoxia regulated miRNAs (HRMs) suggesting hypoxia-inducible-factor (HIF) driven transcription. HIF binding to the candidate cis-elements of specific miRNAs under hypoxia was confirmed by Chromatin immunoprecipitation coupled with qPCR. Role analysis of a subset of upregulated HRMs identified linkage to reported inhibition of differentiation while a downregulated subset of HRMs had a putative role in the promotion of differentiation. MiRNA-target prediction correlation with published hypoxic hESC and hMSC gene expression profiles revealed HRM target genes enriched in the cytokine:cytokine receptor, HIF signalling and pathways in cancer. Overall, our study reveals, novel and distinct hypoxia-driven miRNA signatures in hESCs and hMSCs with the potential for application in optimised culture and differentiation models for both therapeutic application and improved understanding of stem cell biology. PMID:27783707

Compositional classification and sedimentological interpretation of the laminated lacustrine sediments at Baumkrichen (Western Austria) using XRF core scanning data

NASA Astrophysics Data System (ADS)

Barrett, Samuel; Tjallingii, Rik; Bloemsma, Menno; Brauer, Achim; Starnberger, Reinhard; Spötl, Christoph; Dulski, Peter

2015-04-01

The outcrop at Baumkirchen (Austria) encloses part of a unique sequence of laminated lacustrine sediments deposited during the last glacial cycle. A ~250m long composite sediment record recovered at this location now continuously covers the periods ~33 to ~45 ka BP (MIS 3) and ~59 to ~73 ka BP (MIS 4), which are separated by a hiatus. The well-laminated (mm-cm scale) and almost entirely clastic sediments reveal alternations of clayey silt and medium silt to very-fine sand layers. Although radiocarbon and optically stimulated luminescence (OSL) dating provide a robust chronology, accurate dating of the sediment laminations appears to be problematic due to very high sedimentation rates (3-8 cm/yr). X-ray fluorescence (XRF) core scanning provided a detailed ~150m long record of compositional changes of the sediments at Baumkirchen. Changes in the sediments are subtle and classification into different facies based on individual elements is therefore subjective. We applied a statistically robust clustering analysis to provide an objective compositional classification without prior knowledge, based on XRF measurements for 15 analysed elements (all those with an acceptable signal-noise ratio: Zr, Sr, Ca, Mn, Cu, Zn, Rb, Ni, Fe, K, Cr, V, Si, Ba, T). The clustering analysis indicates a distinct compositional change between sediments deposited below and above the stratigraphic hiatus, but also differentiates between individual different laminae. Preliminary results suggest variations in the sequence are largely controlled by the relative occurrence of different kinds of sediment represented by different clusters. Three clusters identify well-laminated sediments, visually similar in appearance, each dominated by an anti-correlation between Ca and one or more of the detrital elements K, Zr, Ti, Si and Fe. Two of these clusters occur throughout the entire sequence, one frequently and the other restricted to short sections, while the third occurs almost exclusively below the hiatus, indicating a geochemically distinct component that possibly represents a specific sediment source. In a similar manner, three other clusters identify event layers with different compositions of which two occur exclusively above the hiatus and one exclusively below. The variations in the occurrence of these clusters revealing distinct event layers suggest variations in dominant sediment source both above and below the hiatus and within the section above it. More detailed comparisons between compositional variations of the individual clusters obtained from biplots and microscopic observations on thin sections, grain-size analyses, and mineralogical analyses are needed to further differentiate between sediment sources and transport mechanisms.

DNA transposon-based gene vehicles - scenes from an evolutionary drive

PubMed Central

2013-01-01

DNA transposons are primitive genetic elements which have colonized living organisms from plants to bacteria and mammals. Through evolution such parasitic elements have shaped their host genomes by replicating and relocating between chromosomal loci in processes catalyzed by the transposase proteins encoded by the elements themselves. DNA transposable elements are constantly adapting to life in the genome, and self-suppressive regulation as well as defensive host mechanisms may assist in buffering ‘cut-and-paste’ DNA mobilization until accumulating mutations will eventually restrict events of transposition. With the reconstructed Sleeping Beauty DNA transposon as a powerful engine, a growing list of transposable elements with activity in human cells have moved into biomedical experimentation and preclinical therapy as versatile vehicles for delivery and genomic insertion of transgenes. In this review, we aim to link the mechanisms that drive transposon evolution with the realities and potential challenges we are facing when adapting DNA transposons for gene transfer. We argue that DNA transposon-derived vectors may carry inherent, and potentially limiting, traits of their mother elements. By understanding in detail the evolutionary journey of transposons, from host colonization to element multiplication and inactivation, we may better exploit the potential of distinct transposable elements. Hence, parallel efforts to investigate and develop distinct, but potent, transposon-based vector systems will benefit the broad applications of gene transfer. Insight and clever optimization have shaped new DNA transposon vectors, which recently debuted in the first DNA transposon-based clinical trial. Learning from an evolutionary drive may help us create gene vehicles that are safer, more efficient, and less prone for suppression and inactivation. PMID:24320156

Disentangling the effects of promised and delivered inducements: relational and transactional contract elements and the mediating role of trust.

PubMed

Montes, Samantha D; Irving, P Gregory

2008-11-01

Psychological contracts contain both relational and transactional elements, each of which is associated with unique characteristics. In the present research, the authors drew on these distinct qualities to develop and test hypotheses regarding differential employee reactions to underfulfillment, fulfillment, and overfulfillment of relational and transactional promises. Further, the authors extended their test of the theoretical distinctions between relational and transactional contracts by assessing the relevance of trust as a key underlying mechanism of relational and transactional psychological contract breach effects. Participants in this 3-wave longitudinal study included 342 full-time temporary employees. In support of existing theoretical distinctions, results indicated that employees reacted differently to varying levels of fulfillment of their relational and transactional contracts and that trust is a more central mechanism of relational, as opposed to transactional, psychological contract breach effects. These findings underscore L.S. Lambert, J. R. Edwards, and D. M. Cable's (2003) recent recommendation that the traditional conceptualization and study of psychological contract breach requires expansion.

Distinct Element Modeling of the Large Block Test

NASA Astrophysics Data System (ADS)

Carlson, S. R.; Blair, S. C.; Wagoner, J. L.

2001-12-01

The Yucca Mountain Site Characterization Project is investigating Yucca Mountain, Nevada as a potential nuclear waste repository site. As part of this effort, the Large Block, a 3m x 3m x 4.5m rectangular prism of Topopah Spring tuff, was excavated at Fran Ridge near Yucca Mountain. The Large Block was heated to a peak temperature of 145\\deg C along a horizontal plane 2.75m below the top of the block over a period of about one-year. Displacements were measured in three orthogonal directions with an array of six Multiple Point Borehole Extensometers (MPBX) and were numerically simulated in three dimensions with 3DEC, a distinct element code. The distinct element method was chosen to incorporate discrete fractures in the simulations. The model domain was extended 23m below the ground surface and, in the subsurface, 23m outward from each vertical face so that fixed displacement boundary conditions could be applied well away from the heated portion of the block. A single continuum model and three distinct element models, incorporating six to twenty eight mapped fractures, were tested. Two thermal expansion coefficients were tested for the six-fracture model: a higher value taken from laboratory measurements and a lower value from an earlier field test. The MPBX data show that the largest displacements occurred in the upper portion of the block despite the higher temperatures near the center. The continuum model was found to under-predict the MPBX displacements except in the east west direction near the base of the block. The high thermal expansion model over-predicted the MPBX displacements except in the north south direction near the top of the block. The highly fractured model under-predicted most of the MPBX displacements and poorly simulated the cool-down portion of the test. Although no model provided the single best fit to all of the MPBX data, the six and seven fracture models consistently provided good fits and in most cases showed much improvement over the other three models. Both provided particularly good fits to the east west displacements in the upper portion of the block throughout the entire test. This exercise demonstrates that distinct element models can surpass continuum models in their ability to simulate fractured rock mass deformation, but care needs to be taken in the selection of fractures incorporated in the models. *This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Numerical analysis of singular solutions of two-dimensional problems of asymmetric elasticity

NASA Astrophysics Data System (ADS)

Korepanov, V. V.; Matveenko, V. P.; Fedorov, A. Yu.; Shardakov, I. N.

2013-07-01

An algorithm for the numerical analysis of singular solutions of two-dimensional problems of asymmetric elasticity is considered. The algorithm is based on separation of a power-law dependence from the finite-element solution in a neighborhood of singular points in the domain under study, where singular solutions are possible. The obtained power-law dependencies allow one to conclude whether the stresses have singularities and what the character of these singularities is. The algorithm was tested for problems of classical elasticity by comparing the stress singularity exponents obtained by the proposed method and from known analytic solutions. Problems with various cases of singular points, namely, body surface points at which either the smoothness of the surface is violated, or the type of boundary conditions is changed, or distinct materials are in contact, are considered as applications. The stress singularity exponents obtained by using the models of classical and asymmetric elasticity are compared. It is shown that, in the case of cracks, the stress singularity exponents are the same for the elasticity models under study, but for other cases of singular points, the stress singularity exponents obtained on the basis of asymmetric elasticity have insignificant quantitative distinctions from the solutions of the classical elasticity.

Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia

PubMed Central

Lin, Jhih-Rong; Cai, Ying; Zhang, Quanwei; Zhang, Wen; Nogales-Cadenas, Rubén; Zhang, Zhengdong D.

2016-01-01

Schizophrenia is a severe mental disorder with a large genetic component. Recent genome-wide association studies (GWAS) have identified many schizophrenia-associated common variants. For most of the reported associations, however, the underlying biological mechanisms are not clear. The critical first step for their elucidation is to identify the most likely disease genes as the source of the association signals. Here, we describe a general computational framework of post-GWAS analysis for complex disease gene prioritization. We identify 132 putative schizophrenia risk genes in 76 risk regions spanning 120 schizophrenia-associated common variants, 78 of which have not been recognized as schizophrenia disease genes by previous GWAS. Even more significantly, 29 of them are outside the risk regions, likely under regulation of transcriptional regulatory elements contained therein. These putative schizophrenia risk genes are transcriptionally active in both brain and the immune system, and highly enriched among cellular pathways, consistent with leading pathophysiological hypotheses about the pathogenesis of schizophrenia. With their involvement in distinct biological processes, these putative schizophrenia risk genes, with different association strengths, show distinctive temporal expression patterns, and play specific biological roles during brain development. PMID:27754856

Dynamic analysis of a geared rotor system considering a slant crack on the shaft

NASA Astrophysics Data System (ADS)

Han, Qinkai; Zhao, Jingshan; Chu, Fulei

2012-12-01

The vibration problems associated with geared systems have been the focus of research in recent years. As the torque is mainly transmitted by the geared system, a slant crack is more likely to appear on the gear shaft. Due to the slant crack and its breathing mechanism, the dynamic behavior of cracked geared system would differ distinctly with that of uncracked system. Relatively less work is reported on slant crack in the geared rotor system during the past research. Thus, the dynamic analysis of a geared rotor-bearing system with a breathing slant crack is performed in the paper. The finite element model of a geared rotor with slant crack is presented. Based on fracture mechanics, the flexibility matrix for the slant crack is derived that accounts for the additional stress intensity factors. Three methods for whirling analysis, parametric instability analysis and steady-state response analysis are introduced. Then, by taking a widely used one-stage geared rotor-bearing system as an example, the whirling frequencies of the equivalent time-invariant system, two types of instability regions and steady-state response under the excitations of unbalance forces and tooth transmission errors, are computed numerically. The effects of crack depth, position and type (transverse or slant) on the system dynamic behaviors are considered in the discussion. The comparative study with slant cracked geared rotor is carried out to explore distinctive features in their modal, parametric instability and frequency response behaviors.

Parvovirus-Derived Endogenous Viral Elements in Two South American Rodent Genomes

PubMed Central

2014-01-01

We describe endogenous viral elements (EVEs) derived from parvoviruses (family Parvoviridae) in the genomes of the long-tailed chinchilla (Chinchilla lanigera) and the degu (Octodon degus). The novel EVEs include dependovirus-related elements and representatives of a clearly distinct parvovirus lineage that also has endogenous representatives in marsupial genomes. In the degu, one dependovirus-derived EVE was found to carry an intact reading frame and was differentially expressed in vivo, with increased expression in the liver. PMID:25078696

Defining the physiologically normal coating and pathological deposit: an analysis of sulfur-containing moieties and pellicle thickness on hydrogel contact lenses.

PubMed

Hart, D E; Plociniak, M P; Grimes, G W

1998-04-01

Historically, biochemical studies of the interaction between tears and hydrogel contact lenses have not been coordinated with the study of the morphological ultrastructure of the phenomena. Moreover, terms that have distinct and different meanings--pellicle, coating, deposit, and biofilm--have been used interchangeably and often incorrectly when applied within the context of the general field of contact lens biotechnology to describe the tear-polymer interaction. We describe our elucidation of morphological and elemental characteristics of the normal pellicle that forms on the lens surface and urge standard use of the word "pellicle" to specify this entity. Fourteen worn hydrogel lenses (8 Group 1 and 6 Group 4 lenses according to the FDA classification) were rinsed, quartered, and fixed or dried, depending on the analysis to be performed. Scanning electron microscopy (SEM) was used to examine the morphology of the pellicle and quantify its thickness. X-ray analysis was used to detect elements associated with the anterior, central, and posterior portions of the lenses and their relative distribution. A distinctive morphological pellicle ranging from 0.1 to 8.6 microns was present on 12 of the 14 lenses. The pellicle was thicker on the Group 4 lenses than on the Group 1 lenses (P < 0.003). However, the pellicle on Group 1 lenses became thicker with increasing lens age (P < 0.02), but not as thick as on Group 4 lenses. Morphologically distinct lipid or jelly bump deposits were observed at the surface of both lenses from a single patient wearing 2 week old Group 4 lenses. Eleven lenses had sulfur-bearing tear components on the anterior zone. Sulfur was deposited within the matrix of nine lenses. The sulfur containing moieties were more prevalent on Group 4 lenses (P < 0.002). More sulfur was assayed on older lenses (P < 0.004). The anterior lens zone had more sulfur-bearing tear components than did the posterior or center zones (P < 0.05). The physiologically normal pellicle is a distinct morphological entity covering the anterior lens surface. Abnormal deposits such as the discrete microgel region, known as jelly bumps, are not part of the physiologically normal pellicle at the anterior lens surface and have the potential to induce pathology. Sulfur-containing moieties within the matrix may represent the breakdown of large proteins and mucoproteins or intact proteins, as well as contaminants such as cosmetics and environmental pollutants. It is also possible that entire small proteins, such as lysozyme, impregnate the matrix. The moieties that become entrapped within the matrix or rigidly adhere to the matrix should be considered true deposits.

LATDYN - PROGRAM FOR SIMULATION OF LARGE ANGLE TRANSIENT DYNAMICS OF FLEXIBLE AND RIGID STRUCTURES

NASA Technical Reports Server (NTRS)

Housner, J. M.

1994-01-01

LATDYN is a computer code for modeling the Large Angle Transient DYNamics of flexible articulating structures and mechanisms involving joints about which members rotate through large angles. LATDYN extends and brings together some of the aspects of Finite Element Structural Analysis, Multi-Body Dynamics, and Control System Analysis; three disciplines that have been historically separate. It combines significant portions of their distinct capabilities into one single analysis tool. The finite element formulation for flexible bodies in LATDYN extends the conventional finite element formulation by using a convected coordinate system for constructing the equation of motion. LATDYN's formulation allows for large displacements and rotations of finite elements subject to the restriction that deformations within each are small. Also, the finite element approach implemented in LATDYN provides a convergent path for checking solutions simply by increasing mesh density. For rigid bodies and joints LATDYN borrows extensively from methodology used in multi-body dynamics where rigid bodies may be defined and connected together through joints (hinges, ball, universal, sliders, etc.). Joints may be modeled either by constraints or by adding joint degrees of freedom. To eliminate error brought about by the separation of structural analysis and control analysis, LATDYN provides symbolic capabilities for modeling control systems which are integrated with the structural dynamic analysis itself. Its command language contains syntactical structures which perform symbolic operations which are also interfaced directly with the finite element structural model, bypassing the modal approximation. Thus, when the dynamic equations representing the structural model are integrated, the equations representing the control system are integrated along with them as a coupled system. This procedure also has the side benefit of enabling a dramatic simplification of the user interface for modeling control systems. Three FORTRAN computer programs, the LATDYN Program, the Preprocessor, and the Postprocessor, make up the collective LATDYN System. The Preprocessor translates user commands into a form which can be used while the LATDYN program provides the computational core. The Postprocessor allows the user to interactively plot and manage a database of LATDYN transient analysis results. It also includes special facilities for modeling control systems and for programming changes to the model which take place during analysis sequence. The documentation includes a Demonstration Problem Manual for the evaluation and verification of results and a Postprocessor guide. Because the program should be viewed as a byproduct of research on technology development, LATDYN's scope is limited. It does not have a wide library of finite elements, and 3-D Graphics are not available. Nevertheless, it does have a measure of "user friendliness". The LATDYN program was developed over a period of several years and was implemented on a CDC NOS/VE & Convex Unix computer. It is written in FORTRAN 77 and has a virtual memory requirement of 1.46 MB. The program was validated on a DEC MICROVAX operating under VMS 5.2.

Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

NASA Astrophysics Data System (ADS)

Dawson, K.; Scheller, S.; Dillon, J. G.; Orphan, V. J.

2016-12-01

Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned 2200 cellular regions of interest (ROIs) into 5 distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment

PubMed Central

Dawson, Katherine S.; Scheller, Silvan; Dillon, Jesse G.; Orphan, Victoria J.

2016-01-01

Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA. PMID:27303371

Distinguishing treatment from research: a functional approach

PubMed Central

Lewens, T

2006-01-01

The best way to distinguish treatment from research is by their functions. This mode of distinction fits well with the basic ethical work that needs to be carried out. The distinction needs to serve as an ethical flag, highlighting areas in which the goals of doctors and patients are more likely than usual to diverge. The distinction also allows us to illuminate and understand some otherwise puzzling elements of debates on research ethics: it shows the peculiarity of exclusive conceptions of the distinction between research and treatment; it allows us to frame questions about therapeutic obligations in the research context, and it allows us to consider whether there may be research obligations in the therapeutic context. PMID:16816045

Effects of depuration on the element concentration in bivalves: Comparison between sympatric Ruditapes decussatus and Ruditapes philippinarum

NASA Astrophysics Data System (ADS)

Freitas, R.; Ramos Pinto, L.; Sampaio, M.; Costa, A.; Silva, M.; Rodrigues, A. M.; Quintino, V.; Figueira, E.

2012-09-01

Organisms living in coastal ecosystems are frequently subjected to anthropogenic pressures such as metals. Metals, especially those not required for metabolic activity (e.g. mercury, lead and cadmium) can be toxic even at quite low concentrations not only to organisms that accumulate them, but also to their consumers. Throughout the world, Ruditapes decussatus and Ruditapes philippinarum have been successfully commercialised for human consumption and for monitoring environmental conditions such as contamination. These two clam species share similar habitats and requirements, successfully competing both in the natural environment and in aquaculture farms. Because differences in metal accumulation may exist between R. decussatus and R. philippinarum, different risks to public health may overcome as well as distinct ecological implications. The effect of depuration on the metal burden and biochemical status of both clams species may also diverge and since the information available is subjective and scarce, the aims of the present study were to: 1) assess the total metal accumulation and intracellular partitioning, at natural conditions, in the two clam species collected at the same site; 2) evaluate the effect of depuration as a mean of reducing the levels of distinct elements, assessing also the effect of depuration time (2 and 7 days); 3) investigate the efficiency of depuration by biochemical status of the two bivalve species, evaluating changes in lipid peroxidation and activity of antioxidant enzymes catalase (CAT), superoxide dismutase (SOD) and of glutathione S-transferase (GST). Metal chelation by metallothioneins (MTs) was also determined. The results obtained showed that concentration of elements in clams was low, presenting very similar concentration levels for all elements. The present work further demonstrated that the total element concentration decreased in the shorter depuration period (2 days) and that R. decussatus and R. philippinarum partitioned elements preferentially in the insoluble fraction. The percentage of elements in the soluble fraction was lower in the longer depuration period, reducing the dietary bioavailability of elements and thus the health risk to consumers of depurated bivalves. In general, LPO, CAT, SOD and GSTs showed a decreased from environmental to depuration conditions, revealing that depuration reduces the oxidative stress that organisms were subjected in the environment. The lower MTs production observed in the longer depuration period, although no significantly different from the remaining periods, may be explained by the distinct metal allocation between both soluble and insoluble fractions.

Data acquisition and analysis in the DOE/NASA Wind Energy Program

NASA Technical Reports Server (NTRS)

Neustadter, H. E.

1980-01-01

Four categories of data systems, each responding to a distinct information need are presented. The categories are: control, technology, engineering and performance. The focus is on the technology data system which consists of the following elements: sensors which measure critical parameters such as wind speed and direction, output power, blade loads and strains, and tower vibrations; remote multiplexing units (RMU) mounted on each wind turbine which frequency modulate, multiplex and transmit sensor outputs; the instrumentation available to record, process and display these signals; and centralized computer analysis of data. The RMU characteristics and multiplexing techniques are presented. Data processing is illustrated by following a typical signal through instruments such as the analog tape recorder, analog to digital converter, data compressor, digital tape recorder, video (CRT) display, and strip chart recorder.

Comprehensive analysis of the optical Kerr coefficient of graphene

DOE PAGES

Soh, Daniel B. S.; Hamerly, Ryan; Mabuchi, Hideo

2016-08-25

We present a comprehensive analysis of the nonlinear optical Kerr effect in graphene. We directly solve the S-matrix element to calculate the absorption rate, utilizing the Volkov-Keldysh-type crystal wave functions. We then convert to the nonlinear refractive index coefficients through the Kramers-Kronig relation. In this formalism, the source of Kerr nonlinearity is the interplay of optical fields that cooperatively drive the transition from valence to conduction band. This formalism makes it possible to identify and compute the rates of distinct nonlinear processes that contribute to the Kerr nonlinear refractive index coefficient. The four identified mechanisms are two-photon absorption, Raman transition,more » self-coupling, and quadratic ac Stark effect. As a result, we present a comparison of our theory with recent experimental and theoretical results.« less

Mechanical response of silk crystalline units from force-distribution analysis.

PubMed

Xiao, Senbo; Stacklies, Wolfram; Cetinkaya, Murat; Markert, Bernd; Gräter, Frauke

2009-05-20

The outstanding mechanical toughness of silk fibers is thought to be caused by embedded crystalline units acting as cross links of silk proteins in the fiber. Here, we examine the robustness of these highly ordered beta-sheet structures by molecular dynamics simulations and finite element analysis. Structural parameters and stress-strain relationships of four different models, from spider and Bombyx mori silk peptides, in antiparallel and parallel arrangement, were determined and found to be in good agreement with x-ray diffraction data. Rupture forces exceed those of any previously examined globular protein many times over, with spider silk (poly-alanine) slightly outperforming Bombyx mori silk ((Gly-Ala)(n)). All-atom force distribution analysis reveals both intrasheet hydrogen-bonding and intersheet side-chain interactions to contribute to stability to similar extent. In combination with finite element analysis of simplified beta-sheet skeletons, we could ascribe the distinct force distribution pattern of the antiparallel and parallel silk crystalline units to the difference in hydrogen-bond geometry, featuring an in-line or zigzag arrangement, respectively. Hydrogen-bond strength was higher in antiparallel models, and ultimately resulted in higher stiffness of the crystal, compensating the effect of the mechanically disadvantageous in-line hydrogen-bond geometry. Atomistic and coarse-grained force distribution patterns can thus explain differences in mechanical response of silk crystals, opening up the road to predict full fiber mechanics.

Endogenous Retrovirus Insertion in the KIT Oncogene Determines White and White spotting in Domestic Cats

PubMed Central

David, Victor A.; Menotti-Raymond, Marilyn; Wallace, Andrea Coots; Roelke, Melody; Kehler, James; Leighty, Robert; Eizirik, Eduardo; Hannah, Steven S.; Nelson, George; Schäffer, Alejandro A.; Connelly, Catherine J.; O’Brien, Stephen J.; Ryugo, David K.

2014-01-01

The Dominant White locus (W) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus, Dominant White, and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting, whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis, the alternatives of wild-type sequence, FERV1 element, and LTR-only define a triallelic marker. Taking into account pedigree relationships, deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats (n = 270), representing 30 cat breeds, supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris (P < 0.0001) and white spotting (P < 0.0001), respectively. PMID:25085922

Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats.

PubMed

David, Victor A; Menotti-Raymond, Marilyn; Wallace, Andrea Coots; Roelke, Melody; Kehler, James; Leighty, Robert; Eizirik, Eduardo; Hannah, Steven S; Nelson, George; Schäffer, Alejandro A; Connelly, Catherine J; O'Brien, Stephen J; Ryugo, David K

2014-08-01

The Dominant White locus (W) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus, Dominant White, and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting, whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis, the alternatives of wild-type sequence, FERV1 element, and LTR-only define a triallelic marker. Taking into account pedigree relationships, deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats (n = 270), representing 30 cat breeds, supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris (P < 0.0001) and white spotting (P < 0.0001), respectively. Copyright © 2014 David et al.

Removing but not adding elements of a context affects generalization of instrumental responses.

PubMed

Bernal-Gamboa, Rodolfo; Nieto, Javier; Uengoer, Metin

2018-01-05

Three experiments with rats investigated whether adding or removing elements of a context affects generalization of instrumental behavior. Each of the experiments used a free operant procedure. In Experiments 1 and 2, rats were trained to press a lever for food in a distinctive context. Then, transfer of lever pressing was tested in a context created either by adding an element to the context of initial acquisition or by removing one of the acquisition context's elements. In Experiment 3, a similar generalization test was conducted after rats received acquisition and extinction within the same context. For Experiments 1 and 2, we observed that removing elements from the acquisition context disrupted acquisition performance, whereas the addition of elements to the context did not. Experiment 3 revealed that removing elements from but not adding elements to the original context improved extinction performance. Our results are consistent with an elemental view of context representation.

[: an expert report by Dr. Egas Moniz on homosexuality].

PubMed

Molina Artaloytia, Francisco

2016-01-01

At the beginning of the 20th century, the noted Nobel prize-winning Portuguese neurologist Egas Moniz made an expert analysis on homosexuality in a marriage annulment case of major value as an example of the effective application of sexological knowledge of that period. Contemporary republican legislation established marriage annulment in medical terms and punished relations between persons of the same sex, or contra natura. In his report, Moniz attempted to interpret distinctive elements of the life of the subject using sexological categories, illustrating the interaction between these categories and the changing forms adopted by homosexuality (or homosexual people) of the time.

Analysis of ERTS-1 imagery and its application to evaluation of Wyoming's natural resources

NASA Technical Reports Server (NTRS)

Houston, R. S. (Principal Investigator); Marrs, R. W.

1973-01-01

The author has identified the following significant results. Significant results of the Wyoming ERTS-1 investigation during the first six months (July-December 1972) included: (1) successful segregation of Precambrian metasedimentary/metavolcanic rocks from igneous rocks, (2) discovery of iron formation within the metasedimentary sequence, (3) mapping of previously unreported tectonic elements of major significance, (4) successful mapping of large scale fracture systems of the Wind River Mountains, (5) successful distinction of some metamorphic, igneous, and sedimentary lithologies by color additive viewing, (6) mapping of large scale glacial features, and (7) development of techniques for mapping small urban areas.

Analysis of ERTS-1 imagery of Wyoming and its application to evaluation of Wyoming's natural resources

NASA Technical Reports Server (NTRS)

Marrs, R. W.

1973-01-01

The author has identified the following significant results. Significant results of the Wyoming investigation during the first six months include: (1) successful segregation of Precambrian metasedimentary/metavolcanic rocks from igneous rocks; (2) discovery of iron formation within the metasedimentary sequence; (3) mapping of previously unreported tectonic elements of major significance; (4) successful mapping of large scale fractures of the Wind River Mountains; (5) sucessful distinction of some metamorphic, igneous, and sedimentary lithologies by color-additive viewing of ERTS images; (6) mapping and interpretation of glacial features in western Wyoming; and (7) development of techniques for mapping small urban areas.

Synaptophysin regulates the kinetics of synaptic vesicle endocytosis in central neurons

PubMed Central

Kwon, Sung E.; Chapman, Edwin R.

2011-01-01

Summary Despite being the most abundant synaptic vesicle membrane protein, the function of synaptophysin remains enigmatic. For example, synaptic transmission was reported to be completely normal in synaptophysin knockout mice; however, direct experiments to monitor the synaptic vesicle cycle have not been carried out. Here, using optical imaging and electrophysiological experiments, we demonstrate that synaptophysin is required for kinetically efficient endocytosis of synaptic vesicles in cultured hippocampal neurons. Truncation analysis revealed that distinct structural elements of synaptophysin differentially regulate vesicle retrieval during and after stimulation. Thus, synaptophysin regulates at least two phases of endocytosis to ensure vesicle availability during and after sustained neuronal activity. PMID:21658579

Ferromanganese nodules from MANOP Sites H, S, and R-Control of mineralogical and chemical composition by multiple accretionary processes

USGS Publications Warehouse

Dymond, J.; Lyle, M.; Finney, B.; Piper, D.Z.; Murphy, K.; Conard, R.; Pisias, N.

1984-01-01

The chemical composition of ferromanganese nodules from the three nodule-bearing MANOP sites in the Pacific can be accounted for in a qualitative way by variable contributions of distinct accretionary processes. These accretionary modes are: 1. (1) hydrogenous, i.e., direct precipitation or accumulation of colloidal metal oxides in seawater, 2. (2) oxic diagenesis which refers to a variety of ferromanganese accretion processes occurring in oxic sediments; and 3. (3) suboxic diagenesis which results from reduction of Mn+4 by oxidation of organic matter in the sediments. Geochemical evidence suggests processes (1) and (2) occur at all three MANOP nodule-bearing sites, and process (3) occurs only at the hemipelagic site, H, which underlies the relatively productive waters of the eastern tropical Pacific. A normative model quantitatively accounts for the variability observed in nearly all elements. Zn and Na, however, are not well explained by the three end-member model, and we suggest that an additional accretionary process results in greater variability in the abundances of these elements. Variable contributions from the three accretionary processes result in distinct top-bottom compositional differences at the three sites. Nodule tops from H are enriched in Ni, Cu, and Zn, instead of the more typical enrichments of these elements in nodule bottoms. In addition, elemental correlations typical of most pelagic nodules are reversed at site H. The three accretionary processes result in distinct mineralogies. Hydrogenous precipitation produces ??MnO2. Oxic diagenesis, however, produces Cu-Ni-rich todorokite, and suboxic diagenesis results in an unstable todorokite which transforms to a 7 A?? phase ("birnessite") upon dehydration. The presence of Cu and Ni as charge-balancing cations influence the stability of the todorokite structure. In the bottoms of H nodules, which accrete dominantly by suboxic diagenesis, Na+ and possibly Mn+2 provide much of the charge balance for the todorokite structure. Limited growth rate data for H nodules suggest suboxic accretion is the fastest of the three processes, with rates at least 200 mm/106 yr. Oxic accretion is probably 10 times slower and hydrogenous 100 times slower. Since these rates predict more suboxic component in bulk nodules than is calculated by the normative analysis, we propose that suboxic accretion is a non-steady-state process. Variations in surface water productivity cause pulses of particulate flux to the sea floor which result in transient Mn reduction in the surface sediments and reprecipitation on nodule surfaces. ?? 1984.

Ferromanganese nodules from MANOP Sites H, S, and R - Control of mineralogical and chemical composition by multiple accretionary processes

NASA Astrophysics Data System (ADS)

Dymond, Jack; Lyle, Mitchell; Finney, Bruce; Piper, David Z.; Murphy, Kim; Conard, Roberta; Pisias, Nicklas

1984-05-01

The chemical composition of ferromanganese nodules from the three nodule-bearing MANOP sites in the Pacific can be accounted for in a qualitative way by variable contributions of distinct accretionary processes. These accretionary modes are: (1) hydrogenous, i.e., direct precipitation or accumulation of colloidal metal oxides in seawater, (2) oxic diagenesis which refers to a variety of ferromanganese accretion processes occurring in oxic sediments; and (3) suboxic diagenesis which results from reduction of Mn +4 by oxidation of organic matter in the sediments. Geochemical evidence suggests processes (1) and (2) occur at all three MANOP nodule-bearing sites, and process (3) occurs only at the hemipelagic site, H, which underlies the relatively productive waters of the eastern tropical Pacific. A normative model quantitatively accounts for the variability observed in nearly all elements. Zn and Na, however, are not well explained by the three end-member model, and we suggest that an additional accretionary process results in greater variability in the abundances of these elements. Variable contributions from the three accretionary processes result in distinct top-bottom compositional differences at the three sites. Nodule tops from H are enriched in Ni, Cu, and Zn, instead of the more typical enrichments of these elements in nodule bottoms. In addition, elemental correlations typical of most pelagic nodules are reversed at site H. The three accretionary processes result in distinct mineralogies. Hydrogenous precipitation produces δMnO 2. Oxic diagenesis, however, produces Cu-Ni-rich todorokite, and suboxic diagenesis results in an unstable todorokite which transforms to a 7 Å phase ("birnessite") upon dehydration. The presence of Cu and Ni as charge-balancing cations influence the stability of the todorokite structure. In the bottoms of H nodules, which accrete dominantly by suboxic diagenesis, Na + and possibly Mn +2 provide much of the charge balance for the todorokite structure. Limited growth rate data for H nodules suggest suboxic accretion is the fastest of the three processes, with rates at least 200 mm/10 6 yr. Oxic accretion is probably 10 times slower and hydrogenous 100 times slower. Since these rates predict more suboxic component in bulk nodules than is calculated by the normative analysis, we propose that suboxic accretion is a non-steady-state process. Variations in surface water productivity cause pulses of particulate flux to the sea floor which result in transient Mn reduction in the surface sediments and reprecipitation on nodule surfaces.

Specimen preparation for NanoSIMS analysis of biological materials

NASA Astrophysics Data System (ADS)

Grovenor, C. R. M.; Smart, K. E.; Kilburn, M. R.; Shore, B.; Dilworth, J. R.; Martin, B.; Hawes, C.; Rickaby, R. E. M.

2006-07-01

In order to achieve reliable and reproducible analysis of biological materials by SIMS, it is critical both that the chosen specimen preparation method does not modify substantially the in vivo chemistry that is the focus of the study and that any chemical information obtained can be calibrated accurately by selection of appropriate standards. In Oxford, we have been working with our new Cameca NanoSIMS50 on two very distinct classes of biological materials; the first where the sample preparation problems are relatively undemanding - human hair - but calibration for trace metal analysis is a critical issue and, the second, marine coccoliths and hyperaccumulator plants where reliable specimen preparation by rapid freezing and controlled drying to preserve the distribution of diffusible species is the first and most demanding requirement, but worthwhile experiments on tracking key elements can still be undertaken even when it is clear that some redistribution of the most diffusible ions has occurred.

A Discordant Melody of Sameness.

ERIC Educational Resources Information Center

Carroll, William J.

2003-01-01

Explores why, in meeting the competition from public and proprietary institutions, small liberal arts colleges should avoid their current homogenization and focus on core, distinctive elements of excellence. (EV)

The r-Stirling Numbers.

DTIC Science & Technology

1982-12-01

partitions, the restriction being that the first r elements must be in distinct cycles and respectively distinct subsets. The combinatorial and algebraic ...symmetric functions The Stirling numbers of the first kind, ("], for ixed n, are the elementary symmetric functions or the numbers 1,...,n (see, e.g., [4 or...5J). The r-Stirling numbers of the Iirst kind are the elementary symmetric runctions or the numbers r,... ,n. --- -4i: ? - , , .i

Isotopically distinct reservoirs in the solar nebula: Isotope anomalies in Vigarano meteorite inclusions

NASA Technical Reports Server (NTRS)

Loss, R. D.; Lugmair, G. W.; Davis, A. M.; Macpherson, G. J.

1994-01-01

The isotopic compositions of Mg, Ca, Ti, Cr, Zn, Sr, Ba, Nd, and Sm were measured in four relatively unaltered refractory inclusions from the Vigarano carbonaceous chondrite meteorite. Three of the inclusions (USNM 1623-2, 1623-3, and 1623-8) show similar Mg, Ca, Ti, and Cr isotopic compositions to those found in most inclusions in the Allende carbonaceous chondrite. This indicates that these Vigarano inclusions sampled the same isotopic reservoirs as the majority of the Allende inclusions that isotope signatures in the latter were not significantly modified by the secondary alteration that permeates most Allende inclusions. In contrast, inclusion 1623-5 has large deficits in Mg-26, Ca-48, and Ti-50 and small but distinct Cr-54, Zn-66, Sr-84, Ba-135, Ba-137, and Sm-144 anomalies. The magnitudes of these unusual anomalies in the refractory elements are within analytical uncertainty of those found in the Allende 'FUN" inclusion C1, yet 1623-5 has a very different bulk chemical composition from C1. The fact that 1623-5 and C1 have identical isotopic anomalies yet have significantly distinct major and trace element contents provide convincing evidence for the presence of isotopically distinct reservoirs in the early solar system.

Elements of a collaborative systems model within the aerospace industry

NASA Astrophysics Data System (ADS)

Westphalen, Bailee R.

2000-10-01

Scope and method of study. The purpose of this study was to determine the components of current aerospace collaborative efforts. There were 44 participants from two selected groups surveyed for this study. Nineteen were from the Oklahoma Air National Guard based in Oklahoma City representing the aviation group. Twenty-five participants were from the NASA Johnson Space Center in Houston representing the aerospace group. The surveys for the aviation group were completed in reference to planning missions necessary to their operations. The surveys for the aerospace group were completed in reference to a well-defined and focused goal from a current mission. A questionnaire was developed to survey active participants of collaborative systems in order to consider various components found within the literature. Results were analyzed and aggregated through a database along with content analysis of open-ended question comments from respondents. Findings and conclusions. This study found and determined elements of a collaborative systems model in the aerospace industry. The elements were (1) purpose or mission for the group or team; (2) commitment or dedication to the challenge; (3) group or team meetings and discussions; (4) constraints of deadlines and budgets; (5) tools and resources for project and simulations; (6) significant contributors to the collaboration; (7) decision-making formats; (8) reviews of project; (9) participants education and employment longevity; (10) cross functionality of team or group members; (11) training on the job plus teambuilding; (12) other key elements identified relevant by the respondents but not included in the model such as communication and teamwork; (13) individual and group accountability; (14) conflict, learning, and performance; along with (15) intraorganizational coordination. These elements supported and allowed multiple individuals working together to solve a common problem or to develop innovation that could not have been accomplished individually. Comparing the relationship of the elements of the aerospace collaborative model with those of the various authors in the literature, it is found that the aerospace model is a more comprehensive configuration of elements and has added to the definition of collaboration found in the literature. Further, findings of relevant elements were indicated by the high response incidence of those individuals within the collaborative system. They were elements that were nearly unanimously identified as relevant by those within aerospace collaborative systems included having a stated purpose or mission for the project; working within completion deadlines; and coordinating with other departments within the organization. Furthermore, relevant terms correlating to the model as indicated by the high incidence of appearance in the respondents' comments were training, communication, commitment, and teamwork. There were also found to be variable distinctions specific to each collaborative context. The survey results suggested the multilevel overlapping of the multiple elements within the aerospace collaborative system model along with distinct context variables. Further research is necessary to refine the model and to provide additional information upon this established foundation.

