Change in fish fauna as indication of aquatic ecosystem condition in Rio Grande de Morelia-Lago de Cuitzeo Basin, Mexico

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

Soto-Galera, E.; Paulo-Maya, J.; Lopez-Lopez, E.

1999-07-01

The Rio Grande de Morelia-Lago de Cuitzeo basin in west central Mexico has experienced major increases in water pollution from a rapidly growing human population. The authors examined changes in the long-term distribution of fishes in relation to water quality and quantity in order to assess the condition and health of aquatic ecosystems in the basin. Sampling between 1985 and 1993 revealed that five (26%) of the 19 native fish species known from the basin had been extirpated. Two of these were endemics, Chirostoma charari and C. compressum, and they are presumed extinct. Twelve (63%) of the remaining species hadmore » declines in distribution. Sixteen (80%) of the 20 localities sampled had lost species. The greatest declines occurred in Lago de Cuitzeo proper and in the lower portion of the Rio Grande de Morelia watershed. Species losses from the lake were attributable to drying and hypereutrophication of the lake because of substantial reductions in the amount and quality of tributary inputs, whereas losses from the Rio Grande de Morelia watershed were the result of pollution from agricultural, municipal, and industrial sources, especially in the region around the city of Morelia. Three localities in the upper portion of the Rio Grande de Morelia watershed--Cointzio reservoir, La Mintzita spring, and Insurgente Morelos stream--contained most of the remaining fish species diversity in the basin and deserve additional protection. Fish faunal changes indicated major declines in the health of aquatic ecosystems in the Morelia-Cuitzeo basin.« less

Identification of snake arenaviruses in live boas and pythons in a zoo in Germany.

PubMed

Aqrawi, T; Stöhr, A C; Knauf-Witzens, T; Krengel, A; Heckers, K O; Marschang, R E

2015-01-01

Recent studies have described the detection and characterisation of new, snake specific arenaviruses in boas and pythons with inclusion body disease (IBD). The objective of this study was to detect arenaviral RNA in live snakes and to determine if these were associated with IBD in all cases. Samples for arenavirus detection in live animals were compared. Detected viruses were compared in order to understand their genetic variability. Esophageal swabs and whole blood was collected from a total of 28 boas and pythons. Samples were tested for arenaviral RNA by RT-PCR. Blood smears from all animals were examined for the presence of inclusion bodies. Internal tissues from animals that died or were euthanized during the study were examined for inclusions and via RT-PCR for arenaviral RNA. All PCR products were sequenced and the genomic sequences phylogenetically analysed. Nine live animals were found to be arenavirus-positive. Two additional snakes tested positive following necropsy. Five new arenaviruses were detected and identified. The detected viruses were named "Boa Arenavirus Deutschland (Boa Av DE) numbers 1-4" and one virus detected in a python (Morelia viridis) was named "Python Av DE1". Results from sequence analyses revealed considerable similarities to a portion of the glycoprotein genes of recently identified boid snake arenaviruses. Both oral swabs and whole blood can be used for the detection of arenaviruses in snakes. In most cases, but not in all, the presence of arenaviral RNA correlated with the presence of inclusions in the tissues of infected animals. There was evidence that some animals may be able to clear arenavirus infection without development of IBD. This is the first detection of arenaviruses in live snakes. The detection of arenaviruses in live snakes is of importance for both disease detection and prevention and for use in quarantine situations. The findings in this study support the theory that arenaviruses are the cause of IBD, but indicate that in some cases it may be possible for animals to clear arenavirus infections without developing IBD.

Toward a Tree-of-Life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

PubMed

Graham Reynolds, R; Niemiller, Matthew L; Revell, Liam J

2014-02-01

Snakes in the families Boidae and Pythonidae constitute some of the most spectacular reptiles and comprise an enormous diversity of morphology, behavior, and ecology. While many species of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain contentious and fluid. A major effort in evolutionary and conservation biology is to assemble a comprehensive Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known life on Earth. No previously published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65% of python species. Using both novel and previously published sequence data, we have produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, contextualized within a larger phylogeny of henophidian snakes. We obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon. We analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny for these species. We found significant evidence of discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and we found support for elevating two previously suggested boid species. We suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species), review relationships between our study and the many other molecular phylogenetic studies of henophidian snakes, and present a taxonomic database and alignment which may be easily used and built upon by other researchers. Copyright © 2013 Elsevier Inc. All rights reserved.

Is There a Tectonic Component On The Subsidence Process In Morelia, Mexico?

NASA Astrophysics Data System (ADS)

Cabral-Cano, E.; Arciniega-Ceballos, A.; Diaz-Molina, O.; Garduno-Monroy, V.; Avila-Olivera, J.; Hernández-Madrigal, V.; Hernández-Quintero, E.

2009-12-01

Subsidence and faulting have affected cities in central Mexico for decades. This process causes substantial damages to the urban infrastructure, housing and large buildings, and is an important factor to be consider when planning urban development, land use zoning and hazard mitigation strategies. In Mexico, studies using InSAR and GPS based observations have shown that high subsidence areas are usually associated with the presence of thick lacustrine and fluvial deposits. In most cases the subsidence is closely associated with intense groundwater extraction that results in sediment consolidation. However, recent studies in the colonial city of Morelia in central Mexico show a different scenario, where groundwater extraction cannot solely explain the observed surface deformation. Our results indicate that a more complex interplay between sediment consolidation and tectonic forces is responsible for the subsidence and fault distribution within the city. The city of Morelia has experienced fault development recognized since the 80’s. This situation has led to the recognition of 9 NE-SW trending faults that cover most of its urbanized area. Displacement maps derived from differential InSAR analysis show that the La Colina fault is the highest subsiding area in Morelia with maximum annual rates over -35 mm/yr. However, lithological mapping and field reconnaissance clearly show basalts outcropping this area of high surface deformation. The subsurface characterization of the La Colina fault was carried out along 27 Ground Penetrating Radar (GPR) sections and 6 seismic tomography profiles. Assuming a constant, linear past behavior of the subsidence as observed by InSAR techniques, and based on the interpretation of the fault dislocation imaged by the shallow GPR and seismic tomography, it is suggested that the La Colina fault may have been active for the past 220-340 years and clearly pre-dates the intense water well extraction from the past century. These conditions suggest the existence of a tectonic component overlapped to the soil consolidation and its related subsidence. Therefore, these results suggest that the fault system observed within the city of Morelia may be an active segment of the Morelia-Acambay tectonic fault system.

Cutaneous and Subcutaneous Soft Tissue Tumours in Snakes: A Retrospective Study of 33 Cases.

PubMed

Dietz, J; Heckers, K O; Aupperle, H; Pees, M

2016-07-01

Cutaneous and subcutaneous soft tissue tumours have been rarely described in detail in snakes. Several malignant entities show strikingly similar histological patterns and therefore the term soft tissue sarcoma (STS) has become a standard histopathological diagnosis. The present study characterizes soft tissue tumours in 33 snakes. Samples included 29 surgically excised masses and four carcasses. Additionally, six animals were humanely destroyed and submitted for necropsy examination following tumour recurrence. Benign neoplasms (n = 8) were described as lipomas of varying differentiation. Recurrence was observed in two of five snakes in which the clinical course was recorded. Malignant neoplasms (n = 25) were diagnosed as STS and graded according to a three-point system previously applied to canine STS. Five (20%) of the primary tumours were classified as grade 1, eleven (44%) as grade 2 and nine (36%) as grade 3 sarcomas. Clinically, recurrence of STS was observed in 11 of 17 cases with available follow-up information. Pathologically, multiple cutaneous metastases were found in one grass snake (Natrix natrix), while visceral metastases were observed in one carpet python (Morelia spilota) and two corn snakes (Pantherophis guttatus). Metastatic risk appears to increase with histological grade. Surgical excision generally represents the current therapy of choice for STS. This study includes the first reports of conventional lipomas in a ribbon snake (Thamnophis radix), angiolipomas in a black-headed python (Aspidites melanocephalus) and a corn snake as well as of STS in a Jamaican boa (Epicrates subflavus), emerald tree boa (Corallus caninus), grass snake (N. natrix), African house snake (Lamprophis fuliginosus), California kingsnake (Lampropeltis getula californiae) and common garter snake (Thamnophis sirtalis). Copyright © 2016 Elsevier Ltd. All rights reserved.

La influencia de "los de abajo" en tres procesos de cambio linguistico en el espanol de Morelia, Michoacan (The Influence of "the Underclass" on Three Processes of Linguistic Change in the Spanish of Morelia, Michoacan).

ERIC Educational Resources Information Center

Gutierrez, Manuel J.

1994-01-01

Examines the role of the educational and socioeconomic levels of the speakers in advancing linguistic change. The study reviews three grammatical phenomena found at distinct stages of change. Individuals at the lower socioeconomic and educational strata of society embrace innovations in language more readily than their affluent and educated…

Subsidence Induced Faulting Hazard risk maps in Mexico City and Morelia, central Mexico

NASA Astrophysics Data System (ADS)

Cabral-Cano, E.; Solano-Rojas, D.; Hernández-Espriu, J.; Cigna, F.; Wdowinski, S.; Osmanoglu, B.; Falorni, G.; Bohane, A.; Colombo, D.

2012-12-01

Subsidence and surface faulting have affected urban areas in Central Mexico for decades and the process has intensified as a consequence of urban sprawl and economic growth. This process causes substantial damages to the urban infrastructure and housing structures and in several cities it is becoming a major factor to be considered when planning urban development, land use zoning and hazard mitigation strategies in the next decades. Subsidence is usually associated with aggressive groundwater extraction rates and a general decrease of aquifer static level that promotes soil consolidation, deformation and ultimately, surface faulting. However, local stratigraphic and structural conditions also play an important role in the development and extension of faults. Despite its potential for damaging housing, and other urban infrastructure, the economic impact of this phenomena is poorly known, in part because detailed, city-wide subsidence induced faulting risk maps have not been published before. Nevertheless, modern remote sensing techniques are most suitable for this task. We present the results of a risk analysis for subsidence induced surface faulting in two cities in central Mexico: Morelia and Mexico City. Our analysis in Mexico City and Morelia is based on a risk matrix using the horizontal subsidence gradient from a Persistent Scatterer InSAR (Morelia) and SqueeSAR (Mexico City) analysis and 2010 census population distribution data from Mexico's National Institute of Statistics and Geography. Defining subsidence induced surface faulting vulnerability within these urbanized areas is best determined using both magnitude and horizontal subsidence gradient. Our Morelia analysis (597,000 inhabitants with localized subsidence rates up to 80 mm/yr) shows that 7% of the urbanized area is under a high to very high risk level, and 14% of its population (11.7% and 2.3% respectively) lives within these areas. In the case of the Mexico City (15'490,000 inhabitants for the Mexico city Metropolitan area included within our map, and up to 370 mm/yr subsidence rate) our risk map shows that 13.5% of the urbanized area is under a high to very high risk level, and 26.2% of its population (22.1% and 4.4% respectively) lives within these areas.

Phylogenetic relationship of Hepatozoon blood parasites found in snakes from Africa, America and Asia.

PubMed

Haklová, B; Majláthová, V; Majláth, I; Harris, D J; Petrilla, V; Litschka-Koen, T; Oros, M; Peťko, B

2014-03-01

The blood parasites from the genus Hepatozoon Miller, 1908 (Apicomplexa: Adeleida: Hepatozoidae) represent the most common intracellular protozoan parasites found in snakes. In the present study, we examined 209 individuals of snakes, from different zoogeographical regions (Africa, America, Asia and Europe), for the occurrence of blood parasites using both molecular and microscopic examination methods, and assess phylogenetic relationships of all Hepatozoon parasites from snakes for the first time. In total, 178 blood smears obtained from 209 individuals, representing 40 species, were examined, from which Hepatozoon unicellular parasites were found in 26 samples (14·6% prevalence). Out of 180 samples tested by molecular method polymerase chain reaction (PCR), the presence of parasites was observed in 21 individuals (prevalence 11·6%): 14 snakes from Africa belonging to six genera (Dendroaspis, Dispholidus, Mehelya, Naja, Philothamnus and Python), five snakes from Asia from the genus Morelia and two snakes from America, from two genera (Coluber and Corallus). The intensity of infection varied from one to 1433 infected cells per 10 000 erythrocytes. Results of phylogenetic analyses (Bayesian and Maximum Likelihood) revealed the existence of five haplotypes divided into four main lineages. The present data also indicate neither geographical pattern of studied Hepatozoon sp., nor congruency in the host association.

The Diamond Beamline Controls and Data Acquisition Software Architecture

NASA Astrophysics Data System (ADS)

Rees, N.

2010-06-01

The software for the Diamond Light Source beamlines[1] is based on two complementary software frameworks: low level control is provided by the Experimental Physics and Industrial Control System (EPICS) framework[2][3] and the high level user interface is provided by the Java based Generic Data Acquisition or GDA[4][5]. EPICS provides a widely used, robust, generic interface across a wide range of hardware where the user interfaces are focused on serving the needs of engineers and beamline scientists to obtain detailed low level views of all aspects of the beamline control systems. The GDA system provides a high-level system that combines an understanding of scientific concepts, such as reciprocal lattice coordinates, a flexible python syntax scripting interface for the scientific user to control their data acquisition, and graphical user interfaces where necessary. This paper describes the beamline software architecture in more detail, highlighting how these complementary frameworks provide a flexible system that can accommodate a wide range of requirements.

Bicycle Facilities That Address Safety, Crime, and Economic Development: Perceptions from Morelia, Mexico.

PubMed

Alveano-Aguerrebere, Inés; Javier Ayvar-Campos, Francisco; Farvid, Maryam; Lusk, Anne

2017-12-22

México is a developing nation and, in the city of Morelia, the concept of the bicyclist as a road user appeared only recently in the Municipal Traffic Regulations. Perhaps the right bicycle infrastructure could address safety, crime, and economic development. To identify the best infrastructure, six groups in Morelia ranked and commented on pictures of bicycle environments that exist in bicycle-friendly nations. Perceptions about bike paths, but only those with impossible-to-be-driven-over solid barriers, were associated with safety from crashes, lowering crime, and contributing to economic development. Shared use paths were associated with lowering the probability of car/bike crashes but lacked the potential to deter crime and foster the local economy. Joint bus and bike lanes were associated with lower safety because of the unwillingness by Mexican bus drivers to be courteous to bicyclists. Gender differences about crash risk biking in the road with the cars (6 best/0 worst scenario) were statistically significant (1.4 for male versus 0.69 for female; p < 0.001). For crashes, crime, and economic development, perceptions about bicycle infrastructure were different in this developing nation perhaps because policy, institutional context, and policing (ticketing for unlawful parking) are not the same as in a developed nation. Countries such as Mexico should consider building cycle tracks with solid barriers to address safety, crime, and economic development.