Viruses and mobile elements as drivers of evolutionary transitions

PubMed Central

2016-01-01

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431520

Laser spectrum detection methods for substance of Mars surface

NASA Astrophysics Data System (ADS)

Zhang, Dan; Xue, Bin; Zhao, Yi-yi

2014-11-01

The chemical element and mineral rock's abundance and distribution are the basic material of planetary geology evolution research [1], hence preterit detection for composition of Mars surface substance contains both elements sorts and mineral ingredients. This article introduced new ways to detect Mars elements and mineral components, Laser Induced Breakdown Spectroscopy (LIBS) and Raman Spectroscopy (RS) which have distinct advantages, such as work over a long distance, detect rapidly, accuratly and nondestructively. LIBS and RS both use laser excitation to shoot the substance of Mars exciting new wavelengths. The techniques of LIBS and RS in laboratory are mature, besides the technique of LIBS is being used in MSL (Chemcam) now and RS will be used in ExoMars. Comparing LIBS and RS's detection results with XRF and APXS, Mossbauer spectrometer, these existed Mars surface material detection instruments,and the Infrared spectrometer, Mid-IR, they have more accurate detection results. So LIBS and RS are competent for Mars surface substance detection instead of X-ray spectrometer and Mossbauer spectrometer which were already used in 'Viking 1' and 'Opportunity'. Only accurate detection results about Mars surface substance can lead to scientist's right analysis in inversing geological evolution of the planet.

Viruses and mobile elements as drivers of evolutionary transitions.

PubMed

Koonin, Eugene V

2016-08-19

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Authors.

Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism

PubMed Central

Berntson, Gary G.; Norman, Greg J.; Hawkley, Louise C.; Cacioppo, John T.

2012-01-01

Evolution has sculpted the incredibly complex human nervous system, among the most complex functions of which extend beyond the individual to an intricate social structure. Although these functions are deterministic, those determinants are legion, heavily interacting and dependent on a specific evolutionary trajectory. That trajectory was directed by the adaptive significance of quasi-random genetic variations, but was also influenced by chance and caprice. With a different evolutionary pathway, the same neural elements could subserve functions distinctly different from what they do in extant human brains. Consequently, the properties of higher level neural networks cannot be derived readily from the properties of the lower level constituent elements, without studying these elements in the aggregate. Thus, a multi-level approach to integrative neuroscience may offer an optimal strategy. Moreover, the process of calibrative reductionism, by which concepts and understandings from one level of organization or analysis can mutually inform and ‘calibrate’ those from other levels (both higher and lower), may represent a viable approach to the application of reductionism in science. This is especially relevant in social neuroscience, where the basic subject matter of interest is defined by interacting organisms across diverse environments. PMID:23386961

Characterization of the Etna volcanic emissions through an active biomonitoring technique (moss-bags): part 1--major and trace element composition.

PubMed

Calabrese, S; D'Alessandro, W; Bellomo, S; Brusca, L; Martin, R S; Saiano, F; Parello, F

2015-01-01

Active biomonitoring using moss-bags was applied to an active volcanic environment for the first time. Bioaccumulation originating from atmospheric deposition was evaluated by exposing mixtures of washed and air-dried mosses (Sphagnum species) at 24 sites on Mt. Etna volcano (Italy). Concentrations of major and a large suite of trace elements were analysed by inductively coupled mass and optical spectrometry (ICP-MS and ICP-OES) after total acid digestion. Of the 49 elements analysed those which closely reflect summit volcanic emissions were S, Tl, Bi, Se, Cd, As, Cu, B, Na, Fe, Al. Enrichment factors and cluster analysis allowed clear distinction between volcanogenic, geogenic and anthropogenic inputs that affect the local atmospheric deposition. This study demonstrates that active biomonitoring with moss-bags is a suitable and robust technique for implementing inexpensive monitoring in scarcely accessible and harsh volcanic environments, giving time-averaged quantitative results of the local exposure to volcanic emissions. This task is especially important in the study area because the summit area of Mt. Etna is visited by nearly one hundred thousand tourists each year who are exposed to potentially harmful volcanic emissions. Copyright © 2014 Elsevier Ltd. All rights reserved.

High-Performance Ion Mobility Spectrometry Using Hourglass Electrodynamic Funnel And Internal Ion Funnel

DOEpatents

Smith, Richard D.; Tang, Keqi; Shvartsburg, Alexandre A.

2004-11-16

A method and apparatus enabling increased sensitivity in ion mobility spectrometry/mass spectrometry instruments which substantially reduces or eliminates the loss of ions in ion mobility spectrometer drift tubes utilizing an hourglass electrodynamic ion funnel at the entrance to the drift tube and/or an internal ion funnel at the exit of the drift tube. An hourglass electrodynamic funnel is formed of at least an entry element, a center element, and an exit element, wherein the aperture of the center element is smaller than the aperture of the entry element and the aperture of the exit elements. Ions generated in a relatively high pressure region by an ion source at the exterior of the hourglass electrodynamic funnel are transmitted to a relatively low pressure region at the entrance of the hourglass funnel through a conductance limiting orifice. Alternating and direct electrical potentials are applied to the elements of the hourglass electrodynamic funnel thereby drawing ions into and through the hourglass electrodynamic funnel thereby introducing relatively large quantities of ions into the drift tube while maintaining the gas pressure and composition at the interior of the drift tube as distinct from those at the entrance of the electrodynamic funnel and allowing a positive gas pressure to be maintained within the drift tube, if desired. An internal ion funnel is provided within the drift tube and is positioned at the exit of said drift tube. The advantage of the internal ion funnel is that ions that are dispersed away from the exit aperture within the drift tube, such as those that are typically lost in conventional drift tubes to any subsequent analysis or measurement, are instead directed through the exit of the drift tube, vastly increasing the amount of ions exiting the drift tube.

[Spatial variations of biogenic elements in coastal wetland sediments of the Jiulong River Estuary].

PubMed

Yu, Xiao-Qing; Yang, Jun; Liu, Le-Mian; Tian, Yuan; Yu, Zheng; Wang, Chang-Fu

2012-11-01

To reveal the spatial distribution of biogenic elements and their influencing factors in the typical subtropical coastal wetland, both surface and core sediment samples were collected from the Jiulong River Estuary, southeast China in summer 2009. The biogenic elements including carbon, nitrogen, phosphorus, sulfur (C, N, P, S) were determined by Element Analyzer and Flow Injection Analyzer. The concentrations of TC, TN, TP, and TS were (12.64 +/- 2.66) g x kg(-1), (1.57 +/- 0.29) g x kg(-1), (0.48 +/- 0.06) g x kg(-1), and (2.61 +/- 1.37) g x kg(-1), respectively. Further, these biogenic elements showed a distinct spatial pattern which closely related with the vegetation type and tide level. Values of TC, TN, TP in the surface sediment of mangrove vegetation zones were higher than those in the cord-grass and mudflat zones, while TC, TN, TP concentrations in the high tide level regions were higher than those in the middle and low tide level regions. The TS concentration was the highest in cord-grass vegetation and middle tidal level zones. The TC and TN values in sedimentary core decreased gradually with depth, and they were the highest in the mangrove sites, followed by cord-grass and mudflat sites at the same depth. In mudflat sedimentary core, the average content of TP was the lowest, whereas TS was the highest. Redundancy analysis revealed that vegetation type, pH and tide level were the main factors influencing the distribution of biogenic elements in surface sediments of the Jiulong River Estuary, by explaining 24.0%, 19.0% and 11.6% of total variation in the four biogenic elements (C, N, P and S), respectively.

Emergence of Sequence Type 779 Methicillin-Resistant Staphylococcus aureus Harboring a Novel Pseudo Staphylococcal Cassette Chromosome mec (SCCmec)-SCC-SCCCRISPR Composite Element in Irish Hospitals

PubMed Central

Kinnevey, Peter M.; Shore, Anna C.; Brennan, Grainne I.; Sullivan, Derek J.; Ehricht, Ralf; Monecke, Stefan; Slickers, Peter

2013-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) has been a major cause of nosocomial infection in Irish hospitals for 4 decades, and replacement of predominant MRSA clones has occurred several times. An MRSA isolate recovered in 2006 as part of a larger study of sporadic MRSA exhibited a rare spa (t878) and multilocus sequence (ST779) type and was nontypeable by PCR- and DNA microarray-based staphylococcal cassette chromosome mec (SCCmec) element typing. Whole-genome sequencing revealed the presence of a novel 51-kb composite island (CI) element with three distinct domains, each flanked by direct repeat and inverted repeat sequences, including (i) a pseudo SCCmec element (16.3 kb) carrying mecA with a novel mec class region, a fusidic acid resistance gene (fusC), and two copper resistance genes (copB and copC) but lacking ccr genes; (ii) an SCC element (17.5 kb) carrying a novel ccrAB4 allele; and (iii) an SCC element (17.4 kb) carrying a novel ccrC allele and a clustered regularly interspaced short palindromic repeat (CRISPR) region. The novel CI was subsequently identified by PCR in an additional 13 t878/ST779 MRSA isolates, six from bloodstream infections, recovered between 2006 and 2011 in 11 hospitals. Analysis of open reading frames (ORFs) carried by the CI showed amino acid sequence similarity of 44 to 100% to ORFs from S. aureus and coagulase-negative staphylococci (CoNS). These findings provide further evidence of genetic transfer between S. aureus and CoNS and show how this contributes to the emergence of novel SCCmec elements and MRSA strains. Ongoing surveillance of this MRSA strain is warranted and will require updating of currently used SCCmec typing methods. PMID:23147725

Innate Pattern Recognition and Categorization in a Jumping Spider

PubMed Central

Dolev, Yinnon; Nelson, Ximena J.

2014-01-01

The East African jumping spider Evarcha culicivora feeds indirectly on vertebrate blood by preferentially preying upon blood-fed Anopheles mosquitoes, the vectors of human malaria1, using the distinct resting posture and engorged abdomen characteristic of these specific prey as key elements for their recognition. To understand perceptual categorization of objects by these spiders, we investigated their predatory behavior toward different digital stimuli - abstract ‘stick figure’ representations of Anopheles constructed solely by known key identification elements, disarranged versions of these, as well as non-prey items and detailed images of alternative prey. We hypothesized that the abstract images representing Anopheles would be perceived as potential prey, and would be preferred to those of non-preferred prey. Spiders perceived the abstract stick figures of Anopheles specifically as their preferred prey, attacking them significantly more often than non-preferred prey, even when the comprising elements of the Anopheles stick figures were disarranged and disconnected from each other. However, if the relative angles between the elements of the disconnected stick figures of Anopheles were altered, the otherwise identical set of elements was no longer perceived as prey. These data show that E. culicivora is capable of making discriminations based on abstract concepts, such as the hypothetical angle formed by discontinuous elements. It is this inter-element angle rather than resting posture that is important for correct identification of Anopheles. Our results provide a glimpse of the underlying processes of object recognition in animals with minute brains, and suggest that these spiders use a local processing approach for object recognition, rather than a holistic or global approach. This study provides an excellent basis for a comparative analysis on feature extraction and detection by animals as diverse as bees and mammals. PMID:24893306

Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions.

PubMed

McDowell, Stephen C; Akmakjian, Garo; Sladek, Chris; Mendoza-Cozatl, David; Morrissey, Joe B; Saini, Nick; Mittler, Ron; Baxter, Ivan; Salt, David E; Ward, John M; Schroeder, Julian I; Guerinot, Mary Lou; Harper, Jeffrey F

2013-01-01

The concentrations of mineral nutrients in seeds are critical to both the life cycle of plants as well as human nutrition. These concentrations are strongly influenced by soil conditions, as shown here by quantifying the concentration of 14 elements in seeds from Arabidopsis thaliana plants grown under four different soil conditions: standard, or modified with NaCl, heavy metals, or alkali. Each of the modified soils resulted in a unique change to the seed ionome (the mineral nutrient content of the seeds). To help identify the genetic networks regulating the seed ionome, changes in elemental concentrations were evaluated using mutants corresponding to 760 genes as well as 10 naturally occurring accessions. The frequency of ionomic phenotypes supports an estimate that as much as 11% of the A. thaliana genome encodes proteins of functional relevance to ion homeostasis in seeds. A subset of mutants were analyzed with two independent alleles, providing five examples of genes important for regulation of the seed ionome: SOS2, ABH1, CCC, At3g14280 and CNGC2. In a comparison of nine different accessions to a Col-0 reference, eight accessions were observed to have reproducible differences in elemental concentrations, seven of which were dependent on specific soil conditions. These results indicate that the A. thaliana seed ionome is distinct from the vegetative ionome, and that elemental analysis is a sensitive approach to identify genes controlling ion homeostasis, including those that regulate gene expression, phospho-regulation, and ion transport.

Identification and Transcript Analysis of the TCP Transcription Factors in the Diploid Woodland Strawberry Fragaria vesca

PubMed Central

Wei, Wei; Hu, Yang; Cui, Meng-Yuan; Han, Yong-Tao; Gao, Kuan; Feng, Jia-Yue

2016-01-01

Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors play versatile functions in multiple processes of plant growth and development. However, no systematic study has been performed in strawberry. In this study, 19 FvTCP genes were identified in the diploid woodland strawberry (Fragaria vesca) accession Heilongjiang-3. Phylogenetic analysis suggested that the FvTCP genes were classified into two main classes, with the second class further divided into two subclasses, which was supported by the exon-intron organizations and the conserved motif structures. Promoter analysis revealed various cis-acting elements related to growth and development, hormone and/or stress responses. We analyzed FvTCP gene transcript accumulation patterns in different tissues and fruit developmental stages. Among them, 12 FvTCP genes exhibited distinct tissue-specific transcript accumulation patterns. Eleven FvTCP genes were down-regulated in different fruit developmental stages, while five FvTCP genes were up-regulated. Transcripts of FvTCP genes also varied with different subcultural propagation periods and were induced by hormone treatments and biotic and abiotic stresses. Subcellular localization analysis showed that six FvTCP-GFP fusion proteins showed distinct localizations in Arabidopsis mesophyll protoplasts. Notably, transient over-expression of FvTCP9 in strawberry fruits dramatically affected the expression of a series of genes implicated in fruit development and ripening. Taken together, the present study may provide the basis for functional studies to reveal the role of this gene family in strawberry growth and development. PMID:28066489

Tyrosine Recombinase Retrotransposons and Transposons.

PubMed

Poulter, Russell T M; Butler, Margi I

2015-04-01

Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold Dictyostelium discoideum. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes.

Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

PubMed Central

Kim, Eun Bae

2014-01-01

Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31 E. faecium and 38 E. faecalis strains. Hierarchical clustering of 7,017 orthologs found in the E. faecium pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC E. faecium genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes. E. faecium ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL E. faecium genomes. In contrast, differences were not observed between NC and CL E. faecalis genomes despite their having larger genomes than E. faecium. Our findings show that unlike E. faecalis, NC and CL E. faecium strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments. PMID:24141120

Hsp40 function in yeast prion propagation: Amyloid diversity necessitates chaperone functional complexity.

PubMed

Sporn, Zachary A; Hines, Justin K

2015-01-01

Yeast prions are heritable protein-based elements, most of which are formed of amyloid aggregates that rely on the action of molecular chaperones for transmission to progeny. Prions can form distinct amyloid structures, known as 'strains' in mammalian systems, that dictate both pathological progression and cross-species infection barriers. In yeast these same amyloid structural polymorphisms, called 'variants', dictate the intensity of prion-associated phenotypes and stability in mitosis. We recently reported that [PSI(+)] prion variants differ in the fundamental domain requirements for one chaperone, the Hsp40/J-protein Sis1, which are mutually exclusive between 2 different yeast prions, demonstrating a functional plurality for Sis1. Here we extend that analysis to incorporate additional data that collectively support the hypothesis that Sis1 has multiple functional roles that can be accomplished by distinct sets of domains. These functions are differentially required by distinct prions and prion variants. We also present new data regarding Hsp104-mediated prion elimination and show that some Sis1 functions, but not all, are conserved in the human homolog Hdj1/DNAJB1. Importantly, of the 10 amyloid-based prions indentified to date in Saccharomyces cerevisiae, the chaperone requirements of only 4 are known, leaving a great diversity of amyloid structures, and likely modes of amyloid-chaperone interaction, largely unexplored.

Cooperative interactions between hippocampal and striatal systems support flexible navigation

PubMed Central

Brown, Thackery I; Ross, Robert S; Tobyne, Sean M; Stern, Chantal E

2012-01-01

Research in animals and humans has demonstrated that the hippocampus is critical for retrieving distinct representations of overlapping sequences of information. There is recent evidence that the caudate nucleus and orbitofrontal cortex are also involved in disambiguation of overlapping spatial representations. The hippocampus and caudate are functionally distinct regions, but both have anatomical links with the orbitofrontal cortex. The present study used an fMRI-based functional connectivity analysis in humans to examine the functional relationship between the hippocampus, caudate, and orbitofrontal cortex when participants use contextual information to navigate well-learned spatial routes which share common elements. Participants were trained outside the scanner to navigate virtual mazes from a first-person perspective. Overlapping condition mazes began and ended at distinct locations, but converged in the middle to share some hallways with another maze. Non-overlapping condition mazes did not share any hallways with any other maze. Successful navigation through the overlapping hallways required contextual information identifying the current navigational route to guide the appropriate response for a given trial. Results revealed greater functional connectivity between the hippocampus, caudate, and orbitofrontal cortex for overlapping mazes compared to non-overlapping mazes. The current findings suggest that the hippocampus and caudate interact with prefrontal structures cooperatively for successful contextually-dependent navigation. PMID:22266411

Characterizing coal beds in western Kentucky with the Al-La-Sc coherent triad

USGS Publications Warehouse

Chyi, L.L.; Medlin, J.H.

1996-01-01

Cyclic sedimentation and lateral facies changes make coal bed correlations inconclusive and difficult. This uncertainty can be further complicated if a coal basin has been structurally deformed. Coal macerals can be studied to indicate the nature and degree of coalification. Their use in coal bed correlation, however, is limited. Most of the trace elements and their ratios that have been studied show significant within-bed lateral and stratigraphic variations, and thus are not effective in correlating coal beds regionally. Geochemically coherent groups of elements, such as rare earth elements (REE) and platinum group elements (PGE), appear to be highly differentiated in coal-forming environments. Geochemical coherent elemental triads appear to be useful for coal bed identification or fingerprinting. The best triad which was demonstrated to be effective in coal bed characterization in western Kentucky, is that of Al, La and Sc. These three elements are highly correlated with one another and they can be determined accurately and simultaneously with instrumental neutron activation analysis (INAA). The elemental triad Al-La-Sc is used to identify and fingerprint three key coal beds in western Kentucky: the Springfield (western Kentucky No. 9), the Davis (western Kentucky No. 6), and the Mining City and Dawson Springs are both considered to be the No. 4 coal bed in western Kentucky). Four distinct groupings can be recognized by use of the Al-La-Sc triad. The Dawson Springs coals have the highest Al/(La + Sc) ratios, followed by the Springfield, the Davis and the Mining City. The Mining City coal bed generally has the highest La/Sc ratio. However, the Dawson Springs is not correlated with the Mining City using the triad analysis, even though they have reportedly similar stratigraphic positions in the western Kentucky coal basin. The Al-La-Sc triad appears to be effective in discriminating between the Springfield and the Davis coal beds throughout the entire Illinois Basin. Furthermore, the range of concentration variation of the AL-La-Sc triad suggests individual groupings of the No. 4 coal in western Kentucky. In addition to characterizing these coal beds, the Al-La-Sc triad may be used to confirm stratigraphic correlations.

Discrimination of microbiological samples using femtosecond laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Baudelet, Matthieu; Yu, Jin; Bossu, Myriam; Jovelet, Julien; Wolf, Jean-Pierre; Amodeo, Tanguy; Fréjafon, Emeric; Laloi, Patrick

2006-10-01

Using femtosecond laser-induced breakdown spectroscopy, the authors have analyzed five different species of bacterium. Line emissions from six trace mineral elements, Na, Mg, P, K, Ca, and Fe, have been clearly detected. Their intensities correspond to relative concentrations of these elements contained in the analyzed samples. The authors demonstrate that the concentration profile of trace elements allows unambiguous discrimination of different bacteria. Quantitative differentiation has been made by representing bacteria in a six-dimension hyperspace with each of its axis representing a detected trace element. In such hyperspace, representative points of different species of bacterium are gathered in different and distinct volumes.

The Last Step of Syringyl Monolignol Biosynthesis in Angiosperms Is Regulated by a Novel Gene Encoding Sinapyl Alcohol Dehydrogenase

PubMed Central

Li, Laigeng; Cheng, Xiao Fei; Leshkevich, Jacqueline; Umezawa, Toshiaki; Harding, Scott A.; Chiang, Vincent L.

2001-01-01

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) has been thought to mediate the reduction of both coniferaldehyde and sinapaldehyde into guaiacyl and syringyl monolignols in angiosperms. Here, we report the isolation of a novel aspen gene (PtSAD) encoding sinapyl alcohol dehydrogenase (SAD), which is phylogenetically distinct from aspen CAD (PtCAD). Liquid chromatography–mass spectrometry-based enzyme functional analysis and substrate level–controlled enzyme kinetics consistently demonstrated that PtSAD is sinapaldehyde specific and that PtCAD is coniferaldehyde specific. The enzymatic efficiency of PtSAD for sinapaldehyde was ∼60 times greater than that of PtCAD. These data suggest that in addition to CAD, discrete SAD function is essential to the biosynthesis of syringyl monolignol in angiosperms. In aspen stem primary tissues, PtCAD was immunolocalized exclusively to xylem elements in which only guaiacyl lignin was deposited, whereas PtSAD was abundant in syringyl lignin–enriched phloem fiber cells. In the developing secondary stem xylem, PtCAD was most conspicuous in guaiacyl lignin–enriched vessels, but PtSAD was nearly absent from these elements and was conspicuous in fiber cells. In the context of additional protein immunolocalization and lignin histochemistry, these results suggest that the distinct CAD and SAD functions are linked spatiotemporally to the differential biosynthesis of guaiacyl and syringyl lignins in different cell types. SAD is required for the biosynthesis of syringyl lignin in angiosperms. PMID:11449052

The last step of syringyl monolignol biosynthesis in angiosperms is regulated by a novel gene encoding sinapyl alcohol dehydrogenase.

PubMed

Li, L; Cheng, X F; Leshkevich, J; Umezawa, T; Harding, S A; Chiang, V L

2001-07-01

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) has been thought to mediate the reduction of both coniferaldehyde and sinapaldehyde into guaiacyl and syringyl monolignols in angiosperms. Here, we report the isolation of a novel aspen gene (PtSAD) encoding sinapyl alcohol dehydrogenase (SAD), which is phylogenetically distinct from aspen CAD (PtCAD). Liquid chromatography-mass spectrometry-based enzyme functional analysis and substrate level-controlled enzyme kinetics consistently demonstrated that PtSAD is sinapaldehyde specific and that PtCAD is coniferaldehyde specific. The enzymatic efficiency of PtSAD for sinapaldehyde was approximately 60 times greater than that of PtCAD. These data suggest that in addition to CAD, discrete SAD function is essential to the biosynthesis of syringyl monolignol in angiosperms. In aspen stem primary tissues, PtCAD was immunolocalized exclusively to xylem elements in which only guaiacyl lignin was deposited, whereas PtSAD was abundant in syringyl lignin-enriched phloem fiber cells. In the developing secondary stem xylem, PtCAD was most conspicuous in guaiacyl lignin-enriched vessels, but PtSAD was nearly absent from these elements and was conspicuous in fiber cells. In the context of additional protein immunolocalization and lignin histochemistry, these results suggest that the distinct CAD and SAD functions are linked spatiotemporally to the differential biosynthesis of guaiacyl and syringyl lignins in different cell types. SAD is required for the biosynthesis of syringyl lignin in angiosperms.

Functional Specialization of Cellulose Synthase Isoforms in a Moss Shows Parallels with Seed Plants1[OPEN

PubMed Central

Li, Xingxing; Huang, Shixin; Van de Meene, Allison M.L.; Tran, Mai L.; Killeavy, Erin; Mercure, Danielle; Burton, Rachel A.

2017-01-01

The secondary cell walls of tracheary elements and fibers are rich in cellulose microfibrils that are helically oriented and laterally aggregated. Support cells within the leaf midribs of mosses deposit cellulose-rich secondary cell walls, but their biosynthesis and microfibril organization have not been examined. Although the Cellulose Synthase (CESA) gene families of mosses and seed plants diversified independently, CESA knockout analysis in the moss Physcomitrella patens revealed parallels with Arabidopsis (Arabidopsis thaliana) in CESA functional specialization, with roles for both subfunctionalization and neofunctionalization. The similarities include regulatory uncoupling of the CESAs that synthesize primary and secondary cell walls, a requirement for two or more functionally distinct CESA isoforms for secondary cell wall synthesis, interchangeability of some primary and secondary CESAs, and some CESA redundancy. The cellulose-deficient midribs of ppcesa3/8 knockouts provided negative controls for the structural characterization of stereid secondary cell walls in wild type P. patens. Sum frequency generation spectra collected from midribs were consistent with cellulose microfibril aggregation, and polarization microscopy revealed helical microfibril orientation only in wild type leaves. Thus, stereid secondary walls are structurally distinct from primary cell walls, and they share structural characteristics with the secondary walls of tracheary elements and fibers. We propose a mechanism for the convergent evolution of secondary walls in which the deposition of aggregated and helically oriented microfibrils is coupled to rapid and highly localized cellulose synthesis enabled by regulatory uncoupling from primary wall synthesis. PMID:28768816

Granulite-facies rocks in the Whatley Mill gneiss, Pine Mountain basement massif, Eastern Alabama

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daniell, N.; Salpas, P.A.

1993-03-01

The Pine Mountain basement massif is a granulite terrane exposed in a tectonic window through the Inner Piedmont of western Georgia and eastern Alabama. Investigations of the westernmost extent of the massif, the Whatley Mill Gneiss, have revealed four distinct lithologies: (1) an augen gneiss, the type lithology; (2) mylonite that develops in the shear zones cutting the unit; (3) a phaneritic rock showing weak to no foliation; (4) enclaves of biotite gneiss within the weakly-foliated rock. Additionally, the weakly-foliated rock comprises two distinct phases which are in sharp contact along curved and undulating boundaries: phase 1 is a coarser-grainedmore » rock; phase 2 is a finer-grained rock of the same mineralogy as phase 1 except it contains rare hypersthene. This first recorded observation of hypersthene unequivocally confirms the granulite-facies origin of the unit. Major and trace element compositions of the phase 1 rock are identical to those of the augen gneiss. The phase 2 rock, has a distinct composition with higher SiO[sub 2] and lower incompatible trace elements than the phase 1 rock. The enclaves display a range in major elements but higher incompatible elements than the other lithologies. Geochemical and petrologic relationships leads one to interpret: (1) the weakly-foliated rock retains many of its primary igneous features including its two phases and enclaves; (2) the two phases of the weakly-foliated rock arose as a result of injection of one magma (phase 2) into a cooler, crystal mush solidifying from another magma (phase 1); (3) the enclaves represent either autoliths of xenoliths; (4) the augen gneiss arose by isochemical deformation of the phase 1 rock.« less

The Role of Recombination in the Origin and Evolution of Alu Subfamilies

PubMed Central

Teixeira-Silva, Ana; Silva, Raquel M.; Carneiro, João; Amorim, António; Azevedo, Luísa

2013-01-01

Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome. PMID:23750218

Lead, platinum and other heavy elements in the primary cosmic radiation: HEAO-3 results

NASA Technical Reports Server (NTRS)

Waddington, C. J.; Binns, W. R.; Brewster, N. R.; Fixsen, D. J.; Garrard, T. L.; Israel, M. H.; Klarmann, J.; Newport, B. J.; Stone, E. C.

1986-01-01

An observation of the abundances of cosmic-ray lead and platinum-group nuclei using data from the HEAO-3 Heavy Nuclei Experiment (HNE) which consisted of ion chambers mounted on both sides of a plastic Cherenkov counter (Binns et al., 1981) is reported. Further analysis with more stringent selections, inclusion of additional data, and a calibration at the LBL Bevalac, have allowed the determination of the abundance ratio of lead and the platinum group of elements for particles that had a cutoff rigidity R(c) 5 GV. The observed ratio for Pb/Pt is distinctly lower than that predicted by any of the standard models for cosmic ray sources. It is possible that the difference is not an indication that the cosmic ray source composition is greatly different from that of the solar system, but rather that there is less Pb in the solar system and in the r-process than is assumed in the standard models.

Ab initio studies of isolated boron substitutional defects in graphane

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Chetty, N.

2017-10-01

We have systematically studied energetics, structural and electronic properties of different configurations of the B atoms substituting C-H pairs located on a single hexagonal ring in a graphane system using the first-principles density functional theory (DFT). A total number of 12 distinct B dopants configurations were identified and characterized. Based on the formation energy analysis, we found that relative stability of B dopants depends greatly on the defect configurations. Our results suggest that the B substitutions prefer to be distributed randomly but avoiding the formation of homo-elemental B-B bonds in a graphane system, at any concentration. Generally, the values of band gap decrease as the number of B dopants increases, but the low energy configurations have large band gaps compared to those that have homo-elemental bonds. As a result, the band gap of graphane can be fine tuned through the change in the structural arrangement of B atoms. The adequate control of the electronic structure of graphane through doping should be essential for technological device applications.

Serial grouping of 2D-image regions with object-based attention in humans.

PubMed

Jeurissen, Danique; Self, Matthew W; Roelfsema, Pieter R

2016-06-13

After an initial stage of local analysis within the retina and early visual pathways, the human visual system creates a structured representation of the visual scene by co-selecting image elements that are part of behaviorally relevant objects. The mechanisms underlying this perceptual organization process are only partially understood. We here investigate the time-course of perceptual grouping of two-dimensional image-regions by measuring the reaction times of human participants and report that it is associated with the gradual spread of object-based attention. Attention spreads fastest over large and homogeneous areas and is slowed down at locations that require small-scale processing. We find that the time-course of the object-based selection process is well explained by a 'growth-cone' model, which selects surface elements in an incremental, scale-dependent manner. We discuss how the visual cortical hierarchy can implement this scale-dependent spread of object-based attention, leveraging the different receptive field sizes in distinct cortical areas.

The Design Process of Physical Security as Applied to a U.S. Border Point of Entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, G.G.

1998-10-26

This paper describes the design process of physical security as applied to a U.S. Border Port of Entry (PoE). Included in this paper are descriptions of the elements that compose U.S. border security. The physical security design will describe the various elements that make up the process as well as the considerations that must be taken into account when dealing with system integration of those elements. The distinctions between preventing unlawful entry and exit of illegal contraband will be emphasized.

Parvovirus-derived endogenous viral elements in two South American rodent genomes.

PubMed

Arriagada, Gloria; Gifford, Robert J

2014-10-01

We describe endogenous viral elements (EVEs) derived from parvoviruses (family Parvoviridae) in the genomes of the long-tailed chinchilla (Chinchilla lanigera) and the degu (Octodon degus). The novel EVEs include dependovirus-related elements and representatives of a clearly distinct parvovirus lineage that also has endogenous representatives in marsupial genomes. In the degu, one dependovirus-derived EVE was found to carry an intact reading frame and was differentially expressed in vivo, with increased expression in the liver. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states.

PubMed

Korkmaz, Ali Giray; Popov, Todor; Peisl, Loulou; Codrea, Marius Cosmin; Nahnsen, Sven; Steimle, Alexander; Velic, Ana; Macek, Boris; von Bergen, Martin; Bernhardt, Joerg; Frick, Julia-Stefanie

2018-05-30

Dendritic cells (DCs) can shape the immune system towards an inflammatory or tolerant state depending on the bacterial antigens and the environment they encounter. In this study we provide a proteomic catalogue of differentially expressed proteins between distinct DC maturation states, brought about by bacteria that differ in their endotoxicity. To achieve this, we have performed proteomics and phosphoproteomics on murine DC cultures. Symbiont and pathobiont bacteria were used to direct dendritic cells into a semi-mature and fully-mature state, respectively. The comparison of semi-mature and fully-mature DCs revealed differential expression in 103 proteins and differential phosphorylation in 118 phosphosites, including major regulatory factors of central immune processes. Our analyses predict that these differences are mediated by upstream elements such as SOCS1, IRF3, ABCA1, TLR4, and PTGER4. Our analyses indicate that the symbiont bacterial strain affects DC proteome in a distinct way, by downregulating inflammatory proteins and activating anti-inflammatory upstream regulators. Biological significance In this study we have investigated the responses of immune cells to distinct bacterial stimuli. We have used the symbiont bacterial strain B. vulgatus and the pathobiont E. coli strain to stimulate cultured primary dendritic cells and performed a shotgun proteome analysis to investigate the protein expression and phosphorylation level differences on a genome level. We have observed expression and phosphorylation level differences in key immune regulators, transcription factors and signal transducers. Moreover, our subsequent bioinformatics analysis indicated regulation at several signaling pathways such as PPAR signaling, LXR/RXR activation and glucocorticoid signaling pathways, which are not studied in detail in an inflammation and DC maturation context. Our phosphoproteome analysis showed differential phosphorylation in 118 phosphosites including those belonging to epigenetic regulators, transcription factors and major cell cycle regulators. We anticipate that our study will facilitate further investigation of immune cell proteomes under different inflammatory and non-inflammatory conditions. Copyright © 2017. Published by Elsevier B.V.

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.

PubMed

Edwards, Scott V; Cloutier, Alison; Baker, Allan J

2017-11-01

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis. © The Author(s) 2017. Published by Oxford University Press on behalf of the Systematic Biologists.

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics

PubMed Central

Cloutier, Alison; Baker, Allan J.

2017-01-01

Abstract Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600–∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis. PMID:28637293

The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons

PubMed Central

Vázquez, Martín; Ben-Dov, Claudia; Lorenzi, Hernan; Moore, Troy; Schijman, Alejandro; Levin, Mariano J.

2000-01-01

The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2β genes. It is present in about 1,500–3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensus nucleotide sequence and structure for the element, consisting of three regions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3′ end of several mRNAs, always transcribed from the sense strand, contributing the polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. VIPER's 5′ end is formed by the first 182 bp of SIRE, whereas its 3′ end is formed by the last 220 bp of the element. Both SIRE moieties are connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite. PMID:10688909

Molecular Population Genetics of the Alcohol Dehydrogenase Gene Region of DROSOPHILA MELANOGASTER

PubMed Central

Aquadro, Charles F.; Desse, Susan F.; Bland, Molly M.; Langley, Charles H.; Laurie-Ahlberg, Cathy C.

1986-01-01

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21–200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L) t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations. PMID:3026893

A Differential Chemical Element Analysis of the Metal-poor Globular Cluster NGC 6397

NASA Astrophysics Data System (ADS)

Koch, Andreas; McWilliam, Andrew

2011-08-01

We present chemical abundances in three red giants and two turnoff (TO) stars in the metal-poor Galactic globular cluster (GC) NGC 6397 based on spectroscopy obtained with the Magellan Inamori Kyocera Echelle high-resolution spectrograph on the Magellan 6.5 m Clay telescope. Our results are based on a line-by-line differential abundance analysis relative to the well-studied red giant Arcturus and the Galactic halo field star Hip 66815. At a mean of -2.10 ± 0.02 (stat.) ±0.07 (sys.), the differential iron abundance is in good agreement with other studies in the literature based on gf-values. As in previous differential works we find a distinct departure from ionization equilibrium in that the abundances of Fe I and Fe II differ by ~0.1 dex, with opposite signs for the red giant branch (RGB) and TO stars. The α-element ratios are enhanced to 0.4 (RGB) and 0.3 dex (TO), respectively, and we also confirm strong variations in the O, Na, and Al/Fe abundance ratios. Accordingly, the light-element abundance patterns in one of the red giants can be attributed to pollution by an early generation of massive Type II supernovae. TO and RGB abundances are not significantly different, with the possible exception of Mg and Ti, which are, however, amplified by the patterns in one TO star additionally belonging to this early generation of GC stars. We discuss interrelations of these light elements as a function of the GC metallicity. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

The transcriptional landscape of hematopoietic stem cell ontogeny

PubMed Central

McKinney-Freeman, Shannon; Cahan, Patrick; Li, Hu; Lacadie, Scott A.; Huang, Hsuan-Ting; Curran, Matthew; Loewer, Sabine; Naveiras, Olaia; Kathrein, Katie L.; Konantz, Martina; Langdon, Erin M.; Lengerke, Claudia; Zon, Leonard I.; Collins, James J.; Daley, George Q.

2012-01-01

Transcriptome analysis of adult hematopoietic stem cells (HSC) and their progeny has revealed mechanisms of blood differentiation and leukemogenesis, but a similar analysis of HSC development is lacking. Here, we acquired the transcriptomes of developing HSC purified from >2500 murine embryos and adult mice. We found that embryonic hematopoietic elements clustered into three distinct transcriptional states characteristic of the definitive yolk sac, HSCs undergoing specification, and definitive HSCs. We applied a network biology-based analysis to reconstruct the gene regulatory networks of sequential stages of HSC development and functionally validated candidate transcriptional regulators of HSC ontogeny by morpholino-mediated knock-down in zebrafish embryos. Moreover, we found that HSCs from in vitro differentiated embryonic stem cells closely resemble definitive HSC, yet lack a Notch-signaling signature, likely accounting for their defective lymphopoiesis. Our analysis and web resource (http://hsc.hms.harvard.edu) will enhance efforts to identify regulators of HSC ontogeny and facilitate the engineering of hematopoietic specification. PMID:23122293

Salivary gland carcinosarcoma: oligonucleotide array CGH reveals similar genomic profiles in epithelial and mesenchymal components.

PubMed

Vékony, Hedy; Leemans, C René; Ylstra, Bauke; Meijer, Gerrit A; van der Waal, Isaäc; Bloemena, Elisabeth

2009-03-01

In this study, we present a case of parotid gland de novo carcinosarcoma. Salivary gland carcinosarcoma (or true malignant mixed tumor) is a rare biphasic neoplasm, composed of both malignant epithelial and malignant mesenchymal components. It is yet unclear whether these two phenotypes occur by collision of two independent tumors or if they are of clonal origin. To analyze the clonality of the different morphologic tumor components, oligonucleotide microarray-based comparative genomic hybridization (oaCGH) was performed on the carcinoma and the sarcoma entity separately. This technique enables a high-resolution, genome-wide overview of the chromosomal alterations in the distinct tumor elements. Analysis of both fractions showed a high number of DNA copy number changes. Losses were more prevalent than gains (82 and 49, respectively). The carcinomatous element displayed more chromosomal aberrations than the sarcomatous component. Specific amplifications of MUC20 (in mesenchymal element) and BMI-1 (in both elements) loci were observed. Overall homology between the two genomic profiles was 75%. DNA copy number profiles of the epithelial and mesenchymal components in this salivary gland carcinosarcoma displayed extensive overlap, indicating a monoclonal origin. Since losses are shared to a larger extent than gains, they seem to be more essential for initial oncogenic events. Furthermore, specific amplifications of a mucin and a Polycomb group gene imply these proteins in the tumorigenesis of carcinosarcomas.

SXT/R391 integrative and conjugative elements in Proteus species reveal abundant genetic diversity and multidrug resistance

PubMed Central

Li, Xinyue; Du, Yu; Du, Pengcheng; Dai, Hang; Fang, Yujie; Li, Zhenpeng; Lv, Na; Zhu, Baoli; Kan, Biao; Wang, Duochun

2016-01-01

SXT/R391 integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are found in most members of Enterobacteriaceae. Here, we determined fifteen SXT/R391 ICEs carried by Proteus isolates from food (4.2%) and diarrhoea patients (17.3%). BLASTn searches against GenBank showed that the fifteen SXT/R391 ICEs were closely related to that from different Enterobacteriaceae species, including Proteus mirabilis. Using core gene phylogenetic analysis, the fifteen SXT/R391 ICEs were grouped into six distinct clusters, including a dominant cluster and three clusters that have not been previously reported in Proteus isolates. The SXT/R391 ICEs shared a common structure with a set of conserved genes, five hotspots and two variable regions, which contained more foreign genes, including drug-resistance genes. Notably, a class A β-lactamase gene was identified in nine SXT/R391 ICEs. Collectively, the ICE-carrying isolates carried resistance genes for 20 tested drugs. Six isolates were resistant to chloramphenicol, kanamycin, streptomycin, trimethoprim-sulfamethoxazole, sulfisoxazole and tetracycline, which are drug resistances commonly encoded by ICEs. Our results demonstrate abundant genetic diversity and multidrug resistance of the SXT/R391 ICEs carried by Proteus isolates, which may have significance for public health. It is therefore necessary to continuously monitor the antimicrobial resistance and related mobile elements among Proteus isolates. PMID:27892525

Six-Message Electromechanical Display System

NASA Technical Reports Server (NTRS)

Howard, Richard T.

2007-01-01

A proposed electromechanical display system would be capable of presenting as many as six distinct messages. In the proposed system, each display element would include a cylinder having a regular hexagonal cross section.

Natural variation of piRNA expression affects immunity to transposable elements.

PubMed

Ryazansky, Sergei; Radion, Elizaveta; Mironova, Anastasia; Akulenko, Natalia; Abramov, Yuri; Morgunova, Valeriya; Kordyukova, Maria Y; Olovnikov, Ivan; Kalmykova, Alla

2017-04-01

In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon HeT-A, which we have observed in one particular transposon-resistant R strain.

AERODYNAMIC AND BLADING DESIGN OF MULTISTAGE AXIAL FLOW COMPRESSORS

NASA Technical Reports Server (NTRS)

Crouse, J. E.

1994-01-01

The axial-flow compressor is used for aircraft engines because it has distinct configuration and performance advantages over other compressor types. However, good potential performance is not easily obtained. The designer must be able to model the actual flows well enough to adequately predict aerodynamic performance. This computer program has been developed for computing the aerodynamic design of a multistage axial-flow compressor and, if desired, the associated blading geometry input for internal flow analysis. The aerodynamic solution gives velocity diagrams on selected streamlines of revolution at the blade row edges. The program yields aerodynamic and blading design results that can be directly used by flow and mechanical analysis codes. Two such codes are TSONIC, a blade-to-blade channel flow analysis code (COSMIC program LEW-10977), and MERIDL, a more detailed hub-to-shroud flow analysis code (COSMIC program LEW-12966). The aerodynamic and blading design program can reduce the time and effort required to obtain acceptable multistage axial-flow compressor configurations by generating good initial solutions and by being compatible with available analysis codes. The aerodynamic solution assumes steady, axisymmetric flow so that the problem is reduced to solving the two-dimensional flow field in the meridional plane. The streamline curvature method is used for the iterative aerodynamic solution at stations outside of the blade rows. If a blade design is desired, the blade elements are defined and stacked within the aerodynamic solution iteration. The blade element inlet and outlet angles are established by empirical incidence and deviation angles to the relative flow angles of the velocity diagrams. The blade element centerline is composed of two segments tangentially joined at a transition point. The local blade angle variation of each element can be specified as a fourth-degree polynomial function of path distance. Blade element thickness can also be specified with fourth-degree polynomial functions of path distance from the maximum thickness point. Input to the aerodynamic and blading design program includes the annulus profile, the overall compressor mass flow, the pressure ratio, and the rotative speed. A number of input parameters are also used to specify and control the blade row aerodynamics and geometry. The output from the aerodynamic solution has an overall blade row and compressor performance summary followed by blade element parameters for the individual blade rows. If desired, the blade coordinates in the streamwise direction for internal flow analysis codes and the coordinates on plane sections through blades for fabrication drawings may be stored and printed. The aerodynamic and blading design program for multistage axial-flow compressors is written in FORTRAN IV for batch execution and has been implemented on an IBM 360 series computer with a central memory requirement of approximately 470K of 8 bit bytes. This program was developed in 1981.

Nano- and micro-electromechanical switch dynamics

NASA Astrophysics Data System (ADS)

Pulskamp, Jeffrey S.; Proie, Robert M.; Polcawich, Ronald G.

2013-01-01

This paper reports theoretical analysis and experimental results on the dynamics of piezoelectric MEMS mechanical logic relays. The multiple degree of freedom analytical model, based on modal decomposition, utilizes modal parameters obtained from finite element analysis and an analytical model of piezoelectric actuation. The model accounts for exact device geometry, damping, drive waveform variables, and high electric field piezoelectric nonlinearity. The piezoelectrically excited modal force is calculated directly and provides insight into design optimization for switching speed. The model accurately predicts the propagation delay dependence on actuation voltage of mechanically distinct relay designs. The model explains the observed discrepancies in switching speed of these devices relative to single degree of freedom switching speed models and suggests the strong potential for improved switching speed performance in relays designed for mechanical logic and RF circuits through the exploitation of higher order vibrational modes.

Cell type-specific termination of transcription by transposable element sequences.

PubMed

Conley, Andrew B; Jordan, I King

2012-09-30

Transposable elements (TEs) encode sequences necessary for their own transposition, including signals required for the termination of transcription. TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. Rarefaction curve analysis suggests that there may be twice as many TE-derived termination sites (TE-TTS) genome-wide among all human cell types. The local chromatin environment for these TE-TTS is similar to that seen for 3' UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. However, those TE-TTS located within the introns of human genes were found to be far more cell type-specific than the canonical TTS. TE-TTS were much more likely to be found in the sense orientation than other intragenic TE sequences of the same TE family and TE-TTS in the sense orientation terminate transcription more efficiently than those found in the antisense orientation. Alu sequences were found to provide a large number of relatively weak TTS, whereas LTR elements provided a smaller number of much stronger TTS. TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. Thus, TE sequences provide a powerful mechanism for the diversification of transcriptional profiles between cell types and among evolutionary lineages, since most TE-TTS are evolutionarily young. The extent of transcription termination by TEs seen here, along with the preference for sense-oriented TE insertions to provide TTS, is consistent with the observed antisense orientation bias of human TEs.

Dissolved Rare Earth Elements in the US GEOTRACES North Atlantic Section

NASA Astrophysics Data System (ADS)

Shiller, A. M.

2016-12-01

The rare earth elements (REEs) are a unique chemical set wherein there are systematic changes in geochemical behavior across the series. Furthermore, while most REEs are in the +III oxidation state, Ce and Eu can be in other oxidation states leading to distinct characteristics of those elements. Thus, the geochemical properties of the REEs make them particularly useful tools for inquiring into various geochemical processes. As part of the US GEOTRACES effort, we determined dissolved REEs and Y at 32 stations across the North Atlantic during US cruises GT10 and GT11 along a meridional transect from Lisbon to the Cape Verde Islands and a zonal transect from Cape Cod to the Mauritanian coast. While profiles are similar to previous reports, the high spatial resolution of the section allows for better elucidation of processes. Light rare earths (LREEs) show removal in the upper water column with a minimum at the chlorophyll maximum. LREE concentrations then increase into the oxygen minimum followed by a slight decrease and fairly constant concentrations in the mid-water column followed by an increase into the deep and bottom waters. Heavy rare earths (HREEs) show a more monotonic increase with depth. We also take advantage of a previously published water mass analysis for the section to estimate that most of the deep water changes can be explained by conservative mixing of waters with different pre-formed REE concentrations. Nonetheless, the pattern of LREE shallow water removal followed by regeneration, possible re-scavenging, and then deep water input is still preserved. Other features of note include an increase in LREEs in the strong oxygen minimum zone off Mauritania, consistent with an association of REE cycling with the redox cycles of Fe and Mn. Also along the eastern margin, but below the oxygen minimum, a small but distinct increase in the cerium and europium anomalies is observed, consistent with terrigenous input. In hydrothermally influenced waters along the mid-Atlantic Ridge, there are increases in Ce/Ce*, Eu/Eu*, and Y/Ho but a decrease in Nd/Yb and in REE concentrations. Surface water distributions are more consistent with elements influenced by margin inputs than with atmospheric input.

Trends in Gypsiferous Aerosol Downwind of White Sands, New Mexico

NASA Astrophysics Data System (ADS)

White, W. H.; Trzepla, K.; Yatkin, S.; Gill, T. E.; Jin, L.

2013-12-01

White Sands is a known 'hotspot' of dust emissions in southwestern North America where an active gypsum dunefield abuts erodible playa sediments. Aerosols entrained from White Sands are sometimes visible on satellite images as distinct, light-colored plumes crossing the Sacramento Mountains to the northeast. The U.S. Forest Service operates an aerosol sampler at White Mountain in the lee of the Sacramento range as part of the IMPROVE network (Interagency Monitoring of PROtected Visual Environments). In recent years a spring pulse of sulfate aerosol has appeared at White Mountain, eclipsing the regional summer peak attributed to atmospheric reactions of sulfur dioxide emissions. A significant fraction of this spring sulfate is contributed by gypsum and other salts from White Sands, with clearly increased concentrations of calcium, strontium, and chloride. The increase in these species coincides with a drought following a period of above-average precipitation. White Sands and White Mountain thus provide an unusually well-defined natural laboratory: a climatically sensitive dust source that is both well characterized and chemically distinct from its surroundings, with a signature that remains identifiably distinct at a long-term observatory ~100 km downwind. This paper examines the routine PM2.5 (fine-particle, Dp < 2.5 um) composition data available from White Mountain and other regional IMPROVE sites (e.g. Bosque del Apache), supplemented by some elemental analysis of collocated PM10 samples. The ambient data are compared with chemical analyses of surface samples from White Sands, bulk dry dustfall and soil surface composition at White Mountain, satellite observations of dust plumes, and available meteorological records. Together, the observations document significant, episodic aeolian transport of gypsum and other salts across the Sacramento Mountains. Figure 1. Left: Monthly average concentrations of every-third-day 24h samples. Top right: MODIS image, 2/28/2012, http://earthobservatory.nasa.gov/NaturalHazards/view.php?id=77294). Bottom right: Correlation (r) matrix for 2011 daily elemental data from White Mountain (n = 105).

The Means: Cytometry and Mass Spectrometry Converge in a Single Cell Deep Profiling Platform

PubMed Central

Weis-Garcia, Frances; Bandura, Dmitry; Baranov, Vladimir; Ornatsky, Olga; Tanner, Scott

2013-01-01

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is a distinct flavor of mass spectrometry that has had little association with cell biology: it remains the state of the art for the determination of the atomic composition of materials. Unrelatedly, flow cytometry is the superior method for distinguishing the heterogeneity of cells through the determination of antigen signatures using tagged antibodies. Simply replacing fluorophore tags with stable isotopes of the heavy metals, and measuring these cell-by-cell with ICP-MS, dramatically increases the number of probes that can be simultaneously measured in cytometry and enables a transformative increase in the resolution of rare cell populations in complex biological samples. While this can be thought of as a novel incarnation of single-cell targeted proteomics, the metal-labeling reagents, ICP-MS of single cells, and accompanying informatics comprise a new field of technology termed Mass Cytometry. While the conception of mass cytometry is simple the embodiment to address the issues of multi-parameter flow cytometry has been far more challenging. There are many elements, and many more stable isotopes of those elements, that might be used as distinct reporter tags. Still, there are many approaches to conjugating metals to antibodies (or other affinity reagents) and work in this area along with developing new applications is ongoing. The mass resolution and linear (quantitative) dynamic range of ICP-MS allows those many stable isotopes to be measured simultaneously and without the spectral overlap issues that limit fluorescence assay. However, the adaptation of ICP-MS to allow high-speed simultaneous measurement with single cell distinction at high throughput required innovation of the cell introduction system, ion optics (sampling, transmission and beam-shaping), mass analysis, and signal handling and processing. An overview of “the nuts and bolts” of Mass Cytometry is presented.

On volatile element trends in gas-rich meteorites

NASA Technical Reports Server (NTRS)

Bart, G.; Lipschutz, M. E.

1979-01-01

Ten volatile elements (and non-volatile Co) in co-existing light and dark portions of 5 gas-rich chondrites were studied. Patterns of distinct but non-uniform enrichment by dark admixing material are revealed. The dark admixing material is enriched in Cs; Bi and Tl covary in it. It is compositionally unique from known types of primitive materials and is apparently not derived by secondary processes from such materials.

Requirement for ErbB2/ErbB signaling in developing cartilage and bone.

PubMed

Fisher, Melanie C; Clinton, Gail M; Maihle, Nita J; Dealy, Caroline N

2007-08-01

During endochondral ossification, the skeletal elements of vertebrate limbs form and elongate via coordinated control of chondrocyte and osteoblast differentiation and proliferation. The role of signaling by the ErbB family of receptor tyrosine kinases, which consists of ErbB1 (epidermal growth factor receptor or EGFR), ErbB2, ErbB3 and ErbB4, has been little studied during cartilage and bone development. Signaling by the ErbB network generates a diverse array of cellular responses via formation of ErbB dimers activated by distinct ligands that produce distinct signal outputs. Herstatin is a soluble ErbB2 receptor that acts in a dominant negative fashion to inhibit ErbB signaling by binding to endogenous ErbB receptors, preventing functional dimer formation. Here, we examine the effects of Herstatin on limb skeletal element development in transgenic mice, achieved via Prx1 promoter-driven expression in limb cartilage and bone. The limb skeletal elements of Prx1-Herstatin embryos are shortened, and chondrocyte maturation and osteoblast differentiation are delayed. In addition, proliferation by chondrocytes and periosteal cells of Prx1-Herstatin limb skeletal elements is markedly reduced. Our study identifies requirements for ErbB signaling in the maintenance of chondrocyte and osteoblast proliferation involved in the timely progression of chondrocyte maturation and periosteal osteoblast differentiation.

Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System.

PubMed

Pecora, Nicole D; Li, Ning; Allard, Marc; Li, Cong; Albano, Esperanza; Delaney, Mary; Dubois, Andrea; Onderdonk, Andrew B; Bry, Lynn

2015-07-28

Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital resources to prevent spread and improve patient outcomes. Whole-genome sequencing allows refined tracking of both chromosomal traits and associated mobile genetic elements that harbor resistance genes. To enhance surveillance of CREs, clinical isolates with phenotypic resistance to carbapenem antibiotics underwent whole-genome sequencing. Analysis of 41 isolates of Klebsiella pneumoniae and Enterobacter cloacae, collected over a 3-year period, identified K. pneumoniae carbapenemase (KPC) genes encoding KPC-2, -3, and -4 and OXA-48 carbapenemases. All occurred within transposons, including multiple Tn4401 transposon isoforms, embedded within more than 10 distinct plasmids representing incompatibility (Inc) groups IncR, -N, -A/C, -H, and -X. Using short-read sequencing, draft maps were generated of new KPC-carrying vectors, several of which were derivatives of the IncN plasmid pBK31551. Two strains also had Tn4401 chromosomal insertions. Integrated analyses of plasmid profiles and chromosomal single-nucleotide polymorphism (SNP) profiles refined the strain patterns and provided a baseline hospital mobilome to facilitate analysis of new isolates. When incorporated with patient epidemiological data, the findings identified limited outbreaks against a broader 3-year period of sporadic external entry of many different strains and resistance vectors into the hospital. These findings highlight the utility of genomic analyses in internal and external surveillance efforts to stem the transmission of drug-resistant strains within and across health care institutions. We demonstrate how detection of resistance genes within mobile elements and resistance-carrying strains furthers active surveillance efforts for drug resistance. Whole-genome sequencing is increasingly available in hospital laboratories and provides a powerful and nuanced means to define the local landscape of drug resistance. In this study, isolates of Klebsiella pneumoniae and Enterobacter cloacae with resistance to carbapenem antibiotics were sequenced. Multiple carbapenemase genes were identified that resided in distinct transposons and plasmids. This mobilome, or population of mobile elements capable of mobilizing drug resistance, further highlighted the degree of strain heterogeneity while providing a detailed timeline of carbapenemase entry into the hospital over a 3-year period. These surveillance efforts support effective targeting of infection control resources and the development of institution-specific repositories of resistance genes and the mobile elements that carry them. Copyright © 2015 Pecora et al.

Psychophysical evidence for the number sense.

PubMed

Burr, David C; Anobile, Giovanni; Arrighi, Roberto

2017-02-19

It is now clear that most animals, including humans, possess an ability to rapidly estimate number. Some have questioned whether this ability arises from dedicated numerosity mechanisms, or is derived indirectly from judgements of density or other attributes. We describe a series of psychophysical experiments, largely using adaptation techniques, which demonstrate clearly the existence of a number sense in humans. The number sense is truly general, extending over space, time and sensory modality, and is closely linked with action. We further show that when multiple cues are present, numerosity emerges as the natural dimension for discrimination. However, when element density increases past a certain level, the elements become too crowded to parse, and the scene is perceived as a texture rather than array of elements. The two different regimes are psychophysically discriminable in that they follow distinct psychophysical laws, and show different dependencies on eccentricity, luminance levels and effects of perceptual grouping. The distinction is important, as the ability to discriminate numerosity, but not texture, correlates with formal maths skills.This article is part of the discussion meeting issue 'The origins of numerical abilities'. © 2017 The Authors.

Psychophysical evidence for the number sense

PubMed Central

2018-01-01

It is now clear that most animals, including humans, possess an ability to rapidly estimate number. Some have questioned whether this ability arises from dedicated numerosity mechanisms, or is derived indirectly from judgements of density or other attributes. We describe a series of psychophysical experiments, largely using adaptation techniques, which demonstrate clearly the existence of a number sense in humans. The number sense is truly general, extending over space, time and sensory modality, and is closely linked with action. We further show that when multiple cues are present, numerosity emerges as the natural dimension for discrimination. However, when element density increases past a certain level, the elements become too crowded to parse, and the scene is perceived as a texture rather than array of elements. The two different regimes are psychophysically discriminable in that they follow distinct psychophysical laws, and show different dependencies on eccentricity, luminance levels and effects of perceptual grouping. The distinction is important, as the ability to discriminate numerosity, but not texture, correlates with formal maths skills. This article is part of the discussion meeting issue ‘The origins of numerical abilities’. PMID:29292350

Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions

PubMed Central

Benner, Christopher; Hutt, Kasey R.; Stunnenberg, Rieka; Garcia-Bassets, Ivan

2013-01-01

Genome-wide maps of DNase I hypersensitive sites (DHSs) reveal that most human promoters contain perpetually active cis-regulatory elements between −150 bp and +50 bp (−150/+50 bp) relative to the transcription start site (TSS). Transcription factors (TFs) recruit cofactors (chromatin remodelers, histone/protein-modifying enzymes, and scaffold proteins) to these elements in order to organize the local chromatin structure and coordinate the balance of post-translational modifications nearby, contributing to the overall regulation of transcription. However, the rules of TF-mediated cofactor recruitment to the −150/+50 bp promoter regions remain poorly understood. Here, we provide evidence for a general model in which a series of cis-regulatory elements (here termed ‘cardinal’ motifs) prefer acting individually, rather than in fixed combinations, within the −150/+50 bp regions to recruit TFs that dictate cofactor signatures distinctive of specific promoter subsets. Subsequently, human promoters can be subclassified based on the presence of cardinal elements and their associated cofactor signatures. In this study, furthermore, we have focused on promoters containing the nuclear respiratory factor 1 (NRF1) motif as the cardinal cis-regulatory element and have identified the pervasive association of NRF1 with the cofactor lysine-specific demethylase 1 (LSD1/KDM1A). This signature might be distinctive of promoters regulating nuclear-encoded mitochondrial and other particular genes in at least some cells. Together, we propose that decoding a signature-based, expanded model of control at proximal promoter regions should lead to a better understanding of coordinated regulation of gene transcription. PMID:24244184

Incorporation of Trace Elements in Ancient and Modern Human Bone: An X-Ray Absorption Spectroscopy Study

NASA Astrophysics Data System (ADS)

Pingitore, N. E.; Cruz-Jimenez, G.; Price, T. D.

2001-12-01

X-ray absorption spectroscopy (XAS) affords the opportunity to probe the atomic environment of trace elements in human bone. We are using XAS to investigate the mode(s) of incorporation of Sr, Zn, Pb, and Ba in both modern and ancient (and thus possibly altered) human and animal bone. Because burial and diagenesis may add trace elements to bone, we performed XAS analysis on samples of pristine contemporary and ancient, buried human and animal bone. We assume that deposition of these elements during burial occurs by processes distinct from those in vivo, and this will be reflected in their atomic environments. Archaeologists measure strontium in human and animal bone as a guide to diet. Carnivores show lower Sr/Ca ratios than their herbivore prey due to discrimination against Sr relative to Ca up the food chain. In an initial sample suite no difference was observed between modern and buried bone. Analysis of additional buried samples, using a more sensitive detector, revealed significant differences in the distance to the second and third neighbors of the Sr in some of the buried samples. Distances to the first neighbor, oxygen, were similar in all samples. Zinc is also used in paleo-diet studies. Initial x-ray absorption spectroscopy of a limited suite of bones did not reveal any differences between modern and buried samples. This may reflect the limited number of samples examined or the low levels of Zn in typical aqueous solutions in soils. Signals from barium and lead were too low to record useful XAS spectra. Additional samples will be studied for Zn, Ba, and Pb. We conducted our XAS experiments on beam lines 4-1 and 4-3 at the Stanford Synchrotron Radiation Laboratory. Data were collected in the fluorescence mode, using a Lytle detector and appropriate filter, and a solid state, 13-element Ge-detector.

Dehomogenized Elastic Properties of Heterogeneous Layered Materials in AFM Indentation Experiments.

PubMed

Lee, Jia-Jye; Rao, Satish; Kaushik, Gaurav; Azeloglu, Evren U; Costa, Kevin D

2018-06-05

Atomic force microscopy (AFM) is used to study mechanical properties of biological materials at submicron length scales. However, such samples are often structurally heterogeneous even at the local level, with different regions having distinct mechanical properties. Physical or chemical disruption can isolate individual structural elements but may alter the properties being measured. Therefore, to determine the micromechanical properties of intact heterogeneous multilayered samples indented by AFM, we propose the Hybrid Eshelby Decomposition (HED) analysis, which combines a modified homogenization theory and finite element modeling to extract layer-specific elastic moduli of composite structures from single indentations, utilizing knowledge of the component distribution to achieve solution uniqueness. Using finite element model-simulated indentation of layered samples with micron-scale thickness dimensions, biologically relevant elastic properties for incompressible soft tissues, and layer-specific heterogeneity of an order of magnitude or less, HED analysis recovered the prescribed modulus values typically within 10% error. Experimental validation using bilayer spin-coated polydimethylsiloxane samples also yielded self-consistent layer-specific modulus values whether arranged as stiff layer on soft substrate or soft layer on stiff substrate. We further examined a biophysical application by characterizing layer-specific microelastic properties of full-thickness mouse aortic wall tissue, demonstrating that the HED-extracted modulus of the tunica media was more than fivefold stiffer than the intima and not significantly different from direct indentation of exposed media tissue. Our results show that the elastic properties of surface and subsurface layers of microscale synthetic and biological samples can be simultaneously extracted from the composite material response to AFM indentation. HED analysis offers a robust approach to studying regional micromechanics of heterogeneous multilayered samples without destructively separating individual components before testing. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Porcine calbindin-D9k gene: expression in endometrium, myometrium, and placenta in the absence of a functional estrogen response element in intron A.

PubMed

Krisinger, J; Jeung, E B; Simmen, R C; Leung, P C

1995-01-01

The expression of Calbindin-D9k (CaBP-9k) in the pig uterus and placenta was measured by Northern blot analysis and reverse transcription polymerase chain reaction (PCR), respectively. Progesterone (P4) administration to ovariectomized pigs decreased CaBP-9k mRNA levels. Expression of endometrial CaBP-9k mRNA was high on pregnancy Days 10-12 and below the detection limit on Days 15 and 18. On Day 60, expression could be detected at low levels. In myometrium and placenta, CaBP-9k mRNA expression was not detectable by Northern analysis using total RNA. Reverse-transcribed RNA from both tissues demonstrated the presence of CaBP-9k transcripts by means of PCR. The partial CaBP-9k gene was amplified by PCR and cloned to determine the sequence of intron A. In contrast to the rat CaBP-9k gene, the pig gene does not contain a functional estrogen response element (ERE) within this region. A similar ERE-like sequence located at the identical location was examined by gel retardation analysis and failed to bind the estradiol receptor. A similar disruption of this ERE-like sequence has been described in the human CaBP-9k gene, which is not expressed at any level in placenta, myometrium, or endometrium. It is concluded that the pig CaBP-9k gene is regulated in these reproductive tissues in a manner distinct from that in rat and human tissues. The regulation is probably due to a regulatory region outside of intron A, which in the rat gene contains the key cis element for uterine expression of the CaBP-9k gene.

A phenylalanine ammonia-lyase ortholog (PkPAL1) from Picrorhiza kurrooa Royle ex. Benth: molecular cloning, promoter analysis and response to biotic and abiotic elicitors.

PubMed

Bhat, Wajid Waheed; Razdan, Sumeer; Rana, Satiander; Dhar, Niha; Wani, Tariq Ahmad; Qazi, Parvaiz; Vishwakarma, Ram; Lattoo, Surrinder K

2014-09-01

Picrorhiza kurrooa Royle ex Benth. is a highly reputed medicinal herb utilised in the preparation of a number of herbal drug formulations, principally due to the presence of novel monoterpene iridoid glycosides kenned as picrosides. Phenylalanine ammonia-lyase catalyses an important rate-limiting step in phenylpropanoid pathway and supplies precursors like cinnamic acid, vanillic acid, ferulic acid, etc., to a variety of secondary metabolites including picrosides. The imperilled status of P. kurrooa coupled with lack of information regarding biogenesis of picrosides necessitates deciphering the biosynthetic pathway for picrosides. In the present study, a PAL gene, designated PkPAL1 was isolated from P. kurrooa. The cDNA is 2312 bp in length, consisting of an ORF of 2142 bp encoding for a 713 amino acid protein having a predicted molecular weight of 77.66 kDa and an isoelectric point of pH 6.82. qRT-PCR analysis of various tissues of P. kurrooa showed that PkPAL1 transcript levels were highest in the leaves, consistent with picroside accumulation pattern. Using Genome walking, a 718 bp promoter region was also isolated resulting in identification of distinct cis-regulatory elements including TGA-element, TGACG-motif, CGTCA-motif, etc. qRT-PCR indicated up-regulation of PkPAL1 by methyl jasmonate, salicylic acid, 2,4-dicholorophenoxy acetic acid and UV-B elicitations that corroborated positively with the identified cis-elements within the promoter region. Moreover, altitude was found to have a positive effect on the PkPAL1 transcript levels, driving the expression of PkPAL1 abundantly. Based on docking analysis, we identified eight residues as potentially essential for substrate binding in PkPAL1. Copyright © 2014 Elsevier B.V. All rights reserved.

Interface bonding of shotcrete reinforced brick masonry assemblages. Volume 2: Appendices

NASA Astrophysics Data System (ADS)

Robinson, D. W.; Kahn, L. F.

1982-09-01

The first of four appendices contains interviews with local masonry experts. It is reported that when stucco is applied to masonry walls, an increased resistance to lateral and implane forces results. The dangers of a solfate attack on brick masonry are examined, and it is pointed out that exposure to sulfate attack for 50 to 100 years can destroy the physical strength of a cement product. Distinctions are drawn between large core, small core, and double row core brick, and it is noted that the predominate brick used is the large core. The other appendices contain design, construction, and material properties for 46 specimens, a generalized finite element analysis, and plots for four specimens.

Multi-Mode Excitation and Data Reduction for Fatigue Crack Characterization in Conducting Plates

NASA Technical Reports Server (NTRS)

Wincheski, B.; Namkung, M.; Fulton, J. P.; Clendenin, C. G.

1992-01-01

Advances in the technique of fatigue crack characterization by resonant modal analysis have been achieved through a new excitation mechanism and data reduction of multiple resonance modes. A non-contacting electromagnetic device is used to apply a time varying Lorentz force to thin conducting sheets. The frequency and direction of the Lorentz force are such that resonance modes are generated in the test sample. By comparing the change in frequency between distinct resonant modes of a sample, detecting and sizing of fatigue cracks are achieved and frequency shifts caused by boundary condition changes can be discriminated against. Finite element modeling has been performed to verify experimental results.

Beyond self-esteem: influence of multiple motives on identity construction.

PubMed

Vignoles, Vivian L; Regalia, Camillo; Manzi, Claudia; Golledge, Jen; Scabini, Eugenia

2006-02-01

Diverse theories suggest that people are motivated to maintain or enhance feelings of self-esteem, continuity, distinctiveness, belonging, efficacy, and meaning in their identities. Four studies tested the influence of these motives on identity construction, by using a multilevel regression design. Participants perceived as more central those identity elements that provided a greater sense of self-esteem, continuity, distinctiveness, and meaning; this was found for individual, relational, and group levels of identity, among various populations, and by using a prospective design. Motives for belonging and efficacy influenced identity definition indirectly through their direct influences on identity enactment and through their contributions to self-esteem. Participants were happiest about those identity elements that best satisfied motives for self-esteem and efficacy. These findings point to the need for an integrated theory of identity motivation. Copyright 2006 APA, all rights reserved.

A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:-

PubMed Central

Mastrorilli, Eleonora; Pietrucci, Daniele; Barco, Lisa; Ammendola, Serena; Petrin, Sara; Longo, Alessandra; Mantovani, Claudio; Battistoni, Andrea; Ricci, Antonia; Desideri, Alessandro; Losasso, Carmen

2018-01-01

Over the past decades, Salmonella 4,[5],12:i:- has rapidly emerged and it is isolated with high frequency in the swine food chain. Although many studies have documented the epidemiological success of this serovar, few investigations have tried to explain this phenomenon from a genetic perspective. Here a comparative whole-genome analysis of 50 epidemiologically unrelated S. 4,[5],12:i:-, isolated in Italy from 2010 to 2016 was performed, characterizing them in terms of genetic elements potentially conferring resistance, tolerance and persistence characteristics. Phylogenetic analyses indicated interesting distinctions among the investigated isolates. The most striking genetic trait characterizing the analyzed isolates is the widespread presence of heavy metals tolerance gene cassettes: most of the strains possess genes expected to confer resistance to copper and silver, whereas about half of the isolates also contain the mercury tolerance gene merA. A functional assay showed that these genes might be useful for preventing the toxic effects of metals, thus supporting the hypothesis that they can contribute to the success of S. 4,[5],12:i:- in farming environments. In addition, the analysis of the distribution of type II toxin-antitoxin families indicated that these elements are abundant in this serovar, suggesting that this is another factor that might favor its successful spread. PMID:29719530

X-Ray Emission from "Uranium" Stars

NASA Technical Reports Server (NTRS)

Schlegel, Eric; Mushotzky, Richard (Technical Monitor)

2005-01-01

The project aims to secure XMM observations of two targets with extremely low abundances of the majority of heavy elements (e.g., log[Fe/H] $\\sim$-4), but that show absorption lines of uranium. The presence of an r-process element such as uranium requires a binary star system in which the companion underwent a supernova explosion. A binary star system raises the distinct possibility of the existence of a compact object, most likely a neutron star, in the binary, assuming it survived the supernova blast. The presence of a compact object then suggests X-ray emission if sufficient matter accretes to the compact object. The observations were completed less than one year ago following a series of reobservations to correct for significant flaring that occurred during the original observations. The ROSAT all-sky survey was used to report on the initial assessment of X-ray emission from these objects; only upper limits were reported. These upper limits were used to justify the XMM observing time, but with the expectation that upper limits would merely be pushed lower. The data analysis hinges critically on the quality and degree of precision with which the background is handled. During the past year, I have spent some time learning the ins and outs of XMM data analysis. In the coming year, I can apply that learning to the analysis of the 'uranium' stars.

Composition and similarity of global anomodont-bearing tetrapod faunas

NASA Astrophysics Data System (ADS)

Fröbisch, Jörg

2009-08-01

Anomodont synapsids represent the dominant herbivores of Permian and Triassic terrestrial vertebrate ecosystems. Their taxonomic diversity and morphological disparity in combination with their cosmopolitan distribution makes them an ideal study object for macroevolutionary patterns across the most devastating extinction event in earth history. This study provides a thorough review of anomodont-bearing tetrapod faunas to form the basis for a faunal similarity analysis and future studies of anomodont diversity. The stratigraphic correlation and composition of all known anomodont assemblages is revisited, including a discussion of the validity of the globally distributed anomodont species. The similarity analysis of anomodont faunas is performed on the basis of presence-absence data of anomodont taxa, using explorative methods such as cluster analysis (UPGMA) and non-metric multidimensional scaling (NMDS). The recovered faunal groupings indicate a common biostratigraphic age and furthermore reflect biogeographic patterns. Even though endemism and faunal provinciality was a constant element in anomodont faunas of the Permian and Triassic, the available evidence indicates that the end-Permian extinction resulted in a distinct uniformity that was unique to Early Triassic anomodont faunas. This is in particular characterized by the global distribution and overwhelming abundance of the disaster taxon Lystrosaurus. In contrast, cosmopolitan anomodonts also existed in the Late Permian (e.g., Diictodon) and Middle Triassic (e.g., Shansiodon), but those taxa coexisted with endemic faunal elements rather than dominated the fauna as Lystrosaurus did.

Cultural meanings of nature: an analysis of contemporary motion pictures.

PubMed

Pollio, Howard R; Anderson, John; Levasseur, Priscilla; Thweatt, Michael

2003-03-01

To evaluate current cultural meanings of nature, the authors asked 65 undergraduate students to "list 3 movies in which nature was an important aspect of the film." They also were asked to specify the natural element that stood out to them and describe "how it related to the overall theme of the movie." Two independent groups of raters skilled in interpretive analysis developed thematic meanings from these responses. Following this, in a 2nd study, a different group of participants rated the 18 most frequently mentioned natural elements on thematic scales derived from the initial interpretive analysis. Participants in the 1st study mentioned 33 different movies at least twice and 5 themes that captured the meaning of nature in these films. Correlational results derived from the 2nd study indicated that rating scales reflecting these 5 themes formed 2 distinct groups; the first group described settings in which nature is experienced as adversarial and plays a significant role in dramatic action, and the second group defined settings in which nature is viewed either as a place of refuge or simply as a locale in which ongoing narrative action occurs. The general conclusion reached in both studies concerns the often noted but not always appreciated fact that movies--similar to everyday events and actions--always take place in specific settings and that neither life events nor dramatic narratives can be understood apart from specific settings.

Identity salience and the influence of differential activation of the social self-schema on advertising response.

PubMed

Forehand, Mark R; Deshpandé, Rohit; Reed, Americus

2002-12-01

The authors examined how identity primes and social distinctiveness influence identity salience (i.e., the activation of a social identity within an individual's social self-schema) and subsequent responses to targeted advertising. Across 2 studies, individuals who were exposed to an identity prime (an ad element that directs attention to the individual's social identity) and who were socially distinctive (minorities in the immediate social context) expressed systematically different evaluations of spokespersons and the advertisements that featured them. Specifically, Asian (Caucasian) participants responded most positively (negatively) to Asian spokespeople and Asian-targeted advertising when the participants were both primed and socially distinctive. No main effects of identity primes or social distinctiveness were found. The implications of these findings for identity theory, advertising practice, and intervention communications are discussed.

The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.

PubMed

Abd El Ghany, Moataz; Chander, Jagadish; Mutreja, Ankur; Rashid, Mamoon; Hill-Cawthorne, Grant A; Ali, Shahjahan; Naeem, Raeece; Thomson, Nicholas R; Dougan, Gordon; Pain, Arnab

2014-07-01

Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century. Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters. The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates.

Stress-induced injuries and trace element concentrations in vascular leaf plants from an urban environment (Palermo, Italy).

PubMed

Alaimo, Maria Grazia; Colombo, Paolo; Firetto, Anna; Trapani, Salvatore; Vizzì, Daniela; Melati, M Rita

2003-01-01

We examined leaf injuries and measured trace element concentrations in vascular plants from an urban ecosystem with distinct stress valences (the city of Palermo), and compared them with samples of the same species from sites where the stress potential is lower. Urban pollution influences macro-, micro- and toxic element concentrations in leaves. Therefore these leaves can be used as markers of the chemical and biological effects of atmospheric pollution. We studied the trace element content in the leaves of two species, oleander and oak, both fairly tolerant plants and good indicators and bio-monitors of pollution contaminants. Samples were collected at various sites in different periods.

An Apollo 15 Mare Basalt Fragment and Lunar Mare Provinces

NASA Technical Reports Server (NTRS)

Ryder, Graham; Burling, Trina Cox

1996-01-01

Lunar sample 15474,4 is a tiny fragment of olivine-augite vitrophyre that is a mare basalt. Although petroraphically distinct from all other Apollo 15 samples, it has been ignored since its first brief description. Our new petrographic and mineral chemical data show that the olivines and pyroxenes are distinct from those in other basalts. The basalt cooled and solidified extremely rapidly; some of the olivine might be cumulate or crystallized prior to extrusion. Bulk-chemical data show that the sample is probably similar to an evolved Apollo 15 olivine-normative basalt in major elements but is distinct in its rare earth element pattern. Its chemical composition and petrography both show that 15474,4 cannot be derived from other Apollo 15 mare basalts by shallow-level crystal fractionation. It represents a distinct extrusion of magma. Nonetheless, the chemical features that 15474,4 has in common with other Apollo 15 mare basalts, including the high FeO/Sc, the general similarity of the rare earth element pattern, and the common (and chondritic) TiO2/Sm ratio, emphasize the concept of a geochemical province at the Apollo 15 site that is distinct from basalts and provinces elsewhere. In making a consistent picture for the derivation of all of the Apollo 15 basalts, both the commonalities and the differences among the basalts must be explained. The Apollo 15 commonalities and differences suggest that the sources must have consisted of major silicate phases with the same composition but with varied amounts of a magma trapped from a contemporary magma ocean. They probably had a high olivine/pyroxene ratio and underwent small and reasonably consistent degrees of partial melting to produce the basalts. These inferences may be inconsistent with models that suggest greatly different depths of melting among basalts, primitive sources for the green glasses, or extensive olivine fractionation during ascent. An integrated approach to lunar mare provinces, of which the Apollo 15 mare basalts constitute only one, offers advances in our understanding of the physical and chemical processes of source formation and mare production but has so far not been utilized.