Geological characterization and environmental implications of the placement of the Morelia Dump, Michoacán, Central Mexico.

PubMed

Israde-Alcantara, Isabel; Buenrostro Delgado, Otoniel; Carrillo Chavez, Alejandro

2005-06-01

The landfill of Morelia, the capital city of the state of Michoacán in central-western Mexico, is located 12 km west of the city and has operated since 1997 without a structure engineered and designed to control the generation in situ of biogas and leachates. A geological evaluation of the landfill site is presented in this paper. The results indicate that the site lacks ideal impermeable subsurface strata. The subsurface strata consist of highly fractured basaltic lava flows (east-west fault and fracture system trend) and sand-size cineritic material with high permeability and porosity. Geochemical analysis of groundwater from Morelia's municipal aquifer shows a high concentration of heavy metals (Cd, Pb, As) exceeding the Mexican environmental regulations, along with the presence of some organic pollutants (phenols). Analyses of samples of the landfill's permanent leachate ponds show very high concentrations of the same contaminants. Samples were taken from the leachate pond and from nearby water-wells during the rainy season (summer 1997) and the dry season (spring 1997, 1998, and 1999). In all cases, the concentration of contaminants registered exceeded the standards for drinking water of the World Health Organization (American Public Health Association, American Water Works Association, and Water Pollution Control Federation, 2000). Some metal contaminants could be leaching directly from the landfill.

Bicycle Facilities That Address Safety, Crime, and Economic Development: Perceptions from Morelia, Mexico

PubMed Central

Alveano-Aguerrebere, Inés; Farvid, Maryam; Lusk, Anne

2017-01-01

México is a developing nation and, in the city of Morelia, the concept of the bicyclist as a road user appeared only recently in the Municipal Traffic Regulations. Perhaps the right bicycle infrastructure could address safety, crime, and economic development. To identify the best infrastructure, six groups in Morelia ranked and commented on pictures of bicycle environments that exist in bicycle-friendly nations. Perceptions about bike paths, but only those with impossible-to-be-driven-over solid barriers, were associated with safety from crashes, lowering crime, and contributing to economic development. Shared use paths were associated with lowering the probability of car/bike crashes but lacked the potential to deter crime and foster the local economy. Joint bus and bike lanes were associated with lower safety because of the unwillingness by Mexican bus drivers to be courteous to bicyclists. Gender differences about crash risk biking in the road with the cars (6 best/0 worst scenario) were statistically significant (1.4 for male versus 0.69 for female; p < 0.001). For crashes, crime, and economic development, perceptions about bicycle infrastructure were different in this developing nation perhaps because policy, institutional context, and policing (ticketing for unlawful parking) are not the same as in a developed nation. Countries such as Mexico should consider building cycle tracks with solid barriers to address safety, crime, and economic development. PMID:29271873

Shallow Faulting in Morelia, Mexico, Based on Seismic Tomography and Geodetically Detected Land Subsidence

NASA Astrophysics Data System (ADS)

Cabral-Cano, E.; Arciniega-Ceballos, A.; Vergara-Huerta, F.; Chaussard, E.; Wdowinski, S.; DeMets, C.; Salazar-Tlaczani, L.

2013-12-01

Subsidence has been a common occurrence in several cities in central Mexico for the past three decades. This process causes substantial damage to the urban infrastructure and housing in several cities and it is a major factor to be considered when planning urban development, land-use zoning and hazard mitigation strategies. Since the early 1980's the city of Morelia in Central Mexico has experienced subsidence associated with groundwater extraction in excess of natural recharge from rainfall. Previous works have focused on the detection and temporal evolution of the subsidence spatial distribution. The most recent InSAR analysis confirms the permanence of previously detected rapidly subsiding areas such as the Rio Grande Meander area and also defines 2 subsidence patches previously undetected in the newly developed suburban sectors west of Morelia at the Fraccionamiento Del Bosque along, south of Hwy. 15 and another patch located north of Morelia along Gabino Castañeda del Rio Ave. Because subsidence-induced, shallow faulting develops at high horizontal strain localization, newly developed a subsidence areas are particularly prone to faulting and fissuring. Shallow faulting increases groundwater vulnerability because it disrupts discharge hydraulic infrastructure and creates a direct path for transport of surface pollutants into the underlying aquifer. Other sectors in Morelia that have been experiencing subsidence for longer time have already developed well defined faults such as La Colina, Central Camionera, Torremolinos and La Paloma faults. Local construction codes in the vicinity of these faults define a very narrow swath along which housing construction is not allowed. In order to better characterize these fault systems and provide better criteria for future municipal construction codes we have surveyed the La Colina and Torremolinos fault systems in the western sector of Morelia using seismic tomographic techniques. Our results indicate that La Colina Fault include secondary faults at depths up to 4-8m below the surface and located up to 24m away from the main fault trace. The Torremolinos fault system includes secondary faults, which are present up to 8m deep and 12-18m away from the main fault trace. Even though the InSAR analysis provides an unsurpassed synoptic view, a higher temporal resolution observation of fault movement has been pursued using the MOIT continuously operating GPS station, which is located within 100 m from the La Colina main fault trace. GPS data is also particularly useful to decompose horizontal and vertical motion in the absence of both ascending and descending SAR data acquisitions. Observations since July 2009 show a total general displacement trend of -39mm/yr and a total horizontal differential motion of 41.8 mm/yr and -4.7mm/yr in its latitudinal and Longitudinal components respectively in respect to the motion observed at the MOGA GPS station located 5.0 km to the SSE within an area which is not affected by subsidence. In addition to the overall trend, high amplitude excursions at the MOIT station with individual residual amplitudes up to 20mm, 25mm, and 60mm in its latitudinal, longitudinal and vertical components respectively vertical are observed. The correlation of fault motion excursions in relationship to the rainfall records will be analyzed.

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

Not Available

This outreach publication highlights federal program milestones and accomplishments of the DOE Geothermal Technologies Program for 2003. This is a special 8-page Spanish supplement for the audience at the Geothermal Resources Council/Geothermal Energy Association Annual Meeting and Industry Exhibit, Morelia, Mexico.

The Morelia-Acambay Fault System

NASA Astrophysics Data System (ADS)

Velázquez Bucio, M.; Soria-Caballero, D.; Garduño-Monroy, V.; Mennella, L.

2013-05-01

The Trans-Mexican Volcanic Belt (TMVB) is one of the most actives and representative zones of Mexico geologically speaking. Research carried out in this area gives stratigraphic, seismologic and historical evidence of its recent activity during the quaternary (Martinez and Nieto, 1990). Specifically the Morelia-Acambay faults system (MAFS) consist in a series of normal faults of dominant direction E - W, ENE - WSW y NE - SW which is cut in center west of the Trans-Mexican Volcanic Belt. This fault system appeared during the early Miocene although the north-south oriented structures are older and have been related to the activity of the tectonism inherited from the "Basin and Range" system, but that were reactivated by the east- west faults. It is believed that the activity of these faults has contributed to the creation and evolution of the longed lacustrine depressions such as: Chapala, Zacapu, Cuitzeo, Maravatio y Acambay also the location of monogenetic volcanoes that conformed the Michoacan-Guanajuato volcanic field (MGVF) and tend to align in the direction of the SFMA dominant effort. In a historical time different segments of the MAFS have been the epicenter of earthquakes from moderated to strong magnitude like the events of 1858 in Patzcuaro, Acambay in 1912, 1979 in Maravatio and 2007 in Morelia, among others. Several detailed analysis and semi-detailed analysis through a GIS platform based in the vectorial archives and thematic charts 1:50 000 scaled from the data base of the INEGI which has allowed to remark the influence of the MAFS segments about the morphology of the landscape and the identification of other structures related to the movement of the existent faults like fractures, alignments, collapses and others from the zone comprehended by the northwest of Morelia in Michoacán to the East of Acambay, Estado de México. Such analysis suggests that the fault segments possess a normal displacement plus a left component. In addition it can be associated to an alignment or different structures oblique directed to the principal fault trace which sometimes shows inverted moves suggest that the MAFS is a system with ''en echelon'' geometry which respond to transtensive tectonic activity. Recent research based in cinematic indicators from some of the most important faults of the MAFS concludes with evidence of the existence of a transtensive deformation in the center section of the TMVB, which can be explained through the oblique convergence model of plates Northamerica, Rivera and Cocos added to the division of the subduction angle at the North of the Mesoamerican trench.

75 FR 38069 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-01

... Python Species, and Four Anaconda Species as Injurious Reptiles AGENCY: Fish and Wildlife Service... regulations to add Indian python (Python molurus, including Burmese python Python molurus bivittatus), reticulated python (Broghammerus reticulatus or Python reticulatus), Northern African python (Python sebae...

Testing Deceptive Honeypots

DTIC Science & Technology

2014-09-01

get install python2.7 python- openssl python-gevent libevent-dev python2.7-dev build-essential make liblapack-dev libmysqlclient-dev python-chardet...apt-get install python-dev openssl python- openssl python-pyasn1 python-twisted • apt-get install subversion • apt-get install authbind 4

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

NASA Astrophysics Data System (ADS)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

Constraints to leisure travel and visitation to natural areas: An international comparison of four cities.In: Chavez, Deborah J.; Winter, Patricia L.; Absher, James D., eds

Treesearch

Patrick T. Tierney; Deborah J. Chavez; James D. Absher

2008-01-01

Leisure travel and visitation to natural areas and constraints to undertaking these activities are important concerns for recreation resource managers and tourism businesses. Surveys were administered to Los Angeles, Barcelona, Glasgow, and Morelia, Mexico, residents to ascertain leisure travel and undeveloped natural area visitation levels and constraints. A...

76 FR 40082 - Semiannual Regulatory Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-07

...; Constrictor Species From Python, Boa, and Eunectes Genera. Bureau of Ocean Energy Management, Regulation, and... Wildlife Evaluation; Constrictor Species from Python, Boa, and Eunectes Genera Legal Authority: 18 U.S.C... are: Indian python (including Burmese python), reticulated python, Northern African python, Southern...

Sierpinski and Carmichael Numbers

DTIC Science & Technology

2013-01-16

Carrie Finch Mathematics Department Washington and Lee University Lexington, VA 24450, USA finchc@wlu.edu Florian Luca Centro de Matemáticas...Universidad Nacional Autónoma de México C.P. 58089, Morelia, Michoacán, México fluca@matmor.unam.mx Carl Pomerance Department of Mathematics Dartmouth...Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any

Correlation analysis of symmetry breaking in the surface nanostructure ordering: case study of the ventral scale of the snake Morelia viridis

NASA Astrophysics Data System (ADS)

Kovalev, A.; Filippov, A.; Gorb, S. N.

2016-03-01

In contrast to the majority of inorganic or artificial materials, there is no ideal long-range ordering of structures on the surface in biological systems. Local symmetry of the ordering on biological surfaces is also often broken. In the present paper, the particular symmetry violation was analyzed for dimple-like nano-pattern on the belly scales of the skin of the pythonid snake Morelia viridis using correlation analysis and statistics of the distances between individual nanostructures. The results of the analysis performed on M. viridis were compared with a well-studied nano-nipple pattern on the eye of the sphingid moth Manduca sexta, used as a reference. The analysis revealed non-random, but very specific symmetry violation. In the case of the moth eye, the nano-nipple arrangement forms a set of domains, while in the case of the snake skin, the nano-dimples arrangement resembles an ordering of particles (molecules) in amorphous (glass) state. The function of the nano-dimples arrangement may be to provide both friction and strength isotropy of the skin. A simple model is suggested, which provides the results almost perfectly coinciding with the experimental ones. Possible mechanisms of the appearance of the above nano-formations are discussed.

77 FR 7968 - Semiannual Regulatory Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-13

...; Constrictor Species From Python, Boa, and Eunectes Genera. National Park Service--Proposed Rule Stage... Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera Legal Authority: 18 U.S.C. 42 Abstract... wildlife under the Lacey Act: Indian python (including Burmese python), reticulated python, Northern...

Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades

USGS Publications Warehouse

McCleery, Robert A.; Sovie, Adia; Reed, Robert N.; Cunningham, Mark W.; Hunter, Margaret E.; Hart, Kristen M.

2015-01-01

To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range.

sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology.

PubMed

Scott-Brown, James; Papachristodoulou, Antonis

2017-07-21

We present sbml-diff, a tool that is able to read a model of a biochemical reaction network in SBML format and produce a range of diagrams showing different levels of detail. Each diagram type can be used to visualize a single model or to visually compare two or more models. The default view depicts species as ellipses, reactions as rectangles, rules as parallelograms, and events as diamonds. A cartoon view replaces the symbols used for reactions on the basis of the associated Systems Biology Ontology terms. An abstract view represents species as ellipses and draws edges between them to indicate whether a species increases or decreases the production or degradation of another species. sbml-diff is freely licensed under the three-clause BSD license and can be downloaded from https://github.com/jamesscottbrown/sbml-diff and used as a python package called from other software, as a free-standing command-line application, or online using the form at http://sysos.eng.ox.ac.uk/tebio/upload.

Betrayal: radio-tagged Burmese pythons reveal locations of conspecifics in Everglades National Park

USGS Publications Warehouse

Smith, Brian J.; Cherkiss, Michael S.; Hart, Kristen M.; Rochford, Michael R.; Selby, Thomas H.; Snow, Ray W; Mazzotti, Frank J.

2016-01-01

The “Judas” technique is based on the idea that a radio-tagged individual can be used to “betray” conspecifics during the course of its routine social behavior. The Burmese python (Python bivittatus) is an invasive constrictor in southern Florida, and few methods are available for its control. Pythons are normally solitary, but from December–April in southern Florida, they form breeding aggregations containing up to 8 individuals, providing an opportunity to apply the technique. We radio-tracked 25 individual adult pythons of both sexes during the breeding season from 2007–2012. Our goals were to (1) characterize python movements and determine habitat selection for betrayal events, (2) quantify betrayal rates of Judas pythons, and (3) compare the efficacy of this tool with current tools for capturing pythons, both in terms of cost per python removed (CPP) and catch per unit effort (CPUE). In a total of 33 python-seasons, we had 8 betrayal events (24 %) in which a Judas python led us to new pythons. Betrayal events occurred more frequently in lowland forest (including tree islands) than would be expected by chance alone. These 8 events resulted in the capture of 14 new individuals (1–4 new pythons per event). Our effort comparison shows that while the Judas technique is more costly than road cruising surveys per python removed, the Judas technique yields more large, reproductive females and is effective at a time of year that road cruising is not, making it a potential complement to the status quo removal effort.

A field test of attractant traps for invasive Burmese pythons (Python molurus bivittatus) in southern Florida

USGS Publications Warehouse

Reed, R.N.; Hart, K.M.; Rodda, G.H.; Mazzotti, F.J.; Snow, R.W.; Cherkiss, M.; Rozar, R.; Goetz, S.

2011-01-01

Context. Invasive Burmese pythons (Python molurus bivittatus) are established over thousands of square kilometres of southern Florida, USA, and consume a wide range of native vertebrates. Few tools are available to control the python population, and none of the available tools have been validated in the field to assess capture success as a proportion of pythons available to be captured. Aims. Our primary aim was to conduct a trap trial for capturing invasive pythons in an area east of Everglades National Park, where many pythons had been captured in previous years, to assess the efficacy of traps for population control.Wealso aimed to compare results of visual surveys with trap capture rates, to determine capture rates of non-target species, and to assess capture rates as a proportion of resident pythons in the study area. Methods.Weconducted a medium-scale (6053 trap nights) experiment using two types of attractant traps baited with live rats in the Frog Pond area east of Everglades National Park.Wealso conducted standardised and opportunistic visual surveys in the trapping area. Following the trap trial, the area was disc harrowed to expose pythons and allow calculation of an index of the number of resident pythons. Key results. We captured three pythons and 69 individuals of various rodent, amphibian, and reptile species in traps. Eleven pythons were discovered during disc harrowing operations, as were large numbers of rodents. Conclusions. The trap trial captured a relatively small proportion of the pythons that appeared to be present in the study area, although previous research suggests that trap capture rates improve with additional testing of alternative trap designs. Potential negative impacts to non-target species were minimal. Low python capture rates may have been associated with extremely high local prey abundances during the trap experiment. Implications. Results of this trial illustrate many of the challenges in implementing and interpreting results from tests of control tools for large cryptic predators such as Burmese pythons. ?? CSIRO 2011.

Seismic Regionalization of Michoacan, Mexico and Recurrence Periods for Earthquakes

NASA Astrophysics Data System (ADS)

Magaña García, N.; Figueroa-Soto, Á.; Garduño-Monroy, V. H.; Zúñiga, R.

2017-12-01

Michoacán is one of the states with the highest occurrence of earthquakes in Mexico and it is a limit of convergence triggered by the subduction of Cocos plate over the North American plate, located in the zone of the Pacific Ocean of our country, in addition to the existence of active faults inside of the state like the Morelia-Acambay Fault System (MAFS).It is important to make a combination of seismic, paleosismological and geological studies to have good planning and development of urban complexes to mitigate disasters if destructive earthquakes appear. With statistical seismology it is possible to characterize the degree of seismic activity as well as to estimate the recurrence periods for earthquakes. For this work, seismicity catalog of Michoacán was compiled and homogenized in time and magnitude. This information was obtained from world and national agencies (SSN, CMT, etc), some data published by Mendoza and Martínez-López (2016) and starting from the seismic catalog homogenized by F. R. Zúñiga (Personal communication). From the analysis of the different focal mechanisms reported in the literature and geological studies, the seismic regionalization of the state of Michoacán complemented the one presented by Vázquez-Rosas (2012) and the recurrence periods for earthquakes within the four different seismotectonic regions. In addition, stable periods were determined for the b value of the Gutenberg-Richter (1944) using the Maximum Curvature and EMR (Entire Magnitude Range Method, 2005) techniques, which allowed us to determine recurrence periods: years for earthquakes upper to 7.5 for the subduction zone (A zone) with EMR technique and years with MAXC technique for the same years for earthquakes upper to 5 for B1 zone with EMR technique and years with MAXC technique; years for earthquakes upper to 7.0 for B2 zone with EMR technique and years with MAXC technique; and the last one, the Morelia-Acambay Fault Sistem zone (C zone) years for earthquakes upper to 5 with EMR technique and years with MAXC technique. This recurrence periods are very similar to periods calculated by Garduño-Monroy (2009) and Sunye-Puchol (2015) using paleoseismological methods. If we consider that the MAFS cross Zacapu, Pátzcuaro, Morelia, Cuitzeo, Maravatío and Acambay, the affected population would be around 1132807 habitants.

Cold-induced mortality of invasive Burmese pythons in south Florida

USGS Publications Warehouse

Mazzotti, Frank J.; Cherkiss, Michael S.; Hart, Kristen M.; Snow, Ray W.; Rochford, Michael R.; Dorcas, Michael E.; Reed, Robert N.

2011-01-01

A recent record cold spell in southern Florida (2–11 January 2010) provided an opportunity to evaluate responses of an established population of Burmese pythons (Python molurus bivittatus) to a prolonged period of unusually cold weather. We observed behavior, characterized thermal biology, determined fate of radio-telemetered (n = 10) and non-telemetered (n = 104) Burmese pythons, and analyzed habitat and environmental conditions experienced by pythons during and after a historic cold spell. Telemetered pythons had been implanted with radio-transmitters and temperature-recording data loggers prior to the cold snap. Only one of 10 telemetered pythons survived the cold snap, whereas 59 of 99 (60%) non-telemetered pythons for which we determined fate survived. Body temperatures of eight dead telemetered pythons fluctuated regularly prior to 9 January 2010, then declined substantially during the cold period (9–11 January) and exhibited no further evidence of active thermoregulation indicating they were likely dead. Unusually cold temperatures in January 2010 were clearly associated with mortality of Burmese pythons in the Everglades. Some radio-telemetered pythons appeared to exhibit maladaptive behavior during the cold spell, including attempting to bask instead of retreating to sheltered refugia. We discuss implications of our findings for persistence and spread of introduced Burmese pythons in the United States and for maximizing their rate of removal.

Report on the observed response of Javan lutungs (Trachypithecus auratus mauritius) upon encountering a reticulated python (Python reticulatus).

PubMed

Tsuji, Yamato; Prayitno, Bambang; Suryobroto, Bambang

2016-04-01

We observed an encounter between a reticulated python (Python reticulatus) and a group of wild Javan lutungs (Trachypithecus auratus mauritius) at the Pangandaran Nature Reserve, West Java, Indonesia. A python (about 2 m in length) moved toward a group of lutungs in the trees. Upon seeing the python, an adult male and several adult female lutungs began to emit alarm calls. As the python approached, two adult and one sub-adult female jumped onto a branch near the python and began mobbing the python by shaking the branch. During the mobbing, other individuals in the group (including an adult lutung male) remained nearby but did not participate. The python then rolled into a ball-like shape and stopped moving, at which point the lutungs moved away. The total duration of the encounter was about 40 min, during which time the lutungs stopped feeding and grooming. Group cohesiveness during and after the encounter was greater than that before the encounter, indicating that lutungs adjust their daily activity in response to potential predation risk.

Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades.

PubMed

McCleery, Robert A; Sovie, Adia; Reed, Robert N; Cunningham, Mark W; Hunter, Margaret E; Hart, Kristen M

2015-04-22

To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades

PubMed Central

McCleery, Robert A.; Sovie, Adia; Reed, Robert N.; Cunningham, Mark W.; Hunter, Margaret E.; Hart, Kristen M.

2015-01-01

To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range. PMID:25788598

Respiratory disease in ball pythons (Python regius) experimentally infected with ball python nidovirus.

PubMed

Hoon-Hanks, Laura L; Layton, Marylee L; Ossiboff, Robert J; Parker, John S L; Dubovi, Edward J; Stenglein, Mark D

2018-04-01

Circumstantial evidence has linked a new group of nidoviruses with respiratory disease in pythons, lizards, and cattle. We conducted experimental infections in ball pythons (Python regius) to test the hypothesis that ball python nidovirus (BPNV) infection results in respiratory disease. Three ball pythons were inoculated orally and intratracheally with cell culture isolated BPNV and two were sham inoculated. Antemortem choanal, oroesophageal, and cloacal swabs and postmortem tissues of infected snakes were positive for viral RNA, protein, and infectious virus by qRT-PCR, immunohistochemistry, western blot and virus isolation. Clinical signs included oral mucosal reddening, abundant mucus secretions, open-mouthed breathing, and anorexia. Histologic lesions included chronic-active mucinous rhinitis, stomatitis, tracheitis, esophagitis and proliferative interstitial pneumonia. Control snakes remained negative and free of clinical signs throughout the experiment. Our findings establish a causal relationship between nidovirus infection and respiratory disease in ball pythons and shed light on disease progression and transmission. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Ultrasound imaging of the anterior section of the eye of five different snake species.

PubMed

Lauridsen, Henrik; Da Silva, Mari-Ann O; Hansen, Kasper; Jensen, Heidi M; Warming, Mads; Wang, Tobias; Pedersen, Michael

2014-12-30

Nineteen clinically normal snakes: six ball pythons (Python regius), six Burmese pythons (Python bivittatus), one Children's python (Antaresia childreni), four Amazon tree boas (Corallus hortulanus), and two Malagasy ground boas (Acrantophis madagascariensis) were subjected to ultrasound imaging with 21 MHz (ball python) and 50 MHz (ball python, Burmese python, Children's python, Amazon tree boa, Malagasy ground boa) transducers in order to measure the different structures of the anterior segment in clinically normal snake eyes with the aim to review baseline values for clinically important ophthalmic structures. The ultrasonographic measurements included horizontal spectacle diameter, spectacle thickness, depth of sub-spectacular space and corneal thickness. For comparative purposes, a formalin-fixed head of a Burmese python was subjected to micro computed tomography. In all snakes, the spectacle was thinner than the cornea. There was significant difference in spectacle diameter, and spectacle and corneal thickness between the Amazon tree boa and the Burmese and ball pythons. There was no difference in the depth of the sub-spectacular space. The results obtained in the Burmese python with the 50 MHz transducer were similar to the results obtained with micro computed tomography. Images acquired with the 21 MHz transducer included artifacts which may be misinterpreted as ocular structures. Our measurements of the structures in the anterior segment of the eye can serve as orientative values for snakes examined for ocular diseases. In addition, we demonstrated that using a high frequency transducer minimizes the risk of misinterpreting artifacts as ocular structures.

A New Python Library for Spectroscopic Analysis with MIDAS Style

NASA Astrophysics Data System (ADS)

Song, Y.; Luo, A.; Zhao, Y.

2013-10-01

The ESO MIDAS is a system for astronomers to analyze data which many astronomers are using. Python is a high level script language and there are many applications for astronomical data process. We are releasing a new Python library which realizes some MIDAS commands in Python. People can use it to write a MIDAS style Python code. We call it PydasLib. It is a Python library based on ESO MIDAS functions, which is easily used by astronomers who are familiar with the usage of MIDAS.

Unilateral microphthalmia or anophthalmia in eight pythons (Pythonidae).

PubMed

Da Silva, Mari-Ann O; Bertelsen, Mads F; Wang, Tobias; Pedersen, Michael; Lauridsen, Henrik; Heegaard, Steffen

2015-01-01

To provide morphological descriptions of microphthalmia or anophthalmia in eight pythons using microcomputerized tomography (μCT), magnetic resonance imaging (MRI), and histopathology. Seven Burmese pythons (Python bivittatus) and one ball python (P. regius) with clinically normal right eyes and an abnormal or missing left eye. At the time of euthanasia, four of the eight snakes underwent necropsy. Hereafter, the heads of two Burmese pythons and one ball python were examined using μCT, and another Burmese python was subjected to MRI. Following these procedures, the heads of these four pythons along with the heads of an additional three Burmese pythons were prepared for histology. All eight snakes had left ocular openings seen as dermal invaginations between 0.2 and 2.0 mm in diameter. They also had varying degrees of malformations of the orbital bones and a limited presence of nervous, glandular, and muscle tissue in the posterior orbit. Two individuals had small but identifiable eyes. Furthermore, remnants of the pigmented embryonic framework of the hyaloid vessels were found in the anophthalmic snakes. Necropsies revealed no other macroscopic anomalies. Eight pythons with unilateral left-sided microphthalmia or anophthalmia had one normal eye and a left orbit with malformed or incompletely developed ocular structures along with remnants of fetal structures. These cases lend further information to a condition that is often seen in snakes, but infrequently described. © 2014 American College of Veterinary Ophthalmologists.

Pythons in Burma: Short-tailed python (Reptilia: Squamata)

USGS Publications Warehouse

Zug, George R.; Gotte, Steve W.; Jacobs, Jeremy F.

2011-01-01

Short-tailed pythons, Python curtus species group, occur predominantly in the Malayan Peninsula, Sumatra, and Borneo. The discovery of an adult female in Mon State, Myanmar, led to a review of the distribution of all group members (spot-mapping of all localities of confirmed occurrence) and an examination of morphological variation in P. brongersmai. The resulting maps demonstrate a limited occurrence of these pythons within peninsular Malaya, Sumatra, and Borneo with broad absences in these regions. Our small samples limit the recognition of regional differentiation in the morphology of P. brongersmai populations; however, the presence of unique traits in the Myanmar python and its strong allopatry indicate that it is a unique genetic lineage, and it is described as Python kyaiktiyo new species.

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

SmartImport.py is a Python source-code file that implements a replacement for the standard Python module importer. The code is derived from knee.py, a file in the standard Python diestribution , and adds functionality to improve the performance of Python module imports in massively parallel contexts.

PyMOOSE: Interoperable Scripting in Python for MOOSE

PubMed Central

Ray, Subhasis; Bhalla, Upinder S.