Anatomical, chemical, and ecological factors affecting tree species choice in dendrochemistry studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cutter, B.E.; Guyette, R.P.

1993-07-01

Recently, element concentrations in tree rings have been used to monitor metal contamination, fertilization, and the effects of acid precipitation on soils. This has stimulated interest in which tree species may be suitable for use in studies of long-term trends in environmental chemistry. Potential radial translocation of elements across living boundaries can be a confounding factor in assessing environmental change. The selection of species which minimizes radial translocation of elements can be critical to the success of dendrochemical research. Criteria for selection of species with characteristics favorable for dendrochemical analysis are categorized into (1) habitat-based factors, (2) xylem-based factors, andmore » (3) element-based factors. A wide geographic range and ecological amplitude provide an advantage in calibration and better controls on the effects of soil chemistry. The most important xylem-based criteria are heartwood moisture content, permeability, and the nature of the sapwood-heartwood transition. The element of interest is important in determining suitable tree species because all elements are not equally mobile or detectable in the xylem. Ideally, the tree species selected for dendrochemical study will be long-lived, grow on a wide range of sites over a large geographic distribution, have a distinct heartwood with a low number of rings in the sapwood, a low heartwood moisture content, and have low radial permeability. Recommended temperate zone North American species include white oak (Quercus alba L.), post oak (Q. stellate Wangenh.), eastern redcedar (funiperus virginiana L.), old-growth Douglas-fir [Pseudoaugu menziesii (Mirb.) Franco] and big sagebrush (Artemisia tridentata Nutt.). In addition, species such as bristlecone pine (Pinus aristata Engelm. syn. longaeva), old-growth redwood [Sequoia sempervirens (D. Don) Endl.], and giant sequoia [S. gigantea (Lindl.) Deene] may be suitable for local purposes. 118 refs., 2 tabs.« less

The evolution and disintegration of matter

USGS Publications Warehouse

Clarke, Frank Wigglesworth

1925-01-01

In any attempt to study the evolution of matter it is necessary to begin with its simplest known forms, the so-called chemical elements. During a great part of the nineteenth century many philosophical chemists held a vague belief that these elements were not distinct entities but manifestations of one primal substance-the protyle, as it is sometimes called. Other chemists, more conservative, looked askance at all such speculations and held fast to what they regarded as established facts. To them an element was something distinct from other kinds of matter, a substance which could neither be decomposed nor transmuted into anything else. This belief, however, was based entirely upon negative evidence-the inadequacy of our existing resources to produce such sweeping changes. Many important facts were ignored, and especially the fact that the elements are connected by very intimate relations, such as are best shown in the periodic law of Mendeleef, who, from gaps in his table of atomic weights, predicted the existence of three unknown metals, which have since been discovered. For these metals, scandium, gallium, and germanium, he foretold not only their atomic weights but also their most characteristic physical properties and the sort of compounds that each one would form. His prophecies have been verified in every essential particular. One obvious conclusion was soon drawn from Mendeleef's "law," although he was too cautious to admit it, namely, that the chemical elements must have had some community of origin. The philosophical speculations as to their nature were fully justified.

Elemental Abundance Distributions in Basalt Clays and Meteorites: Is It a Biosignature?

NASA Technical Reports Server (NTRS)

Fisk, M. R.; Storrie-Lombardi, M. C.; Joseph, J.

2005-01-01

Volcanic glass altered by microorganisms exhibits distinctive textures differing significantly from abiotic alteration [1-4]. We have previously presented morphological evidence of bioweathering in sub-oceanic basalt glass [5] and olivine [6], and noted similar alterations in Nakhla [7]. We have also introduced an autonomous Bayesian probabilistic classification methodology to identify biotic and abiotic alteration in sub-oceanic basalts using elemental abundance data [8]. We now present data from multiple sub-oceanic sites addressing the more general question of utilizing elemental abundance distribution in clays as a valid biosignature for the exploration of putative clay alteration products in meteorites.

Atmospheric metal pollution records in the Kovářská Bog (Czech Republic) as an indicator of anthropogenic activities over the last three millennia.

PubMed

Bohdálková, Leona; Bohdálek, Petr; Břízová, Eva; Pacherová, Petra; Kuběna, Aleš Antonín

2018-08-15

Three peat cores were extracted from the Kovářská Bog in the central Ore Mountains to study anthropogenic pollution generated by mining and metallurgy. The core profiles were 14 C dated, and concentrations of selected elements were determined by ICP MS and HG-AAS. Principal component analysis indicated that Pb, Cu, As and Ag may be useful elements for the reconstruction of historical atmospheric pollution. Total and anthropogenic accumulation rates (ARs) of Pb, Cu and As estimated for the last ca. 3500years showed similar chronologies, and revealed twelve periods of elevated ARs of Pb, As and Cu related to possible mining and metallurgic activities. In total, four periods of elevated ARs of Pb, Cu and As were detected during the Middle and Late Bronze Ages, including a distinct Late Bronze Age pollution event between 1030BCE and 910BCE. The Iron Age included three episodes of increased ARs of Pb and As; the first and the most distinctive episode, recorded between 730 and 440BCE, was simultaneous with the Bylany culture during the Hallstatt Period. The Roman Age was characterized by one pollution event, two events were detected in the Middle Ages, and the last two during the modern period. Enhanced element ARs in the late 12th and 15th centuries clearly documented the onset of two periods of intense mining in the Ore Mountains. Metal ARs culminated in ca. 1600CE, and subsequently decreased after the beginning of the Thirty Years' War. The last boom of mining between 1700CE and 1830CE represented the last period of important metallurgical operations. Late Medieval and modern period metal ARs are in good agreement with written documents. Earlier pollution peaks suggest that local metal production could have a much longer tradition than commonly believed; however, archaeological or written evidence is scarce or lacking. Copyright © 2018 Elsevier B.V. All rights reserved.

Coordinate action of distinct sequence elements localizes checkpoint kinase Hsl1 to the septin collar at the bud neck in Saccharomyces cerevisiae

PubMed Central

Finnigan, Gregory C.; Sterling, Sarah M.; Duvalyan, Angela; Liao, Elizabeth N.; Sargsyan, Aspram; Garcia, Galo; Nogales, Eva; Thorner, Jeremy

2016-01-01

Passage through the eukaryotic cell cycle requires processes that are tightly regulated both spatially and temporally. Surveillance mechanisms (checkpoints) exert quality control and impose order on the timing and organization of downstream events by impeding cell cycle progression until the necessary components are available and undamaged and have acted in the proper sequence. In budding yeast, a checkpoint exists that does not allow timely execution of the G2/M transition unless and until a collar of septin filaments has properly assembled at the bud neck, which is the site where subsequent cytokinesis will occur. An essential component of this checkpoint is the large (1518-residue) protein kinase Hsl1, which localizes to the bud neck only if the septin collar has been correctly formed. Hsl1 reportedly interacts with particular septins; however, the precise molecular determinants in Hsl1 responsible for its recruitment to this cellular location during G2 have not been elucidated. We performed a comprehensive mutational dissection and accompanying image analysis to identify the sequence elements within Hsl1 responsible for its localization to the septins at the bud neck. Unexpectedly, we found that this targeting is multipartite. A segment of the central region of Hsl1 (residues 611–950), composed of two tandem, semiredundant but distinct septin-associating elements, is necessary and sufficient for binding to septin filaments both in vitro and in vivo. However, in addition to 611–950, efficient localization of Hsl1 to the septin collar in the cell obligatorily requires generalized targeting to the cytosolic face of the plasma membrane, a function normally provided by the C-terminal phosphatidylserine-binding KA1 domain (residues 1379–1518) in Hsl1 but that can be replaced by other, heterologous phosphatidylserine-binding sequences. PMID:27193302

Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae

PubMed Central

Mukherjee, Munmun; Kakarla, Prathusha; Kumar, Sanath; Gonzalez, Esmeralda; Floyd, Jared T.; Inupakutika, Madhuri; Devireddy, Amith Reddy; Tirrell, Selena R.; Bruns, Merissa; He, Guixin; Lindquist, Ingrid E.; Sundararajan, Anitha; Schilkey, Faye D.; Mudge, Joann; Varela, Manuel F.

2015-01-01

Pathogenic strains of Vibrio cholerae are responsible for endemic and pandemic outbreaks of the disease cholera. The complete toxigenic mechanisms underlying virulence in Vibrio strains are poorly understood. The hypothesis of this work was that virulent versus non-virulent strains of V. cholerae harbor distinctive genomic elements that encode virulence. The purpose of this study was to elucidate genomic differences between the O1 serotypes and non-O1 V. cholerae PS15, a non-toxigenic strain, in order to identify novel genes potentially responsible for virulence. In this study, we compared the whole genome of the non-O1 PS15 strain to the whole genomes of toxigenic serotypes at the phylogenetic level, and found that the PS15 genome was distantly related to those of toxigenic V. cholerae. Thus we focused on a detailed gene comparison between PS15 and the distantly related O1 V. cholerae N16961. Based on sequence alignment we tentatively assigned chromosome numbers 1 and 2 to elements within the genome of non-O1 V. cholerae PS15. Further, we found that PS15 and O1 V. cholerae N16961 shared 98% identity and 766 genes, but of the genes present in N16961 that were missing in the non-O1 V. cholerae PS15 genome, 56 were predicted to encode not only for virulence–related genes (colonization, antimicrobial resistance, and regulation of persister cells) but also genes involved in the metabolic biosynthesis of lipids, nucleosides and sulfur compounds. Additionally, we found 113 genes unique to PS15 that were predicted to encode other properties related to virulence, disease, defense, membrane transport, and DNA metabolism. Here, we identified distinctive and novel genomic elements between O1 and non-O1 V. cholerae genomes as potential virulence factors and, thus, targets for future therapeutics. Modulation of such novel targets may eventually enhance eradication efforts of endemic and pandemic disease cholera in afflicted nations. PMID:25722857

Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.

PubMed

Mukherjee, Munmun; Kakarla, Prathusha; Kumar, Sanath; Gonzalez, Esmeralda; Floyd, Jared T; Inupakutika, Madhuri; Devireddy, Amith Reddy; Tirrell, Selena R; Bruns, Merissa; He, Guixin; Lindquist, Ingrid E; Sundararajan, Anitha; Schilkey, Faye D; Mudge, Joann; Varela, Manuel F

Pathogenic strains of Vibrio cholerae are responsible for endemic and pandemic outbreaks of the disease cholera. The complete toxigenic mechanisms underlying virulence in Vibrio strains are poorly understood. The hypothesis of this work was that virulent versus non-virulent strains of V. cholerae harbor distinctive genomic elements that encode virulence. The purpose of this study was to elucidate genomic differences between the O1 serotypes and non-O1 V. cholerae PS15, a non-toxigenic strain, in order to identify novel genes potentially responsible for virulence. In this study, we compared the whole genome of the non-O1 PS15 strain to the whole genomes of toxigenic serotypes at the phylogenetic level, and found that the PS15 genome was distantly related to those of toxigenic V. cholerae . Thus we focused on a detailed gene comparison between PS15 and the distantly related O1 V. cholerae N16961. Based on sequence alignment we tentatively assigned chromosome numbers 1 and 2 to elements within the genome of non-O1 V. cholerae PS15. Further, we found that PS15 and O1 V. cholerae N16961 shared 98% identity and 766 genes, but of the genes present in N16961 that were missing in the non-O1 V. cholerae PS15 genome, 56 were predicted to encode not only for virulence-related genes (colonization, antimicrobial resistance, and regulation of persister cells) but also genes involved in the metabolic biosynthesis of lipids, nucleosides and sulfur compounds. Additionally, we found 113 genes unique to PS15 that were predicted to encode other properties related to virulence, disease, defense, membrane transport, and DNA metabolism. Here, we identified distinctive and novel genomic elements between O1 and non-O1 V. cholerae genomes as potential virulence factors and, thus, targets for future therapeutics. Modulation of such novel targets may eventually enhance eradication efforts of endemic and pandemic disease cholera in afflicted nations.

Dynamic Reweighting of Auditory Modulation Filters.

PubMed

Joosten, Eva R M; Shamma, Shihab A; Lorenzi, Christian; Neri, Peter

2016-07-01

Sound waveforms convey information largely via amplitude modulations (AM). A large body of experimental evidence has provided support for a modulation (bandpass) filterbank. Details of this model have varied over time partly reflecting different experimental conditions and diverse datasets from distinct task strategies, contributing uncertainty to the bandwidth measurements and leaving important issues unresolved. We adopt here a solely data-driven measurement approach in which we first demonstrate how different models can be subsumed within a common 'cascade' framework, and then proceed to characterize the cascade via system identification analysis using a single stimulus/task specification and hence stable task rules largely unconstrained by any model or parameters. Observers were required to detect a brief change in level superimposed onto random level changes that served as AM noise; the relationship between trial-by-trial noisy fluctuations and corresponding human responses enables targeted identification of distinct cascade elements. The resulting measurements exhibit a dynamic complex picture in which human perception of auditory modulations appears adaptive in nature, evolving from an initial lowpass to bandpass modes (with broad tuning, Q∼1) following repeated stimulus exposure.

Numerical Investigation of Shock Wave Propagation in Bone-Like Tissue

NASA Astrophysics Data System (ADS)

Nelms, Matt; Rajendran, Arunachalam

In this investigation, the effects of shock wave propagation in bone-like biomineralized tissue was investigated. The Alligator gar (Atractosteus spatula) exoskeleton is comprised of many disparate scales that provide a biological analog for potential design of flexible protective material systems. The penetration resistant fish scale was modeled by simulating a plate impact test configuration using ABAQUS®finite element (FE) software. The gar scale is identified as a two-phase, (1) hydroxyapatite mineral and (2) collagen protein, biological composite with two distinct layers where a stiff, ceramic-like ganoine overlays a soft, highly ductile bone. The geometry and variation of elastic modulus were determined from high-resolution scanning electron microscopy and dynamic nanoindentation experimentation to develop an idealized computational model for RVE-based FE simulations. The numerical analysis shows the effects of different functional material property variations on the stress histories and energy dissipation generated by wave propagation. Given the constitutive behaviors of the two layers are distinctly different, a brittle tensile damage model was employed to describe the ganoine and Drucker-Prager plasticity was used for the nonlinear response of the bone.

Nickel-iron spherules in tektites - Non-meteoritic in origin

NASA Technical Reports Server (NTRS)

Ganapathy, R.; Larimer, J. W.

1983-01-01

The concentrations of several diagnostic trace elements were determined in two comparatively large NiFe spherules extracted from tektites. The purpose of the study was to obtain some clues about the chemistry of the projectile that is presumed responsible for the formation of these tektites. However, the trace element pattern is distinctly terrestrial implying that the spherules are the result of in-situ reduction of the host rock and are not meteoritic in origin.

Elemental Concentrations in the Seed of Mutants and Natural Variants of Arabidopsis thaliana Grown under Varying Soil Conditions

PubMed Central

McDowell, Stephen C.; Akmakjian, Garo; Sladek, Chris; Mendoza-Cozatl, David; Morrissey, Joe B.; Saini, Nick; Mittler, Ron; Baxter, Ivan; Salt, David E.; Ward, John M.; Schroeder, Julian I.; Guerinot, Mary Lou; Harper, Jeffrey F.

2013-01-01

The concentrations of mineral nutrients in seeds are critical to both the life cycle of plants as well as human nutrition. These concentrations are strongly influenced by soil conditions, as shown here by quantifying the concentration of 14 elements in seeds from Arabidopsis thaliana plants grown under four different soil conditions: standard, or modified with NaCl, heavy metals, or alkali. Each of the modified soils resulted in a unique change to the seed ionome (the mineral nutrient content of the seeds). To help identify the genetic networks regulating the seed ionome, changes in elemental concentrations were evaluated using mutants corresponding to 760 genes as well as 10 naturally occurring accessions. The frequency of ionomic phenotypes supports an estimate that as much as 11% of the A. thaliana genome encodes proteins of functional relevance to ion homeostasis in seeds. A subset of mutants were analyzed with two independent alleles, providing five examples of genes important for regulation of the seed ionome: SOS2, ABH1, CCC, At3g14280 and CNGC2. In a comparison of nine different accessions to a Col-0 reference, eight accessions were observed to have reproducible differences in elemental concentrations, seven of which were dependent on specific soil conditions. These results indicate that the A. thaliana seed ionome is distinct from the vegetative ionome, and that elemental analysis is a sensitive approach to identify genes controlling ion homeostasis, including those that regulate gene expression, phospho-regulation, and ion transport. PMID:23671651

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

PubMed Central

Smith, Emily M.; Lajoie, Bryan R.; Jain, Gaurav; Dekker, Job

2016-01-01

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. PMID:26748519

Trace element geochemistry of altered volcanic ash layers (tonsteins) in late Permian coal-bearing formations of eastern Yunnan and western Guizhou Provinces, China

USGS Publications Warehouse

Zhou, Y.; Bohor, B.F.; Ren, Y.

2000-01-01

Trace element compositions were determined (by instrumental neutron activation analysis; INAA) in 30 samples of synsedimentary volcanic ash-derived tonsteins and detrital claystones from coal seams within the late Permian coal-bearing formation of eastern Yunnan and western Guizhou Provinces, China. The characteristics of trace-element geochemistry in the tonsteins can be distinguished from those of detrital claystones because of the former's unique volcanic-ash origin. The detrital claystones are characterized by their relatively high content of V, Ti, Sc, Cr, Co and Ni, relatively low content of Th and U, Th/U ratio, and small negative Eu anomaly (Eu/Eu* 0.63-0.93). Overall, these trace element characteristics are consistent with a mafic source similar to the composition of basalt rocks in the erosional region on the western edge of the study area. In contrast, the tonsteins are low in V, Ti, Sc, Cr, Co and Ni contents and have a high Th/U ratio with a distinct negative Eu anomaly (Eu/Eu* normally in the range of 0.2-0.4), consistent with a silicic magmatic source. Within the group of tonsteins, those from the lower section (P2.1) of the coal-bearing formation are relatively high in Ti, Zr, Hf, Nb, Ta and rare earth elements (REE), as compared to those from the middle and upper sections (P2.2+3). In trace-element discrimination diagrams (scatter plots) of Hf-Ta, Ti-Ta, Ti-V, Hf-Sc, Lu-Hf and Lu-Th, tonsteins from the P2.1 horizon always fall in isolated distribution areas, separate from the tonsteins of the P2.2+3 horizon. These results suggest that the source materials of tonsteins from the two separate horizons were probably derived from volcanic ash falls of two distinctly different natures. Based on a comparison of the concentrations and assemblages of trace elements between various magmatic rocks, the source materials of tonsteins from P2.1 horizon were mostly composed of calc-alkalic, silica-poor volcanic ash (similar to rhyodacitic magma), whereas those from P2.+3 were apparently more siliceous and K-rich (rhyolitic magma). Thus, tonsteins from the two different horizons are characterized by unique geochemical properties, which remain constant over a wide lateral extent. Integration of trace-elemental compositions with mineralogical and textural observations makes possible the establishment of tonstein stratigraphy, thus, facilitating more precise and reliable coal-seam correlations. (C) 2000 Elsevier Science B.V. All rights reserved.Trace element compositions were determined in 30 samples of synsedimentary volcanic ash-derived tonsteins and detrital claystones from coal seams within the late Permian coal-bearing formation of eastern Yunnan and western Guizhou Provinces, China. The characteristics of trace-element geochemistry in the tonsteins can be distinguished from those of detrital claystones because of the former's unique volcanic-ash origin. The detrital claystones are characterized by their relatively high content of V, Ti, Sc, CR, Co and Ni, relatively low content of Th and U, Th/U ratio, and small negative Eu anomaly.

Binding mechanism investigations guiding the synthesis of novel condensed 1,4-dihydropyridine derivatives with L-/T-type calcium channel blocking activity.

PubMed

Schaller, David; Gündüz, Miyase Gözde; Zhang, Fang Xiong; Zamponi, Gerald W; Wolber, Gerhard

2018-05-23

Nifedipine and isradipine are prominent examples of calcium channel blockers with a 1,4-dihydropyridine (DHP) scaffold. Although successfully used in clinics since decades for the treatment of hypertension, the binding mechanism to their target, the L-type voltage-gated calcium channel Cav1.2, is still incompletely understood. Recently, novel DHP derivatives with a condensed ring system have been discovered that show distinct selectivity profiles to different calcium channel subtypes. This property renders this DHP class as a promising tool to achieve selectivity towards distinct calcium channel subtypes. In this study, we identified a common binding mode for prominent DHPs nifedipine and isradipine using docking and pharmacophore analysis that is also able to explain the structure-activity relationship of a small subseries of DHP derivatives with a condensed ring system. These findings were used to guide the synthesis of twenty-two novel DHPs. An extensive characterization using 1 H NMR, 13 C NMR, mass spectra and elemental analysis was followed by whole cell patch clamp assays for analyzing activity at Cav1.2 and Cav3.2. Two compounds were identified with significant activity against Cav1.2. Additionally, we identified four compounds active against Cav3.2 of which three were selective over Cav1.2. Novel binding modes were analyzed using docking and pharmacophore analysis as well as molecular dynamics simulations. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Satellite Characterization of Biomass Burning: Fourier Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscope Study of Combustion Experiments

NASA Astrophysics Data System (ADS)

Padilla, D.; Steiner, J. C.

2005-12-01

Fourier Transform Infrared (FTIR) examination of the combustion products of selected forest materials using a meeker burner flame at temperatures up to 500 degrees Celsius produces a cluster of broad distinct peaks throughout the 400 to 4000 cm-1 wavenumber interval. Distinct bands bracketed by wavenumbers 400-700, 1500-1700, 2200-2400 and 3300-3600 cm-1 show variable intensity with an average difference between the least absorbing and most strongly absorbing species of approximately fifty percent. Given that spectral band differences of ten percent are within the range of modern satellite spectrometers, these band differences are of potential value for discriminating between fires that are impacting a range of vegetation types. Corresponding scanning electron microscope and energy dispersive micro-chemical (SEM/ED) analysis establishes that the evolved soot particles exhibit a characteristic rounded morphology, are carbon rich and host a wide range of adsorbed elements, including calcium, aluminum, potassium, silicon, sulfur and trace nitrogen. Combustion experiments involving leaves and branches as a subset of the biomass experiments at 200-500 degrees Celsius yield a similar broad background, but with peak shifts for maxima residing at less than 1700 cm-1. Additional peaks appear in the ranges 1438-1444, 875 and 713 cm-1. These peak are of potential use for discriminating between hot and smoldering fires, and between soot and smoke yields from green woods and whole-wood or lumber. The spectral shifts noted for low temperature smoldering conditions are in the vicinity of those cited for green vegetation and may not be resolved by present satellite platforms. Nevertheless, the experimental peak data set is of potential use for discriminating between a conflagration or accentuated fire and one characterized by smoldering at low temperature. SEM/ED analysis of the combusted leaf, branch, bark and various crown assemblages yields comparable morphological and geochemical signatures although potassium and light elements are slightly concentrated in effluent from the leafy matrix.

Nano characterization of gunshot residues from Brazilian ammunition.

PubMed

Melo, Lis G A; Martiny, Andrea; Pinto, André L

2014-07-01

Gunshot residues (GSR) from a total of nine different caliber ammunitions produced in Brazil were analyzed and characterized by transmission (TEM) and scanning electron microscopy (SEM). GSR particles are composed of spherical particles of several micrometers of diameter containing distinct amounts of lead, barium and antimony, along with other organic and inorganic elements arising from the primer, gunpowder, the gun and the bullet itself. This study was carried out to obtain additional information on the properties of GSR nanoparticles originated from different types of regular ammunition produced in Brazil by CBC. Besides the SEM, we have used a TEM, exploring its high magnification capability and ability to explore internal structure and chemical composition of submicron particles. We observed that CBC ammunition generated smaller particles than usually reported for other ammunitions and that the three component particles are not a majority. TEM analysis revealed that GSR are partially composed of sub-micron particles as well. The electron diffraction pattern from these particles confirmed them to be mainly composed of lead oxides crystalline nanoparticles that may be agglomerated into larger particles. Energy dispersive X-ray spectroscopy revealed that most of them were composed of two elements, especially PbSb. Ba was not a common element found in the nanoparticles. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

The perception of food quality. Profiling Italian consumers.

PubMed

Mascarello, Giulia; Pinto, Anna; Parise, Nicoletta; Crovato, Stefania; Ravarotto, Licia

2015-06-01

This study aims to analyse the elements which, according to Italian consumers, contribute most to defining the quality of a food product. A sample of 1000 consumers, in charge of purchases for the household, was interviewed by telephone. The data analysis has made it possible to categorise Italian consumers into two main groups: on the one hand those who mainly use criteria associated with organoleptic elements, and, on the other, those who make their choice based on place and methods of production. Both categories were studied with a view to identifying their distinctive socio-demographic and behavioural features. Geographical provenance, age, propensity to read the label on products, scientific knowledge and self-assessment of knowledge on food safety-related issues emerged as the main differences between the two groups. The perception of quality appears to affect purchase decisions and dietary patterns. The description of the consumer groups who use the same elements to define quality provided a useful insight into consumer choices and potential risk-exposure behaviours. The study of these aspects is therefore relevant for the purpose of designing effective and targeted communication actions, not only for companies but also for public institutions in charge of safeguarding public health. Copyright © 2015 Elsevier Ltd. All rights reserved.

Canonical WNT signalling determines lineage specificity in Wilms tumour.

PubMed

Fukuzawa, R; Anaka, M R; Weeks, R J; Morison, I M; Reeve, A E

2009-02-26

Wilms tumours (WTs) have two distinct types of histology with or without ectopic mesenchymal elements, suggesting that WTs arise from either the mesenchymal or epithelial nephrogenic lineages. Regardless of the presence or absence of CTNNB1 mutations, nuclear accumulation of beta-catenin is often observed in WTs with ectopic mesenchymal elements. Here, we addressed the relationship between the WNT-signalling pathway and lineage in WTs by examining CTNNB1 and WT1 mutations, nuclear accumulation of beta-catenin, tumour histology and gene expression profiles. In addition, we screened for mutations in WTX, which has been proposed to be a negative regulator of the canonical WNT-signalling pathway. Unsupervised clustering analysis identified two classes of tumours: mesenchymal lineage WNT-dependent tumours, and epithelial lineage WNT-independent tumours. In contrast to the mesenchymal lineage specificity of CTNNB1 mutations, WTX mutations were surprisingly observed in both lineages. WTX-mutant WTs with ectopic mesenchymal elements had nuclear accumulation of beta-catenin, upregulation of WNT target genes and an association with CTNNB1 mutations in exon 7 or 8. However, epithelial lineage WTs with WTX mutations had no indications of active WNT signalling, suggesting that the involvement of WTX in the WNT-signalling pathway may be lineage dependent, and that WTX may have an alternative function to its role in the canonical WNT-signalling pathway.

Transactivation of a cellular promoter by the NS1 protein of the parvovirus minute virus of mice through a putative hormone-responsive element.

PubMed Central

Vanacker, J M; Corbau, R; Adelmant, G; Perros, M; Laudet, V; Rommelaere, J

1996-01-01

The promoter of the thyroid hormone receptor alpha gene (c-erbA-1) is activated by the nonstructural protein 1 (NS1) of parvovirus minute virus of mice (prototype strain [MVMp]) in ras-transformed FREJ4 cells that are permissive for lytic MVMp replication. This stimulation may be related to the sensitivity of host cells to MVMp, as it does not take place in parental FR3T3 cells, which are resistant to the parvovirus killing effect. The analysis of a series of deletion and point mutants of the c-erbA-1 promoter led to the identification of an upstream region that is necessary for NS1-driven transactivation. This sequence harbors a putative hormone-responsive element and is sufficient to render a minimal promoter NS1 inducible in FREJ4 but not in FR3T3 cells, and it is involved in distinct interactions with proteins from the respective cell lines. The NS1-responsive element of the c-erbA-1 promoter bears no homology with sequences that were previously reported to be necessary for NS1 DNA binding and transactivation. Altogether, our data point to a novel, cell-specific mechanism of promoter activation by NS1. PMID:8642664

Hermes Transposon Distribution and Structure in Musca domestica

PubMed Central

Subramanian, Ramanand A.; Cathcart, Laura A.; Krafsur, Elliot S.; Atkinson, Peter W.

2009-01-01

Hermes are hAT transposons from Musca domestica that are very closely related to the hobo transposons from Drosophila melanogaster and are useful as gene vectors in a wide variety of organisms including insects, planaria, and yeast. hobo elements show distinct length variations in a rapidly evolving region of the transposase-coding region as a result of expansions and contractions of a simple repeat sequence encoding 3 amino acids threonine, proline, and glutamic acid (TPE). These variations in length may influence the function of the protein and the movement of hobo transposons in natural populations. Here, we determine the distribution of Hermes in populations of M. domestica as well as whether Hermes transposase has undergone similar sequence expansions and contractions during its evolution in this species. Hermes transposons were found in all M. domestica individuals sampled from 14 populations collected from 4 continents. All individuals with Hermes transposons had evidence for the presence of intact transposase open reading frames, and little sequence variation was observed among Hermes elements. A systematic analysis of the TPE-homologous region of the Hermes transposase-coding region revealed no evidence for length variation. The simple sequence repeat found in hobo elements is a feature of this transposon that evolved since the divergence of hobo and Hermes. PMID:19366812

Thermodynamic and Spectroscopic Studies of Trivalent f -element Complexation with Ethylenediamine- N,N '-di(acetylglycine)- N,N '-diacetic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heathman, Colt R.; Grimes, Travis S.; Zalupski, Peter R.

In this study, the coordination behavior and thermodynamic features of complexation of trivalent lanthanides and americium by ethylenediamine- N,N'-di(acetylglycine)- N,N'-diacetic acid (EDDAG-DA) (bisamide-substituted-EDTA) were investigated by potentiometric and spectroscopic techniques. Acid dissociation constants (K a) and complexation constants (β) of lanthanides (except Pm) were determined by potentiometric analysis. Absorption spectroscopy was used to determine stability constants for the binding of trivalent americium and neodymium by EDDAG-DA under similar conditions. The potentiometry revealed 5 discernible protonation constants and 3 distinct metal–ligand complexes (identified as ML –, MHL, and MH 2L +). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identifiedmore » a constant inner-sphere hydration number of 3, suggesting that glycine functionalities contained in the amide pendant arms are not involved in metal complexation and are protonated under more acidic conditions. The thermodynamic studies identified that f-element coordination by EDDAG-DA is similar to that observed for ethylenediamine- N,N,N',N'-tetraacetic acid (EDTA). However, coordination via two amidic oxygens of EDDAG-DA lowers its trivalent f-element complex stability by roughly 3 orders of magnitude relative to EDTA.« less

Chemical composition of PM2.5 at an urban site of Chengdu in southwestern China

NASA Astrophysics Data System (ADS)

Tao, Jun; Cheng, Tiantao; Zhang, Renjian; Cao, Junji; Zhu, Lihua; Wang, Qiyuan; Luo, Lei; Zhang, Leiming

2013-07-01

PM2.5 aerosols were sampled in urban Chengdu from April 2009 to January 2010, and their chemical compositions were characterized in detail for elements, water soluble inorganic ions, and carbonaceous matter. The annual average of PM2.5 was 165 μg m-3, which is generally higher than measurements in other Chinese cities, suggesting serious particulate pollution issues in the city. Water soluble ions contributed 43.5% to the annual total PM2.5 mass, carbonaceous aerosols including elemental carbon and organic carbon contributed 32.0%, and trace elements contributed 13.8%. Distinct daily and seasonal variations were observed in the mass concentrations of PM2.5 and its components, reflecting the seasonal variations of different anthropogenic and natural sources. Weakly acidic to neutral particles were found for PM2.5. Major sources of PM2.5 identified from source apportionment analysis included coal combustion, traffic exhaust, biomass burning, soil dust, and construction dust emissions. The low nitrate: sulfate ratio suggested that stationary emissions were more important than vehicle emissions. The reconstructed masses of ammonium sulfate, ammonium nitrate, particulate carbonaceous matter, and fine soil accounted for 79% of the total measured PM2.5 mass; they also accounted for 92% of the total measured particle scattering.

Thermodynamic and Spectroscopic Studies of Trivalent f -element Complexation with Ethylenediamine- N,N '-di(acetylglycine)- N,N '-diacetic Acid

DOE PAGES

Heathman, Colt R.; Grimes, Travis S.; Zalupski, Peter R.

2016-03-21

In this study, the coordination behavior and thermodynamic features of complexation of trivalent lanthanides and americium by ethylenediamine- N,N'-di(acetylglycine)- N,N'-diacetic acid (EDDAG-DA) (bisamide-substituted-EDTA) were investigated by potentiometric and spectroscopic techniques. Acid dissociation constants (K a) and complexation constants (β) of lanthanides (except Pm) were determined by potentiometric analysis. Absorption spectroscopy was used to determine stability constants for the binding of trivalent americium and neodymium by EDDAG-DA under similar conditions. The potentiometry revealed 5 discernible protonation constants and 3 distinct metal–ligand complexes (identified as ML –, MHL, and MH 2L +). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identifiedmore » a constant inner-sphere hydration number of 3, suggesting that glycine functionalities contained in the amide pendant arms are not involved in metal complexation and are protonated under more acidic conditions. The thermodynamic studies identified that f-element coordination by EDDAG-DA is similar to that observed for ethylenediamine- N,N,N',N'-tetraacetic acid (EDTA). However, coordination via two amidic oxygens of EDDAG-DA lowers its trivalent f-element complex stability by roughly 3 orders of magnitude relative to EDTA.« less

Thermal Effects Modeling Developed for Smart Structures

NASA Technical Reports Server (NTRS)

Lee, Ho-Jun

1998-01-01

Applying smart materials in aeropropulsion systems may improve the performance of aircraft engines through a variety of vibration, noise, and shape-control applications. To facilitate the experimental characterization of these smart structures, researchers have been focusing on developing analytical models to account for the coupled mechanical, electrical, and thermal response of these materials. One focus of current research efforts has been directed toward incorporating a comprehensive thermal analysis modeling capability. Typically, temperature affects the behavior of smart materials by three distinct mechanisms: Induction of thermal strains because of coefficient of thermal expansion mismatch 1. Pyroelectric effects on the piezoelectric elements; 2. Temperature-dependent changes in material properties; and 3. Previous analytical models only investigated the first two thermal effects mechanisms. However, since the material properties of piezoelectric materials generally vary greatly with temperature (see the graph), incorporating temperature-dependent material properties will significantly affect the structural deflections, sensory voltages, and stresses. Thus, the current analytical model captures thermal effects arising from all three mechanisms through thermopiezoelectric constitutive equations. These constitutive equations were incorporated into a layerwise laminate theory with the inherent capability to model both the active and sensory response of smart structures in thermal environments. Corresponding finite element equations were formulated and implemented for both the beam and plate elements to provide a comprehensive thermal effects modeling capability.

Chemical and Sr isotopic characterization of North America uranium ores: Nuclear forensic applications

DOE PAGES

Balboni, Enrica; Jones, Nina; Spano, Tyler; ...

2016-08-31

This study reports major, minor, and trace element data and Sr isotope ratios for 11 uranium ore (uraninite, UO 2+x) samples and one processed uranium ore concentrate (UOC) from various U.S. deposits. The uraninite investigated represent ores formed via different modes of mineralization (e.g., high- and low-temperature) and within various geological contexts, which include magmatic pegmatites, metamorphic rocks, sandstone-hosted, and roll front deposits. In situ trace element data obtained by laser ablation-ICP-MS and bulk sample Sr isotopic ratios for uraninite samples investigated here indicate distinct signatures that are highly dependent on the mode of mineralization and host rock geology. Relativemore » to their high-temperature counterparts, low-temperature uranium ores record high U/Th ratios (>1000), low total rare earth element (REE) abundances (<1 wt%), high contents (>300 ppm) of first row transition metals (Sc, Ti, V, Cr, Mn, Co, Ni), and radiogenic 87Sr/ 86Sr ratios (>0.7200). Comparison of chondrite normalized REE patterns between uraninite and corresponding processed UOC from the same locality indicates identical patterns at different absolute concentrations. Lastly, this result ultimately confirms the importance of establishing geochemical signatures of raw, uranium ore materials for attribution purposes in the forensic analysis of intercepted nuclear materials.« less

Chemical and Sr isotopic characterization of North America uranium ores: Nuclear forensic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balboni, Enrica; Jones, Nina; Spano, Tyler

This study reports major, minor, and trace element data and Sr isotope ratios for 11 uranium ore (uraninite, UO 2+x) samples and one processed uranium ore concentrate (UOC) from various U.S. deposits. The uraninite investigated represent ores formed via different modes of mineralization (e.g., high- and low-temperature) and within various geological contexts, which include magmatic pegmatites, metamorphic rocks, sandstone-hosted, and roll front deposits. In situ trace element data obtained by laser ablation-ICP-MS and bulk sample Sr isotopic ratios for uraninite samples investigated here indicate distinct signatures that are highly dependent on the mode of mineralization and host rock geology. Relativemore » to their high-temperature counterparts, low-temperature uranium ores record high U/Th ratios (>1000), low total rare earth element (REE) abundances (<1 wt%), high contents (>300 ppm) of first row transition metals (Sc, Ti, V, Cr, Mn, Co, Ni), and radiogenic 87Sr/ 86Sr ratios (>0.7200). Comparison of chondrite normalized REE patterns between uraninite and corresponding processed UOC from the same locality indicates identical patterns at different absolute concentrations. Lastly, this result ultimately confirms the importance of establishing geochemical signatures of raw, uranium ore materials for attribution purposes in the forensic analysis of intercepted nuclear materials.« less

Morphine biosynthesis in opium poppy involves two cell types: sieve elements and laticifers.