2008-01-01

Python is emerging as a common scripting language for simulators. This opens up many possibilities for interoperability in the form of analysis, interfaces, and communications between simulators. We report the integration of Python scripting with the Multi-scale Object Oriented Simulation Environment (MOOSE). MOOSE is a general-purpose simulation system for compartmental neuronal models and for models of signaling pathways based on chemical kinetics. We show how the Python-scripting version of MOOSE, PyMOOSE, combines the power of a compiled simulator with the versatility and ease of use of Python. We illustrate this by using Python numerical libraries to analyze MOOSE output online, and by developing a GUI in Python/Qt for a MOOSE simulation. Finally, we build and run a composite neuronal/signaling model that uses both the NEURON and MOOSE numerical engines, and Python as a bridge between the two. Thus PyMOOSE has a high degree of interoperability with analysis routines, with graphical toolkits, and with other simulators. PMID:19129924

Humoral regulation of heart rate during digestion in pythons (Python molurus and Python regius).

PubMed

Enok, Sanne; Simonsen, Lasse Stærdal; Pedersen, Signe Vesterskov; Wang, Tobias; Skovgaard, Nini

2012-05-15

Pythons exhibit a doubling of heart rate when metabolism increases several times during digestion. Pythons, therefore, represent a promising model organism to study autonomic cardiovascular regulation during the postprandial state, and previous studies show that the postprandial tachycardia is governed by a release of vagal tone as well as a pronounced stimulation from nonadrenergic, noncholinergic (NANC) factors. Here we show that infusion of plasma from digesting donor pythons elicit a marked tachycardia in fasting snakes, demonstrating that the NANC factor resides in the blood. Injections of the gastrin and cholecystokinin receptor antagonist proglumide had no effect on double-blocked heart rate or blood pressure. Histamine has been recognized as a NANC factor in the early postprandial period in pythons, but the mechanism of its release has not been identified. Mast cells represent the largest repository of histamine in vertebrates, and it has been speculated that mast cells release histamine during digestion. Treatment with the mast cell stabilizer cromolyn significantly reduced postprandial heart rate in pythons compared with an untreated group but did not affect double-blocked heart rate. While this study indicates that histamine induces postprandial tachycardia in pythons, its release during digestion is not stimulated by gastrin or cholecystokinin nor is its release from mast cells a stimulant of postprandial tachycardia.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.

PubMed

Gautier, Laurent

2010-12-21

Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/.

Prospects and limitations of citizen science in invasive species management: A case study with Burmese pythons in Everglades National Park

USGS Publications Warehouse

Falk, Bryan; Snow, Raymond W.; Reed, Robert

2016-01-01

Citizen-science programs have the potential to contribute to the management of invasive species, including Python molurus bivittatus (Burmese Python) in Florida. We characterized citizen-science–generated Burmese Python information from Everglades National Park (ENP) to explore how citizen science may be useful in this effort. As an initial step, we compiled and summarized records of Burmese Python observations and removals collected by both professional and citizen scientists in ENP during 2000–2014 and found many patterns of possible significance, including changes in annual observations and in demographic composition after a cold event. These patterns are difficult to confidently interpret because the records lack search-effort information, however, and differences among years may result from differences in search effort. We began collecting search-effort information in 2014 by leveraging an ongoing citizen-science program in ENP. Program participation was generally low, with most authorized participants in 2014 not searching for the snakes at all. We discuss the possible explanations for low participation, especially how the low likelihood of observing pythons weakens incentives to search. The monthly rate of Burmese Python observations for 2014 averaged ~1 observation for every 8 h of searching, but during several months, the rate was 1 python per >40 h of searching. These low observation-rates are a natural outcome of the snakes’ low detectability—few Burmese Pythons are likely to be observed even if many are present. The general inaccessibility of the southern Florida landscape also severely limits the effectiveness of using visual searches to find and remove pythons for the purposes of population control. Instead, and despite the difficulties in incentivizing voluntary participation, the value of citizen-science efforts in the management of the Burmese Python population is in collecting search-effort information.

A modern Python interface for the Generic Mapping Tools

NASA Astrophysics Data System (ADS)

Uieda, L.; Wessel, P.

2017-12-01

Figures generated by The Generic Mapping Tools (GMT) are present in countless publications across the Earth sciences. The command-line interface of GMT lends the tool its flexibility but also creates a barrier to entry for begginers. Meanwhile, adoption of the Python programming language has grown across the scientific community. This growth is largely due to the simplicity and low barrier to entry of the language and its ecosystem of tools. Thus, it is not surprising that there have been at least three attempts to create Python interfaces for GMT: gmtpy (github.com/emolch/gmtpy), pygmt (github.com/ian-r-rose/pygmt), and PyGMT (github.com/glimmer-cism/PyGMT). None of these projects are currently active and, with the exception of pygmt, they do not use the GMT Application Programming Interface (API) introduced in GMT 5. The two main Python libraries for plotting data on maps are the matplotlib Basemap toolkit (matplotlib.org/basemap) and Cartopy (scitools.org.uk/cartopy), both of which rely on matplotlib (matplotlib.org) as the backend for generating the figures. Basemap is known to have limitations and is being discontinued. Cartopy is an improvement over Basemap but is still bound by the speed and memory constraints of matplotlib. We present a new Python interface for GMT (GMT/Python) that makes use of the GMT API and of new features being developed for the upcoming GMT 6 release. The GMT/Python library is designed according to the norms and styles of the Python community. The library integrates with the scientific Python ecosystem by using the "virtual files" from the GMT API to implement input and output of Python data types (numpy "ndarray" for tabular data and xarray "Dataset" for grids). Other features include an object-oriented interface for creating figures, the ability to display figures in the Jupyter notebook, and descriptive aliases for GMT arguments (e.g., "region" instead of "R" and "projection" instead of "J"). GMT/Python can also serve as a backend for developing new high-level interfaces, which can help make GMT more accessible to beginners and more intuitive for Python users. GMT/Python is an open-source project hosted on Github (github.com/GenericMappingTools/gmt-python) and is in early stages of development. A first release will accompany the release of GMT 6, which is expected for early 2018.

PyMidas: Interface from Python to Midas

NASA Astrophysics Data System (ADS)

Maisala, Sami; Oittinen, Tero

2014-01-01

PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.

Endocardial fibrosarcoma in a reticulated python (Python reticularis).

PubMed

Gumber, Sanjeev; Nevarez, Javier G; Cho, Doo-Youn

2010-11-01

A female, reticulated python (Python reticularis) of unknown age was presented with a history of lethargy, weakness, and distended coelom. Physical examination revealed severe dystocia and stomatitis. The reticulated python was euthanized due to a poor clinical prognosis. Postmortem examination revealed marked distention of the reproductive tract with 26 eggs (10-12 cm in diameter), pericardial effusion, and a slightly firm, pale tan mass (3-4 cm in diameter) adhered to the endocardium at the base of aorta. Based on histopathologic and transmission electron microscopic findings, the diagnosis of endocardial fibrosarcoma was made.

Leveraging Python Interoperability Tools to Improve Sapphire's Usability

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

Gezahegne, A; Love, N S

2007-12-10

The Sapphire project at the Center for Applied Scientific Computing (CASC) develops and applies an extensive set of data mining algorithms for the analysis of large data sets. Sapphire's algorithms are currently available as a set of C++ libraries. However many users prefer higher level scripting languages such as Python for their ease of use and flexibility. In this report, we evaluate four interoperability tools for the purpose of wrapping Sapphire's core functionality with Python. Exposing Sapphire's functionality through a Python interface would increase its usability and connect its algorithms to existing Python tools.

The zoonotic implications of pentastomiasis in the royal python (python regius).

PubMed

Ayinmode, Ab; Adedokun, Ao; Aina, A; Taiwo, V

2010-09-01

Pentastomes are worm-like endoparasites of the phylum Pentastomida found principally in the respiratory tract of reptiles, birds, and mammals. They cause a zoonotic disease known as pentastomiasis in humans and other mammals. The autopsy of a Nigerian royal python (Python regius) revealed two yellowish-white parasites in the lungs, tissue necrosis and inflammatory lesions. The parasite was confirmed to be Armillifer spp (Pentastomid); this is the first recorded case of pentastomiasis in the royal python (Python regius) in Nigeria. This report may be an alert of the possibility of on-going zoonotic transmission of pentastomiasis from snake to man, especially in the sub-urban/rural areas of Nigeria and other West African countries where people consume snake meat.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

PubMed

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

Python in Astronomy 2016

NASA Astrophysics Data System (ADS)

Jenness, Tim; Robitaille, Thomas; Tollerud, Erik; Mumford, Stuart; Cruz, Kelle

2016-04-01

The second Python in Astronomy conference will be held from 21-25 March 2016 at the University of Washington eScience Institute in Seattle, WA, USA. Similarly to the 2015 meeting (which was held at the Lorentz Center), we are aiming to bring together researchers, Python developers, users, and educators. The conference will include presentations, tutorials, unconference sessions, and coding sprints. In addition to sharing information about state-of-the art Python Astronomy packages, the workshop will focus on improving interoperability between astronomical Python packages, providing training for new open-source contributors, and developing educational materials for Python in Astronomy. The meeting is therefore not only aimed at current developers, but also users and educators who are interested in being involved in these efforts.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

PubMed Central

2010-01-01

Background Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. Results The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Conclusions Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/ PMID:21210978

Consumption of bird eggs by invasive Burmese Pythons in Florida

USGS Publications Warehouse

Dove, Carla J.; Reed, Robert N.; Snow, Ray W.

2012-01-01

Burmese Pythons (Python molurus bivittatus or P. bivittatus) have been reported to consume 25 species of adult birds in Everglades National Park, Florida (Dove et al. 2011), but until now no records documented this species eating bird eggs. Here we report three recent cases of bird-egg consumption by Burmese Pythons and discuss egg-eating in basal snakes.

Acariasis on pet Burmese python, Python molurus bivittatus in Malaysia.

PubMed

Mariana, A; Vellayan, S; Halimaton, I; Ho, T M

2011-03-01

To identify the acari present on pet Burmese pythons in Malaysia and to determine whether there is any potential public health risk related to handling of the snakes. Two sub-adult Burmese pythons kept as pets for a period of about 6 to 7 months by different owners, were brought to an exotic animal practice for treatment. On a complete medical examination, some ticks and mites (acari) were detected beneath the dorsal and ventral scales along body length of the snakes. Ticks were directly identified and mites were mounted prior to identification. A total of 12 ticks represented by 3 males, 2 females and 7 nymphal stages of Rhipicephalus sanguineus (R. sanguineus) were extracted from the first python while the other one was with 25 female Ophionyssus natricis (O. natricis) mesostigmatid mites. Only adult female mites were found. These mites are common ectoparasites of Burmese pythons. Both the acarine species found on the Burmese pythons are known vectors of pathogens. This is the first record that R. sanguineus has been reported from a pet Burmese python in Malaysia. Copyright © 2011 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

The Discovery of XY Sex Chromosomes in a Boa and Python.

PubMed

Gamble, Tony; Castoe, Todd A; Nielsen, Stuart V; Banks, Jaison L; Card, Daren C; Schield, Drew R; Schuett, Gordon W; Booth, Warren

2017-07-24

For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1-3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7]. Here we demonstrate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromosomes, based on the discovery of male-specific genetic markers in both species. We use these markers, along with transcriptomic and genomic data, to identify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independently in each lineage. This discovery highlights the dynamic evolution of vertebrate sex chromosomes and further enhances the value of snakes as a model for studying sex chromosome evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Python in the NERSC Exascale Science Applications Program for Data

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

Ronaghi, Zahra; Thomas, Rollin; Deslippe, Jack

We describe a new effort at the National Energy Re- search Scientific Computing Center (NERSC) in performance analysis and optimization of scientific Python applications targeting the Intel Xeon Phi (Knights Landing, KNL) many- core architecture. The Python-centered work outlined here is part of a larger effort called the NERSC Exascale Science Applications Program (NESAP) for Data. NESAP for Data focuses on applications that process and analyze high-volume, high-velocity data sets from experimental/observational science (EOS) facilities supported by the US Department of Energy Office of Science. We present three case study applications from NESAP for Data that use Python. These codesmore » vary in terms of “Python purity” from applications developed in pure Python to ones that use Python mainly as a convenience layer for scientists without expertise in lower level programming lan- guages like C, C++ or Fortran. The science case, requirements, constraints, algorithms, and initial performance optimizations for each code are discussed. Our goal with this paper is to contribute to the larger conversation around the role of Python in high-performance computing today and tomorrow, highlighting areas for future work and emerging best practices« less

Responses of python gastrointestinal regulatory peptides to feeding

PubMed Central

Secor, Stephen M.; Fehsenfeld, Drew; Diamond, Jared; Adrian, Thomas E.

2001-01-01

In the Burmese python (Python molurus), the rapid up-regulation of gastrointestinal (GI) function and morphology after feeding, and subsequent down-regulation on completing digestion, are expected to be mediated by GI hormones and neuropeptides. Hence, we examined postfeeding changes in plasma and tissue concentrations of 11 GI hormones and neuropeptides in the python. Circulating levels of cholecystokinin (CCK), glucose-dependent insulinotropic peptide (GIP), glucagon, and neurotensin increase by respective factors of 25-, 6-, 6-, and 3.3-fold within 24 h after feeding. In digesting pythons, the regulatory peptides neurotensin, somatostatin, motilin, and vasoactive intestinal peptide occur largely in the stomach, GIP and glucagon in the pancreas, and CCK and substance P in the small intestine. Tissue concentrations of CCK, GIP, and neurotensin decline with feeding. Tissue distributions and molecular forms (as determined by gel-permeation chromatography) of many python GI peptides are similar or identical to those of their mammalian counterparts. The postfeeding release of GI peptides from tissues, and their concurrent rise in plasma concentrations, suggests that they play a role in regulating python-digestive responses. These large postfeeding responses, and similarities of peptide structure with mammals, make pythons an attractive model for studying GI peptides. PMID:11707600

Fatty acids identified in the Burmese python promote beneficial cardiac growth.

PubMed

Riquelme, Cecilia A; Magida, Jason A; Harrison, Brooke C; Wall, Christopher E; Marr, Thomas G; Secor, Stephen M; Leinwand, Leslie A

2011-10-28

Burmese pythons display a marked increase in heart mass after a large meal. We investigated the molecular mechanisms of this physiological heart growth with the goal of applying this knowledge to the mammalian heart. We found that heart growth in pythons is characterized by myocyte hypertrophy in the absence of cell proliferation and by activation of physiological signal transduction pathways. Despite high levels of circulating lipids, the postprandial python heart does not accumulate triglycerides or fatty acids. Instead, there is robust activation of pathways of fatty acid transport and oxidation combined with increased expression and activity of superoxide dismutase, a cardioprotective enzyme. We also identified a combination of fatty acids in python plasma that promotes physiological heart growth when injected into either pythons or mice.

First record of invasive Burmese Python oviposition and brooding inside an anthropogenic structure

USGS Publications Warehouse

Hanslowe, Emma; Falk, Bryan; Collier, Michelle A. M.; Josimovich, Jillian; Rahill, Thomas; Reed, Robert

2016-01-01

We discovered an adult female Python bivittatus (Burmese Python) coiled around a clutch of 25 eggs in a cement culvert in Flamingo, FL, in Everglades National Park. To our knowledge, this is the first record of an invasive Burmese Python laying eggs and brooding inside an anthropogenic structure in Florida. A 92% hatch-success rate suggests that the cement culvert provided suitable conditions for oviposition, embryonic development, and hatching. Given the plenitude of such anthropogenic structures across the landscape, available sites for oviposition and brooding may not be limiting for the invasive Burmese Python population.

A field test of attractant traps for invasive Burmese pythons (Python molurus bivittatus) in southern Florida

USGS Publications Warehouse

Reed, Robert N.; Hart, Kristen M.; Rodda, Gordon H.; Mazzotti, Frank J.; Snow, Ray W.; Cherkiss, Michael; Rozar, Rondald; Goetz, Scott

2011-01-01

Conclusions: The trap trial captured a relatively small proportion of the pythons that appeared to be present in the study area, although previous research suggests that trap capture rates improve with additional testing of alternative trap designs. Potential negative impacts to non-target species were minimal. Low python capture rates may have been associated with extremely high local prey abundances during the trap experiment. Implications: Results of this trial illustrate many of the challenges in implementing and interpreting results from tests of control tools for large cryptic predators such as Burmese pythons.

Re-imagining a Stata/Python Combination

NASA Technical Reports Server (NTRS)

Fiedler, James

2013-01-01

At last year's Stata Conference, I presented some ideas for combining Stata and the Python programming language within a single interface. Two methods were presented: in one, Python was used to automate Stata; in the other, Python was used to send simulated keystrokes to the Stata GUI. The first method has the drawback of only working in Windows, and the second can be slow and subject to character input limits. In this presentation, I will demonstrate a method for achieving interaction between Stata and Python that does not suffer these drawbacks, and I will present some examples to show how this interaction can be useful.

Python erythrocytes are resistant to α-hemolysin from Escherichia coli.

PubMed

Larsen, Casper K; Skals, Marianne; Wang, Tobias; Cheema, Muhammad U; Leipziger, Jens; Praetorius, Helle A

2011-12-01

α-Hemolysin (HlyA) from Escherichia coli lyses mammalian erythrocytes by creating nonselective cation pores in the membrane. Pore insertion triggers ATP release and subsequent P2X receptor and pannexin channel activation. Blockage of either P2X receptors or pannexin channels reduces HlyA-induced hemolysis. We found that erythrocytes from Python regius and Python molurus are remarkably resistant to HlyA-induced hemolysis compared to human and Trachemys scripta erythrocytes. HlyA concentrations that induced maximal hemolysis of human erythrocytes did not affect python erythrocytes, but increasing the HlyA concentration 40-fold did induce hemolysis. Python erythrocytes were more resistant to osmotic stress than human erythrocytes, but osmotic stress tolerance per se did not confer HlyA resistance. Erythrocytes from T. scripta, which showed higher osmotic resistance than python erythrocytes, were as susceptible to HlyA as human erythrocytes. Therefore, we tested whether python erythrocytes lack the purinergic signalling known to amplify HlyA-induced hemolysis in human erythrocytes. P. regius erythrocytes increased intracellular Ca²⁺ concentration and reduced cell volume when exposed to 3 mM ATP, indicating the presence of a P2X₇-like receptor. In addition, scavenging extracellular ATP or blocking P2 receptors or pannexin channels reduced the HlyA-induced hemolysis. We tested whether the low HlyA sensitivity resulted from low affinity of HlyA to the python erythrocyte membrane. We found comparable incorporation of HlyA into human and python erythrocyte membranes. Taken together, the remarkable HlyA resistance of python erythrocytes was not explained by increased osmotic resistance, lack of purinergic hemolysis amplification, or differences in HlyA affinity.

MEG and EEG data analysis with MNE-Python.

PubMed

Gramfort, Alexandre; Luessi, Martin; Larson, Eric; Engemann, Denis A; Strohmeier, Daniel; Brodbeck, Christian; Goj, Roman; Jas, Mainak; Brooks, Teon; Parkkonen, Lauri; Hämäläinen, Matti

2013-12-26

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne.

Pycellerator: an arrow-based reaction-like modelling language for biological simulations.

PubMed

Shapiro, Bruce E; Mjolsness, Eric

2016-02-15

We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales-Menten-Henri (MMH) and Gene-Regulation (GRN) to Monod-Wyman-Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface. Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica. All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases. Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

MEG and EEG data analysis with MNE-Python

PubMed Central

Gramfort, Alexandre; Luessi, Martin; Larson, Eric; Engemann, Denis A.; Strohmeier, Daniel; Brodbeck, Christian; Goj, Roman; Jas, Mainak; Brooks, Teon; Parkkonen, Lauri; Hämäläinen, Matti

2013-01-01

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne. PMID:24431986

ERDC MSRC Resource. High Performance Computing for the Warfighter. Fall 2006

DTIC Science & Technology

2006-01-01

to as Aggregated Combat Modeling, putting us at the campaign level).” Incorporating UIT within DAC The DAC system is written in Python and uses...API calls with two Python classes, UITConnectionFactory and UITConnection. UITConnectionFactory supports Kerberos authentication and establishes a...API calls within these Python classes, we insulated the DAC code from the Python SOAP interface requirements and details of the ERDC MSRC Resource

Stata Hybrids: Updates and Ideas

NASA Technical Reports Server (NTRS)

Fieldler, James

2014-01-01

At last year's Stata conference I presented two projects for using Python with Stata: a plugin that embeds the Python programming language within Stata and code for using Stata data sets in Python. In this talk I will describe some small improvements being made to these projects, and I will present other ideas for combining tools with Stata. Some of these ideas use Python, some use JavaScript and a web browser.

Supersize me: Remains of three white-tailed deer (Odocoileus virginianus) in an invasive Burmese python (Python molurus bivittatus) in Florida

USGS Publications Warehouse

Boback, Scott M.; Snow, Ray W.; Hsu, Teresa; Peurach, Suzanne C.; Dove, Carla J.; Reed, Robert N.

2016-01-01

Snakes have become successful invaders in a wide variety of ecosystems worldwide. In southern Florida, USA, the Burmese python (Python molurus bivittatus) has become established across thousands of square kilometers including all of Everglades National Park (ENP). Both experimental and correlative data have supported a relationship between Burmese python predation and declines or extirpations of mid- to large-sized mammals in ENP. In June 2013 a large python (4.32 m snout-vent length, 48.3 kg) was captured and removed from the park. Subsequent necropsy revealed a massive amount of fecal matter (79 cm in length, 6.5 kg) within the snake’s large intestine. A comparative examination of bone, teeth, and hooves extracted from the fecal contents revealed that this snake consumed three white-tailed deer (Odocoileus virginianus). This is the first report of an invasive Burmese python containing the remains of multiple white-tailed deer in its gut. Because the largest snakes native to southern Florida are not capable of consuming even mid-sized mammals, pythons likely represent a novel predatory threat to white-tailed deer in these habitats. This work highlights the potential impact of this large-bodied invasive snake and supports the need for more work on invasive predator-native prey relationships.

Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

USGS Publications Warehouse

Falk, Bryan; Reed, Robert N.

2015-01-01

Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons

Hemodynamic consequences of cardiac malformations in two juvenile ball pythons (Python regius).

PubMed

Jensen, Bjarke; Wang, Tobias

2009-12-01

Two cases of bifid ventricles and cardiac malformations in juvenile ball python (Python regius) were investigated by blood pressure measurements and macro- and microscopic sectioning. A study of a normal ball python was included for reference. In both cases, all cardiac chambers were enlarged and abnormally shaped. Internal assessment of the ventricles revealed a pronounced defect of the muscular ridge, which normally is responsible for separating the systemic and pulmonary circuits. Consistent with the small muscular ridge, systolic pressures were identical in the pulmonary and systemic arteries, but, the snakes, nevertheless, lived to reach body weights severalfold of their hatchling weight.

Practical Approach for Hyperspectral Image Processing in Python

NASA Astrophysics Data System (ADS)

Annala, L.; Eskelinen, M. A.; Hämäläinen, J.; Riihinen, A.; Pölönen, I.

2018-04-01

Python is a very popular programming language among data scientists around the world. Python can also be used in hyperspectral data analysis. There are some toolboxes designed for spectral imaging, such as Spectral Python and HyperSpy, but there is a need for analysis pipeline, which is easy to use and agile for different solutions. We propose a Python pipeline which is built on packages xarray, Holoviews and scikit-learn. We have developed some of own tools, MaskAccessor, VisualisorAccessor and a spectral index library. They also fulfill our goal of easy and agile data processing. In this paper we will present our processing pipeline and demonstrate it in practice.

Comparison of the genetic variability of Blastocystis subtypes between human carriers from two contrasting climatic regions of México.

PubMed

Villegas-Gómez, Isaac; Martínez-Hernández, Fernando; Urrea-Quezada, Alejandro; González-Díaz, Mariana; Durazo, María; Hernández, Jesús; Orozco-Mosqueda, Guadalupe Erendira; Villalobos, Guiehdani; Maravilla, Pablo; Valenzuela, Olivia

2016-10-01

Blastocystis sp. is an anaerobic intestinal microorganism commonly identified in the feces of several animals, including humans. Blastocystis exhibits high genetic polymorphism and at least 17 subtypes (ST) have been identified; ST1-ST3 are frequently found in the Americas. Furthermore, in vitro assays have shown that temperature and humidity can affect the viability of Blastocystis cysts. In this study, we describe the genetic variability and genetic differentiation among and within Blastocystis STs in adults and children from the cities of Hermosillo and Morelia cities, which represent arid and humid subtropical climatic regions of México, respectively. Phylogenetic and genetic diversity was assessed by analyzing a region of the small subunit ribosomal DNA (SSU rDNA) gene as a marker. Blastocystis ST3 and ST1 were associated with children from Hermosillo and Morelia, respectively. An analysis of the nucleotide diversity (π) and haplotype polymorphism (θ) indexes showed that they were similar within each ST, but different between ST1 and ST3. Interestingly, the group of symptomatic carriers from Hermosillo showed scarce mean nucleotide diversity compared to the asymptomatic carriers (0.0039±0.0030 and 0.0329±0.0286, respectively). Furthermore, the gene flow and genetic differentiation indexes between the children and adults suggested that the Blastocystis haplotypes in the adult carriers were "highly mobile" among humans, while the haplotypes found in the children were more isolated and genetically differentiated between them. Copyright © 2016 Elsevier B.V. All rights reserved.

Using Python as a first programming environment for computational physics in developing countries

NASA Astrophysics Data System (ADS)

Akpojotor, Godfrey; Ehwerhemuepha, Louis; Echenim, Myron; Akpojotor, Famous

2011-03-01

Python unique features such its interpretative, multiplatform and object oriented nature as well as being a free and open source software creates the possibility that any user connected to the internet can download the entire package into any platform, install it and immediately begin to use it. Thus Python is gaining reputation as a preferred environment for introducing students and new beginners to programming. Therefore in Africa, the Python African Tour project has been launched and we are coordinating its use in computational science. We examine here the challenges and prospects of using Python for computational physics (CP) education in developing countries (DC). Then we present our project on using Python to simulate and aid the learning of laboratory experiments illustrated here by modeling of the simple pendulum and also to visualize phenomena in physics illustrated here by demonstrating the wave motion of a particle in a varying potential. This project which is to train both the teachers and our students on CP using Python can easily be adopted in other DC.

Pizza.py Toolkit

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

Plimpton, Steve; Jones, Matt; Crozier, Paul

2006-01-01

Pizza.py is a loosely integrated collection of tools, many of which provide support for the LAMMPS molecular dynamics and ChemCell cell modeling packages. There are tools to create input files. convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots. Software packages that are wrapped by Pizza.py. so they can invoked from within Python, include GnuPlot, MatLab, Raster3d. and RasMol. Pizza.py is written in Python and runs on any platform that supports Python. Pizza.py enhances the standard Python interpreter in a few simple ways. Its tools are Python modules which can be invokedmore » interactively, from scripts, or from GUIs when appropriate. Some of the tools require additional Python packages to be installed as part of the users Python. Others are wrappers on software packages (as listed above) which must be available on the users system. It is easy to modify or extend Pizza.py with new functionality or new tools, which need not have anything to do with LAMMPS or ChemCell.« less

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

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

Python for Ecology

EPA Science Inventory

Python is a high-level scripting language that is becoming increasingly popular for scientific computing. This all-day workshop is designed to introduce the basics of Python programming to ecologists. Some scripting/programming experience is recommended (e.g. familiarity with R)....

Automating Disk Forensic Processing with SleuthKit, XML and Python

DTIC Science & Technology

2009-05-01

1 Automating Disk Forensic Processing with SleuthKit, XML and Python Simson L. Garfinkel Abstract We have developed a program called fiwalk which...files themselves. We show how it is relatively simple to create automated disk forensic applications using a Python module we have written that reads...software that the portable device may contain. Keywords: Computer Forensics; XML; Sleuth Kit; Python I. INTRODUCTION In recent years we have found many

Python Scripts for Automation of Current-Voltage Testing of Semiconductor Devices (FY17)

DTIC Science & Technology

2017-01-01

ARL-TR-7923 ● JAN 2017 US Army Research Laboratory Python Scripts for Automation of Current- Voltage Testing of Semiconductor...manual device-testing procedures is reduced or eliminated through automation. This technical report includes scripts written in Python , version 2.7, used ...nothing. 3.1.9 Exit Program The script exits the entire program. Line 505, sys.exit(), uses the sys package that comes with Python to exit system

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

PubMed Central

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-01-01

Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. PMID:18328109

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

PubMed

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-03-09

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

Python to learn programming

NASA Astrophysics Data System (ADS)

Bogdanchikov, A.; Zhaparov, M.; Suliyev, R.