PubMed

Onoyovwe, Akpevwe; Hagel, Jillian M; Chen, Xue; Khan, Morgan F; Schriemer, David C; Facchini, Peter J

2013-10-01

Immunofluorescence labeling and shotgun proteomics were used to establish the cell type-specific localization of morphine biosynthesis in opium poppy (Papaver somniferum). Polyclonal antibodies for each of six enzymes involved in converting (R)-reticuline to morphine detected corresponding antigens in sieve elements of the phloem, as described previously for all upstream enzymes transforming (S)-norcoclaurine to (S)-reticuline. Validated shotgun proteomics performed on whole-stem and latex total protein extracts generated 2031 and 830 distinct protein families, respectively. Proteins corresponding to nine morphine biosynthetic enzymes were represented in the whole stem, whereas only four of the final five pathway enzymes were detected in the latex. Salutaridine synthase was detected in the whole stem, but not in the latex subproteome. The final three enzymes converting thebaine to morphine were among the most abundant active latex proteins despite a limited occurrence in laticifers suggested by immunofluorescence labeling. Multiple charge isoforms of two key O-demethylases in the latex were revealed by two-dimensional immunoblot analysis. Salutaridine biosynthesis appears to occur only in sieve elements, whereas conversion of thebaine to morphine is predominant in adjacent laticifers, which contain morphine-rich latex. Complementary use of immunofluorescence labeling and shotgun proteomics has substantially resolved the cellular localization of morphine biosynthesis in opium poppy.

Heavy metal and nutrient uptake in plants colonizing post-flotation copper tailings.

PubMed

Kasowska, Dorota; Gediga, Krzysztof; Spiak, Zofia

2018-01-01

Copper ore mining and processing release hazardous post-flotation wastes that are difficult for remediation. The studied tailings were extremely rich in Cu (1800 mg kg -1 ) and contaminated with Co and Mn, and contained very little available forms of P, Fe, and Zn. The plants growing in tailings were distinctly enriched in Cu, Cd, Co, Ni, and Pb, and the concentration of copper achived the critical toxicity level in shoots of Cerastium arvense and Polygonum aviculare. The redundancy analysis demonstrated significant relationship between the concentration of available forms of studied elements in substrate and the chemical composition of plant shoots. Results of the principal component analysis enabled to distinguish groups of plants which significantly differed in the pattern of element accumulation. The grass species Agrostis stolonifera and Calamagrostis epigejos growing in the tailings accumulated significantly lower amounts of Cu, but they also had the lowest levels of P, Fe, and Zn in comparison to dicotyledonous. A. stolonifera occurred to be the most suitable species for phytostabilization of the tailings with regard to its low shoot Cu content and more efficient acquisition of limiting nutrients in relation to C. epigejos. The amendments improving texture, phosphorus fertilization, and the introduction of native leguminous species were recommended for application in the phytoremediation process of the tailings.

Histological and Finite Element Analysis of Cell Death due to Irreversible Electroporation

PubMed Central

Long, G.; Bakos, G.; Shires, P. K.; Gritter, L.; Crissman, J. W.; Harris, J. L.; Clymer, J. W.

2014-01-01

Irreversible electroporation (IRE) has been shown to be an effective method of killing cells locally. In contrast to radiofrequency ablation, the mechanism by which cells are thought to die via IRE is the creation of pores in cell membranes, without substantial increase in tissue temperature. To determine the degree to which cell death is non-thermal, we evaluated IRE in porcine hepatocytes in vivo. Using pulse widths of 10μs, bursts of 3 kV square-wave pulses were applied through a custom probe to the liver of an anesthetized pig. Affected tissue was evaluated histologically via stainings of hematoxylin & eosin (H&E), nitroblue tetrazolium (NBT) to monitor cell respiration and TUNEL to gauge apoptosis. Temperature was measured during the application of electroporation, and heat transfer was modeled via finite element analysis. Cell death was calculated via Arrhenius kinetics. Four distinct zones were observed within the ring return electrode; heat-fixed tissue, coagulation, necrotic, and viable. The Arrhenius damage integral estimated complete cell death only in the first zone, where the temperature exceeded 70°C, and partial or no cell death in the other zones, where maximum temperature was approximately 45°C. Except for a limited area near the electrode tip, cell death in IRE is predominantly due to a non-thermal mechanism. PMID:24000980

Mid-Award Progress Report for Department of Energy Office of Science Graduate Student Research Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffman, M. K.

The purpose of the work proposed for this study is to investigate the behavior and transport mechanisms for cesium-137 in soils collected from contaminated sites with distinct source release scenarios. More specifically, this study aims to determine with which elements and minerals cesium-137 associates in these various environments to more reliably predict its migration in the subsurface. This will be achieved using a state-of-the-art analysis technique available at Lawrence Livermore National Laboratory (LLNL) known as NanoSIMS. Nano-scale secondary ion mass spectrometry, or NanoSIMS, is a destructive surface analysis technique in which positive secondary ions are generated from the surface ofmore » a sample and then quantified based on their mass-to-charge ratio (m/z) using mass spectrometry. The data collected about the secondary ions can then be used to create isotope-specific spatial maps with a resolution of a few hundred nanometers and depth profiles that show the variation of the secondary ion intensity with sputtering time. This should be an ideal technique for locating cesium-137 in a sample, as cesium is an easily ionized element, meaning the yield of secondary cesium (Cs) ions produced should be high and making the identification of cesium-137 straight forward.« less

The application of the Wigner Distribution to wave type identification in finite length beams

NASA Technical Reports Server (NTRS)

Wahl, T. J.; Bolton, J. Stuart

1994-01-01

The object of the research described in this paper was to develop a means of identifying the wave-types propagating between two points in a finite length beam. It is known that different structural wave-types possess different dispersion relations: i.e., that their group speeds and the frequency dependence of their group speeds differ. As a result of those distinct dispersion relationships, different wave-types may be associated with characteristic features when structural responses are examined in the time frequency domain. Previously, the time-frequency character of analytically generated structural responses of both single element and multi-element structures were examined by using the Wigner Distribution (WD) along with filtering techniques that were designed to detect the wave-types present in the responses. In the work to be described here, the measure time-frequency response of finite length beam is examined using the WD and filtering procedures. This paper is organized as follows. First the concept of time-frequency analysis of structural responses is explained. The WD is then introduced along with a description of the implementation of a discrete version. The time-frequency filtering techniques are then presented and explained. The results of applying the WD and the filtering techniques to the analysis of a transient response is then presented.

Heat exchanger with ceramic elements

DOEpatents

Corey, John A.

1986-01-01

An annular heat exchanger assembly includes a plurality of low thermal growth ceramic heat exchange members with inlet and exit flow ports on distinct faces. A mounting member locates each ceramic member in a near-annular array and seals the flow ports on the distinct faces into the separate flow paths of the heat exchanger. The mounting member adjusts for the temperature gradient in the assembly and the different coefficients of thermal expansion of the members of the assembly during all operating temperatures.

Development of deformation band clusters in porous quartz sandstones - Contribution from microstructural analysis and numerical modeling

NASA Astrophysics Data System (ADS)

Philit, S.; Soliva, R.; Chemenda, A. I.

2017-12-01

Because sandstones form good reservoirs for hydrocarbon, water or C02 storage, the understanding of the deformation processes in sandstones is major. The deformation band clusters result from the localization of the deformation in porous sandstones under the form of gathered low-permeability cataclastic deformation bands. It has recently been shown that this localization is favored in extensional tectonics. The clusters measure tens to hundreds of meters in extent and propagate vertically as long as the sandstone is clean. Because the clusters can form several kilometers long networks, they are likely to hamper fluid flow during reservoir exploitation. Yet, the processes of band accumulation linked to the evolution of the clusters to a potential faulting are poorly understood. An integrated study coupling a microscopic analysis of the deformed granular material in clusters from 7 sites in the world and distinct element numerical modeling permits to propose a model for cluster growth. Our microscopic analysis reveals that the clusters display varying degree of cataclasis, with the most important degrees in the bands. This cataclasis is accompanied by porosity reduction (more reduced in thrust Andersonian regime), and increased Particle Size Distribution. This testifies of an important packing and implies an increased number of particle coordination. During deformation, the grain shape is both smoothened and roughened; the averaged values of the roundness and circularity indicate a rapid roughening of the clasts at the first stages of deformation followed by a slight smoothening. The roughening of the clasts in densely packed material induces high friction and strengthens the material. High residual porosity at some band edges suggests a local dilatant behavior of sheared material. Our distinct element numerical models and other particle models in the literature confirm this observation. The development of force chains with low particle coordination at these locations would weaken the stress resistance at the contact points. Hence, the cluster growth would be promoted by the successive localization of bands the edges of preexisting bands. Faulting could occur at any stage of the cluster development, probably favored along interfaces of minimized strength with smooth geometry.

Interdisciplinary cognitive task analysis: a strategy to develop a comprehensive endoscopic retrograde cholangiopancreatography protocol for use in fellowship training.

PubMed

Canopy, Erin; Evans, Matt; Boehler, Margaret; Roberts, Nicole; Sanfey, Hilary; Mellinger, John

2015-10-01

Endoscopic retrograde cholangiopancreatography is a challenging procedure performed by surgeons and gastroenterologists. We employed cognitive task analysis to identify steps and decision points for this procedure. Standardized interviews were conducted with expert gastroenterologists (7) and surgeons (4) from 4 institutions. A procedural step and cognitive decision point protocol was created from audio-taped transcriptions and was refined by 5 additional surgeons. Conceptual elements, sequential actions, and decision points were iterated for 5 tasks: patient preparation, duodenal intubation, selective cannulation, imaging interpretation with related therapeutic intervention, and complication management. A total of 180 steps were identified. Gastroenterologists identified 34 steps not identified by surgeons, and surgeons identified 20 steps not identified by gastroenterologists. The findings suggest that for complex procedures performed by diverse practitioners, more experts may help delineate distinctive emphases differentiated by training background and type of practice. Copyright © 2015 Elsevier Inc. All rights reserved.

Observe, simplify, titrate, model, and synthesize: A paradigm for analyzing behavior

PubMed Central

Alberts, Jeffrey R.

2013-01-01

Phenomena in behavior and their underlying neural mechanisms are exquisitely complex problems. Infrequently do we reflect on our basic strategies of investigation and analysis, or formally confront the actual challenges of achieving an understanding of the phenomena that inspire research. Philip Teitelbaum is distinct in his elegant approaches to understanding behavioral phenomena and their associated neural processes. He also articulated his views on effective approaches to scientific analyses of brain and behavior, his vision of how behavior and the nervous system are patterned, and what constitutes basic understanding. His rubrics involve careful observation and description of behavior, simplification of the complexity, analysis of elements, and re-integration through different forms of synthesis. Research on the development of huddling behavior by individual and groups of rats is reviewed in a context of Teitelbaum’s rubrics of research, with the goal of appreciating his broad and positive influence on the scientific community. PMID:22481081

Elemental and Microscopic Analysis of Naturally Occurring C-O-Si Hetero-Fullerene-Like Structures.

PubMed

Hullavarad, Nilima V; Hullavarad, Shiva S; Fochesatto, Javier

2015-03-01

Carbon exhibits an ability to form a wide range of structures in nature. Under favorable conditions, carbon condenses to form hollow, spheroid fullerenes in an inert atmosphere. Using high resolution FESEM, we have concealed the existence of giant hetero-fullerene like structures in the natural form. Clear, distinct features of connected hexagons and pentagons were observed. Energy dispersive X-ray analysis depth-profile of natural fullerene structures indicates that Russian-doll-like configurations composed of C, 0, and Si rings exist in nature. The analysis is based on an outstanding molecular feature found in the size fraction of aerosols having diameters 150 nm to 1.0 µm. The fullerene like structures, which are ~ 150 nm in diameter, are observed in large numbers. To the best of our knowledge, this is the first direct detailed observation of natural fullerene-like structures. This article reports inadvertent observation of naturally occurring hetero-fullerene-like structures in the Arctic.

Phytoremediation of Soil Trace Elements

USDA-ARS?s Scientific Manuscript database

Phytoremediation includes several distinct approaches to using plants to achieve soil remediation goals. Phytoextraction uses rare hyperaccumulator plants to accumulate in their shoots enough metals per year to achieve decontamination goals. Phytomining uses hyperaccumulators and biomass burn to pro...

Transposable elements as genetic regulatory substrates in early development.

PubMed

Gifford, Wesley D; Pfaff, Samuel L; Macfarlan, Todd S

2013-05-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. Published by Elsevier Ltd.

Transposable elements as genetic regulatory substrates in early development

PubMed Central

Gifford, Wesley D.; Pfaff, Samuel L.; Macfarlan, Todd S.

2014-01-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. PMID:23411159

The Role of Triads in the Evolution of the Periodic Table: Past and Present

NASA Astrophysics Data System (ADS)

Scerri, Eric

2008-04-01

The purpose of this article is to propose a new design for the presentation of the periodic system of the elements. It is a system that highlights the fundamental importance of elements as basic substances rather than elements as simple substances, a distinction that is explained in the article. The proposed table is a variant of the Janet or left-step periodic table. Furthermore the fundamental nature of atomic number triads of elements is put to use in obtaining a new perfect triad by relocating hydrogen among the halogens to give the triad H, F, Cl. The relative virtues of this table, as compared with the medium-long form and the left-step table, are discussed.

Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships.

PubMed

Koton, Yael; Gordon, Michal; Chalifa-Caspi, Vered; Bisharat, Naiel

2014-01-01

In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically distinct group within the E-cluster. The unique epidemiological circumstances facilitated disease outbreak and brought this genotype to the attention of the scientific community.

Surprise but not coherence: sensitivity to verbal humor in right-hemisphere patients.

PubMed

Brownell, H H; Michel, D; Powelson, J; Gardner, H

1983-01-01

Verbal humor deficits were investigated in right-hemisphere-damaged patients. It was hypothesized that the appreciation of jokes presupposes two elements: sensitivity to the surprise element entailed in the punch line of a joke and apprehension of the coherence which results when the punch line has been integrated with the body of the joke. The possible dissociation between these elements was tested by asking subjects to select from four alternatives the appropriate ending to a joke. Right-hemisphere patients exhibited a selective attraction to endings which contained an element of surprise but which were not otherwise coherent with the body of the joke. This finding suggests that right-hemisphere patients have difficulty in integrating content across parts of a narrative and confirms the psychological reality of the proposed distinction between the surprise and coherence elements of humor processing.

Lead Isotope Compositions of Acid Residues from Olivine-Phyric Shergottite Tissint: Implications for Heterogeneous Shergottite Source Reservoirs

NASA Technical Reports Server (NTRS)

Moriwaki, R.; Usui, T.; Yokoyama, T.; Simon, J. I.; Jones, J. H.

2015-01-01

Geochemical studies of shergottites suggest that their parental magmas reflect mixtures between at least two distinct geochemical source reservoirs, producing correlations between radiogenic isotope compositions and trace element abundances. These correlations have been interpreted as indicating the presence of a reduced, incompatible element- depleted reservoir and an oxidized, incompatible- element-enriched reservoir. The former is clearly a depleted mantle source, but there is ongoing debate regarding the origin of the enriched reservoir. Two contrasting models have been proposed regarding the location and mixing process of the two geochemical source reservoirs: (1) assimilation of oxidized crust by mantle derived, reduced magmas, or (2) mixing of two distinct mantle reservoirs during melting. The former requires the ancient Martian crust to be the enriched source (crustal assimilation), whereas the latter requires isolation of a long-lived enriched mantle domain that probably originated from residual melts formed during solidification of a magma ocean (heterogeneous mantle model). This study conducts Pb isotope and trace element concentration analyses of sequential acid-leaching fractions (leachates and the final residues) from the geochemically depleted olivine-phyric shergottite Tissint. The results suggest that the Tissint magma is not isotopically uniform and sampled at least two geochemical source reservoirs, implying that either crustal assimilation or magma mixing would have played a role in the Tissint petrogenesis.

Sulfur redox chemistry governs diurnal antimony and arsenic cycles at Champagne Pool, Waiotapu, New Zealand

NASA Astrophysics Data System (ADS)

Ullrich, Maria K.; Pope, James G.; Seward, Terry M.; Wilson, Nathaniel; Planer-Friedrich, Britta

2013-07-01

Champagne Pool, a sulfidic hot spring in New Zealand, exhibits distinct diurnal variations in antimony (Sb) and arsenic (As) concentrations, with daytime high and night-time low concentrations. To identify the underlying mobilization mechanisms, five sites along the drainage channel of Champagne Pool were sampled every 2 h during a 24 h period. Temporal variations in elemental concentrations and Sb, As, and sulfur (S) speciation were monitored in the discharging fluid. Total trace element concentrations in filtered and unfiltered samples were analyzed using ICP-MS, and Sb, As and S species were determined by IC-ICP-MS. Sulfur speciation in the drainage channel was dominated by thiosulfate and sulfide at night, while sulfate dominated during the day. The distinct diurnal changes suggest that the transformations are caused by phototrophic sulfur-oxidizing bacteria. These bacteria metabolize thiosulfate and sulfide in daylight to form sulfate and, as suggested by modeling with PhreeqC, elemental sulfur. Sulfide consumption during the day results in undersaturation of antimony sulfides, which triggers the additional release of dissolved Sb. For As, diurnal cycles were much more pronounced in speciation than in total concentrations, with di- and trithioarsenate forming at night due to excess sulfide, and monothioarsenate forming from arsenite and elemental sulfur during the day. Sulfur speciation was thus found to control Sb and As in terms of both solubility and speciation.

Effect of joint spacing and joint dip on the stress distribution around tunnels using different numerical methods

NASA Astrophysics Data System (ADS)

Nikadat, Nooraddin; Fatehi Marji, Mohammad; Rahmannejad, Reza; Yarahmadi Bafghi, Alireza

2016-11-01

Different conditions may affect the stability of tunnels by the geometry (spacing and orientation) of joints in the surrounded rock mass. In this study, by comparing the results obtained by the three novel numerical methods i.e. finite element method (Phase2), discrete element method (UDEC) and indirect boundary element method (TFSDDM), the effects of joint spacing and joint dips on the stress distribution around rock tunnels are numerically studied. These comparisons indicate the validity of the stress analyses around circular rock tunnels. These analyses also reveal that for a semi-continuous environment, boundary element method gives more accurate results compared to the results of finite element and distinct element methods. In the indirect boundary element method, the displacements due to joints of different spacing and dips are estimated by using displacement discontinuity (DD) formulations and the total stress distribution around the tunnel are obtained by using fictitious stress (FS) formulations.

Environmental assessment of Al-Hammar Marsh, Southern Iraq.

PubMed

Al-Gburi, Hind Fadhil Abdullah; Al-Tawash, Balsam Salim; Al-Lafta, Hadi Salim

2017-02-01

(a) To determine the spatial distributions and levels of major and minor elements, as well as heavy metals, in water, sediment, and biota (plant and fish) in Al-Hammar Marsh, southern Iraq, and ultimately to supply more comprehensive information for policy-makers to manage the contaminants input into the marsh so that their concentrations do not reach toxic levels. (b) to characterize the seasonal changes in the marsh surface water quality. (c) to address the potential environmental risk of these elements by comparison with the historical levels and global quality guidelines (i.e., World Health Organization (WHO) standard limits). (d) to define the sources of these elements (i.e., natural and/or anthropogenic) using combined multivariate statistical techniques such as Principal Component Analysis (PCA) and Agglomerative Hierarchical Cluster Analysis (AHCA) along with pollution analysis (i.e., enrichment factor analysis). Water, sediment, plant, and fish samples were collected from the marsh, and analyzed for major and minor ions, as well as heavy metals, and then compared to historical levels and global quality guidelines (WHO guidelines). Then, multivariate statistical techniques, such as PCA and AHCA, were used to determine the element sourcing. Water analyses revealed unacceptable values for almost all physio-chemical and biological properties, according to WHO standard limits for drinking water. Almost all major ions and heavy metal concentrations in water showed a distinct decreasing trend at the marsh outlet station compared to other stations. In general, major and minor ions, as well as heavy metals exhibit higher concentrations in winter than in summer. Sediment analyses using multivariate statistical techniques revealed that Mg, Fe, S, P, V, Zn, As, Se, Mo, Co, Ni, Cu, Sr, Br, Cd, Ca, N, Mn, Cr, and Pb were derived from anthropogenic sources, while Al, Si, Ti, K, and Zr were primarily derived from natural sources. Enrichment factor analysis gave results compatible with multivariate statistical techniques findings. Analysis of heavy metals in plant samples revealed that there is no pollution in plants in Al-Hammar Marsh. However, the concentrations of heavy metals in fish samples showed that all samples were contaminated by Pb, Mn, and Ni, while some samples were contaminated by Pb, Mn, and Ni. Decreasing of Tigris and Euphrates discharges during the past decades due to drought conditions and upstream damming, as well as the increasing stress of wastewater effluents from anthropogenic activities, led to degradation of the downstream Al-Hammar Marsh water quality in terms of physical, chemical, and biological properties. As such properties were found to consistently exceed the historical and global quality objectives. However, element concentration decreasing trend at the marsh outlet station compared to other stations indicate that the marsh plays an important role as a natural filtration and bioremediation system. Higher element concentrations in winter were due to runoff from the washing of the surrounding Sabkha during flooding by winter rainstorms. Finally, the high concentrations of heavy metals in fish samples can be attributed to bioaccumulation and biomagnification processes.

Evolution of the Moon's Mantle and Crust as Reflected in Trace-Element Microbeam Studies of Lunar Magmatism

NASA Astrophysics Data System (ADS)

Shearer, C. K.; Floss, C.

Ion microprobe trace-element studies of lunar cumulates [ferroan anorthosites (FAN), highlands Mg suite (HMS), and highlands alkali suite (HAS)] and volcanic glasses have provided an additional perspective in reconstructing lunar magmatism and early differentiation. Calculated melt compositions for the FANs indicate that a simple lunar magma ocean (LMO) model does not account for differences between FANs with highly magnesian mafic minerals and “typical” ferroan anorthosites. The HMS and HAS appear to have crystallized from magmas that had incompatible trace-element concentrations equal to or greater than KREEP. Partial melting of distinct, hybridized sources is consistent with these calculated melt compositions. However, the high-Mg silicates with relatively low Ni content that are observed in the HMS are suggestive of other possible processes (reduction, metal removal). The compositions of the picritic glasses indicate that they were produced by melting of hybrid cumulate sources produced by mixing of early and late LMO cumulates. The wide compositional range of near-primitive mare basalts indicates small degrees of localized melting preserved the signature of distinct mantle reservoirs. The relationship between ilmenite anomalies and 182W in the mare basalts suggests that the LMO crystallized over a short period of time.

Immersive visualization of rail simulation data.

DOT National Transportation Integrated Search

2016-01-01

The prime objective of this project was to create scientific, immersive visualizations of a Rail-simulation. This project is a part of a larger initiative that consists of three distinct parts. The first step consists of performing a finite element a...

Integrating Multidisciplinary Engineering Knowledge

ERIC Educational Resources Information Center

Wolff, Karin; Luckett, Kathy

2013-01-01

In order to design two distinct engineering qualification levels for an existing University of Technology programme, empirical evidence based on the current diploma is necessary to illuminate the nature of and the relationship between the "contextual" and "conceptual" elements underpinning a multidisciplinary engineering…

Mathematical Geology

ERIC Educational Resources Information Center

Merriam, Daniel F.

1978-01-01

Geomathematics is a developing field that is being used in practical applications. Classification is an important element and the dynamic-cluster method (DCM), a nonhierarchial procedure, was introduced this past year. A method for testing the degree of cluster distinctness was developed also. (MA)

Nd and Sm isotopic composition of spent nuclear fuels from three material test reactors

DOE PAGES

Sharp, Nicholas; Ticknor, Brian W.; Bronikowski, Michael; ...

2016-11-17

Rare earth elements such as neodymium and samarium are ideal for probing the neutron environment that spent nuclear fuels are exposed to in nuclear reactors. The large number of stable isotopes can provide distinct isotopic signatures for differentiating the source material for nuclear forensic investigations. The rare-earth elements were isolated from the high activity fuel matrix via ion exchange chromatography in a shielded cell. The individual elements were then separated using cation exchange chromatography. In conclusion, the neodymium and samarium aliquots were analyzed via MC–ICP–MS, resulting in isotopic compositions with a precision of 0.01–0.3%.

Nd and Sm isotopic composition of spent nuclear fuels from three material test reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharp, Nicholas; Ticknor, Brian W.; Bronikowski, Michael

Rare earth elements such as neodymium and samarium are ideal for probing the neutron environment that spent nuclear fuels are exposed to in nuclear reactors. The large number of stable isotopes can provide distinct isotopic signatures for differentiating the source material for nuclear forensic investigations. The rare-earth elements were isolated from the high activity fuel matrix via ion exchange chromatography in a shielded cell. The individual elements were then separated using cation exchange chromatography. In conclusion, the neodymium and samarium aliquots were analyzed via MC–ICP–MS, resulting in isotopic compositions with a precision of 0.01–0.3%.

Elements of Pacific public health laws: an analysis of the public health acts of Papua New Guinea, Vanuatu, the Solomon Islands, and Fiji.

PubMed

Howse, Genevieve

2012-09-01

Pacific countries are sovereign nations with distinctive histories, ethnicity, customs, primary resources, economies, and health systems. Despite these and other acknowledged differences, similarities exist in many areas such as geography, legal history, and culture. Many share the experience of colonization, with imported British laws and the subsequent experience of independence. Most Pacific countries are also developing countries. This article broadly describes approaches to legislating in public health in Papua New Guinea, Fiji, Vanuatu, and the Solomon Islands and notes common elements in their public health laws, in particular, in relation to administration, allocation of powers and responsibilities, interaction with local government, communicable disease control, and nuisance. The article concludes that many Pacific public health laws could deliver better support for current health policy, more sensitivity to the culture and customs of the region, and better management of public health risk through laws that are better suited to their Pacific environment, easier to understand, more flexible, and more relevant to current health policy.

Update on the Chemical Composition Of Crystalline, Smectite, and Amorphous Components for Rocknest Soil and John Klein and Cumberland Mudstone Drill Fines at Gale Crater, Mars

NASA Technical Reports Server (NTRS)

Morris, R. V.; Ming, D. W.; Gellert, R.; Vaniman, D. T.; Bish, D. L.; Blake, D. F.; Chipera, S. J.; Morrison, S. M.; Downs, R. T.; Rampe, E. B.;

Serial grouping of 2D-image regions with object-based attention in humans

PubMed Central

Jeurissen, Danique; Self, Matthew W; Roelfsema, Pieter R

2016-01-01

After an initial stage of local analysis within the retina and early visual pathways, the human visual system creates a structured representation of the visual scene by co-selecting image elements that are part of behaviorally relevant objects. The mechanisms underlying this perceptual organization process are only partially understood. We here investigate the time-course of perceptual grouping of two-dimensional image-regions by measuring the reaction times of human participants and report that it is associated with the gradual spread of object-based attention. Attention spreads fastest over large and homogeneous areas and is slowed down at locations that require small-scale processing. We find that the time-course of the object-based selection process is well explained by a 'growth-cone' model, which selects surface elements in an incremental, scale-dependent manner. We discuss how the visual cortical hierarchy can implement this scale-dependent spread of object-based attention, leveraging the different receptive field sizes in distinct cortical areas. DOI: http://dx.doi.org/10.7554/eLife.14320.001 PMID:27291188

Quebec platelet disorder is linked to the urokinase plasminogen activator gene (PLAU) and increases expression of the linked allele in megakaryocytes

PubMed Central

Diamandis, Maria; Paterson, Andrew D.; Rommens, Johanna M.; Veljkovic, D. Kika; Blavignac, Jessica; Bulman, Dennis E.; Waye, John S.; Derome, Francine; Rivard, Georges E.

2009-01-01

Quebec platelet disorder (QPD) is an autosomal dominant disorder with high penetrance that is associated with increased risks for bleeding. The hallmark of QPD is a gain-of-function defect in fibrinolysis due to increased platelet content of urokinase plasminogen activator (uPA) without systemic fibrinolysis. We hypothesized that increased expression of uPA by differentiating QPD megakaryocytes is linked to PLAU. Genetic marker analyses indicated that QPD was significantly linked to a 2-Mb region on chromosome 10q containing PLAU with a maximum multipoint logarithm of the odds (LOD) score of +11 between markers D10S1432 and D10S1136. Analysis of PLAU by sequencing and Southern blotting excluded mutations within PLAU and its known regulatory elements as the cause of QPD. Analyses of uPA mRNA indicated that QPD distinctly increased transcript levels of the linked PLAU allele with megakaryocyte differentiation. These findings implicate a mutation in an uncharacterized cis element near PLAU as the cause of QPD. PMID:18988861

Quebec platelet disorder is linked to the urokinase plasminogen activator gene (PLAU) and increases expression of the linked allele in megakaryocytes.

PubMed

Diamandis, Maria; Paterson, Andrew D; Rommens, Johanna M; Veljkovic, D Kika; Blavignac, Jessica; Bulman, Dennis E; Waye, John S; Derome, Francine; Rivard, Georges E; Hayward, Catherine P M

2009-02-12

Quebec platelet disorder (QPD) is an autosomal dominant disorder with high penetrance that is associated with increased risks for bleeding. The hallmark of QPD is a gain-of-function defect in fibrinolysis due to increased platelet content of urokinase plasminogen activator (uPA) without systemic fibrinolysis. We hypothesized that increased expression of uPA by differentiating QPD megakaryocytes is linked to PLAU. Genetic marker analyses indicated that QPD was significantly linked to a 2-Mb region on chromosome 10q containing PLAU with a maximum multipoint logarithm of the odds (LOD) score of +11 between markers D10S1432 and D10S1136. Analysis of PLAU by sequencing and Southern blotting excluded mutations within PLAU and its known regulatory elements as the cause of QPD. Analyses of uPA mRNA indicated that QPD distinctly increased transcript levels of the linked PLAU allele with megakaryocyte differentiation. These findings implicate a mutation in an uncharacterized cis element near PLAU as the cause of QPD.

Variation of Electric Properties Between Surface Permanent Magnet and Interior Permanent Magnet Motor

NASA Astrophysics Data System (ADS)

Woo, Byung-Chul; Hong, Do-Kwan; Lee, Ji-Young

The most distinctive advantage of transverse flux motor(TFM) is high torque density which has prompted many researches into studying various design variants. TFM is well suited for low speed direct drive applications due to its high torque density. This paper deals with simulation based comparisons between a surface permanent magnet transverse flux motor(SPM-TFM) and an interior permanent magnet transverse flux motor(IPM-TFM). A commercial finite element analysis(FEA) software Maxwell 3D is used for electromagnetic field computation to fully analyze complex geometry of the TFMs. General characteristics, such as cogging torque, rated torque and torque ripple characteristics of the two TFMs are analyzed and compared by extensive 3D FEA.

Wigner analysis of three dimensional pupil with finite lateral aperture

PubMed Central

Chen, Hsi-Hsun; Oh, Se Baek; Zhai, Xiaomin; Tsai, Jui-Chang; Cao, Liang-Cai; Barbastathis, George; Luo, Yuan

2015-01-01

A three dimensional (3D) pupil is an optical element, most commonly implemented on a volume hologram, that processes the incident optical field on a 3D fashion. Here we analyze the diffraction properties of a 3D pupil with finite lateral aperture in the 4-f imaging system configuration, using the Wigner Distribution Function (WDF) formulation. Since 3D imaging pupil is finite in both lateral and longitudinal directions, the WDF of the volume holographic 4-f imager theoretically predicts distinct Bragg diffraction patterns in phase space. These result in asymmetric profiles of diffracted coherent point spread function between degenerate diffraction and Bragg diffraction, elucidating the fundamental performance of volume holographic imaging. Experimental measurements are also presented, confirming the theoretical predictions. PMID:25836443

Colorimetric Recognition of Aldehydes and Ketones.

PubMed

Li, Zheng; Fang, Ming; LaGasse, Maria K; Askim, Jon R; Suslick, Kenneth S

2017-08-07

A colorimetric sensor array has been designed for the identification of and discrimination among aldehydes and ketones in vapor phase. Due to rapid chemical reactions between the solid-state sensor elements and gaseous analytes, distinct color difference patterns were produced and digitally imaged for chemometric analysis. The sensor array was developed from classical spot tests using aniline and phenylhydrazine dyes that enable molecular recognition of a wide variety of aliphatic or aromatic aldehydes and ketones, as demonstrated by hierarchical cluster, principal component, and support vector machine analyses. The aldehyde/ketone-specific sensors were further employed for differentiation among and identification of ten liquor samples (whiskies, brandy, vodka) and ethanol controls, showing its potential applications in the beverage industry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

High Performance Ion Mobility Spectrometry Using Hourglass Electrodynamic Funnel And Internal Ion Funnel

DOEpatents

Smith, Richard D.; Tang, Keqi; Shvartsburg, Alexandre A.

2005-11-22

A method and apparatus enabling increased sensitivity in ion mobility spectrometry/mass spectrometry instruments which substantially reduces or eliminates the loss of ions in ion mobility spectrometer drift tubes utilizing a device for transmitting ions from an ion source which allows the transmission of ions without significant delay to an hourglass electrodynamic ion funnel at the entrance to the drift tube and/or an internal ion funnel at the exit of the drift tube. An hourglass electrodynamic funnel is formed of at least an entry element, a center element, and an exit element, wherein the aperture of the center element is smaller than the aperture of the entry element and the aperture of the exit elements. Ions generated in a relatively high pressure region by an ion source at the exterior of the hourglass electrodynamic funnel are transmitted to a relatively low pressure region at the entrance of the hourglass funnel through a conductance limiting orifice. Alternating and direct electrical potentials are applied to the elements of the hourglass electrodynamic funnel thereby drawing ions into and through the hourglass electrodynamic funnel thereby introducing relatively large quantities of ions into the drift tube while maintaining the gas pressure and composition at the interior of the drift tube as distinct from those at the entrance of the electrodynamic funnel and allowing a positive gas pressure to be maintained within the drift tube, if desired. An internal ion funnel is provided within the drift tube and is positioned at the exit of said drift tube. The advantage of the internal ion funnel is that ions that are dispersed away from the exit aperture within the drift tube, such as those that are typically lost in conventional drift tubes to any subsequent analysis or measurement, are instead directed through the exit of the drift tube, vastly increasing the amount of ions exiting the drift tube.

Age and whole rock glass compositions of proximal pyroclastics from the major explosive eruptions of Somma-Vesuvius: A review as a tool for distal tephrostratigraphy

NASA Astrophysics Data System (ADS)

Santacroce, Roberto; Cioni, Raffaello; Marianelli, Paola; Sbrana, Alessandro; Sulpizio, Roberto; Zanchetta, Giovanni; Donahue, Douglas J.; Joron, Jean Louis

2008-10-01

A review of compositional data of the major explosive eruptions of Vesuvius is presented, comparing compositions (major elements) of whole rock with glass shards from the proximal deposits, hopefully useful for long-distance correlation. A critical review of published and new geochronological data is also provided. All available 14C ages are calibrated to give calendar ages useful for the reconstruction of the volcanological evolution of the volcanic complex. The pyroclastic deposits of the four major Plinian eruptions (22,000 yr cal BP "Pomici di Base", 8900 yr cal BP "Mercato Pumice", 4300 yr cal BP "Avellino Pumice", and A.D. 79 "Pompeii Pumice") are widely dispersed and allow a four-folded, Plinian to Plinian, stratigraphic division: 1. B-M (between Pomici di Base and Mercato); 2. M-A (between Mercato and Avellino); 3. A-P (between Avellino and Pompeii); 4. P-XX (from the Pompeii Pumice to the last erupted products of the XXth century). Within each interval, the age, lithologic and compositional features of pyroclastic deposits of major eruptions, potentially useful for tephrostratigraphic purposes on distal areas, are briefly discussed. The Vesuvius rocks are mostly high Potassic products, widely variable in terms of their silica saturation. They form three groups, different for both composition and age: 1. slightly undersaturated, older than Mercato eruption; 2. mildly undersaturated, from Mercato to Pompeii eruptions; 3. highly undersaturated, younger than Pompeii eruption. For whole rock analyses, the peculiar variations in contents of some major and trace elements as well as different trends in element/element ratios, allow a clear, unequivocal, easy diagnosis of the group they belong. Glass analyses show large compositional overlap between different groups, but selected element vs. element plots are distinctive for the three groups. The comparative analysis of glass and whole rock major element compositions provides reliable geochemical criteria helping in the recognition, frequently not obvious, of distal products from the different single eruptions.

Structural characterization of a novel full-length transcript promoter from Horseradish Latent Virus (HRLV) and its transcriptional regulation by multiple stress responsive transcription factors.

PubMed

Khan, Ahamed; Shrestha, Ankita; Bhuyan, Kashyap; Maiti, Indu B; Dey, Nrisingha

2018-01-01

The promoter fragment described in this study can be employed for strong transgene expression under both biotic and abiotic stress conditions. Plant-infecting Caulimoviruses have evolved multiple regulatory mechanisms to address various environmental stimuli during the course of evolution. One such mechanism involves the retention of discrete stress responsive cis-elements which are required for their survival and host-specificity. Here we describe the characterization of a novel Caulimoviral promoter isolated from Horseradish Latent Virus (HRLV) and its regulation by multiple stress responsive Transcription factors (TFs) namely DREB1, AREB1 and TGA1a. The activity of full length transcript (Flt-) promoter from HRLV (- 677 to + 283) was investigated in both transient and transgenic assays where we identified H12 (- 427 to + 73) as the highest expressing fragment having ~ 2.5-fold stronger activity than the CaMV35S promoter. The H12 promoter was highly active and near-constitutive in the vegetative and reproductive parts of both Tobacco and Arabidopsis transgenic plants. Interestingly, H12 contains a distinct cluster of cis-elements like dehydration-responsive element (DRE-core; GCCGAC), an ABA-responsive element (ABRE; ACGTGTC) and as-1 element (TGACG) which are known to be induced by cold, drought and pathogen/SA respectively. The specific binding of DREB1, AREB1 and TGA1a to DRE, ABRE and as-1 elements respectively were confirmed by the gel-binding assays using H12 promoter-specific probes. Detailed mutational analysis of the H12 promoter suggested that the presence of DRE-core and as-1 element was indispensable for its activity which was further confirmed by the transactivation assays. Our studies imply that H12 could be a valuable genetic tool for regulated transgene expression under diverse environmental conditions.

Classifiers utilized to enhance acoustic based sensors to identify round types of artillery/mortar

NASA Astrophysics Data System (ADS)

Grasing, David; Desai, Sachi; Morcos, Amir

2008-04-01

Feature extraction methods based on the statistical analysis of the change in event pressure levels over a period and the level of ambient pressure excitation facilitate the development of a robust classification algorithm. The features reliably discriminates mortar and artillery variants via acoustic signals produced during the launch events. Utilizing acoustic sensors to exploit the sound waveform generated from the blast for the identification of mortar and artillery variants as type A, etcetera through analysis of the waveform. Distinct characteristics arise within the different mortar/artillery variants because varying HE mortar payloads and related charges emphasize varying size events at launch. The waveform holds various harmonic properties distinct to a given mortar/artillery variant that through advanced signal processing and data mining techniques can employed to classify a given type. The skewness and other statistical processing techniques are used to extract the predominant components from the acoustic signatures at ranges exceeding 3000m. Exploiting these techniques will help develop a feature set highly independent of range, providing discrimination based on acoustic elements of the blast wave. Highly reliable discrimination will be achieved with a feedforward neural network classifier trained on a feature space derived from the distribution of statistical coefficients, frequency spectrum, and higher frequency details found within different energy bands. The processes that are described herein extend current technologies, which emphasis acoustic sensor systems to provide such situational awareness.