2013-04-01

Today we have a lot of programming languages that can realize our needs, but the most important question is how to teach programming to beginner students. In this paper we suggest using Python for this purpose, because it is a programming language that has neatly organized syntax and powerful tools to solve any task. Moreover it is very close to simple math thinking. Python is chosen as a primary programming language for freshmen in most of leading universities. Writing code in python is easy. In this paper we give some examples of program codes written in Java, C++ and Python language, and we make a comparison between them. Firstly, this paper proposes advantages of Python language in relation to C++ and JAVA. Then it shows the results of a comparison of short program codes written in three different languages, followed by a discussion on how students understand programming. Finally experimental results of students' success in programming courses are shown.

PyEEG: an open source Python module for EEG/MEG feature extraction.

PubMed

Bao, Forrest Sheng; Liu, Xin; Zhang, Christina

2011-01-01

Computer-aided diagnosis of neural diseases from EEG signals (or other physiological signals that can be treated as time series, e.g., MEG) is an emerging field that has gained much attention in past years. Extracting features is a key component in the analysis of EEG signals. In our previous works, we have implemented many EEG feature extraction functions in the Python programming language. As Python is gaining more ground in scientific computing, an open source Python module for extracting EEG features has the potential to save much time for computational neuroscientists. In this paper, we introduce PyEEG, an open source Python module for EEG feature extraction.

PyEEG: An Open Source Python Module for EEG/MEG Feature Extraction

PubMed Central

Bao, Forrest Sheng; Liu, Xin; Zhang, Christina

2011-01-01

Computer-aided diagnosis of neural diseases from EEG signals (or other physiological signals that can be treated as time series, e.g., MEG) is an emerging field that has gained much attention in past years. Extracting features is a key component in the analysis of EEG signals. In our previous works, we have implemented many EEG feature extraction functions in the Python programming language. As Python is gaining more ground in scientific computing, an open source Python module for extracting EEG features has the potential to save much time for computational neuroscientists. In this paper, we introduce PyEEG, an open source Python module for EEG feature extraction. PMID:21512582

BoF - Python in Astronomy

NASA Astrophysics Data System (ADS)

Barrett, P. E.

This BoF will be chaired by Paul Barrett and will begin with an introduction to Python in astronomy, be followed by reports of current Python projects, and conclude with a discussion about the current state of Python in astronomy. The introduction will give a brief overview of the language, highlighting modules, resources, and aspects of the language that are important to scientific programming and astronomical data analysis. The closing discussion will provide an opportunity for questions and comments.

Urbanization may limit impacts of an invasive predator on native mammal diversity

USGS Publications Warehouse

Reichert, Brian E.; Sovie, Adia R.; Udell, Brad J.; Hart, Kristen M.; Borkhataria, Rena R.; Bonneau, Mathieu; Reed, Robert; McCleery, Robert A.

2017-01-01

AimOur understanding of the effects of invasive species on faunal diversity is limited in part because invasions often occur in modified landscapes where other drivers of community diversity can exacerbate or reduce the net impacts of an invader. Furthermore, rigorous assessments of the effects of invasive species on native communities that account for variation in sampling, species-specific detection and occurrence of rare species are lacking. Invasive Burmese pythons (Python molurus bivittatus) may be causing declines in medium- to large-sized mammals throughout the Greater Everglades Ecosystem (GEE); however, other factors such as urbanization, habitat changes and drastic alteration in water flow may also be influential in structuring mammal communities. The aim of this study was to gain an understanding of how mammal communities simultaneously facing invasive predators and intensively human-altered landscapes are influenced by these drivers and their interactions.LocationFlorida, USA.MethodsWe used data from trail cameras and scat searches with a hierarchical community model that accounts for undetected species to determine the relative influence of introduced Burmese pythons, urbanization, local hydrology, habitat types and interactive effects between pythons and urbanization on mammal species occurrence, site-level species richness, and turnover.ResultsPython density had significant negative effects on all species except coyotes. Despite these negative effects, occurrence of some generalist species increased significantly near urban areas. At the community level, pythons had the greatest impact on species richness, while turnover was greatest along the urbanization gradient where communities were increasingly similar as distance to urbanization decreased.Main conclusionsWe found evidence for an antagonistic interaction between pythons and urbanization where the impacts of pythons were reduced near urban development. Python-induced changes to mammal communities may be mediated near urban development, but elsewhere in the GEE, pythons are likely causing a fundamental restructuring of the food web, declines in ecosystem function, and creating complex and unpredictable cascading effects.

Pythons metabolize prey to fuel the response to feeding.

PubMed Central

Starck, J. Matthias; Moser, Patrick; Werner, Roland A.; Linke, Petra

2004-01-01

We investigated the energy source fuelling the post-feeding metabolic upregulation (specific dynamic action, SDA) in pythons (Python regius). Our goal was to distinguish between two alternatives: (i) snakes fuel SDA by metabolizing energy depots from their tissues; or (ii) snakes fuel SDA by metabolizing their prey. To characterize the postprandial response of pythons we used transcutaneous ultrasonography to measure organ-size changes and respirometry to record oxygen consumption. To discriminate unequivocally between the two hypotheses, we enriched mice (= prey) with the stable isotope of carbon (13C). For two weeks after feeding we quantified the CO2 exhaled by pythons and determined its isotopic 13C/12C signature. Ultrasonography and respirometry showed typical postprandial responses in pythons. After feeding, the isotope ratio of the exhaled breath changed rapidly to values that characterized enriched mouse tissue, followed by a very slow change towards less enriched values over a period of two weeks after feeding. We conclude that pythons metabolize their prey to fuel SDA. The slowly declining delta13C values indicate that less enriched tissues (bone, cartilage and collagen) from the mouse become available after several days of digestion. PMID:15255044

Pynamic: the Python Dynamic Benchmark

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

Lee, G L; Ahn, D H; de Supinksi, B R

2007-07-10

Python is widely used in scientific computing to facilitate application development and to support features such as computational steering. Making full use of some of Python's popular features, which improve programmer productivity, leads to applications that access extremely high numbers of dynamically linked libraries (DLLs). As a result, some important Python-based applications severely stress a system's dynamic linking and loading capabilities and also cause significant difficulties for most development environment tools, such as debuggers. Furthermore, using the Python paradigm for large scale MPI-based applications can create significant file IO and further stress tools and operating systems. In this paper, wemore » present Pynamic, the first benchmark program to support configurable emulation of a wide-range of the DLL usage of Python-based applications for large scale systems. Pynamic has already accurately reproduced system software and tool issues encountered by important large Python-based scientific applications on our supercomputers. Pynamic provided insight for our system software and tool vendors, and our application developers, into the impact of several design decisions. As we describe the Pynamic benchmark, we will highlight some of the issues discovered in our large scale system software and tools using Pynamic.« less

Experimentally derived salinity tolerance of hatchling Burmese pythons (Python molurus bivittatus) from the Everglades, Florida (USA)

USGS Publications Warehouse

Hart, Kristen M.; Schofield, Pamela J.; Gregoire, Denise R.

2012-01-01

In a laboratory setting, we tested the ability of 24 non-native, wild-caught hatchling Burmese pythons (Python molurus bivittatus) collected in the Florida Everglades to survive when given water containing salt to drink. After a one-month acclimation period in the laboratory, we grouped snakes into three treatments, giving them access to water that was fresh (salinity of 0, control), brackish (salinity of 10), or full-strength sea water (salinity of 35). Hatchlings survived about one month at the highest marine salinity and about five months at the brackish-water salinity; no control animals perished during the experiment. These results are indicative of a "worst-case scenario", as in the laboratory we denied access to alternate fresh-water sources that may be accessible in the wild (e.g., through rainfall). Therefore, our results may underestimate the potential of hatchling pythons to persist in saline habitats in the wild. Because of the effect of different salinity regimes on survival, predictions of ultimate geographic expansion by non-native Burmese pythons that consider salt water as barriers to dispersal for pythons may warrant re-evaluation, especially under global climate change and associated sea-level-rise scenarios.

Experimentally derived salinity tolerance of hatchling Burmese pythons (Python molurus bivittatus) from the Everglades, Florida (USA)

USGS Publications Warehouse

Hart, K.M.; Schofield, P.J.; Gregoire, D.R.

2012-01-01

In a laboratory setting, we tested the ability of 24 non-native, wild-caught hatchling Burmese pythons (Python molurus bivittatus) collected in the Florida Everglades to survive when given water containing salt to drink. After a one-month acclimation period in the laboratory, we grouped snakes into three treatments, giving them access to water that was fresh (salinity of 0, control), brackish (salinity of 10), or full-strength sea water (salinity of 35). Hatchlings survived about one month at the highest marine salinity and about five months at the brackish-water salinity; no control animals perished during the experiment. These results are indicative of a "worst-case scenario", as in the laboratory we denied access to alternate fresh-water sources that may be accessible in the wild (e.g., through rainfall). Therefore, our results may underestimate the potential of hatchling pythons to persist in saline habitats in the wild. Because of the effect of different salinity regimes on survival, predictions of ultimate geographic expansion by non-native Burmese pythons that consider salt water as barriers to dispersal for pythons may warrant re-evaluation, especially under global climate change and associated sea-level-rise scenarios. ?? 2011.

Accelerating wave propagation modeling in the frequency domain using Python

NASA Astrophysics Data System (ADS)

Jo, Sang Hoon; Park, Min Jun; Ha, Wan Soo

2017-04-01

Python is a dynamic programming language adopted in many science and engineering areas. We used Python to simulate wave propagation in the frequency domain. We used the Pardiso matrix solver to solve the impedance matrix of the wave equation. Numerical examples shows that Python with numpy consumes longer time to construct the impedance matrix using the finite element method when compared with Fortran; however we could reduce the time significantly to be comparable to that of Fortran using a simple Numba decorator.

HOPE: Just-in-time Python compiler for astrophysical computations

NASA Astrophysics Data System (ADS)

Akeret, Joel; Gamper, Lukas; Amara, Adam; Refregier, Alexandre

2014-11-01

HOPE is a specialized Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimization on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. By using HOPE, the user benefits from being able to write common numerical code in Python while getting the performance of compiled implementation.

CyNEST: a maintainable Cython-based interface for the NEST simulator

PubMed Central

Zaytsev, Yury V.; Morrison, Abigail

2014-01-01

NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, 2007). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., 1999). The introduction of PyNEST (Eppler et al., 2008), the Python interface for NEST, enabled users to control simulations using Python. As the majority of NEST users found PyNEST easier to use and to combine with other applications, it immediately displaced SLI as the default NEST interface. However, developing and maintaining PyNEST has become increasingly difficult over time. This is partly because adding new features requires writing low-level C++ code intermixed with calls to the Python/C API, which is unrewarding. Moreover, the Python/C API evolves with each new version of Python, which results in a proliferation of version-dependent code branches. In this contribution we present the re-implementation of PyNEST in the Cython language, a superset of Python that additionally supports the declaration of C/C++ types for variables and class attributes, and provides a convenient foreign function interface (FFI) for invoking C/C++ routines (Behnel et al., 2011). Code generation via Cython allows the production of smaller and more maintainable bindings, including increased compatibility with all supported Python releases without additional burden for NEST developers. Furthermore, this novel approach opens up the possibility to support alternative implementations of the Python language at no cost given a functional Cython back-end for the corresponding implementation, and also enables cross-compilation of Python bindings for embedded systems and supercomputers alike. PMID:24672470

Cosmic Microwave Background Anisotropy Measurement from Python V

NASA Astrophysics Data System (ADS)

Coble, K.; Dodelson, S.; Dragovan, M.; Ganga, K.; Knox, L.; Kovac, J.; Ratra, B.; Souradeep, T.

2003-02-01

We analyze observations of the microwave sky made with the Python experiment in its fifth year of operation at the Amundsen-Scott South Pole Station in Antarctica. After modeling the noise and constructing a map, we extract the cosmic signal from the data. We simultaneously estimate the angular power spectrum in eight bands ranging from large (l~40) to small (l~260) angular scales, with power detected in the first six bands. There is a significant rise in the power spectrum from large to smaller (l~200) scales, consistent with that expected from acoustic oscillations in the early universe. We compare this Python V map to a map made from data taken in the third year of Python. Python III observations were made at a frequency of 90 GHz and covered a subset of the region of the sky covered by Python V observations, which were made at 40 GHz. Good agreement is obtained both visually (with a filtered version of the map) and via a likelihood ratio test.

Scripting MODFLOW model development using Python and FloPy

USGS Publications Warehouse

Bakker, Mark; Post, Vincent E. A.; Langevin, Christian D.; Hughes, Joseph D.; White, Jeremy; Starn, Jeffrey; Fienen, Michael N.

2016-01-01

Graphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW-based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture-fraction analysis with a real-world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy.

Size, but not experience, affects the ontogeny of constriction performance in ball pythons (Python regius).

PubMed

Penning, David A; Dartez, Schuyler F

2016-03-01

Constriction is a prey-immobilization technique used by many snakes and is hypothesized to have been important to the evolution and diversification of snakes. However, very few studies have examined the factors that affect constriction performance. We investigated constriction performance in ball pythons (Python regius) by evaluating how peak constriction pressure is affected by snake size, sex, and experience. In one experiment, we tested the ontogenetic scaling of constriction performance and found that snake diameter was the only significant factor determining peak constriction pressure. The number of loops applied in a coil and its interaction with snake diameter did not significantly affect constriction performance. Constriction performance in ball pythons scaled differently than in other snakes that have been studied, and medium to large ball pythons are capable of exerting significantly higher pressures than those shown to cause circulatory arrest in prey. In a second experiment, we tested the effects of experience on constriction performance in hatchling ball pythons over 10 feeding events. By allowing snakes in one test group to gain constriction experience, and manually feeding snakes under sedation in another test group, we showed that experience did not affect constriction performance. During their final (10th) feedings, all pythons constricted similarly and with sufficiently high pressures to kill prey rapidly. At the end of the 10 feeding trials, snakes that were allowed to constrict were significantly smaller than their non-constricting counterparts. © 2016 Wiley Periodicals, Inc.