Artillery/mortar type classification based on detected acoustic transients

NASA Astrophysics Data System (ADS)

Morcos, Amir; Grasing, David; Desai, Sachi

2008-04-01

Feature extraction methods based on the statistical analysis of the change in event pressure levels over a period and the level of ambient pressure excitation facilitate the development of a robust classification algorithm. The features reliably discriminates mortar and artillery variants via acoustic signals produced during the launch events. Utilizing acoustic sensors to exploit the sound waveform generated from the blast for the identification of mortar and artillery variants as type A, etcetera through analysis of the waveform. Distinct characteristics arise within the different mortar/artillery variants because varying HE mortar payloads and related charges emphasize varying size events at launch. The waveform holds various harmonic properties distinct to a given mortar/artillery variant that through advanced signal processing and data mining techniques can employed to classify a given type. The skewness and other statistical processing techniques are used to extract the predominant components from the acoustic signatures at ranges exceeding 3000m. Exploiting these techniques will help develop a feature set highly independent of range, providing discrimination based on acoustic elements of the blast wave. Highly reliable discrimination will be achieved with a feed-forward neural network classifier trained on a feature space derived from the distribution of statistical coefficients, frequency spectrum, and higher frequency details found within different energy bands. The processes that are described herein extend current technologies, which emphasis acoustic sensor systems to provide such situational awareness.

Artillery/mortar round type classification to increase system situational awareness

NASA Astrophysics Data System (ADS)

Desai, Sachi; Grasing, David; Morcos, Amir; Hohil, Myron

2008-04-01

Feature extraction methods based on the statistical analysis of the change in event pressure levels over a period and the level of ambient pressure excitation facilitate the development of a robust classification algorithm. The features reliably discriminates mortar and artillery variants via acoustic signals produced during the launch events. Utilizing acoustic sensors to exploit the sound waveform generated from the blast for the identification of mortar and artillery variants as type A, etcetera through analysis of the waveform. Distinct characteristics arise within the different mortar/artillery variants because varying HE mortar payloads and related charges emphasize varying size events at launch. The waveform holds various harmonic properties distinct to a given mortar/artillery variant that through advanced signal processing and data mining techniques can employed to classify a given type. The skewness and other statistical processing techniques are used to extract the predominant components from the acoustic signatures at ranges exceeding 3000m. Exploiting these techniques will help develop a feature set highly independent of range, providing discrimination based on acoustic elements of the blast wave. Highly reliable discrimination will be achieved with a feedforward neural network classifier trained on a feature space derived from the distribution of statistical coefficients, frequency spectrum, and higher frequency details found within different energy bands. The processes that are described herein extend current technologies, which emphasis acoustic sensor systems to provide such situational awareness.

Challenges in the size analysis of a silica nanoparticle mixture as candidate certified reference material

NASA Astrophysics Data System (ADS)

Kestens, Vikram; Roebben, Gert; Herrmann, Jan; Jämting, Åsa; Coleman, Victoria; Minelli, Caterina; Clifford, Charles; De Temmerman, Pieter-Jan; Mast, Jan; Junjie, Liu; Babick, Frank; Cölfen, Helmut; Emons, Hendrik

2016-06-01

A new certified reference material for quality control of nanoparticle size analysis methods has been developed and produced by the Institute for Reference Materials and Measurements of the European Commission's Joint Research Centre. The material, ERM-FD102, consists of an aqueous suspension of a mixture of silica nanoparticle populations of distinct particle size and origin. The characterisation relied on an interlaboratory comparison study in which 30 laboratories of demonstrated competence participated with a variety of techniques for particle size analysis. After scrutinising the received datasets, certified and indicative values for different method-defined equivalent diameters that are specific for dynamic light scattering (DLS), centrifugal liquid sedimentation (CLS), scanning and transmission electron microscopy (SEM and TEM), atomic force microscopy (AFM), particle tracking analysis (PTA) and asymmetrical-flow field-flow fractionation (AF4) were assigned. The value assignment was a particular challenge because metrological concepts were not always interpreted uniformly across all participating laboratories. This paper presents the main elements and results of the ERM-FD102 characterisation study and discusses in particular the key issues of measurand definition and the estimation of measurement uncertainty.

Using scale and feather traits for module construction provides a functional approach to chicken epidermal development.

PubMed

Bao, Weier; Greenwold, Matthew J; Sawyer, Roger H

2017-11-01

Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules.

Effects of human-induced alteration of groundwater flow on concentrations of naturally-occurring trace elements at water-supply wells

USGS Publications Warehouse

Ayotte, J.D.; Szabo, Z.; Focazio, M.J.; Eberts, S.M.

2011-01-01

The effects of human-induced alteration of groundwater flow patterns on concentrations of naturally-occurring trace elements were examined in five hydrologically distinct aquifer systems in the USA. Although naturally occurring, these trace elements can exceed concentrations that are considered harmful to human health. The results show that pumping-induced hydraulic gradient changes and artificial connection of aquifers by well screens can mix chemically distinct groundwater. Chemical reactions between these mixed groundwaters and solid aquifer materials can result in the mobilization of trace elements such as U, As and Ra, with subsequent transport to water-supply wells. For example, in the High Plains aquifer near York, Nebraska, mixing of shallow, oxygenated, lower-pH water from an unconfined aquifer with deeper, confined, anoxic, higher-pH water is facilitated by wells screened across both aquifers. The resulting higher-O2, lower-pH mixed groundwater facilitated the mobilization of U from solid aquifer materials, and dissolved U concentrations were observed to increase significantly in nearby supply wells. Similar instances of trace element mobilization due to human-induced mixing of groundwaters were documented in: (1) the Floridan aquifer system near Tampa, Florida (As and U), (2) Paleozoic sedimentary aquifers in eastern Wisconsin (As), (3) the basin-fill aquifer underlying the California Central Valley near Modesto (U), and (4) Coastal Plain aquifers of New Jersey (Ra). Adverse water-quality impacts attributed to human activities are commonly assumed to be related solely to the release of the various anthropogenic contaminants to the environment. The results show that human activities including various land uses, well drilling, and pumping rates and volumes can adversely impact the quality of water in supply wells, when associated with naturally-occurring trace elements in aquifer materials. This occurs by causing subtle but significant changes in geochemistry and associated trace element mobilization as well as enhancing advective transport processes.

Transposable elements as a molecular evolutionary force

NASA Technical Reports Server (NTRS)

Fedoroff, N. V.

1999-01-01

This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes

PubMed Central

Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B.; Blanc, Hervé; Verdier, Yann; Vinh, Joelle

2017-01-01

ABSTRACT Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo. The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, characterizing these EVEs is a prerequisite for their potential use to manipulate the mosquito antiviral response. In the study described here, we focused on EVEs related to the Flavivirus genus, to which dengue and Zika viruses belong, in individual Aedes mosquitoes from geographically distinct areas. We show the existence in vivo of flaviviral EVEs previously identified in mosquito cell lines, and we detected new ones. We show that EVEs have evolved differently in each mosquito population. They produce transcripts and small RNAs but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs in Aedes mosquito populations and contributes to an understanding of their role in the host antiviral system. PMID:28539440

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes.

PubMed

Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B; Blanc, Hervé; Verdier, Yann; Vinh, Joelle; Lambrechts, Louis; Saleh, Maria-Carla

2017-08-01

Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, characterizing these EVEs is a prerequisite for their potential use to manipulate the mosquito antiviral response. In the study described here, we focused on EVEs related to the Flavivirus genus, to which dengue and Zika viruses belong, in individual Aedes mosquitoes from geographically distinct areas. We show the existence in vivo of flaviviral EVEs previously identified in mosquito cell lines, and we detected new ones. We show that EVEs have evolved differently in each mosquito population. They produce transcripts and small RNAs but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs in Aedes mosquito populations and contributes to an understanding of their role in the host antiviral system. Copyright © 2017 Suzuki et al.

Frontage Roads in Texas: Legal Issues, Operational Issues, and Land Use Distinctions

DOT National Transportation Integrated Search

2000-08-01

This research project investigates frontage roads as an element of limited-access highway design. The discussion in this paper reviews legal statutes affecting public access to roadways, summarizes studies on access-right valuation, and considers a v...

Highly Siderophile Elements in Shocked and Unshocked Chondrites

NASA Technical Reports Server (NTRS)

Horan, M. F.; Walker, R. J.; Rubin, A. E.

2001-01-01

High precision abundances of Re, Os, Pt, Ir, Ru, and Pd are combined with Re-Os isotopic data to demonstrate that HSE provide a distinctive fingerprint for each of the chondrite groups. Additional information is contained in the original extended abstract.

The Crystal Stratigraphy of Ontong Java Plateau Plagioclase Pegacrysts: New Insights into the Evolution of LIP Magmas.

NASA Astrophysics Data System (ADS)

Neal, C. R.; Kinman, W. S.

2003-12-01

The Ontong Java Plateau (OJP) is the world's largest LIP made up of 2 isotopically distinct lava types that comprise the Singgalo and Kwaimbaita formations (Tejada et al., 2002, J.Pet 43:449). Some Kwaimbaita basaltic flows contain plagioclase-rich cumulate xenoliths. As plagioclase is stable over a range of magmatic conditions, microanalysis of this phase allows the evolution of the parent magma(s) to be constrained (cf. Davidson & Tepley, 1997, Science 275:826). This crystal stratigraphy approach has been applied to cm-size plagioclase megacrysts from three basaltic units (5B, 6, and 7) recovered at ODP Leg 192 Site 1183. Core-to-rim trace element variations were quantified by LA-ICP-MS, major elements by EPMA, and compositional backscatter SEM imaging was used to investigate the subtle compositional zoning and textural features within the plagioclases. All 5 OJP megacrysts sampled show little core-to-rim anorthite variation (82 mol % An +/- 5%); An-rich plagioclase crystals are resistant to re-equilibration and are more likely to retain magmatic trace element signatures (Blundy & Wood, 1991, GCA 55:193). The Unit 7 (oldest) plagioclase contains a relatively Sr, Ga, REE, and Ti poor core bounded by a resorption surface and a relatively Sr, Ga, REE, and Ti rich zone suggesting this crystal was exposed to 2 compositionally distinct magmas. The Unit 6 plagioclase contains a relatively Sr, Ga, REE, and Ti poor core with increasing abundances toward the rim, consistent with evolution through fractional crystallization. This megacryst also contains a distinct resorption surface bounded by a core-like Sr, REE, and Ti poor zone. The three Unit 5B plagioclases display core-to-rim Sr and Ba increases with little core-to-rim REE and Ga variations. The uppermost Unit 5B crystal (youngest) exhibits a core-to-rim decrease in Ti, while the lower 2 crystals display the opposite relationship. We suggest the textural and trace element variations seen in OJP plagioclase megacrysts are again evidence of magma mixing. Reconstructed liquids suggest at least two distinct mixing end members: an enriched end member, similar to Singgalo-type lavas, and a depleted end member, similar to Kwaimbaita type lavas. As the Singgalo- and Kwaimbaita-type basalts are isotopically distinct (I(Sr) = 0.7041 and 0.7038, resp.), Sr isotope determinations of the different plagioclase zones through microdrilling is planned for the near future to test this hypothesis. If correct, it suggests that both the Kwaimbaita and Singgalo sources were active at the same time, which is in contrast to the stratigraphy determined by whole-rock compositions.

Elemental analyses on porcelains of Tang and Song Dynasties excavated from Yongjinwan zone at Jinsha site

NASA Astrophysics Data System (ADS)

Xia, C. D.; Ge, L. J.; Liu, M. T.; Zhu, J. J.; An, Z.; Bai, B.

2018-02-01

The work presented here carried out elemental analyses on 60 porcelain shards of Tang and Song Dynasties, unearthed from Yongjinwan zone at Jinsha site, Sichuan, China, using a combination of PIXE and RBS methods. Six shards from Liulichang kiln site and 6 from Shifangtang kiln site were also analyzed as reference materials. The factor analyses for the elemental compositions in the bodies and glazes of the total 72 porcelain shards have been performed to explore their similarities and differences. Combining the results of factor analyses on elements in bodies and glazes and the classification by traditional archaeological criteria, the provenances for most of shards unearthed from Yongjinwan zone in Jinsha site could be determined. Majority of shards with a Qiong-kiln style were found as products of Liulichang kiln, this is consistent with Yongjinwan's geographical location and social environment, i.e., Yongjinwan was a suburban settlement nearest to Liulichang kiln in ancient times. Although both products of Liulichang kiln and Shifangtang kiln belonged to Qiong-kiln system and they shared a similar appearance such as red body and celadon glaze, there were distinct differences in chemical composition which could be unraveled by PIXE-RBS measurements and factor analysis. There were no apparent differences of chemical compositions for the same kinds of body and glaze between Tang and Song Dynasties, which may suggest that raw materials and production techniques for the same kinds of body and glaze continued between Tang and Song Dynasties. The chemical characteristics for each kind of body and glaze and the correlations between element composition and porcelain appearance were also obtained in this work.

Tools and techniques for developing tephra stratigraphies in lake cores: A case study from the basaltic Auckland Volcanic Field, New Zealand

NASA Astrophysics Data System (ADS)

Hopkins, Jenni L.; Millet, Marc-Alban; Timm, Christian; Wilson, Colin J. N.; Leonard, Graham S.; Palin, J. Michael; Neil, Helen

2015-09-01

Probabilistic hazard forecasting for a volcanic region relies on understanding and reconstructing the eruptive record (derived potentially from proximal as well as distal volcanoes). Tephrostratigraphy is commonly used as a reconstructive tool by cross-correlating tephra deposits to create a stratigraphic framework that can be used to assess magnitude-frequency relationships for eruptive histories. When applied to widespread rhyolitic deposits, tephra identifications and correlations have been successful; however, the identification and correlation of basaltic tephras are more problematic. Here, using tephras in drill cores from six maars in the Auckland Volcanic Field (AVF), New Zealand, we show how X-ray density scanning coupled with magnetic susceptibility analysis can be used to accurately and reliably identify basaltic glass shard-bearing horizons in lacustrine sediments and which, when combined with the major and trace element signatures of the tephras, can be used to distinguish primary from reworked layers. After reliably identifying primary vs. reworked basaltic horizons within the cores, we detail an improved method for cross-core correlation based on stratigraphy and geochemical fingerprinting. We present major and trace element data for individual glass shards from 57 separate basaltic horizons identified within the cores. Our results suggest that in cases where major element compositions (SiO2, CaO, Al2O3, FeO, MgO) do not provide unambiguous correlations, trace elements (e.g. La, Gd, Yb, Zr, Nb, Nd) and trace element ratios (e.g. [La/Yb]N, [Gd/Yb]N, [Zr/Yb]N) are successful in improving the compositional distinction between the AVF basaltic tephra horizons, thereby allowing an improved eruptive history of the AVF to be reconstructed.

Comparison of Ultra-Conserved Elements in Drosophilids and Vertebrates

PubMed Central

Makunin, Igor V.; Shloma, Viktor V.; Stephen, Stuart J.; Pheasant, Michael; Belyakin, Stepan N.

2013-01-01

Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption. PMID:24349264

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

PubMed

Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job

2016-01-07

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Two distinct cellular proteins interact with the EIa-responsive element of an adenovirus early promoter.

PubMed Central

Jansen-Durr, P; Wintzerith, M; Reimund, B; Hauss, C; Kédinger, C

1990-01-01

EIa-dependent transactivation of the adenovirus EIIa early (EIIaE) promoter is correlated with the activation of the cellular transcription factor E2F. In this study we identified a cellular protein, C alpha, that is distinct from E2F and that binds two sites in the EIIaE promoter, one of which overlaps with the proximal E2F binding site of the EIIaE promoter. The possible involvement of C alpha in the EIa responsiveness of this promoter is discussed. Images PMID:2139142

Age Distribution of Lunar Impact-Melt Rocks in Apollo Drive-Tube 68001/2

NASA Technical Reports Server (NTRS)

Curran, N. M.; Bower, D. M.; Frasl, B.; Cohen, B. A.

2018-01-01

Apollo 16 double-drive tube 68001 /68002 provides impact and volcanic materials along a depth of approximately 60 cm in five compositional distinct units. 68001 /2 offers the potential to study distinct populations of impact melts with depth to understand how 'gardening' affects these samples. We will use unbiased major-element chemistry, mineralogy, and age to understand the impact history of Apollo 16 landing site. The study demonstrates the techniques that landed missions require to identify lithologies of interest (e.g., impact melts).

Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

NASA Technical Reports Server (NTRS)

Rosner, D. E.; Nagarajan, R.

1985-01-01

Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

Magma batches in the Timber Mountain magmatic system, Southwestern Nevada Volcanic Field, Nevada, USA

NASA Astrophysics Data System (ADS)

Mills, James G.; Saltoun, Benjamin W.; Vogel, Thomas A.

1997-09-01

The common occurrence of compositionally and mineralogically zoned ash flow sheets, such as those of the Timber Mountain Group, provides evidence that the source magma bodies were chemically and thermally zoned. The Rainier Mesa and Ammonia Tanks tuffs of the Timber Mountain Group are both large volume (1200 and 900 km 3, respectively) chemically zoned (57-78 wt.% SiO 2) ash flow sheets. Evidence of distinct magma batches in the Timber Mountain system are based on: (1) major- and trace-element variations of whole pumice fragments; (2) major-element variations in phenocrysts; (3) major-element variations in glass matrix; and (4) emplacement temperatures calculated from Fe-Ti oxides and feldspars. There are three distinct groups of pumice fragments in the Rainier Mesa Tuff: a low-silica group and two high-silica groups (a low-Th and a high-Th group). These groups cannot be related by crystal fractionation. The low-silica portion of the Rainier Mesa Tuff is distinct from the low-silica portion of the overlying Ammonia Tanks Tuff, even though the age difference is less than 200,000 years. Three distinct groups occur in the Ammonia Tanks Tuff: a low-silica, intermediate-silica and a high-silica group. Part of the high-silica group may be due to mixing of the two high-silica Rainier Mesa groups. The intermediate-silica group may be due to mixing of the low- and high-silica Ammonia Tanks groups. Three distinct emplacement temperatures occur in the Rainier Mesa Tuff (869, 804, 723 °C) that correspond to the low-silica, high-Th and low-Th magma batches, respectively. These temperature differences could not have been maintained for any length of time in the magma chamber (cf. Turner, J.S., Campbell, I.H., 1986. Convection and mixing in magma chambers. Earth-Sci. Rev. 23, 255-352; Martin, D., Griffiths, R.W., Campbell, I.H., 1987. Compositional and thermal convection in magma chambers. Contrib. Mineral. Petrol. 96, 465-475) and therefore eruption must have occurred soon after emplacement of the magma batches into the chamber. Emplacement temperatures of the pumice fragments from the Ammonia Tanks Tuff show a continuous gradient of temperatures with composition. This continuous temperature gradient is consistent with the model of storage of magma batches in the Ammonia Tanks group that have undergone both thermal and chemical diffusion.

Application of New Partition Coefficients to Modeling Plagioclase

NASA Technical Reports Server (NTRS)

Fagan, A. L.; Neal, C. R.; Rapp, J. F.; Draper, D. S.; Lapen, T. J.

2017-01-01

Previously, studies that determined the partition coefficient for an element, i, between plagioclase and the residual basaltic melt (Di plag) have been conducted using experimental conditions dissimilar from the Moon, and thus these values are not ideal for modeling plagioclase fractionation in a lunar system. However, recent work [1] has determined partition coefficients for plagioclase at lunar oxygen fugacities, and resulted in plagioclase with Anorthite contents =An90; these are significantly more calcic than plagioclase in previous studies, and the An content has a profound effect on partition coefficient values [2,3]. Plagioclase D-values, which are dependent on the An content of the crystal [e.g., 2-6], can be determined using published experimental data and the correlative An contents. Here, we examine new experimental data from [1] to ascertain their effect on the calculation of equilibrium liquids from Apollo 16 sample 60635,2. This sample is a coarse grained, subophitic impact melt composed of 55% plagioclase laths with An94.4-98.7 [7,8], distinctly more calcic than of previous partition coefficient studies (e.g., [3-6, 9-10]). Sample 60635,2 is notable as having several plagioclase trace element analyses containing a negative Europium anomaly (-Eu) in the rare-earth element (REE) profile, rather than the typical positive Eu anomaly (+Eu) [7-8] (Fig. 1). The expected +Eu is due to the similarity in size and charge with Ca2+, thereby allowing Eu2+ to be easily taken up by the plagioclase crystal structure, in contrast to the remaining REE3+. Some 60635,2 plagioclase crystals only have +Eu REE profiles, some only have -Eu REE profiles, and some +Eu and -Eu analyses in different areas on a single crystal [7, 8]. Moreover, there does not seem to be any core-rim association with the +Eu or -Eu analyses, nor does there appear to be a correlation between the size, shape, or location of a particular crystal within the sample and the sign of its Eu anomaly, which suggests a complex evolution. In order to investigate this sample further, we can calculate the equilibrium liquids, but with An contents distinct from previous experimental studies, we must calculate the appropriate partition coefficients for each trace element analysis.

Structural features of diverse Pin-II proteinase inhibitor genes from Capsicum annuum.

PubMed

Mahajan, Neha S; Dewangan, Veena; Lomate, Purushottam R; Joshi, Rakesh S; Mishra, Manasi; Gupta, Vidya S; Giri, Ashok P

2015-02-01

The proteinase inhibitor (PI) genes from Capsicum annuum were characterized with respect to their UTR, introns and promoter elements. The occurrence of PIs with circularly permuted domain organization was evident. Several potato inhibitor II (Pin-II) type proteinase inhibitor (PI) genes have been analyzed from Capsicum annuum (L.) with respect to their differential expression during plant defense response. However, complete gene characterization of any of these C. annuum PIs (CanPIs) has not been carried out so far. Complete gene architectures of a previously identified CanPI-7 (Beads-on-string, Type A) and a member of newly isolated Bracelet type B, CanPI-69 are reported in this study. The 5' UTR (untranslated region), 3'UTR, and intronic sequences of both the CanPI genes were obtained. The genomic sequence of CanPI-7 exhibited, exon 1 (49 base pair, bp) and exon 2 (740 bp) interrupted by a 294-bp long type I intron. We noted the occurrence of three multi-domain PIs (CanPI-69, 70, 71) with circularly permuted domain organization. CanPI-69 was found to possess exon 1 (49 bp), exon 2 (551 bp) and a 584-bp long type I intron. The upstream sequence analysis of CanPI-7 and CanPI-69 predicted various transcription factor-binding sites including TATA and CAAT boxes, hormone-responsive elements (ABRELATERD1, DOFCOREZM, ERELEE4), and a defense-responsive element (WRKY71OS). Binding of transcription factors such as zinc finger motif MADS-box and MYB to the promoter regions was confirmed using electrophoretic mobility shift assay followed by mass spectrometric identification. The 3' UTR analysis for 25 CanPI genes revealed unique/distinct 3' UTR sequence for each gene. Structures of three domain CanPIs of type A and B were predicted and further analyzed for their attributes. This investigation of CanPI gene architecture will enable the better understanding of the genetic elements present in CanPIs.

Finite element modeling of temperature load effects on the vibration of local modes in multi-cable structures

NASA Astrophysics Data System (ADS)

Treyssède, Fabien

2018-01-01

Understanding thermal effects on the vibration of local (cable-dominant) modes in multi-cable structures is a complicated task. The main difficulty lies in the modification by temperature change of cable tensions, which are then undetermined. This paper applies a finite element procedure to investigate the effects of thermal loads on the linear dynamics of prestressed self-weighted multi-cable structures. Provided that boundary conditions are carefully handled, the discretization of cables with nonlinear curved beam elements can properly represent the thermoelastic behavior of cables as well as their linearized dynamics. A three-step procedure that aims to replace applied pretension forces with displacement continuity conditions is used. Despite an increase in the computational cost related to beam rotational degrees of freedom, such an approach has several advantages. Nonlinear beam finite elements are usually available in commercial codes. The overall method follows a thermoelastic geometrically non-linear analysis and hereby includes the main sources of non-linearities in multi-cable structures. The effects of cable bending stiffness, which can be significant, are also naturally accounted for. The accuracy of the numerical approach is assessed thanks to an analytical model for the vibration of a single inclined cable under temperature change. Then, the effects of thermal loads are investigated for two cable bridges, highlighting how natural frequencies can be affected by temperature. Although counterintuitive, a reverse relative change of natural frequency may occur for certain local modes. This phenomenon can be explained by two distinct mechanisms, one related to the physics intrinsic to cables and the other related to the thermal deflection of the superstructure. Numerical results show that cables cannot be isolated from the rest of the structure and the importance of modeling the whole structure for a quantitative analysis of temperature effects on the dynamics of cable bridges.

Early palliative care in advanced lung cancer: a qualitative study.

PubMed

Yoong, Jaclyn; Park, Elyse R; Greer, Joseph A; Jackson, Vicki A; Gallagher, Emily R; Pirl, William F; Back, Anthony L; Temel, Jennifer S

2013-02-25

BACKGROUND Early ambulatory palliative care (PC) is an emerging practice, and its key elements have not been defined. We conducted a qualitative analysis of data from a randomized controlled trial that demonstrated improved quality of life, mood, and survival in patients with newly diagnosed metastatic non-small cell lung cancer who received early PC integrated with standard oncologic care vs standard oncologic care alone. Our objectives were to (1) identify key elements of early PC clinic visits, (2) explore the timing of key elements, and (3) compare the content of PC and oncologic visit notes at the critical time points of clinical deterioration and radiographic disease progression. METHODS We randomly selected 20 patients who received early PC and survived within 4 periods: less than 3 months (n = 5), 3 to 6 months (n = 5), 6 to 12 months (n = 5), and 12 to 24 months (n = 5). We performed content analysis on PC and oncologic visit notes from the electronic health records of these patients. RESULTS Addressing symptoms and coping were the most prevalent components of the PC clinic visits. Initial visits focused on building relationships and rapport with patients and their families and on illness understanding, including prognostic awareness. Discussions about resuscitation preferences and hospice predominantly occurred during later visits. Comparing PC and oncologic care visits around critical time points, both included discussions about symptoms and illness status; however, PC visits emphasized psychosocial elements, such as coping, whereas oncologic care visits focused on cancer treatment and management of medical complications. CONCLUSIONS Early PC clinic visits emphasize managing symptoms, strengthening coping, and cultivating illness understanding and prognostic awareness in a responsive and time-sensitive model. During critical clinical time points, PC and oncologic care visits have distinct features that suggest a key role for PC involvement and enable oncologists to focus on cancer treatment and managing medical complications.

Species Delimitation and Global Biosecurity

PubMed Central

Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

2012-01-01

Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might be drawn. In the species cases here, the results clearly indicate that there is a need for more gene sampling to substantiate either the new cohort of species indicated for B. tabaci or to detect the established subspecies taxonomy of L. dispar. Given the ease of use through the Geneious species delimitation plugins, similar analysis of such multi-gene datasets would be easily accommodated. Overall, the tip to root approach described here is recommended where careful consideration of species delimitation is required to support crucial biosecurity decisions based on accurate species identification. PMID:22267902

Root anatomy and element distribution vary between two Salix caprea isolates with different Cd accumulation capacities

PubMed Central

Vaculík, Marek; Konlechner, Cornelia; Langer, Ingrid; Adlassnig, Wolfram; Puschenreiter, Markus; Lux, Alexander; Hauser, Marie-Theres

2012-01-01

The understanding of the influence of toxic elements on root anatomy and element distribution is still limited. This study describes anatomical responses, metal accumulation and element distribution of rooted cuttings of Salix caprea after exposure to Cd and/or Zn. Differences in the development of apoplastic barriers and tissue organization in roots between two distinct S. caprea isolates with divergent Cd uptake and accumulation capacities in leaves might reflect an adaptive predisposition based on different natural origins. Energy-dispersive X-ray spectroscopy (EDX) revealed that Cd and Zn interfered with the distribution of elements in a tissue- and isolate-specific manner. Zinc, Ca, Mg, Na and Si were enriched in the peripheral bark, K and S in the phloem and Cd in both vascular tissues. Si levels were lower in the superior Cd translocator. Since the cuttings originated from stocks isolated from polluted and unpolluted sites we probably uncovered different strategies against toxic elements. PMID:22325439

14 CFR 27.671 - General.

Code of Federal Regulations, 2011 CFR

2011-01-01

... STANDARDS: NORMAL CATEGORY ROTORCRAFT Design and Construction Control Systems § 27.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 27.671 - General.

Code of Federal Regulations, 2012 CFR

2012-01-01

... STANDARDS: NORMAL CATEGORY ROTORCRAFT Design and Construction Control Systems § 27.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 27.671 - General.

Code of Federal Regulations, 2010 CFR

2010-01-01

... STANDARDS: NORMAL CATEGORY ROTORCRAFT Design and Construction Control Systems § 27.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 29.671 - General.

Code of Federal Regulations, 2013 CFR

2013-01-01

... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Design and Construction Control Systems § 29.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 25.671 - General.

Code of Federal Regulations, 2014 CFR

2014-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 25.671 - General.

Code of Federal Regulations, 2012 CFR

2012-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 25.671 - General.

Code of Federal Regulations, 2010 CFR

2010-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 27.671 - General.

Code of Federal Regulations, 2013 CFR

2013-01-01

... STANDARDS: NORMAL CATEGORY ROTORCRAFT Design and Construction Control Systems § 27.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 27.671 - General.

Code of Federal Regulations, 2014 CFR

2014-01-01

... STANDARDS: NORMAL CATEGORY ROTORCRAFT Design and Construction Control Systems § 27.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

14 CFR 25.671 - General.

Code of Federal Regulations, 2011 CFR

2011-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Design and Construction Control Systems § 25.671 General. (a) Each control and control system must operate with the ease, smoothness, and positiveness appropriate to its function. (b) Each element of each flight control system must be designed, or distinctively and permanently...

A New Material Mapping Procedure for Quantitative Computed Tomography-Based, Continuum Finite Element Analyses of the Vertebra

PubMed Central

Unnikrishnan, Ginu U.; Morgan, Elise F.

2011-01-01

Inaccuracies in the estimation of material properties and errors in the assignment of these properties into finite element models limit the reliability, accuracy, and precision of quantitative computed tomography (QCT)-based finite element analyses of the vertebra. In this work, a new mesh-independent, material mapping procedure was developed to improve the quality of predictions of vertebral mechanical behavior from QCT-based finite element models. In this procedure, an intermediate step, called the material block model, was introduced to determine the distribution of material properties based on bone mineral density, and these properties were then mapped onto the finite element mesh. A sensitivity study was first conducted on a calibration phantom to understand the influence of the size of the material blocks on the computed bone mineral density. It was observed that varying the material block size produced only marginal changes in the predictions of mineral density. Finite element (FE) analyses were then conducted on a square column-shaped region of the vertebra and also on the entire vertebra in order to study the effect of material block size on the FE-derived outcomes. The predicted values of stiffness for the column and the vertebra decreased with decreasing block size. When these results were compared to those of a mesh convergence analysis, it was found that the influence of element size on vertebral stiffness was less than that of the material block size. This mapping procedure allows the material properties in a finite element study to be determined based on the block size required for an accurate representation of the material field, while the size of the finite elements can be selected independently and based on the required numerical accuracy of the finite element solution. The mesh-independent, material mapping procedure developed in this study could be particularly helpful in improving the accuracy of finite element analyses of vertebroplasty and spine metastases, as these analyses typically require mesh refinement at the interfaces between distinct materials. Moreover, the mapping procedure is not specific to the vertebra and could thus be applied to many other anatomic sites. PMID:21823740

Fate and agricultural consequences of leachable elements added to the environment from the 2011 Cordón Caulle tephra fall

NASA Astrophysics Data System (ADS)

Stewart, Carol; Craig, Heather M.; Gaw, Sally; Wilson, Thomas; Villarosa, Gustavo; Outes, Valeria; Cronin, Shane; Oze, Christopher

2016-11-01

The June 2011 eruption of Cordón Caulle volcano, Chile, dispersed tephra over 350,000 km2, including productive agricultural land. This resulted in the death of nearly one million livestock. Two distinct environments were affected: a proximal temperate Andean setting, and the semi-arid Argentine steppe farther from the volcano. The purpose of this study was to better understand the fate and agricultural consequences of leachable elements added to the environment by this large silicic tephra fall. Tephra, soil and surface water samples across the depositional area were collected both immediately after the eruption (tephra and water) and nine months afterwards (tephra, soil and water). Tephra samples were analysed following a new hazard assessment protocol developed by the International Volcanic Health Hazard Network (IVHHN). Water-extractable element concentrations in freshly-collected tephra were very low to low compared to other eruptions, and showed no trends with distance from the volcano. Surface water analyses suggested short-term changes to water composition due to the release of elements from tephra. No effect on the fertility of soils underlying tephra was apparent after nine months. Water-extractable fluorine (F) in freshly-collected tephra ranged from 12 to 167 mg/kg, with a median value of 67 mg/kg. Based on parallels with the 11-12 October 1995 eruption of Ruapehu volcano, New Zealand, we conclude that F toxicity was a possible contributing factor to the large-scale livestock deaths as well as to chronic fluorosis widely reported in wild deer populations across the Cordón Caulle tephra depositional area. Finally, we recommend that effective response to widespread tephra fall over agricultural areas should include: (1) rapid, statistically representative field sampling of tephra, soils, surface water supplies and forage crops; (2) analysis using appropriate and reliable laboratory methods; (3) modelling both short and long-term impacts on the ecosystem, especially for elements that may generate chronic hazard; (4) timely dissemination of results to agricultural agencies; (5) longitudinal sampling and monitoring to adapt impact models; and (6) developing reliable animal fatality diagnoses through autopsies and chemical analysis.

Flexible Retrieval: When True Inferences Produce False Memories

PubMed Central

Carpenter, Alexis C.; Schacter, Daniel L.

2016-01-01

Episodic memory involves flexible retrieval processes that allow us to link together distinct episodes, make novel inferences across overlapping events, and recombine elements of past experiences when imagining future events. However, the same flexible retrieval and recombination processes that underpin these adaptive functions may also leave memory prone to error or distortion, such as source misattributions in which details of one event are mistakenly attributed to another related event. To determine whether the same recombination-related retrieval mechanism supports both successful inference and source memory errors, we developed a modified version of an associative inference paradigm in which participants encoded everyday scenes comprised of people, objects, and other contextual details. These scenes contained overlapping elements (AB, BC) that could later be linked to support novel inferential retrieval regarding elements that had not appeared together previously (AC). Our critical experimental manipulation concerned whether contextual details were probed before or after the associative inference test, thereby allowing us to assess whether a) false memories increased for successful versus unsuccessful inferences, and b) any such effects were specific to after as compared to before participants received the inference test. In each of four experiments that used variants of this paradigm, participants were more susceptible to false memories for contextual details after successful than unsuccessful inferential retrieval, but only when contextual details were probed after the associative inference test. These results suggest that the retrieval-mediated recombination mechanism that underlies associative inference also contributes to source misattributions that result from combining elements of distinct episodes. PMID:27918169

Numerical slope stability simulations of chasma walls in Valles Marineris/Mars using a distinct element method (dem).

NASA Astrophysics Data System (ADS)

Imre, B.

2003-04-01

NUMERICAL SLOPE STABILITY SIMULATIONS OF CHASMA WALLS IN VALLES MARINERIS/MARS USING A DISTINCT ELEMENT METHOD (DEM). B. Imre (1) (1) German Aerospace Center, Berlin Adlershof, bernd.imre@gmx.net The 8- to 10-km depths of Valles Marineris (VM) offer excellent views into the upper Martian crust. Layering, fracturing, lithology, stratigraphy and the content of volatiles have influenced the evolution of the Valles Marineris wallslopes. But these parameters also reflect the development of VM and its wall slopes. The scope of this work is to gain understanding in these parameters by back-simulating the development of wall slopes. For that purpose, the two dimensional Particle Flow Code PFC2D has been chosen (ITASCA, version 2.00-103). PFC2D is a distinct element code for numerical modelling of movements and interactions of assemblies of arbitrarily sized circular particles. Particles may be bonded together to represent a solid material. Movements of particles are unlimited. That is of importance because results of open systems with numerous unknown variables are non-unique and therefore highly path dependent. This DEM allows the simulation of whole development paths of VM walls what makes confirmation of the model more complete (e.g. Oreskes et al., Science 263, 1994). To reduce the number of unknown variables a proper (that means as simple as possible) field-site had to be selected. The northern wall of eastern Candor Chasma has been chosen. This wall is up to 8-km high and represents a significant outcrop of the upper Martian crust. It is quite uncomplex, well-aligned and of simple morphology. Currently the work on the model is at the stage of performing the parameter study. Results will be presented via poster by the EGS-Meeting.

End-Permian mass extinction and palaeoenvironmental changes in Neotethys: Evidence from an oceanic carbonate section in southwestern Tibet

NASA Astrophysics Data System (ADS)

Shen, Shu-zhong; Cao, Chang-qun; Zhang, Yi-chun; Li, Wen-zhong; Shi, G. R.; Wang, Yue; Wu, Ya-sheng; Ueno, K.; Henderson, C. M.; Wang, Xiang-dong; Zhang, Hua; Wang, Xiao-juan; Chen, Jun

2010-08-01

This paper documents a new Permian-Triassic carbonate sequence which recorded the end-Permian mass extinction in the isolated oceanic setting of Neotethys in southwestern Tibet, China. The sequence is over 350 m thick and consists of the Gyanyima and the Lower Lanchengquxia formations in ascending order. The Lopingian (Late Permian) Gyanyima Formation is composed of fossiliferous reddish carbonates dominated by Colaniella grainstone and reef facies including fenestrate/sponge/coral framestone and bafflestone. 156 species are recognized from the Lopingian Gyanyima Formation. Composite ranges of brachiopods, ostracods, rugose corals and foraminifers at the Gyanyima Section suggest that evolution and diversification of Permian marine organisms continued to the end-Permian preceding a major faunal extinction close to the Permian-Triassic boundary (PTB), coincident with a 2-3‰ negative shift of δ13C carb. The timing and accelerating extinction pattern and the negative δ13C carb excursion are largely comparable with those reported from many previously-documented sections on continental shelf environments. Based on a detailed lithofacies analysis, the latest Permian reefal facies is sharply replaced by ostracod/crinoid packstone/grainstone with abrupt abundant occurrences of Early Triassic conodonts at the Gyanyima Section. This is then followed by thrombolitic microbialite, stromatolite, packstone containing abundant spherical microbes, and bivalve/ammonoid packstone of tidal and intertidal facies. This distinct lithofacies and biofacies shift would, therefore, suggest a dramatic faunal community and environmental change across the PTB. Distinct palaeoclimate fluctuations through the P- T interval are also indicated by the alternation of warm- and cool-water faunas through the uppermost part of the succession. The lower part of the Gyanyima Formation is characterized by a warm condition as indicated by Cathaysian-dominated fossils. This was then followed by a mild cooling event as suggested by the occurrence of many distinct peri-Gondwanan elements and absence of compound corals. The latest Changhsingian is characterized exclusively by warm-water faunal elements of Cathaysian affinities, together with the negative shift of δ13C carb, suggesting a rapid warming event at the very end of Permian in association with much more widespread volcanic activities than we thought before.

Genetic element from human surfactant protein SP-C gene confers bronchiolar-alveolar cell specificity in transgenic mice.

PubMed

Glasser, S W; Korfhagen, T R; Wert, S E; Bruno, M D; McWilliams, K M; Vorbroker, D K; Whitsett, J A

1991-10-01

Transgenic mice bearing chimeric genes consisting of 5'-sequences derived from the human surfactant protein C (SP-C) gene and the bacterial chloramphenicol acetyltransferase (CAT) gene were generated. Analysis of CAT activity was utilized to demonstrate tissue-specific and developmental expression of chimeric genes containing 3.7 kb of sequences from the human SP-C gene. Lung-specific expression of the 3.7 SP-C-CAT transgene was observed in eight distinct transgenic mouse lines. Expression of the 3.7 SP-C-CAT transgene was first detected in fetal lung on day 11 of gestation and increased dramatically with advancing gestational age, reaching adult levels of activity before birth. In situ hybridization demonstrated that expression of 3.7 SP-C-CAT mRNA was confined to the distal respiratory epithelium. Antisense CAT hybridization was detected in bronchiolar and type II epithelial cells in the adult lung of the 3.7 SP-C-CAT transgenic mice. In situ hybridization of four distinct 3.7 SP-C-CAT transgenic mouse lines demonstrated bronchiolar-alveolar expression of the chimeric CAT gene, although the relative intensity of expression at each site varied within the lines studied. Glucocorticoids increased murine SP-C mRNA in fetal lung organ culture. Likewise, expression of 3.7 SP-C-CAT transgene increased during fetal lung organ or explant culture and was further enhanced by glucocorticoid in vitro. The 5'-regions of human SP-C conferred developmental, lung epithelial, and glucocorticoid-enhanced expression of bacterial CAT in transgenic mice. The increased expression of SP-C accompanying prenatal lung development and exposure to glucocorticoid is mediated, at least in part, at the transcriptional level, being influenced by cis-active elements contained within the 5'-flanking region of the human SP-C gene.

The State-of-the-art HST Astro-photometric Analysis of the Core of ω Centauri. III. The Main Sequence's Multiple Populations Galore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bellini, A.; Anderson, J.; Van der Marel, R. P.

We take advantage of the exquisite quality of the Hubble Space Telescope 26-filter astro-photometric catalog of the core of ω Cen presented in the first paper of this series and the empirical differential-reddening correction presented in the second paper in order to distill the main sequence into its constituent populations. To this end, we restrict ourselves to the five most useful filters: the magic “trio” of F275W, F336W, and F438W, along with F606W and F814W. We develop a strategy for identifying color systems where different populations stand out most distinctly, then we isolate those populations and examine them in othermore » filters where their subpopulations also come to light. In this way, we have identified at least 15 subpopulations, each of which has a distinctive fiducial curve through our five-dimensional photometric space. We confirm the MSa to be split into two subcomponents, and find that both the bMS and the rMS are split into three subcomponents. Moreover, we have discovered two additional MS groups: the MSd (which has three subcomponents) shares similar properties with the bMS, and the MSe (which has four subcomponents) has properties more similar to those of the rMS. We examine the fiducial curves together and use synthetic spectra to infer relative heavy-element, light-element, and helium abundances for the populations. Our findings show that the stellar populations and star formation history of ω Cen are even more complex than inferred previously. Finally, we provide as a supplement to the original catalog a list that identifies for each star which population it is most likely associated with.« less

Patterns of larval source distribution and mixing in early life stages of Pacific cod (Gadus macrocephalus) in the southeastern Bering Sea

NASA Astrophysics Data System (ADS)

Miller, Jessica A.; DiMaria, Ruth A.; Hurst, Thomas P.

2016-12-01

Effective and sustainable management depends on knowledge of spawning locations and their relative contributions to marine fish populations. Pacific cod (Gadus macrocephalus) in the southeastern Bering Sea aggregate at discrete spawning locations but there is little information on patterns of larval dispersal and the relative contribution of specific spawning areas to nursery habitats. Age-0 Pacific cod from two cohorts (2006 and 2008) were examined to address the following questions: (1) does size, age, and otolith chemistry vary among known capture locations; (2) can variation in elemental composition of the otolith cores (early larval signatures) be used to infer the number of chemically distinct sources contributing to juvenile recruits in the Bering Sea; and (3) to what extent are juvenile collection locations represented by groups of fish with similar chemical histories throughout their early life history? Hierarchical cluster (HCA) and discriminant function analyses (DFA) were used to examine variation in otolith chemistry at discrete periods throughout the early life history. HCA identified five chemically distinct groups of larvae in the 2006 cohort and three groups in 2008; however, three sources accounted for 80-100% of the juveniles in each year. DFA of early larval signatures indicated that there were non-random spatial distributions of early larvae in both years, which may reflect interannual variation in regional oceanography. There was also a detectable and substantial level of coherence in chemical signatures within groups of fish throughout the early life history. The variation in elemental signatures throughout the early life history (hatch to capture) indicates that otolith chemical analysis could be an effective tool to further clarify larval sources and dispersal, identify juvenile nursery habitats, and estimate the contributions of juvenile nursery habitats to the adult population within the southeastern Bering Sea.

A new method for computation of eigenvector derivatives with distinct and repeated eigenvalues in structural dynamic analysis

NASA Astrophysics Data System (ADS)

Li, Zhengguang; Lai, Siu-Kai; Wu, Baisheng

2018-07-01

Determining eigenvector derivatives is a challenging task due to the singularity of the coefficient matrices of the governing equations, especially for those structural dynamic systems with repeated eigenvalues. An effective strategy is proposed to construct a non-singular coefficient matrix, which can be directly used to obtain the eigenvector derivatives with distinct and repeated eigenvalues. This approach also has an advantage that only requires eigenvalues and eigenvectors of interest, without solving the particular solutions of eigenvector derivatives. The Symmetric Quasi-Minimal Residual (SQMR) method is then adopted to solve the governing equations, only the existing factored (shifted) stiffness matrix from an iterative eigensolution such as the subspace iteration method or the Lanczos algorithm is utilized. The present method can deal with both cases of simple and repeated eigenvalues in a unified manner. Three numerical examples are given to illustrate the accuracy and validity of the proposed algorithm. Highly accurate approximations to the eigenvector derivatives are obtained within a few iteration steps, making a significant reduction of the computational effort. This method can be incorporated into a coupled eigensolver/derivative software module. In particular, it is applicable for finite element models with large sparse matrices.

A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence.

PubMed

de Souza, Camila Ferreira; Sabedot, Thais S; Malta, Tathiane M; Stetson, Lindsay; Morozova, Olena; Sokolov, Artem; Laird, Peter W; Wiznerowicz, Maciej; Iavarone, Antonio; Snyder, James; deCarvalho, Ana; Sanborn, Zachary; McDonald, Kerrie L; Friedman, William A; Tirapelli, Daniela; Poisson, Laila; Mikkelsen, Tom; Carlotti, Carlos G; Kalkanis, Steven; Zenklusen, Jean; Salama, Sofie R; Barnholtz-Sloan, Jill S; Noushmehr, Houtan

2018-04-10

Glioma diagnosis is based on histomorphology and grading; however, such classification does not have predictive clinical outcome after glioblastomas have developed. To date, no bona fide biomarkers that significantly translate into a survival benefit to glioblastoma patients have been identified. We previously reported that the IDH mutant G-CIMP-high subtype would be a predecessor to the G-CIMP-low subtype. Here, we performed a comprehensive DNA methylation longitudinal analysis of diffuse gliomas from 77 patients (200 tumors) to enlighten the epigenome-based malignant transformation of initially lower-grade gliomas. Intra-subtype heterogeneity among G-CIMP-high primary tumors allowed us to identify predictive biomarkers for assessing the risk of malignant recurrence at early stages of disease. G-CIMP-low recurrence appeared in 9.5% of all gliomas, and these resembled IDH-wild-type primary glioblastoma. G-CIMP-low recurrence can be characterized by distinct epigenetic changes at candidate functional tissue enhancers with AP-1/SOX binding elements, mesenchymal stem cell-like epigenomic phenotype, and genomic instability. Molecular abnormalities of longitudinal G-CIMP offer possibilities to defy glioblastoma progression. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Activity inference for Ambient Intelligence through handling artifacts in a healthcare environment.

PubMed

Martínez-Pérez, Francisco E; González-Fraga, Jose Ángel; Cuevas-Tello, Juan C; Rodríguez, Marcela D

2012-01-01

Human activity inference is not a simple process due to distinct ways of performing it. Our proposal presents the SCAN framework for activity inference. SCAN is divided into three modules: (1) artifact recognition, (2) activity inference, and (3) activity representation, integrating three important elements of Ambient Intelligence (AmI) (artifact-behavior modeling, event interpretation and context extraction). The framework extends the roaming beat (RB) concept by obtaining the representation using three kinds of technologies for activity inference. The RB is based on both analysis and recognition from artifact behavior for activity inference. A practical case is shown in a nursing home where a system affording 91.35% effectiveness was implemented in situ. Three examples are shown using RB representation for activity representation. Framework description, RB description and CALog system overcome distinct problems such as the feasibility to implement AmI systems, and to show the feasibility for accomplishing the challenges related to activity recognition based on artifact recognition. We discuss how the use of RBs might positively impact the problems faced by designers and developers for recovering information in an easier manner and thus they can develop tools focused on the user.

Activity Inference for Ambient Intelligence Through Handling Artifacts in a Healthcare Environment

PubMed Central

Martínez-Pérez, Francisco E.; González-Fraga, Jose Ángel; Cuevas-Tello, Juan C.; Rodríguez, Marcela D.

2012-01-01

Human activity inference is not a simple process due to distinct ways of performing it. Our proposal presents the SCAN framework for activity inference. SCAN is divided into three modules: (1) artifact recognition, (2) activity inference, and (3) activity representation, integrating three important elements of Ambient Intelligence (AmI) (artifact-behavior modeling, event interpretation and context extraction). The framework extends the roaming beat (RB) concept by obtaining the representation using three kinds of technologies for activity inference. The RB is based on both analysis and recognition from artifact behavior for activity inference. A practical case is shown in a nursing home where a system affording 91.35% effectiveness was implemented in situ. Three examples are shown using RB representation for activity representation. Framework description, RB description and CALog system overcome distinct problems such as the feasibility to implement AmI systems, and to show the feasibility for accomplishing the challenges related to activity recognition based on artifact recognition. We discuss how the use of RBs might positively impact the problems faced by designers and developers for recovering information in an easier manner and thus they can develop tools focused on the user. PMID:22368512

Progress on a generalized coordinates tensor product finite element 3DPNS algorithm for subsonic

NASA Technical Reports Server (NTRS)

Baker, A. J.; Orzechowski, J. A.

1983-01-01

A generalized coordinates form of the penalty finite element algorithm for the 3-dimensional parabolic Navier-Stokes equations for turbulent subsonic flows was derived. This algorithm formulation requires only three distinct hypermatrices and is applicable using any boundary fitted coordinate transformation procedure. The tensor matrix product approximation to the Jacobian of the Newton linear algebra matrix statement was also derived. Tne Newton algorithm was restructured to replace large sparse matrix solution procedures with grid sweeping using alpha-block tridiagonal matrices, where alpha equals the number of dependent variables. Numerical experiments were conducted and the resultant data gives guidance on potentially preferred tensor product constructions for the penalty finite element 3DPNS algorithm.

[Evoked potentials in the human visual cortex when observing whole figures and their elements].

PubMed

Slavutskaia, A V; Mikhaĭlova, E S

2010-01-01

Evoked potentials changes were analyzed in 32 subjects in a task of observing whole and disintegrated images. In the occipital and parietal regions, reactions to a disintegrated image appeared early (within the period of P1 development), and their characteristics were determined by the magnitude of the response to the whole image. In the occipital cortex, a low-amplitude P1 (the 1st group of subjects) increased in response to image disintegration, whereas in cases of a high P1 amplitude (the 2nd group), the tendency to its reduction was observed. In the parietal regions, the effects were distinct only in the 1st group of subjects and different in the right and left hemispheres: in the left hemisphere, the P1 amplitude increased when simpler elements appeared in the image, in the right hemisphere, a change in the spatial disposition of details was more significant. In the inferior temporal cortex, the amplitude of the later wave N1 decreased in response to disintegration, the effect being significant only in the 2nd group of subjects. The appearance of simpler elements in the image resulted in a P3 wave increase in both groups. The results point to topographic and temporal specificity of the reactions of the visual cortex to image disintegration and suggest the existence of various strategies of the visual image analysis at the early stages.

Ectoderm gene activation in sea urchin embryos mediated by the CCAAT-binding factor.

PubMed

Li, Xiaotao; Bhattacharya, Chitralekha; Dayal, Sandeep; Maity, Sankar; Klein, William H

2002-05-01

Transcriptional enhancers are short stretches of DNA that function to achieve highly specific patterns of gene expression. To identify the mechanisms by which enhancers achieve their specificity, we made use of an enhancer from the aboral ectoderm-specific spec2a gene of the sea urchin Strongylocentrotus purpuratus. The spec2a enhancer contains five cis-regulatory elements within 78 base pairs that interact with five distinct DNA-binding proteins to confer aboral ectoderm expression. Here, we present an analysis of the sea urchin CCAAT binding factor (CBF), which binds to a CCAAT motif within the spec2a enhancer. S. purpuratus CBF and SpOtx, a ubiquitously expressed factor, act together at closely placed cis-regulatory elements to mediate spec2a transcription in the ectoderm. SpCBF was the sole factor that bound to the spec2a CCAAT element, and two of the three subunits that make up the CBF holoprotein were cloned and shown to have high sequence conservation with their vertebrate orthologs. Based on its involvement in the regulation of several other sea urchin genes, SpCBF appears to be a major transcription factor in the sea urchin embryo for positive regulation of ectoderm gene expression. In addition to its role in vertebrate cell growth and proliferation, our results indicate that CBF also functions at the early stages of germ layer formation, namely ectoderm differentiation.

Whole-Genome Sequencing of Sake Yeast Saccharomyces cerevisiae Kyokai no. 7

PubMed Central

Akao, Takeshi; Yashiro, Isao; Hosoyama, Akira; Kitagaki, Hiroshi; Horikawa, Hiroshi; Watanabe, Daisuke; Akada, Rinji; Ando, Yoshinori; Harashima, Satoshi; Inoue, Toyohisa; Inoue, Yoshiharu; Kajiwara, Susumu; Kitamoto, Katsuhiko; Kitamoto, Noriyuki; Kobayashi, Osamu; Kuhara, Satoru; Masubuchi, Takashi; Mizoguchi, Haruhiko; Nakao, Yoshihiro; Nakazato, Atsumi; Namise, Masahiro; Oba, Takahiro; Ogata, Tomoo; Ohta, Akinori; Sato, Masahide; Shibasaki, Seiji; Takatsume, Yoshifumi; Tanimoto, Shota; Tsuboi, Hirokazu; Nishimura, Akira; Yoda, Koji; Ishikawa, Takeaki; Iwashita, Kazuhiro; Fujita, Nobuyuki; Shimoi, Hitoshi

2011-01-01

The term ‘sake yeast’ is generally used to indicate the Saccharomyces cerevisiae strains that possess characteristics distinct from others including the laboratory strain S288C and are well suited for sake brewery. Here, we report the draft whole-genome shotgun sequence of a commonly used diploid sake yeast strain, Kyokai no. 7 (K7). The assembled sequence of K7 was nearly identical to that of the S288C, except for several subtelomeric polymorphisms and two large inversions in K7. A survey of heterozygous bases between the homologous chromosomes revealed the presence of mosaic-like uneven distribution of heterozygosity in K7. The distribution patterns appeared to have resulted from repeated losses of heterozygosity in the ancestral lineage of K7. Analysis of genes revealed the presence of both K7-acquired and K7-lost genes, in addition to numerous others with segmentations and terminal discrepancies in comparison with those of S288C. The distribution of Ty element also largely differed in the two strains. Interestingly, two regions in chromosomes I and VII of S288C have apparently been replaced by Ty elements in K7. Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast. PMID:21900213

Episodic-like memory in the rat.

PubMed

Babb, Stephanie J; Crystal, Jonathon D

2006-07-11

A fundamental question in comparative cognition is whether animals remember unique, personal past experiences. It has long been argued that memories for specific events (referred to as episodic memory) are unique to humans. Recently, considerable evidence has accumulated to show that food-storing birds possess critical behavioral elements of episodic memory, referred to as episodic-like memory in acknowledgment of the fact that behavioral criteria do not assess subjective experiences. Here we show that rats have a detailed representation of remembered events and meet behavioral criteria for episodic-like memory. We provided rats with access to locations baited with distinctive (e.g., grape and raspberry) or nondistinctive (regular chow) flavors. Locations with a distinctive flavor replenished after a long but not a short delay, and locations with the nondistinctive flavor never replenished. One distinctive flavor was devalued after encoding its location by prefeeding that flavor (satiation) or by pairing it with lithium chloride (acquired taste aversion), while the other distinctive flavor was not devalued. The rats selectively decreased revisits to the devalued distinctive flavor but not to the nondevalued distinctive flavor. The present studies demonstrate that rats selectively encode the content of episodic-like memories.

Modeling vertebrate diversity in Oregon using satellite imagery

NASA Astrophysics Data System (ADS)

Cablk, Mary Elizabeth

Vertebrate diversity was modeled for the state of Oregon using a parametric approach to regression tree analysis. This exploratory data analysis effectively modeled the non-linear relationships between vertebrate richness and phenology, terrain, and climate. Phenology was derived from time-series NOAA-AVHRR satellite imagery for the year 1992 using two methods: principal component analysis and derivation of EROS data center greenness metrics. These two measures of spatial and temporal vegetation condition incorporated the critical temporal element in this analysis. The first three principal components were shown to contain spatial and temporal information about the landscape and discriminated phenologically distinct regions in Oregon. Principal components 2 and 3, 6 greenness metrics, elevation, slope, aspect, annual precipitation, and annual seasonal temperature difference were investigated as correlates to amphibians, birds, all vertebrates, reptiles, and mammals. Variation explained for each regression tree by taxa were: amphibians (91%), birds (67%), all vertebrates (66%), reptiles (57%), and mammals (55%). Spatial statistics were used to quantify the pattern of each taxa and assess validity of resulting predictions from regression tree models. Regression tree analysis was relatively robust against spatial autocorrelation in the response data and graphical results indicated models were well fit to the data.

Iodothyronine deiodinase gene analysis of the Pacific oyster Crassostrea gigas reveals possible conservation of thyroid hormone feedback regulation mechanism in mollusks

NASA Astrophysics Data System (ADS)

Huang, Wen; Xu, Fei; Qu, Tao; Li, Li; Que, Huayong; Zhang, Guofan

2015-07-01

Iodothyronine deiodinase catalyzes the initiation and termination of thyroid hormones (THs) effects, and plays a central role in the regulation of thyroid hormone level in vertebrates. In non-chordate invertebrates, only one deiodinase has been identified in the scallop Chlamys farreri. Here, two deiodinases were cloned in the Pacific oyster Crassostrea gigas ( CgDx and CgDy). The characteristic in-frame TGA codons and selenocysteine insertion sequence elements in the oyster deiodinase cDNAs supported the activity of them. Furthermore, seven orthologs of deiodinases were found by a tblastn search in the mollusk Lottia gigantea and the annelid Capitella teleta. A phylogenetic analysis revealed that the deiodinase gene originated from an common ancestor and a clade-specific gene duplication occurred independently during the differentiation of the mollusk, annelid, and vertebrate lineages. The distinct spatiotemporal expression patterns implied functional divergence of the two deiodinases. The expression of CgDx and CgDy was influenced by L-thyroxine T4, and putative thyroid hormone responsive elements were found in their promoters, which suggested that the oyster deiodinases were feedback regulated by TH. Epinephrine stimulated the expression level of CgDx and CgDy, suggesting an interaction effect between different hormones. This study provides the first evidence for the existence of a conserved TH feedback regulation mechanism in mollusks, providing insights into TH evolution.

The repetitive landscape of the chicken genome.

PubMed

Wicker, Thomas; Robertson, Jon S; Schulze, Stefan R; Feltus, F Alex; Magrini, Vincent; Morrison, Jason A; Mardis, Elaine R; Wilson, Richard K; Peterson, Daniel G; Paterson, Andrew H; Ivarie, Robert

2005-01-01

Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, and low-copy fractions of the chicken genome. Sequencing high-copy DNA of chicken to about 2.7 x coverage of its estimated sequence complexity led to the initial identification of several new repeat families, which were then used for a survey of the newly released first draft of the complete chicken genome. The analysis provided insight into the diversity and biology of known repeat structures such as CR1 and CNM, for which only limited sequence data had previously been available. Cot sequence data also resulted in the identification of four novel repeats (Birddawg, Hitchcock, Kronos, and Soprano), two new subfamilies of CR1 repeats, and many elements absent from the chicken genome assembly. Multiple autonomous elements were found for a novel Mariner-like transposon, Galluhop, in addition to nonautonomous deletion derivatives. Phylogenetic analysis of the high-copy repeats CR1, Galluhop, and Birddawg provided insight into two distinct genome dispersion strategies. This study also exemplifies the power of the CBCS method to create representative databases for the repetitive fractions of genomes for which only limited sequence data is available.

The repetitive landscape of the chicken genome

PubMed Central

Wicker, Thomas; Robertson, Jon S.; Schulze, Stefan R.; Feltus, F. Alex; Magrini, Vincent; Morrison, Jason A.; Mardis, Elaine R.; Wilson, Richard K.; Peterson, Daniel G.; Paterson, Andrew H.; Ivarie, Robert

2005-01-01

Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, and low-copy fractions of the chicken genome. Sequencing high-copy DNA of chicken to about 2.7× coverage of its estimated sequence complexity led to the initial identification of several new repeat families, which were then used for a survey of the newly released first draft of the complete chicken genome. The analysis provided insight into the diversity and biology of known repeat structures such as CR1 and CNM, for which only limited sequence data had previously been available. Cot sequence data also resulted in the identification of four novel repeats (Birddawg, Hitchcock, Kronos, and Soprano), two new subfamilies of CR1 repeats, and many elements absent from the chicken genome assembly. Multiple autonomous elements were found for a novel Mariner-like transposon, Galluhop, in addition to nonautonomous deletion derivatives. Phylogenetic analysis of the high-copy repeats CR1, Galluhop, and Birddawg provided insight into two distinct genome dispersion strategies. This study also exemplifies the power of the CBCS method to create representative databases for the repetitive fractions of genomes for which only limited sequence data is available. PMID:15256510

Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa.

PubMed

Karlsen, Christian; Hjerde, Erik; Klemetsen, Terje; Willassen, Nils Peder

2017-04-20

Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs. The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles. Our data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.

Chemical studies of H chondrites. 6: Antarctic/non-Antarctic compositional differences revisited

NASA Astrophysics Data System (ADS)

Wolf, Stephen F.; Lipschutz, Michael E.

1995-02-01

We report data for the trace elements Au, Co, Sb, Ga, Rb, Ag, Se, Cs, Te, Zn, Cd, Bi, T1, and In (ordered by putative volatility during nebular condensation and accretion) determined by radiochemical neutron activation analysis of 14 additional H5 and H6 chondrite falls. Data for the 10 most volatile elements (Rb to In) treated by the multivariate techniques of linear discriminant analysis and logistic regression in these and 44 other falls are compared with those of 59 H4-6 chondrites from Antarctica. Various populations are tested by the multivariate techniques, using the previously developed method of randomization-simulation to assess significance levels. An earlier conclusion, based on fewer examples, that H4-6 chondrite falls are compositionally distinguishable from the Antarctic suite is verified by the additional data. This distinctiveness is highly significant because of the presence of samples from Victoria Land in the Antarctic population, which differ compositionally from falls beyond any reasonable doubt. However, it cannot be proven unequivocally that falls and Antarctic samples from Queen Maud Land are compositionally distinguishable. Trivial causes (e.g., analyst bias, weathering) cannot explain the Victoria Land (Antarctic)/non-Antarctic compositional difference for paradigmatic H4-6 chondrites. This seems to reflect a time-dependent variation of near-Earth meteoroid source regions differing in average thermal history.

Chemical studies of H chondrites. 6: Antarctic/non-Antarctic compositional differences revisited

NASA Technical Reports Server (NTRS)

Wolf, Stephen F.; Lipschutz, Michael E.

1995-01-01

We report data for the trace elements Au, Co, Sb, Ga, Rb, Ag, Se, Cs, Te, Zn, Cd, Bi, T1, and In (ordered by putative volatility during nebular condensation and accretion) determined by radiochemical neutron activation analysis of 14 additional H5 and H6 chondrite falls. Data for the 10 most volatile elements (Rb to In) treated by the multivariate techniques of linear discriminant analysis and logistic regression in these and 44 other falls are compared with those of 59 H4-6 chondrites from Antarctica. Various populations are tested by the multivariate techniques, using the previously developed method of randomization-simulation to assess significance levels. An earlier conclusion, based on fewer examples, that H4-6 chondrite falls are compositionally distinguishable from the Antarctic suite is verified by the additional data. This distinctiveness is highly significant because of the presence of samples from Victoria Land in the Antarctic population, which differ compositionally from falls beyond any reasonable doubt. However, it cannot be proven unequivocally that falls and Antarctic samples from Queen Maud Land are compositionally distinguishable. Trivial causes (e.g., analyst bias, weathering) cannot explain the Victoria Land (Antarctic)/non-Antarctic compositional difference for paradigmatic H4-6 chondrites. This seems to reflect a time-dependent variation of near-Earth meteoroid source regions differing in average thermal history.

Discrete-Layer Piezoelectric Plate and Shell Models for Active Tip-Clearance Control

NASA Technical Reports Server (NTRS)

Heyliger, P. R.; Ramirez, G.; Pei, K. C.

1994-01-01

The objectives of this work were to develop computational tools for the analysis of active-sensory composite structures with added or embedded piezoelectric layers. The targeted application for this class of smart composite laminates and the analytical development is the accomplishment of active tip-clearance control in turbomachinery components. Two distinct theories and analytical models were developed and explored under this contract: (1) a discrete-layer plate theory and corresponding computational models, and (2) a three dimensional general discrete-layer element generated in curvilinear coordinates for modeling laminated composite piezoelectric shells. Both models were developed from the complete electromechanical constitutive relations of piezoelectric materials, and incorporate both displacements and potentials as state variables. This report describes the development and results of these models. The discrete-layer theories imply that the displacement field and electrostatic potential through-the-thickness of the laminate are described over an individual layer rather than as a smeared function over the thickness of the entire plate or shell thickness. This is especially crucial for composites with embedded piezoelectric layers, as the actuating and sensing elements within these layers are poorly represented by effective or smeared properties. Linear Lagrange interpolation polynomials were used to describe the through-thickness laminate behavior. Both analytic and finite element approximations were used in the plane or surface of the structure. In this context, theoretical developments are presented for the discrete-layer plate theory, the discrete-layer shell theory, and the formulation of an exact solution for simply-supported piezoelectric plates. Finally, evaluations and results from a number of separate examples are presented for the static and dynamic analysis of the plate geometry. Comparisons between the different approaches are provided when possible, and initial conclusions regarding the accuracy and limitations of these models are given.

Spatial variation of PM elemental composition between and within 20 European study areas--Results of the ESCAPE project.

PubMed

Tsai, Ming-Yi; Hoek, Gerard; Eeftens, Marloes; de Hoogh, Kees; Beelen, Rob; Beregszászi, Timea; Cesaroni, Giulia; Cirach, Marta; Cyrys, Josef; De Nazelle, Audrey; de Vocht, Frank; Ducret-Stich, Regina; Eriksen, Kirsten; Galassi, Claudia; Gražuleviciene, Regina; Gražulevicius, Tomas; Grivas, Georgios; Gryparis, Alexandros; Heinrich, Joachim; Hoffmann, Barbara; Iakovides, Minas; Keuken, Menno; Krämer, Ursula; Künzli, Nino; Lanki, Timo; Madsen, Christian; Meliefste, Kees; Merritt, Anne-Sophie; Mölter, Anna; Mosler, Gioia; Nieuwenhuijsen, Mark J; Pershagen, Göran; Phuleria, Harish; Quass, Ulrich; Ranzi, Andrea; Schaffner, Emmanuel; Sokhi, Ranjeet; Stempfelet, Morgane; Stephanou, Euripides; Sugiri, Dorothea; Taimisto, Pekka; Tewis, Marjan; Udvardy, Orsolya; Wang, Meng; Brunekreef, Bert

2015-11-01

An increasing number of epidemiological studies suggest that adverse health effects of air pollution may be related to particulate matter (PM) composition, particularly trace metals. However, we lack comprehensive data on the spatial distribution of these elements. We measured PM2.5 and PM10 in twenty study areas across Europe in three seasonal two-week periods over a year using Harvard impactors and standardized protocols. In each area, we selected street (ST), urban (UB) and regional background (RB) sites (totaling 20) to characterize local spatial variability. Elemental composition was determined by energy-dispersive X-ray fluorescence analysis of all PM2.5 and PM10 filters. We selected a priori eight (Cu, Fe, K, Ni, S, Si, V, Zn) well-detected elements of health interest, which also roughly represented different sources including traffic, industry, ports, and wood burning. PM elemental composition varied greatly across Europe, indicating different regional influences. Average street to urban background ratios ranged from 0.90 (V) to 1.60 (Cu) for PM2.5 and from 0.93 (V) to 2.28 (Cu) for PM10. Our selected PM elements were variably correlated with the main pollutants (PM2.5, PM10, PM2.5 absorbance, NO2 and NOx) across Europe: in general, Cu and Fe in all size fractions were highly correlated (Pearson correlations above 0.75); Si and Zn in the coarse fractions were modestly correlated (between 0.5 and 0.75); and the remaining elements in the various size fractions had lower correlations (around 0.5 or below). This variability in correlation demonstrated the distinctly different spatial distributions of most of the elements. Variability of PM10_Cu and Fe was mostly due to within-study area differences (67% and 64% of overall variance, respectively) versus between-study area and exceeded that of most other traffic-related pollutants, including NO2 and soot, signaling the importance of non-tailpipe (e.g., brake wear) emissions in PM. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cs-137 geochronology, epithermal neutron activation analysis, and principal component analysis of heavy metals pollution of the Black Sea anoxic continental shelf sediments

NASA Astrophysics Data System (ADS)

Duliu, O. G.; Cristache, C.; Oaie, G.; Culicov, O. A.; Frontasyeva, M. V.

2009-04-01

Anthropogenic Cs-137 Gamma-ray Spectroscopy assay (GrSA) performed at the National Institute of Research and Development for Physics and Nuclear Engineering - Bucharest (Romania) in correlation with Epithermal Neutrons Activation Analysis (ENAA) performed at the Joint Institute of Nuclear Researches - Dubna (Russia) were used to investigate a 50 cm core containing unconsolidated sediments collected at a depth of 600 m off Romanian town of Constantza, located in the anoxic zone of the Black Sea Continental Shelf. A digital radiography showed the presence of about 265 distinct laminae, 1 to 3 mm thick, a fact attesting a stationary sedimentary process, completely free of bioturbation. After being radiographed, the core was sliced into 45 segments whose thickness gradually increased from 0.5 to 5 cm, such that the minimum thickness corresponded to the upper part of the core. From each segment two aliquots of about 0.5 g and 50 g were extracted for subsequent ENAA and Cs-137 GrSA. The Cs-137 vertical profile evidenced two maxima, one of them was very sharp and localized at a depth of 1 cm and the other very broad, almost undistinguished at about 8 cm depth, the first one being attributed to 1986 Chernobyl accident. Based on these date, we have estimated a sedimentation ratio of about 0.5 mm/year, value taken as reference for further assessment of recent pollution history. By means of ENAA we have determined the vertical content of five presumed pollutants, e.i. Zn, As, Br, Sn and Sb and of Sc, as natural, nonpolluting element. In the first case, all five elements presented a more or less similar vertical profile consisting of an almost exponential decrease for the first 10 cm below sediment surface followed by a plateau until the core base, i.e. 50 cm below surface, dependency better described by the equation: c(z) = c0 [1+k exp (-z/Z)] (1) where: where c(z) represents the concentration vertical profile; z represents depth (in absolute value); c0 represents the plateau concentrations; k represents the surface to plateau relative increment of concentration; Z represents concentration decrement: the depth at which the concentration becomes 1+k times greater than plateau one. Final results have shown with clarity that in the case of Zn, As, Br, Sn and Sb, the concentrations near sediment surface were 1.6 to 4.1 times greater then the plateau ones while Sc vertical profile, excepting some small fluctuations observed between 18 to 25 cm below surface, shown to be almost constant. Moreover, the concentration decrements Z of Zn, Br, Sn and Sb were almost coincident within one standard deviation while in the case of As, this coincidence appears within two standard deviation, these facts pleading for a comparable time evolution in the past 100 years. On the other hand, in the case of Sn and As, the maximum concentrations were reached 1 cm below the sediment surface, roughly corresponding to 1990 year, while the concentrations of all other three elements monotonously increases up to sediment surface. Further Principal Components Analysis of the data concerning the vertical distribution of all six elements illustrates the presence of two distinct clusters, one consisting of Zn, As, Br, Sn and Sb and the other on only of Sn, attesting both differences and similarities in the vertical distribution of considered elements. By comparing the experimental concentrations of all five elements with Romania Regulations concerning heavy metal pollution, we remarked that, by respect to these Regulations the only Zn, As, Br and Sb slightly exceeded normal accepted limits while the minimum alert concentrations were exceeded only in few cases by of As and Br, but no elements concentrations reached the intervention threshold. In our opinion, these results reflect the dynamics of the industrial activity in the riparian to Danube River European countries: a steady increase beginning with the last half of the XIX-th century followed by a slightly decline after the fall of Communism.

Comparison of SHOX and associated elements duplications distribution between patients (Lėri-Weill dyschondrosteosis/idiopathic short stature) and population sample.

PubMed

Hirschfeldova, Katerina; Solc, Roman

2017-09-05

The effect of heterozygous duplications of SHOX and associated elements on Lėri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS) development is less distinct when compared to reciprocal deletions. The aim of our study was to compare frequency and distribution of duplications within SHOX and associated elements between population sample and LWD (ISS) patients. A preliminary analysis conducted on Czech population sample of 250 individuals compared to our previously reported sample of 352 ISS/LWD Czech patients indicated that rather than the difference in frequency of duplications it is the difference in their distribution. Particularly, there was an increased frequency of duplications residing to the CNE-9 enhancer in our LWD/ISS sample. To see whether the obtained data are consistent across published studies we made a literature survey to get published cases with SHOX or associated elements duplication and formed the merged LWD, the merged ISS, and the merged population samples. Relative frequency of particular region duplication in each of those merged samples were calculated. There was a significant difference in the relative frequency of CNE-9 enhancer duplications (11 vs. 3) and complete SHOX (exon1-6b) duplications (4 vs. 24) (p-value 0.0139 and p-value 0.000014, respectively) between the merged LWD sample and the merged population sample. We thus propose that partial SHOX duplications and small duplications encompassing CNE-9 enhancer could be highly penetrant alleles associated with ISS and LWD development. Copyright © 2017 Elsevier B.V. All rights reserved.

EnGeoMAP - geological applications within the EnMAP hyperspectral satellite science program

NASA Astrophysics Data System (ADS)

Boesche, N. K.; Mielke, C.; Rogass, C.; Guanter, L.

2016-12-01

Hyperspectral investigations from near field to space substantially contribute to geological exploration and mining monitoring of raw material and mineral deposits. Due to their spectral characteristics, large mineral occurrences and minefields can be identified from space and the spatial distribution of distinct proxy minerals be mapped. In the frame of the EnMAP hyperspectral satellite science program a mineral and elemental mapping tool was developed - the EnGeoMAP. It contains a basic mineral mapping and a rare earth element mapping approach. This study shows the performance of EnGeoMAP based on simulated EnMAP data of the rare earth element bearing Mountain Pass Carbonatite Complex, USA, and the Rodalquilar and Lomilla Calderas, Spain, which host the economically relevant gold-silver, lead-zinc-silver-gold and alunite deposits. The mountain pass image data was simulated on the basis of AVIRIS Next Generation images, while the Rodalquilar data is based on HyMap images. The EnGeoMAP - Base approach was applied to both images, while the mountain pass image data were additionally analysed using the EnGeoMAP - REE software tool. The results are mineral and elemental maps that serve as proxies for the regional lithology and deposit types. The validation of the maps is based on chemical analyses of field samples. Current airborne sensors meet the spatial and spectral requirements for detailed mineral mapping and future hyperspectral space borne missions will additionally provide a large coverage. For those hyperspectral missions, EnGeoMAP is a rapid data analysis tool that is provided to spectral geologists working in mineral exploration.

Analysis of memory consolidation and evocation in rats by proton induced X-ray emission

NASA Astrophysics Data System (ADS)

Jobim, P. F. C.; dos Santos, C. E. I.; Maurmann, N.; Reolon, G. K.; Debastiani, R.; Pedroso, T. R.; Carvalho, L. M.; Dias, J. F.

2014-08-01

It is well known that trace elements such as Mg, Ca, Fe, Cu and Zn have a key role in synapse plasticity and learning. Learning process is conventionally divided in three distinct and complementary stages: memory acquisition, consolidation and evocation. Consolidation is the stabilization of the synaptic trace formed by acquisition, while evocation is the recall of this trace. Ion-based techniques capable of providing information concerning the elemental composition of organic tissues may be helpful to improve our understanding on memory consolidation and evocation processes. In particular, the Particle-Induced X-ray Emission (PIXE) technique can be used to analyze different biological tissues with good accuracy. In this work we explore the versatility of PIXE to measure the elemental concentrations in rat brain tissues in order to establish any possible correlation between them and the memory consolidation and evocation processes. To this end, six groups of middle-age male Wistar rats were trained and tested in a step-down Inhibitory Avoidance conditioning. After the behavior tests, the animals were decapitated in accordance with the legal procedures and their brains were removed and dissected for the PIXE analyses. The results demonstrated that there are differences in the elemental concentration among the groups and such variations may be associated with their availability to the learning processes (by memory consolidation and evocation). Moreover, the control groups circumvent the possibility that a non-specific event involved in learning tasks cause such variations. Our results suggest that PIXE may be a useful tool to investigate memory consolidation and evocation in animal models.

Alliance through Change

ERIC Educational Resources Information Center

Sebalj, Darlene; Hudson, Susan; Ryan, Jan; Wight-Boycott, Juliet

2007-01-01

Following a landmark organisational change event within the University of Western Sydney, when the university ceased operating as a federation of four distinct, inter-related elements and merged to become a single entity, four foundation College Managers made a strategic decision to form an alliance. This alliance significantly enhanced the…

Black Womanhood and Feminist Standpoints.

ERIC Educational Resources Information Center

Allen, Brenda J.

1998-01-01

Discusses challenges and consequences of being a member of two historically oppressed groups in the United States--Blacks and females. Relies on feminist standpoint theory--a distinctive element of contemporary feminist thought about how knowledge is constructed. Focuses on academe as a discursive site for constructing identity. (PA)

Transpersonal Relations: Counseling for the "We" Decade.