78 FR 44275 - Semiannual Regulatory Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-23

... 1018-AV68 Evaluation; Constrictor Species From Python, Boa, and Eunectes Genera. National Park Service... Species From Python, Boa, and Eunectes Genera Legal Authority: 18 U.S.C. 42 Abstract: We are making a... Lacey Act: Reticulated python, DeSchauensee's anaconda, green anaconda, and Beni anaconda. The boa...

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes.

PubMed

Castoe, Todd A; de Koning, Jason A P; Hall, Kathryn T; Yokoyama, Ken D; Gu, Wanjun; Smith, Eric N; Feschotte, Cédric; Uetz, Peter; Ray, David A; Dobry, Jason; Bogden, Robert; Mackessy, Stephen P; Bronikowski, Anne M; Warren, Wesley C; Secor, Stephen M; Pollock, David D

2011-07-28

The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline.

SpiceyPy, a Python Wrapper for SPICE

NASA Astrophysics Data System (ADS)

Annex, A.

2017-06-01

SpiceyPy is an open source Python wrapper for the NAIF SPICE toolkit. It is available for macOS, Linux, and Windows platforms and for Python versions 2.7.x and 3.x as well as Anaconda. SpiceyPy can be installed by running: “pip install spiceypy.”

GillesPy: A Python Package for Stochastic Model Building and Simulation.

PubMed

Abel, John H; Drawert, Brian; Hellander, Andreas; Petzold, Linda R

2016-09-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community.

Double valvular insufficiency in a Burmese python (Python molurus bivittatus, Linnaeus, 1758) suffering from concomitant bacterial pneumonia.

PubMed

Schilliger, Lionel; Tréhiou-Sechi, Emilie; Petit, Amandine M P; Misbach, Charlotte; Chetboul, Valérie

2010-12-01

Ultrasonography, and, to a lesser extent, echocardiography are now well-established, noninvasive, and painless diagnostic tools in herpetologic medicine. Various cardiac lesions have been previously described in reptiles, but valvulopathy is rarely documented in these animals and, consequently, is poorly understood. In this report, sinoatrial and atrioventricular insufficiencies were diagnosed in a 5-yr-old captive dyspneic Burmese python (Python molurus bivittatus) on the basis of echocardiographic and Doppler examination. This case report is the first to document Doppler assessment of valvular regurgitations in a reptile.

GillesPy: A Python Package for Stochastic Model Building and Simulation

PubMed Central

Abel, John H.; Drawert, Brian; Hellander, Andreas; Petzold, Linda R.

2017-01-01

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community. PMID:28630888

Report on the ''ESO Python Boot Camp — Pilot Version''

NASA Astrophysics Data System (ADS)

Dias, B.; Milli, J.

2017-03-01

The Python programming language is becoming very popular within the astronomical community. Python is a high-level language with multiple applications including database management, handling FITS images and tables, statistical analysis, and more advanced topics. Python is a very powerful tool both for astronomical publications and for observatory operations. Since the best way to learn a new programming language is through practice, we therefore organised a two-day hands-on workshop to share expertise among ESO colleagues. We report here the outcome and feedback from this pilot event.

The Python ARM Radar Toolkit (Py-ART), a library for working with weather radar data in the Python programming language

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

Helmus, Jonathan J.; Collis, Scott M.

The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cython for interfacing with existing radar libraries written in C and to speed up computationally demanding algorithms. As a result, the source code for themore » toolkit is available on GitHub and is distributed under a BSD license.« less

NEURON and Python.

PubMed

Hines, Michael L; Davison, Andrew P; Muller, Eilif

2009-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications.

NEURON and Python

PubMed Central

Hines, Michael L.; Davison, Andrew P.; Muller, Eilif

2008-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications. PMID:19198661

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

The Python ARM Radar Toolkit (Py-ART), a library for working with weather radar data in the Python programming language

DOE PAGES

Helmus, Jonathan J.; Collis, Scott M.

2016-07-18

The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cython for interfacing with existing radar libraries written in C and to speed up computationally demanding algorithms. As a result, the source code for themore » toolkit is available on GitHub and is distributed under a BSD license.« less

Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python)

PubMed Central

Rutllant, Josep

2016-01-01

Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism's genome (such as the mouse genome) in order to make physiological inferences about the role of genes and proteins in a less characterized organism's genome (such as the Burmese python). We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. Applications of our research include (1) production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2) enhanced assisted reproduction technology for endangered and captive reptiles; and (3) novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles. Additional enhancements to reptile genomic resources will further enhance their value. PMID:27200191

In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

PubMed Central

2016-01-01

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons. PMID:27698666

Molecular identification of python species: development and validation of a novel assay for forensic investigations.

PubMed

Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

2015-05-01

Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites.

PubMed

Irizarry, Kristopher J L; Bryden, Randall L

2016-01-01

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus . Our results provide insight into pigment phenotypes in pythons.

Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python).

PubMed

Irizarry, Kristopher J L; Rutllant, Josep

2016-01-01

Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism's genome (such as the mouse genome) in order to make physiological inferences about the role of genes and proteins in a less characterized organism's genome (such as the Burmese python). We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. Applications of our research include (1) production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2) enhanced assisted reproduction technology for endangered and captive reptiles; and (3) novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles. Additional enhancements to reptile genomic resources will further enhance their value.

Photodermatitis and photokeratoconjunctivitis in a ball python (Python regius) and a blue-tongue skink (Tiliqua spp.).

PubMed

Gardiner, David W; Baines, Frances M; Pandher, Karamjeet

2009-12-01

A male ball python (Python regius) and a female blue tongue skink (Tiliqua spp.) of unknown age were evaluated for anorexia, lethargy, excessive shedding, corneal opacity (python), and weight loss (skink) of approximately three weeks' duration. These animals represented the worst affected animals from a private herpetarium where many animals exhibited similar signs. At necropsy, the python had bilateral corneal opacity and scattered moderate dysecdysis. The skink had mild dysecdysis, poor body condition, moderate intestinal nematodiasis, and mild liver atrophy. Microscopic evaluation revealed epidermal erosion and ulceration, with severe epidermal basal cell degeneration and necrosis, and superficial dermatitis (python and skink). Severe bilateral ulcerative keratoconjunctivitis with bacterial colonization was noted in the ball python. Microscopic findings within the skin and eyes were suggestive of ultraviolet (UV) radiation damage or of photodermatitis and photokeratoconjunctivitis. Removal of the recently installed new lamps from the terrariums of the surviving reptiles resulted in resolution of clinical signs. Evaluation of a sample lamp of the type associated with these cases revealed an extremely high UV output, including very-short-wavelength UVB, neither found in natural sunlight nor emitted by several other UVB lamps unassociated with photokeratoconjunctivitis. Exposure to high-intensity and/or inappropriate wavelengths of UV radiation may be associated with significant morbidity, and even mortality, in reptiles. Veterinarians who are presented with reptiles with ocular and/or cutaneous disease of unapparent cause should fully evaluate the specifics of the vivarium light sources. Further research is needed to determine the characteristics of appropriate and of toxic UV light for reptiles kept in captivity.

Ultrasonographic anatomy of the coelomic organs of boid snakes (Boa constrictor imperator, Python regius, Python molurus molurus, and Python curtus).

PubMed

Banzato, Tommaso; Russo, Elisa; Finotti, Luca; Milan, Maria C; Gianesella, Matteo; Zotti, Alessandro

2012-05-01

To determine the ultrasonographic features of the coelomic organs of healthy snakes belonging to the Boidae and Pythonidae families. 16 ball pythons (Python regius; 7 males, 8 females, and 1 sexually immature), 10 Indian rock pythons (Python molurus molurus; 5 males, 4 females, and 1 sexually immature), 12 Python curtus (5 males and 7 females), and 8 boa constrictors (Boa constrictor imperator; 4 males and 4 females). All snakes underwent complete ultrasonographic evaluation of the coelomic cavity; chemical restraint was not necessary. A dorsolateral approach to probe placement was chosen to increase image quality and to avoid injury to the snakes and operators. Qualitative and quantitative observations were recorded. The liver, stomach, gallbladder, pancreas, small and large intestines, kidneys, cloaca, and scent glands were identified in all snakes. The hemipenes were identified in 10 of the 21 (48%) male snakes. The spleen was identified in 5 of the 46 (11%) snakes, and ureters were identified in 6 (13%). In 2 sexually immature snakes, the gonads were not visible. One (2%) snake was gravid, and 7 (15%) had small amounts of free fluid in the coelomic cavity. A significant positive correlation was identified between several measurements (diameter and thickness of scent glands, gastric and pyloric walls, and colonic wall) and body length (snout to vent) and body weight. The study findings can be used as an atlas of the ultrasonographic anatomy of the coelomic cavity in healthy boid snakes. Ultrasonography was reasonably fast to perform and was well tolerated in conscious snakes.

Scraping EDGAR with Python

ERIC Educational Resources Information Center

Ashraf, Rasha

2017-01-01

This article presents Python codes that can be used to extract data from Securities and Exchange Commission (SEC) filings. The Python program web crawls to obtain URL paths for company filings of required reports, such as Form 10-K. The program then performs a textual analysis and counts the number of occurrences of words in the filing that…

On Parallel Software Engineering Education Using Python

ERIC Educational Resources Information Center

Marowka, Ami

2018-01-01

Python is gaining popularity in academia as the preferred language to teach novices serial programming. The syntax of Python is clean, easy, and simple to understand. At the same time, it is a high-level programming language that supports multi programming paradigms such as imperative, functional, and object-oriented. Therefore, by default, it is…

Satiety and eating patterns in two species of constricting snakes.

PubMed

Nielsen, Torben P; Jacobsen, Magnus W; Wang, Tobias

2011-01-10

Satiety has been studied extensively in mammals, birds and fish but very little information exists on reptiles. Here we investigate time-dependent satiation in two species of constricting snakes, ball pythons (Python regius) and yellow anacondas (Eunectes notaeus). Satiation was shown to depend on both fasting time and prey size. In the ball pythons fed with mice of a relative prey mass RPM (mass of the prey/mass of the snake×100) of 15%, we observed a satiety response that developed between 6 and 12h after feeding, but after 24h pythons regained their appetite. With an RPM of 10% the pythons kept eating throughout the experiment. The anacondas showed a non-significant tendency for satiety to develop between 6 and 12h after ingesting a prey of 20% RPM. Unlike pythons, anacondas remained satiated after 24h. Handling time (from strike until prey swallowed) increased with RPM. We also found a significant decrease in handling time between the first and the second prey and a positive correlation between handling time and the mass of the snake. 2010 Elsevier Inc. All rights reserved.

Scripting MODFLOW Model Development Using Python and FloPy.

PubMed

Bakker, M; Post, V; Langevin, C D; Hughes, J D; White, J T; Starn, J J; Fienen, M N

2016-09-01

Graphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW-based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture-fraction analysis with a real-world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy. © 2016, National Ground Water Association.

Homing of invasive Burmese pythons in South Florida: evidence for map and compass senses in snakes

PubMed Central

Pittman, Shannon E.; Hart, Kristen M.; Cherkiss, Michael S.; Snow, Ray W.; Fujisaki, Ikuko; Smith, Brian J.; Mazzotti, Frank J.; Dorcas, Michael E.

2014-01-01

Navigational ability is a critical component of an animal's spatial ecology and may influence the invasive potential of species. Burmese pythons (Python molurus bivittatus) are apex predators invasive to South Florida. We tracked the movements of 12 adult Burmese pythons in Everglades National Park, six of which were translocated 21–36 km from their capture locations. Translocated snakes oriented movement homeward relative to the capture location, and five of six snakes returned to within 5 km of the original capture location. Translocated snakes moved straighter and faster than control snakes and displayed movement path structure indicative of oriented movement. This study provides evidence that Burmese pythons have navigational map and compass senses and has implications for predictions of spatial spread and impacts as well as our understanding of reptile cognitive abilities. PMID:24647727

Homing of invasive Burmese pythons in South Florida: evidence for map and compass senses in snakes

USGS Publications Warehouse

Pittman, Shannon E.; Hart, Kristen M.; Cherkiss, Michael S.; Snow, Ray W.; Fujisaki, Ikuko; Mazzotti, Frank J.; Dorcas, Michael E.

2014-01-01

Navigational ability is a critical component of an animal's spatial ecology and may influence the invasive potential of species. Burmese pythons (Python molurus bivittatus) are apex predators invasive to South Florida. We tracked the movements of 12 adult Burmese pythons in Everglades National Park, six of which were translocated 21–36 km from their capture locations. Translocated snakes oriented movement homeward relative to the capture location, and five of six snakes returned to within 5 km of the original capture location. Translocated snakes moved straighter and faster than control snakes and displayed movement path structure indicative of oriented movement. This study provides evidence that Burmese pythons have navigational map and compass senses and has implications for predictions of spatial spread and impacts as well as our understanding of reptile cognitive abilities.

Predators in training: operant conditioning of novel behavior in wild Burmese pythons (Python molurus bivitattus).

PubMed

Emer, Sherri A; Mora, Cordula V; Harvey, Mark T; Grace, Michael S

2015-01-01

Large pythons and boas comprise a group of animals whose anatomy and physiology are very different from traditional mammalian, avian and other reptilian models typically used in operant conditioning. In the current study, investigators used a modified shaping procedure involving successive approximations to train wild Burmese pythons (Python molurus bivitattus) to approach and depress an illuminated push button in order to gain access to a food reward. Results show that these large, wild snakes can be trained to accept extremely small food items, associate a stimulus with such rewards via operant conditioning and perform a contingent operant response to gain access to a food reward. The shaping procedure produced robust responses and provides a mechanism for investigating complex behavioral phenomena in massive snakes that are rarely studied in learning research.

Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons

PubMed Central

Hunter, Margaret E.; Oyler-McCance, Sara J.; Dorazio, Robert M.; Fike, Jennifer A.; Smith, Brian J.; Hunter, Charles T.; Reed, Robert N.; Hart, Kristen M.

2015-01-01

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models. PMID:25874630

Isolation and identification of bacterial populations of zoonotic importance from captive non-venomous snakes in Malaysia.