ERIC Educational Resources Information Center

Stensrud, Robert; Stensrud, Kay

1982-01-01

Reviews elements of Maslow's work and shows how Fromm's distinction between a having and a being mode of experience corresponds with the work of Maslow. Suggests counselors must clarify professional values and concludes that transpersonal psychology offers a way of establishing more positive relationships. (JAC)

A Numerical Study on Toppling Failure of a Jointed Rock Slope by Using the Distinct Lattice Spring Model

NASA Astrophysics Data System (ADS)

Lian, Ji-Jian; Li, Qin; Deng, Xi-Fei; Zhao, Gao-Feng; Chen, Zu-Yu

2018-02-01

In this work, toppling failure of a jointed rock slope is studied by using the distinct lattice spring model (DLSM). The gravity increase method (GIM) with a sub-step loading scheme is implemented in the DLSM to mimic the loading conditions of a centrifuge test. A classical centrifuge test for a jointed rock slope, previously simulated by the finite element method and the discrete element model, is simulated by using the GIM-DLSM. Reasonable boundary conditions are obtained through detailed comparisons among existing numerical solutions with experimental records. With calibrated boundary conditions, the influences of the tensional strength of the rock block, cohesion and friction angles of the joints, as well as the spacing and inclination angles of the joints, on the flexural toppling failure of the jointed rock slope are investigated by using the GIM-DLSM, leading to some insight into evaluating the state of flexural toppling failure for a jointed slope and effectively preventing the flexural toppling failure of jointed rock slopes.

Timing of magmatism following initial convergence at a passive margin, southwestern U.S. Cordillera, and ages of lower crustal magma sources

USGS Publications Warehouse

Barth, A.P.; Wooden, J.L.

2006-01-01

Initiation of the Cordilleran magmatic arc in the southwestern United States is marked by intrusion of granitic plutons, predominantly composed of alkali-calcic Fe- and Sr-enriched quartz monzodiorite and monzonite, that intruded Paleoproterozoic basement and its Paleozoic cratonal-miogeoclinal cover. Three intrusive suites, recognized on the basis of differences in high field strength element and large ion lithophile element abundances, contain texturally complex but chronologically distinctive zircons. These zircons record heterogeneous but geochemically discrete mafic crustal magma sources, discrete Permo-Triassic intrusion ages, and a prolonged postemplacement thermal history within the long-lived Cordilleran arc, leading to episodic loss of radiogenic Pb. Distinctive lower crustal magma sources reflect lateral heterogeneity within the composite lithosphere of the Proterozoic craton. Limited interaction between derived magmas and middle and upper crustal rocks probably reflects the relatively cool thermal structure of the nascent Cordilleran continental margin magmatic arc. ?? 2006 by The University of Chicago. All rights reserved.

Acidocalcisomes of Phytomonas françai possess distinct morphological characteristics and contain iron.

PubMed

Miranda, Kildare; Rodrigues, Claudia O; Hentchel, Joachim; Vercesi, Anibal; Plattner, Helmut; de Souza, Wanderley; Docampo, Roberto

2004-10-01

Acidocalcisomes are acidic calcium storage compartments described initially in trypanosomatid and apicomplexan parasites, and recently found in other unicellular eukaryotes. The aim of this study was to identify the presence of acidocalcisomes in the plant trypanosomatid Phytomonas françai. Electron-dense organelles of P. françai were shown to contain large amounts of oxygen, sodium, magnesium, phosphorus, potassium, calcium, iron, and zinc as determined by X-ray microanalysis, either in situ or when purified using iodixanol gradient centrifugation or by elemental mapping. The presence of iron is not common in other acidocalcisomes. In situ, but not when purified, these organelles showed an elongated shape differing from previously described acidocalcisomes. However, these organelles also possessed a vacuolar H+-pyrophosphatase (V-H+-PPase) as determined by biochemical methods and by immunofluorescence microscopy using antibodies against the enzyme. Together, these results suggest that the electron-dense organelles of P. françai are homologous to the acidocalcisomes described in other trypanosomatids, although with distinct morphology and elemental content.

LA-ICP-MS analysis of isolated phosphatic grains indicates selective rare earth element enrichment during reworking and transport processes

NASA Astrophysics Data System (ADS)

Auer, Gerald; Reuter, Markus; Hauzenberger, Christoph A.; Piller, Werner E.

2016-04-01

Rare earth elements (REE) are a commonly used proxy to reconstruct water chemistry and oxygen saturation during the formation history of authigenic and biogenic phosphates in marine environments. In the modern ocean REE exhibit a distinct pattern with enrichment of heavy REE and strong depletion in Cerium. Studies of ancient phosphates and carbonates, however, showed that this 'modern' pattern is only rarely present in the geological past. Consequently, the wide range of REE enrichment patterns found in ancient marine phosphates lead to the proposition that water chemistry had to have been radically different in the earth's past. A wealth of studies has already shown that both early and late diagenesis can strongly affect REE signatures in phosphates and severely alter primary marine signals. However, no previous research was conducted on how alteration processes occurring prior to final deposition affect marine phosphates. Herein we present a dataset of multiple LA-ICP-MS measurements of REE signatures in isolated phosphate and carbonate grains deposited in a carbonate ramp setting in the central Mediterranean Sea during the middle Miocene "Monterey event". The phosphates are represented by authigenic, biogenic and detrital grains emplaced in bioclastic grain- to packstones dominated by bryozoan and echinoderm fragments, as well as abundant benthic and planktic foraminifers. The results of 39 grain specific LA-ICP-MS measurements in three discrete rock samples reveals four markedly different REE patterns (normalized to the Post Archean Australian Shale standard) in terms of total enrichment and pattern shape. Analyses of REE diagenesis proxies show that diagenetic alteration affected the samples only to a minor degree. Considering grain shape and REE patterns together indicate that authigenic, detrital and biogenic phosphates have distinct REE patterns irrespective of the sample. Our results show that the observed REE patterns in phosphates only broadly reflect water chemistry under certain well constrained circumstances of primary authigenesis. Are these conditions not met, REE patterns are more likely to reflect complex enrichment processes that likely already started to occur during reworking over geologically relatively short time frames. Similarities in the REE patterns of clearly detrital and biogenic phosphate further suggest that the often observed 'hat-shaped' pattern in biogenic phosphates can easily result from increased middle REE (Neodymium to Holmium) scavenging during taphonomic processes prior to final deposition. Finally, cluster analysis coupled with sedimentological considerations proved a valuable tool for the characterization of REE patterns of phosphates in terms of their formation conditions and depositional history, such as the distinction of phosphates formed in situ from reworked and transported phosphate grains.

A glass spherule of questionable impact origin from the Apollo 15 landing site: Unique target mare basalt

USGS Publications Warehouse

Ryder, G.; Delano, J.W.; Warren, P.H.; Kallemeyn, G.W.; Dalrymple, G.B.

1996-01-01

A 6 mm-diameter dark spherule, 15434,28, from the regolith on the Apennine Front at the Apollo 15 landing site has a homogeneous glass interior with a 200 ??m-thick rind of devitrified or crystallized melt. The rind contains abundant small fragments of Apollo 15 olivine-normative mare basalt and rare volcanic Apollo 15 green glass. The glass interior of the spherule has the chemical composition, including a high FeO content and high CaO/Al2O3, of a mare basalt. Whereas the major element and Sc, Ni, and Co abundances are similar to those of low-Ti mare basalts, the incompatible elements and Sr abundances are similar to those of high-Ti mare basalts. The relative abundance patterns of the incompatible trace elements are distinct from any other lunar mare basalts or KREEP; among these distinctions are a much steeper slope of the heavy rare earth elements. The 15434,28 glass has abundances of the volatile element Zn consistent with both impact glasses and crystalline mare basalts, but much lower than in glasses of mare volcanic origin. The glass contains siderophile elements such as Ir in abundances only slightly higher than accepted lunar indigenous levels, and some, such as Au, are just below such upper limits. The age of the glass, determined by the 40Ar/39Ar laser incremental heating technique, is 1647 ?? 11 Ma (2 ??); it is expressed as an age spectrum of seventeen steps over 96% of the 39Ar released, unusual for an impact glass. Trapped argon is negligible. The undamaged nature of the sphere demonstrates that it must have spent most of its life buried in regolith; 38Ar cosmic ray exposure data suggest that it was buried at less than 2m but more than a few centimeters if a single depth is appropriate. That the spherule solidified to a glass is surprising; for such a mare composition, cooling at about 50??C s-1 is required to avoid crystallization, and barely attainable in such a large spherule. The low volatile abundances, slightly high siderophile abundances, and the young age are perhaps all most consistent with an impact origin, but nonetheless not absolutely definitive. The 15434,28 glass is distinct from the common yellow impact glasses at the Apollo 15 landing site, in particular in its lower abundances of incompatible elements and much younger age. If we accept an impact origin, then the trace element relative abundances preclude both typical KREEP and the common Apollo 15 yellow impact glass from contributing more than a few percent of the incompatible elements to potential mixtures. The melted part of any target must have consisted almost entirely of a variety (or varieties) of mare basalt or glass distinct from any known mare basalts or glasses, including Apollo 15 yellow volcanic glass, or mixtures of them. However, the rind inclusions, similar to materials of local origin, do suggest a source near the Apollo 15 landing site. An impact melt cannot have dissolved much, if any, of such inclusions. A lack of regolith materials in the rind and in the melt component suggest an immature source terrain. Thus, even for an impact origin, there is the possibility (though not requirement) that the volcanic target is younger than most mare plains. The crater Hadley C, 25 km away, is a potential source. If the 15434,28 glass is instead directly of volcanic origin, it represents an extremely young mare magma of a type previously undiscovered on the Moon.

Defining personal utility in genomics: A Delphi study.

PubMed

Kohler, J N; Turbitt, E; Lewis, K L; Wilfond, B S; Jamal, L; Peay, H L; Biesecker, L G; Biesecker, B B

2017-09-01

Individual genome sequencing results are valued by patients in ways distinct from clinical utility. Such outcomes have been described as components of "personal utility," a concept that broadly encompasses patient-endorsed benefits, that is operationally defined as non-clinical outcomes. No empirical delineation of these outcomes has been reported. To address this gap, we administered a Delphi survey to adult participants in a National Institute of Health (NIH) clinical exome study to extract the most highly endorsed outcomes constituting personal utility. Forty research participants responded to a Delphi survey to rate 35 items identified by a systematic literature review of personal utility. Two rounds of ranking resulted in 24 items that represented 14 distinct elements of personal utility. Elements most highly endorsed by participants were: increased self-knowledge, knowledge of "the condition," altruism, and anticipated coping. Our findings represent the first systematic effort to delineate elements of personal utility that may be used to anticipate participant expectation and inform genetic counseling prior to sequencing. The 24 items reported need to be studied further in additional clinical genome sequencing studies to assess generalizability in other populations. Further research will help to understand motivations and to predict the meaning and use of results. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Applying ecological models to communities of genetic elements: the case of neutral theory.

PubMed

Linquist, Stefan; Cottenie, Karl; Elliott, Tyler A; Saylor, Brent; Kremer, Stefan C; Gregory, T Ryan

2015-07-01

A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size. © 2015 John Wiley & Sons Ltd.

Structural aspects of the inactive X chromosome.

PubMed

Bonora, Giancarlo; Disteche, Christine M

2017-11-05

A striking difference between male and female nuclei was recognized early on by the presence of a condensed chromatin body only in female cells. Mary Lyon proposed that X inactivation or silencing of one X chromosome at random in females caused this structural difference. Subsequent studies have shown that the inactive X chromosome (Xi) does indeed have a very distinctive structure compared to its active counterpart and all autosomes in female mammals. In this review, we will recap the discovery of this fascinating biological phenomenon and seminal studies in the field. We will summarize imaging studies using traditional microscopy and super-resolution technology, which revealed uneven compaction of the Xi. We will then discuss recent findings based on high-throughput sequencing techniques, which uncovered the distinct three-dimensional bipartite configuration of the Xi and the role of specific long non-coding RNAs in eliciting and maintaining this structure. The relative position of specific genomic elements, including genes that escape X inactivation, repeat elements and chromatin features, will be reviewed. Finally, we will discuss the position of the Xi, either near the nuclear periphery or the nucleolus, and the elements implicated in this positioning.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'. © 2017 The Authors.

Landscape Routes as an Infrastructural Core of Cultural Landscapes; Their Distinctive Role for The Character of Region

NASA Astrophysics Data System (ADS)

Kołodziej, Anna

2017-10-01

Roadside tree avenues are a distinctive element of the landscape of Warmia and Mazury, which is a testament to the history of the region from the Prussian time. Their emergence was imposed top-down and was dictated both by practical and aesthetic reasons. Today they are a problematic heritage in the view of current tendencies of infrastructural development of the country that favour highways and the opportunity to cover the distance between start and destination point as fast as possible. Nevertheless, the literature and conducted scientific studies indicate a change in perception of the in-car experience which underlines a pleasure of travel itself. The research also suggests the growing need for planning route on the basis of the attractiveness of its elements. The work also distinguishes the conditions that must occur for the scenic route be established and put under protection. Moreover, it presents different views of assessing the value of such a road and the cultural landscape in which it is inscribed. It also describes the impact of the individual elements of scenic route on well-being of a participant of road traffic and his perception of the space. This paper attempts to survey the existing trends and actions in development and protection of scenic roads in selected and to present the tree-lined roads of northern Poland on the background of the examples. This has been done on the basis of personal experience and observation, as well as the literature. There have been juxtaposed routes’ common elements and the elements distinctive to individual countries and regions. The results of the survey indicate that the scenic route, as a picture of the economic, historical, social and political situation of the place is an infrastructural core of cultural landscape. It constitutes the uniqueness of the region not only from the biological, but also cultural point of view. Then, apart from the obvious economic importance of scenic routes for the development of non-invasive tourism in the region, there is indicated their important role in shaping local identity. In the light of the above, the paper estimates possibilities for protection of tree-lined roads of northern Poland as the network of scenic routes characteristic for the region.

Multivariate analyses of Erzgebirge granite and rhyolite composition: Implications for classification of granites and their genetic relations

USGS Publications Warehouse

Forster, H.-J.; Davis, J.C.; Tischendorf, G.; Seltmann, R.

1999-01-01

High-precision major, minor and trace element analyses for 44 elements have been made of 329 Late Variscan granitic and rhyolitic rocks from the Erzgebirge metallogenic province of Germany. The intrusive histories of some of these granites are not completely understood and exposures of rock are not adequate to resolve relationships between what apparently are different plutons. Therefore, it is necessary to turn to chemical analyses to decipher the evolution of the plutons and their relationships. A new classification of Erzgebirge plutons into five major groups of granites, based on petrologic interpretations of geochemical and mineralogical relationships (low-F biotite granites; low-F two-mica granites; high-F, high-P2O5 Li-mica granites; high-F, low-P2O5 Li-mica granites; high-F, low-P2O5 biotite granites) was tested by multivariate techniques. Canonical analyses of major elements, minor elements, trace elements and ratio variables all distinguish the groups with differing amounts of success. Univariate ANOVA's, in combination with forward-stepwise and backward-elimination canonical analyses, were used to select ten variables which were most effective in distinguishing groups. In a biplot, groups form distinct clusters roughly arranged along a quadratic path. Within groups, individual plutons tend to be arranged in patterns possibly reflecting granitic evolution. Canonical functions were used to classify samples of rhyolites of unknown association into the five groups. Another canonical analysis was based on ten elements traditionally used in petrology and which were important in the new classification of granites. Their biplot pattern is similar to that from statistically chosen variables but less effective at distinguishing the five groups of granites. This study shows that multivariate statistical techniques can provide significant insight into problems of granitic petrogenesis and may be superior to conventional procedures for petrological interpretation.

Essential and toxic element concentrations in blood and urine and their associations with diet: results from a Norwegian population study including high-consumers of seafood and game.

PubMed

Birgisdottir, B E; Knutsen, H K; Haugen, M; Gjelstad, I M; Jenssen, M T S; Ellingsen, D G; Thomassen, Y; Alexander, J; Meltzer, H M; Brantsæter, A L

2013-10-01

The first aim of the study was to evaluate calculated dietary intake and concentrations measured in blood or urine of essential and toxic elements in relation to nutritional and toxicological reference values. The second aim was to identify patterns of the element concentrations in blood and urine and to identify possible dietary determinants of the concentrations of these elements. Adults with a known high consumption of environmental contaminants (n=111), and a random sample of controls (n=76) answered a validated food frequency questionnaire (FFQ). Complete data on biological measures were available for 179 individuals. Blood and urine samples were analyzed for selenium, iodine, arsenic, mercury, cadmium and lead. Principal component analysis was used to identify underlying patterns of correlated blood and urine concentrations. The calculated intakes of selenium, iodine, inorganic arsenic and mercury were within guideline levels. For cadmium 24% of the high consumer group and 8% of the control group had intakes above the tolerable weekly intake. Concentrations of lead in blood exceeded the bench-mark dose lower confidence limits for some participants. However, overall, the examined exposures did not give rise to nutritional or toxicological concerns. Game consumption was associated with lead in blood (B(ln) 0.021; 95%CI:0.010, 0.031) and wine consumption. Seafood consumption was associated with urinary cadmium in non-smokers (B(ln) 0.009; 95%CI:0.003, 0.015). A novel finding was a distinct pattern of positively associated biological markers, comprising iodine, selenium, arsenic and mercury (eigenvalue 3.8), reflecting seafood intake (B 0.007; 95%CI:0.004, 0.010). The study clearly demonstrates the significance of seafood as a source of both essential nutrients and toxic elements simultaneously and shows that exposure to various essential and toxic elements can be intertwined. © 2013 Elsevier B.V. All rights reserved.

Assessment of urban green space structures and their quality from a multidimensional perspective.

PubMed

Daniels, Benjamin; Zaunbrecher, Barbara S; Paas, Bastian; Ottermanns, Richard; Ziefle, Martina; Roß-Nickoll, Martina

2018-02-15

Facing the growing amount of people living in cities and, at the same time, the need for a compact and sustainable urban development to mitigate urban sprawl, it becomes increasingly important that green spaces in compact cities are designed to meet the various needs within an urban environment. Urban green spaces have a multitude of functions: Maintaining ecological processes and resulting services, e.g. providing habitat for animals and plants, providing a beneficial city microclimate as well as recreational space for citizens. Regarding these requirements, currently existing assessment procedures for green spaces have some major shortcomings, which are discussed in this paper. It is argued why a more detailed spatial level as well as a distinction between natural and artificial varieties of structural elements is justified and needed and how the assessment of urban green spaces benefits from the multidimensional perspective that is applied. By analyzing a selection of structural elements from an ecological, microclimatic and social perspective, indicator values are derived and a new, holistic metrics 1 is proposed. The results of the integrated analysis led to two major findings: first, that for some elements, the evaluation differs to a great extent between the different perspectives (disciplines) and second, that natural and artificial varieties are, in most cases, evaluated considerably different from each other. The differences between the perspectives call for an integrative planning policy which acknowledges the varying contribution of a structural element to different purposes (ecological, microclimatic, social) as well as a discussion about the prioritization of those purposes. The differences in the evaluation of natural vs. artificial elements verify the assumption that indicators which consider only generic elements fail to account for those refinements and are thus less suitable for planning and assessment purposes. Implications, challenges and scenarios for the application of such a metrics are finally discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Growth and patterning in the conodont skeleton

PubMed Central

Donoghue, P. C. J.

1998-01-01

Recent advances in our understanding of conodont palaeobiology and functional morphology have rendered established hypotheses of element growth untenable. In order to address this problem, hard tissue histology is reviewed paying particular attention to the relationships during growth of the component hard tissues comprising conodont elements, and ignoring a priori assumptions of the homologies of these tissues. Conodont element growth is considered further in terms of the pattern of formation, of which four distinct types are described, all possibly derived from a primitive condition after heterochronic changes in the timing of various developmental stages. It is hoped that this may provide further means of unravelling conodont phylogeny. The manner in which the tissues grew is considered homologous with other vertebrate hard tissues, and the elements appear to have grown in a way similar to the growing scales and growing dentition of other vertebrates.

Soil archives of a Fluvisol: Subsurface analysis and soil history of the medieval city centre of Vlaardingen, the Netherlands - an integral approach

NASA Astrophysics Data System (ADS)

Kluiving, Sjoerd; De Ridder, Tim; Van Dasselaar, Marcel; Roozen, Stan; Prins, Maarten; Van Mourik, Jan

2016-04-01

In Medieval times the city of Vlaardingen (the Netherlands) was strategically located on the confluence of three rivers, the Meuse, the Merwede and the Vlaarding. A church of early 8th century was already located here. In a short period of time Vlaardingen developed into an international trading place, the most important place in the former county of Holland. Starting from the 11th century the river Meuse threatened to flood the settlement. These floods have been registered in the archives of the fluvisol and were recognised in a multidisciplinary sedimentary analysis of these archives. To secure the future of this vulnerable soil archive currently an extensive interdisciplinary research (76 mechanical drill holes, grain size analysis (GSA), thermo-gravimetric analysis (TGA), archaeological remains, soil analysis, dating methods, micromorphology, and microfauna has started in 2011 to gain knowledge on the sedimentological and pedological subsurface of the mound as well as on the well-preserved nature of the archaeological evidence. Pedogenic features are recorded with soil descriptive, micromorphological and geochemical (XRF) analysis. The soil sequence of 5 meters thickness exhibits a complex mix of 'natural' as well as 'anthropogenic layering' and initial soil formation that enables to make a distinction for relatively stable periods between periods with active sedimentation. In this paper the results of this large-scale project are demonstrated in a number of cross-sections with interrelated geological, pedological and archaeological stratification. Distinction between natural and anthropogenic layering is made on the occurrence of chemical elements phosphor and potassium. A series of four stratigraphic / sedimentary units record the period before and after the flooding disaster. Given the many archaeological remnants and features present in the lower units, we assume that the medieval landscape was drowned while it was inhabited in the 12th century AD. After a final drowning phase in the 13th century, as a reaction to it, inhabitants started to raise the surface.

The effect of bottom boundary condition type on the behavior of adhesive contact of spherical probe on an elastic film

NASA Astrophysics Data System (ADS)

Zhu, X.; Xu, W.

2017-11-01

This study presents an investigation on the behavior of adhesive contact between a rigid sphere and an elastic film which is either perfectly bonded (case I) or in frictionless contact (case II) with a rigid substrate. By using linear fracture mechanics, we formulate an convenient semi-analytical approach to develop relations between the applied force, penetration depth and contact radius. Finite element analysis (FEA) is used to verify the relationships. Our results reveal that the interfacial boundary conditions between the film and substrate have distinct effects on the adhesive contact behavior between the sphere and the film. The aim of the present study is to provide an instructive inspiration for controlling adhesion strength of the thin film subject to adhesive contact.

Towards an understanding of nuclear morphogenesis.

PubMed

Georgatos, S D

1994-05-01

In the age of "virtual reality," the imperfect microscopic silhouettes of cells and organelles are gradually being replaced by calligraphic computer drawings. In this context, textbooks and introductory slides often depict the cell nucleus as a smooth-shaped, featureless object. However, in reality, the nuclei of different cells possess distinct sizes and morphological features which develop in a programmed fashion as each cell differentiates. To dissect this complex morphogenetic process, we need to identify the basic elements that determine nuclear architecture and the regulatory factors involved. Recently, clues about the identity of these components have been obtained both by systematic analysis and by serendipity. This review summarizes a few recent findings and ideas that may serve as a first forum for future discussions and, I hope, for further work on this topic.

ACCESS 3. Approximation concepts code for efficient structural synthesis: User's guide

NASA Technical Reports Server (NTRS)

Fleury, C.; Schmit, L. A., Jr.

1980-01-01

A user's guide is presented for ACCESS-3, a research oriented program which combines dual methods and a collection of approximation concepts to achieve excellent efficiency in structural synthesis. The finite element method is used for structural analysis and dual algorithms of mathematical programming are applied in the design optimization procedure. This program retains all of the ACCESS-2 capabilities and the data preparation formats are fully compatible. Four distinct optimizer options were added: interior point penalty function method (NEWSUMT); second order primal projection method (PRIMAL2); second order Newton-type dual method (DUAL2); and first order gradient projection-type dual method (DUAL1). A pure discrete and mixed continuous-discrete design variable capability, and zero order approximation of the stress constraints are also included.

Extensive retroviral diversity in shark.

PubMed

Han, Guan-Zhu

2015-04-28

Retroviruses infect a wide range of vertebrates. However, little is known about the diversity of retroviruses in basal vertebrates. Endogenous retrovirus (ERV) provides a valuable resource to study the ecology and evolution of retrovirus. I performed a genome-scale screening for ERVs in the elephant shark (Callorhinchus milii) and identified three complete or nearly complete ERVs and many short ERV fragments. I designate these retroviral elements "C. milli ERVs" (CmiERVs). Phylogenetic analysis shows that the CmiERVs form three distinct lineages. The genome invasions by these retroviruses are estimated to take place more than 50 million years ago. My results reveal the extensive retroviral diversity in the elephant shark. Diverse retroviruses appear to have been associated with cartilaginous fishes for millions of years. These findings have important implications in understanding the diversity and evolution of retroviruses.

Coordinated transcriptional regulation of two key genes in the lignin branch pathway - CAD and CCR - is mediated through MYB- binding sites

PubMed Central

2010-01-01

Background Cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the final steps in the biosynthesis of monolignols, the monomeric units of the phenolic lignin polymers which confer rigidity, imperviousness and resistance to biodegradation to cell walls. We have previously shown that the Eucalyptus gunnii CCR and CAD2 promoters direct similar expression patterns in vascular tissues suggesting that monolignol production is controlled, at least in part, by the coordinated transcriptional regulation of these two genes. Although consensus motifs for MYB transcription factors occur in most gene promoters of the whole phenylpropanoid pathway, functional evidence for their contribution to promoter activity has only been demonstrated for a few of them. Here, in the lignin-specific branch, we studied the functional role of MYB elements as well as other cis-elements identified in the regulatory regions of EgCAD2 and EgCCR promoters, in the transcriptional activity of these gene promoters. Results By using promoter deletion analysis and in vivo footprinting, we identified an 80 bp regulatory region in the Eucalyptus gunnii EgCAD2 promoter that contains two MYB elements, each arranged in a distinct module with newly identified cis-elements. A directed mutagenesis approach was used to introduce block mutations in all putative cis-elements of the EgCAD2 promoter and in those of the 50 bp regulatory region previously delineated in the EgCCR promoter. We showed that the conserved MYB elements in EgCAD2 and EgCCR promoters are crucial both for the formation of DNA-protein complexes in EMSA experiments and for the transcriptional activation of EgCAD2 and EgCCR promoters in vascular tissues in planta. In addition, a new regulatory cis-element that modulates the balance between two DNA-protein complexes in vitro was found to be important for EgCAD2 expression in the cambial zone. Conclusions Our assignment of functional roles to the identified cis-elements clearly demonstrates the importance of MYB cis-elements in the transcriptional regulation of two genes of the lignin-specific pathway and support the hypothesis that MYB elements serve as a common means for the coordinated regulation of genes in the entire lignin biosynthetic pathway. PMID:20584286

HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors.

PubMed

Pocock, Ginger M; Becker, Jordan T; Swanson, Chad M; Ahlquist, Paul; Sherer, Nathan M

2016-04-01

Retroviruses encode cis-acting RNA nuclear export elements that override nuclear retention of intron-containing viral mRNAs including the full-length, unspliced genomic RNAs (gRNAs) packaged into assembling virions. The HIV-1 Rev-response element (RRE) recruits the cellular nuclear export receptor CRM1 (also known as exportin-1/XPO1) using the viral protein Rev, while simple retroviruses encode constitutive transport elements (CTEs) that directly recruit components of the NXF1(Tap)/NXT1(p15) mRNA nuclear export machinery. How gRNA nuclear export is linked to trafficking machineries in the cytoplasm upstream of virus particle assembly is unknown. Here we used long-term (>24 h), multicolor live cell imaging to directly visualize HIV-1 gRNA nuclear export, translation, cytoplasmic trafficking, and virus particle production in single cells. We show that the HIV-1 RRE regulates unique, en masse, Rev- and CRM1-dependent "burst-like" transitions of mRNAs from the nucleus to flood the cytoplasm in a non-localized fashion. By contrast, the CTE derived from Mason-Pfizer monkey virus (M-PMV) links gRNAs to microtubules in the cytoplasm, driving them to cluster markedly to the centrosome that forms the pericentriolar core of the microtubule-organizing center (MTOC). Adding each export element to selected heterologous mRNAs was sufficient to confer each distinct export behavior, as was directing Rev/CRM1 or NXF1/NXT1 transport modules to mRNAs using a site-specific RNA tethering strategy. Moreover, multiple CTEs per transcript enhanced MTOC targeting, suggesting that a cooperative mechanism links NXF1/NXT1 to microtubules. Combined, these results reveal striking, unexpected features of retroviral gRNA nucleocytoplasmic transport and demonstrate roles for mRNA export elements that extend beyond nuclear pores to impact gRNA distribution in the cytoplasm.

HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors

PubMed Central

Pocock, Ginger M.; Becker, Jordan T.; Swanson, Chad M.; Ahlquist, Paul; Sherer, Nathan M.

2016-01-01

Retroviruses encode cis-acting RNA nuclear export elements that override nuclear retention of intron-containing viral mRNAs including the full-length, unspliced genomic RNAs (gRNAs) packaged into assembling virions. The HIV-1 Rev-response element (RRE) recruits the cellular nuclear export receptor CRM1 (also known as exportin-1/XPO1) using the viral protein Rev, while simple retroviruses encode constitutive transport elements (CTEs) that directly recruit components of the NXF1(Tap)/NXT1(p15) mRNA nuclear export machinery. How gRNA nuclear export is linked to trafficking machineries in the cytoplasm upstream of virus particle assembly is unknown. Here we used long-term (>24 h), multicolor live cell imaging to directly visualize HIV-1 gRNA nuclear export, translation, cytoplasmic trafficking, and virus particle production in single cells. We show that the HIV-1 RRE regulates unique, en masse, Rev- and CRM1-dependent “burst-like” transitions of mRNAs from the nucleus to flood the cytoplasm in a non-localized fashion. By contrast, the CTE derived from Mason-Pfizer monkey virus (M-PMV) links gRNAs to microtubules in the cytoplasm, driving them to cluster markedly to the centrosome that forms the pericentriolar core of the microtubule-organizing center (MTOC). Adding each export element to selected heterologous mRNAs was sufficient to confer each distinct export behavior, as was directing Rev/CRM1 or NXF1/NXT1 transport modules to mRNAs using a site-specific RNA tethering strategy. Moreover, multiple CTEs per transcript enhanced MTOC targeting, suggesting that a cooperative mechanism links NXF1/NXT1 to microtubules. Combined, these results reveal striking, unexpected features of retroviral gRNA nucleocytoplasmic transport and demonstrate roles for mRNA export elements that extend beyond nuclear pores to impact gRNA distribution in the cytoplasm. PMID:27070420

Identifying educator behaviours for high quality verbal feedback in health professions education: literature review and expert refinement.

PubMed

Johnson, Christina E; Keating, Jennifer L; Boud, David J; Dalton, Megan; Kiegaldie, Debra; Hay, Margaret; McGrath, Barry; McKenzie, Wendy A; Nair, Kichu Balakrishnan R; Nestel, Debra; Palermo, Claire; Molloy, Elizabeth K

2016-03-22

Health professions education is characterised by work-based learning and relies on effective verbal feedback. However the literature reports problems in feedback practice, including lack of both learner engagement and explicit strategies for improving performance. It is not clear what constitutes high quality, learner-centred feedback or how educators can promote it. We hoped to enhance feedback in clinical practice by distinguishing the elements of an educator's role in feedback considered to influence learner outcomes, then develop descriptions of observable educator behaviours that exemplify them. An extensive literature review was conducted to identify i) information substantiating specific components of an educator's role in feedback asserted to have an important influence on learner outcomes and ii) verbal feedback instruments in health professions education, that may describe important educator activities in effective feedback. This information was used to construct a list of elements thought to be important in effective feedback. Based on these elements, descriptions of observable educator behaviours that represent effective feedback were developed and refined during three rounds of a Delphi process and a face-to-face meeting with experts across the health professions and education. The review identified more than 170 relevant articles (involving health professions, education, psychology and business literature) and ten verbal feedback instruments in health professions education (plus modified versions). Eighteen distinct elements of an educator's role in effective feedback were delineated. Twenty five descriptions of educator behaviours that align with the elements were ratified by the expert panel. This research clarifies the distinct elements of an educator's role in feedback considered to enhance learner outcomes. The corresponding set of observable educator behaviours aim to describe how an educator could engage, motivate and enable a learner to improve. This creates the foundation for developing a method to systematically evaluate the impact of verbal feedback on learner performance.

Beam steering via resonance detuning in coherently coupled vertical cavity laser arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Matthew T., E-mail: matthew.johnson.9@us.af.mil; Siriani, Dominic F.; Peun Tan, Meng

2013-11-11

Coherently coupled vertical-cavity surface-emitting laser arrays offer unique advantages for nonmechanical beam steering applications. We have applied dynamic coupled mode theory to show that the observed temporal phase shift between vertical-cavity surface-emitting array elements is caused by the detuning of their resonant wavelengths. Hence, a complete theoretical connection between the differential current injection into array elements and the beam steering direction has been established. It is found to be a fundamentally unique beam-steering mechanism with distinct advantages in efficiency, compactness, speed, and phase-sensitivity to current.

Coordinate action of distinct sequence elements localizes checkpoint kinase Hsl1 to the septin collar at the bud neck in Saccharomyces cerevisiae.

PubMed

Finnigan, Gregory C; Sterling, Sarah M; Duvalyan, Angela; Liao, Elizabeth N; Sargsyan, Aspram; Garcia, Galo; Nogales, Eva; Thorner, Jeremy

2016-07-15

Passage through the eukaryotic cell cycle requires processes that are tightly regulated both spatially and temporally. Surveillance mechanisms (checkpoints) exert quality control and impose order on the timing and organization of downstream events by impeding cell cycle progression until the necessary components are available and undamaged and have acted in the proper sequence. In budding yeast, a checkpoint exists that does not allow timely execution of the G2/M transition unless and until a collar of septin filaments has properly assembled at the bud neck, which is the site where subsequent cytokinesis will occur. An essential component of this checkpoint is the large (1518-residue) protein kinase Hsl1, which localizes to the bud neck only if the septin collar has been correctly formed. Hsl1 reportedly interacts with particular septins; however, the precise molecular determinants in Hsl1 responsible for its recruitment to this cellular location during G2 have not been elucidated. We performed a comprehensive mutational dissection and accompanying image analysis to identify the sequence elements within Hsl1 responsible for its localization to the septins at the bud neck. Unexpectedly, we found that this targeting is multipartite. A segment of the central region of Hsl1 (residues 611-950), composed of two tandem, semiredundant but distinct septin-associating elements, is necessary and sufficient for binding to septin filaments both in vitro and in vivo. However, in addition to 611-950, efficient localization of Hsl1 to the septin collar in the cell obligatorily requires generalized targeting to the cytosolic face of the plasma membrane, a function normally provided by the C-terminal phosphatidylserine-binding KA1 domain (residues 1379-1518) in Hsl1 but that can be replaced by other, heterologous phosphatidylserine-binding sequences. © 2016 Finnigan et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Multidisciplinary study of Wyoming test sites. [hydrology, biology, geology, lithology, geothermal, and land use

NASA Technical Reports Server (NTRS)

Houston, R. S. (Principal Investigator); Marrs, R. W.; Agard, S. S.; Downing, K. G.; Earle, J. L.; Froman, N. L.; Gordon, R.; Kolm, K. E.; Tomes, B.; Vietti, J.

1974-01-01

The author has identified the following significant results. Investigation of a variety of applications of EREP photographic data demonstrated that EREP S-190 data offer a unique combination of synoptic coverage and image detail. The broad coverage is ideal for regional geologic mapping and tectonic analysis while the detail is adequate for mapping of crops, mines, urban areas, and other relatively small features. The investigative team at the University of Wyoming has applied the EREP S-190 data to: (1) analysis of photolinear elements of the Powder River Basin, southern Montana, and the Wind River Mountains; (2) drainage analysis of the Powder River Basin and Beartooth Mountains; (3) lithologic and geologic mapping in the Powder River Basin, Black Hills, Green River Basin, Bighorn Basin and Southern Bighorn Mountains; (4) location of possible mineralization in the Absaroka Range; and (5) land use mapping near Riverton and Gillette. All of these applications were successful to some degree. Image enhancement procedures were useful in some efforts requiring distinction of small objects or subtle contrasts.

Principal component analysis of dynamic fluorescence images for diagnosis of diabetic vasculopathy

NASA Astrophysics Data System (ADS)

Seo, Jihye; An, Yuri; Lee, Jungsul; Ku, Taeyun; Kang, Yujung; Ahn, Chulwoo; Choi, Chulhee

2016-04-01

Indocyanine green (ICG) fluorescence imaging has been clinically used for noninvasive visualizations of vascular structures. We have previously developed a diagnostic system based on dynamic ICG fluorescence imaging for sensitive detection of vascular disorders. However, because high-dimensional raw data were used, the analysis of the ICG dynamics proved difficult. We used principal component analysis (PCA) in this study to extract important elements without significant loss of information. We examined ICG spatiotemporal profiles and identified critical features related to vascular disorders. PCA time courses of the first three components showed a distinct pattern in diabetic patients. Among the major components, the second principal component (PC2) represented arterial-like features. The explained variance of PC2 in diabetic patients was significantly lower than in normal controls. To visualize the spatial pattern of PCs, pixels were mapped with red, green, and blue channels. The PC2 score showed an inverse pattern between normal controls and diabetic patients. We propose that PC2 can be used as a representative bioimaging marker for the screening of vascular diseases. It may also be useful in simple extractions of arterial-like features.

Continuum mechanics analysis of fracture progression in the vitrified cryoprotective agent DP6

PubMed Central

Steif, Paul S.; Palastro, Matthew C.; Rabin, Yoed

2008-01-01

As part of an ongoing effort to study the continuum mechanics effects associated with cryopreservation, the current report focuses on the prediction of fracture formation in cryoprotective agents. Fractures had been previously observed in 1 mℓ samples of the cryoprotective agent cocktail DP6, contained in a standard 15 mℓ glass vial, and subjected to various cooling rates. These experimental observations were obtained by means of a cryomacroscope, which has been recently presented by the current research team. High and low cooling rates were found to produce very distinct patterns of cracking. The current study seeks to explain the observed patterns on the basis of stresses predicted from finite element analysis, which relies on a simple viscoelastic constitutive model and on estimates of the critical stress for cracking. The current study demonstrates that the stress which results in instantaneous fracture at low cooling rates is consistent with the stress to initiate fracture at high cooling rate. This consistency supports the credibility of the proposed constitutive model and analysis, and the unified criterion for fracturing, that is, a critical stress threshold. PMID:18412493