PubMed

Abba, Yusuf; Ilyasu, Yusuf Maina; Noordin, Mustapha Mohamed

2017-07-01

Captivity of non-venomous snakes such as python and boa are common in zoos, aquariums and as pets in households. Poor captivity conditions expose these reptiles to numerous pathogens which may result in disease conditions. The purpose of this study was to investigate the common bacteria isolated from necropsied captive snakes in Malaysia over a five year period. A total of 27 snake carcasses presented for necropsy at the Universiti Putra Malaysia (UPM) were used in this survey. Samples were aseptically obtained at necropsy from different organs/tissues (lung, liver, heart, kindey, oesophagus, lymph node, stomach, spinal cord, spleen, intestine) and cultured onto 5% blood and McConkey agar, respectively. Gram staining, morphological evaluation and biochemical test such as oxidase, catalase and coagulase were used to tentatively identify the presumptive bacterial isolates. Pythons had the highest number of cases (81.3%) followed by anaconda (14.8%) and boa (3.7%). Mixed infection accounted for 81.5% in all snakes and was highest in pythons (63%). However, single infection was only observed in pythons (18.5%). A total of 82.7%, 95.4% and 100% of the bacterial isolates from python, anaconda and boa, respectively were gram negative. Aeromonas spp was the most frequently isolated bacteria in pythons and anaconda with incidences of 25 (18%) and 8 (36.6%) with no difference (p > 0.05) in incidence, respectively, while Salmonella spp was the most frequently isolated in boa and significantly higher (p < 0.05) than in python and anaconda. Bacteria species were most frequently isolated from the kidney of pythons 35 (25.2%), intestines of anacondas 11 (50%) and stomach of boa 3 (30%). This study showed that captive pythons harbored more bacterial species than anaconda or boa. Most of the bacterial species isolated from these snakes have public health importance and have been incriminated in human infections worldwide. Copyright © 2017 Elsevier Ltd. All rights reserved.

Selected regulation of gastrointestinal acid-base secretion and tissue metabolism for the diamondback water snake and Burmese python.

PubMed

Secor, Stephen M; Taylor, Josi R; Grosell, Martin

2012-01-01

Snakes exhibit an apparent dichotomy in the regulation of gastrointestinal (GI) performance with feeding and fasting; frequently feeding species modestly regulate intestinal function whereas infrequently feeding species rapidly upregulate and downregulate intestinal function with the start and completion of each meal, respectively. The downregulatory response with fasting for infrequently feeding snakes is hypothesized to be a selective attribute that reduces energy expenditure between meals. To ascertain the links between feeding habit, whole-animal metabolism, and GI function and metabolism, we measured preprandial and postprandial metabolic rates and gastric and intestinal acid-base secretion, epithelial conductance and oxygen consumption for the frequently feeding diamondback water snake (Nerodia rhombifer) and the infrequently feeding Burmese python (Python molurus). Independent of body mass, Burmese pythons possess a significantly lower standard metabolic rate and respond to feeding with a much larger metabolic response compared with water snakes. While fasting, pythons cease gastric acid and intestinal base secretion, both of which are stimulated with feeding. In contrast, fasted water snakes secreted gastric acid and intestinal base at rates similar to those of digesting snakes. We observed no difference between fasted and fed individuals for either species in gastric or intestinal transepithelial potential and conductance, with the exception of a significantly greater gastric transepithelial potential for fed pythons at the start of titration. Water snakes experienced no significant change in gastric or intestinal metabolism with feeding. Fed pythons, in contrast, experienced a near-doubling of gastric metabolism and a tripling of intestinal metabolic rate. For fasted individuals, the metabolic rate of the stomach and small intestine was significantly lower for pythons than for water snakes. The fasting downregulation of digestive function for pythons is manifested in a depressed gastric and intestinal metabolism, which selectively serves to reduce basal metabolism and hence promote survival between infrequent meals. By maintaining elevated GI performance between meals, fasted water snakes incur the additional cost of tissue activity, which is expressed in a higher standard metabolic rate.

Python-Based Applications for Hydrogeological Modeling

NASA Astrophysics Data System (ADS)

Khambhammettu, P.

2013-12-01

Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Add-on packages supporting fast array computation (numpy), plotting (matplotlib), scientific /mathematical Functions (scipy), have resulted in a powerful ecosystem for scientists interested in exploratory data analysis, high-performance computing and data visualization. Three examples are provided to demonstrate the applicability of the Python environment in hydrogeological applications. Python programs were used to model an aquifer test and estimate aquifer parameters at a Superfund site. The aquifer test conducted at a Groundwater Circulation Well was modeled with the Python/FORTRAN-based TTIM Analytic Element Code. The aquifer parameters were estimated with PEST such that a good match was produced between the simulated and observed drawdowns. Python scripts were written to interface with PEST and visualize the results. A convolution-based approach was used to estimate source concentration histories based on observed concentrations at receptor locations. Unit Response Functions (URFs) that relate the receptor concentrations to a unit release at the source were derived with the ATRANS code. The impact of any releases at the source could then be estimated by convolving the source release history with the URFs. Python scripts were written to compute and visualize receptor concentrations for user-specified source histories. The framework provided a simple and elegant way to test various hypotheses about the site. A Python/FORTRAN-based program TYPECURVEGRID-Py was developed to compute and visualize groundwater elevations and drawdown through time in response to a regional uniform hydraulic gradient and the influence of pumping wells using either the Theis solution for a fully-confined aquifer or the Hantush-Jacob solution for a leaky confined aquifer. The program supports an arbitrary number of wells that can operate according to arbitrary schedules. The python wrapper invokes the underlying FORTRAN layer to compute transient groundwater elevations and processes this information to create time-series and 2D plots.

Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons

USGS Publications Warehouse

Hunter, Margaret E.; Oyler-McCance, Sara J.; Dorazio, Robert M.; Fike, Jennifer A.; Smith, Brian J.; Hunter, Charles T.; Reed, Robert N.; Hart, Kristen M.

2015-01-01

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.

Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons.

PubMed

Hunter, Margaret E; Oyler-McCance, Sara J; Dorazio, Robert M; Fike, Jennifer A; Smith, Brian J; Hunter, Charles T; Reed, Robert N; Hart, Kristen M

2015-01-01

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.

PubMed

Bald, Till; Barth, Johannes; Niehues, Anna; Specht, Michael; Hippler, Michael; Fufezan, Christian

2012-04-01

pymzML is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data, the standard data format in MS and (iii) a set of functions to compare or handle spectra. pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on http://pymzml.github.com or pypi, is published under LGPL license and requires no additional modules to be installed. christian@fufezan.net.

Myiasis by Megaselia scalaris (Diptera: Phoridae) in a python affected by pulmonitis.

PubMed

Vanin, S; Mazzariol, S; Menandro, M L; Lafisca, A; Turchetto, M

2013-01-01

Myiases are caused by the presence of maggots in vertebrate tissues and organs. Myiases have been studied widely in humans, farm animals, and pets, whereas reports of myiasis in reptiles are scarce. We describe a case of myiasis caused by the Megaselia scalaris (Loew) in an Indian python (Python molurus bivittatus, Kuhl) (Ophida: Boidae). The python, 15 yr old, born and reared in a terrarium in the mainland of Venice (Italy), was affected by diffuse, purulent pneumonia caused by Burkholderia cepacia. The severe infestation of maggots found in the lungs during an autopsy indicated at a myiasis.

Effects of meal size, clutch, and metabolism on the energy efficiencies of juvenile Burmese pythons, Python molurus.

PubMed

Cox, Christian L; Secor, Stephen M

2007-12-01

We explored meal size and clutch (i.e., genetic) effects on the relative proportion of ingested energy that is absorbed by the gut (apparent digestive efficiency), becomes available for metabolism and growth (apparent assimilation efficiency), and is used for growth (production efficiency) for juvenile Burmese pythons (Python molurus). Sibling pythons were fed rodent meals equaling 15%, 25%, and 35% of their body mass and individuals from five different clutches were fed rodent meals equaling 25% of their body mass. For each of 11-12 consecutive feeding trials, python body mass was recorded and feces and urate of each snake was collected, dried, and weighed. Energy contents of meals (mice and rats), feces, urate, and pythons were determined using bomb calorimetry. For siblings fed three different meal sizes, growth rate increased with larger meals, but there was no significant variation among the meal sizes for any of the calculated energy efficiencies. Among the three meal sizes, apparent digestive efficiency, apparent assimilation efficiency, and production efficiency averaged 91.0%, 84.7%, and 40.7%, respectively. In contrast, each of these energy efficiencies varied significantly among the five different clutches. Among these clutches production efficiency was negatively correlated with standard metabolic rate (SMR). Clutches containing individuals with low SMR were therefore able to allocate more of ingested energy into growth.

Clinical and histologic effects of intracardiac administration of propofol for induction of anesthesia in ball pythons (Python regius).

PubMed

McFadden, Michael S; Bennett, R Avery; Reavill, Drury R; Ragetly, Guillaume R; Clark-Price, Stuart C

2011-09-15

To assess the clinical differences between induction of anesthesia in ball pythons with intracardiac administration of propofol and induction with isoflurane in oxygen and to assess the histologic findings over time in hearts following intracardiac administration of propofol. Prospective randomized study. 30 hatchling ball pythons (Python regius). Anesthesia was induced with intracardiac administration of propofol (10 mg/kg [4.5 mg/lb]) in 18 ball pythons and with 5% isoflurane in oxygen in 12 ball pythons. Induction time, time of anesthesia, and recovery time were recorded. Hearts from snakes receiving intracardiac administration of propofol were evaluated histologically 3, 7, 14, 30, and 60 days following propofol administration. Induction time with intracardiac administration of propofol was significantly shorter than induction time with 5% isoflurane in oxygen. No significant differences were found in total anesthesia time. Recovery following intracardiac administration of propofol was significantly longer than recovery following induction of anesthesia with isoflurane in oxygen. Heart tissue evaluated histologically at 3, 7, and 14 days following intracardiac administration of propofol had mild inflammatory changes, and no histopathologic lesions were seen 30 and 60 days following propofol administration. Intracardiac injection of propofol in snakes is safe and provides a rapid induction of anesthesia but leads to prolonged recovery, compared with that following induction with isoflurane. Histopathologic lesions in heart tissues following intracardiac injection of propofol were mild and resolved after 14 days.

Ecological correlates of invasion impact for Burmese pythons in Florida

USGS Publications Warehouse

Reed, R.N.; Willson, J.D.; Rodda, G.H.; Dorcas, M.E.

2012-01-01

An invasive population of Burmese pythons (Python molurus bivittatus) is established across several thousand square kilometers of southern Florida and appears to have caused precipitous population declines among several species of native mammals. Why has this giant snake had such great success as an invasive species when many established reptiles have failed to spread? We scored the Burmese python for each of 15 literature-based attributes relative to predefined comparison groups from a diverse range of taxa and provide a review of the natural history and ecology of Burmese pythons relevant to each attribute. We focused on attributes linked to spread and magnitude of impacts rather than establishment success. Our results suggest that attributes related to body size and generalism appeared to be particularly applicable to the Burmese python's success in Florida. The attributes with the highest scores were: high reproductive potential, low vulnerability to predation, large adult body size, large offspring size and high dietary breadth. However, attributes of ectotherms in general and pythons in particular (including predatory mode, energetic efficiency and social interactions) might have also contributed to invasion success. Although establishment risk assessments are an important initial step in prevention of new establishments, evaluating species in terms of their potential for spreading widely and negatively impacting ecosystems might become part of the means by which resource managers prioritize control efforts in environments with large numbers of introduced species.

Severe mammal declines coincide with proliferation of invasive Burmese pythons in Everglades National Park

USGS Publications Warehouse

Dorcas, Michael E.; Wilson, John D.; Reed, Robert N.; Snow, Ray W.; Rochford, Michael R.; Miller, Melissa A.; Meshaka, Walter E.; Andreadis, Paul T.; Mazzotti, Frank J.; Romagosa, Christina M.; Hart, Kristen M.

2012-01-01

Invasive species represent a significant threat to global biodiversity and a substantial economic burden. Burmese pythons, giant constricting snakes native to Asia, now are found throughout much of southern Florida, including all of Everglades National Park (ENP). Pythons have increased dramatically in both abundance and geographic range since 2000 and consume a wide variety of mammals and birds. Here we report severe apparent declines in mammal populations that coincide temporally and spatially with the proliferation of pythons in ENP. Before 2000, mammals were encountered frequently during nocturnal road surveys within ENP. In contrast, road surveys totaling 56,971 km from 2003–2011 documented a 99.3% decrease in the frequency of raccoon observations, decreases of 98.9% and 87.5% for opossum and bobcat observations, respectively, and failed to detect rabbits. Road surveys also revealed that these species are more common in areas where pythons have been discovered only recently and are most abundant outside the python's current introduced range. These findings suggest that predation by pythons has resulted in dramatic declines in mammals within ENP and that introduced apex predators, such as giant constrictors, can exert significant top-down pressure on prey populations. Severe declines in easily observed and/or common mammals, such as raccoons and bobcats, bode poorly for species of conservation concern, which often are more difficult to sample and occur at lower densities.

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

PubMed

Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

2018-01-01

Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

pyMOOGi - python wrapper for MOOG

NASA Astrophysics Data System (ADS)

Adamow, Monika M.

2017-06-01

pyMOOGi is a python wrapper for MOOG. It allows to use MOOG in a classical, interactive way, but with all graphics handled by python libraries. Some MOOG features have been redesigned, like plotting with abfind driver. Also, new funtions have been added, like automatic rescaling of stellar spectrum for synth driver. pyMOOGi is an open source project.

Short telomeres in hatchling snakes: erythrocyte telomere dynamics and longevity in tropical pythons.

PubMed

Ujvari, Beata; Madsen, Thomas

2009-10-16

Telomere length (TL) has been found to be associated with life span in birds and humans. However, other studies have demonstrated that TL does not affect survival among old humans. Furthermore, replicative senescence has been shown to be induced by changes in the protected status of the telomeres rather than the loss of TL. In the present study we explore whether age- and sex-specific telomere dynamics affect life span in a long-lived snake, the water python (Liasis fuscus). Erythrocyte TL was measured using the Telo TAGGG TL Assay Kit (Roche). In contrast to other vertebrates, TL of hatchling pythons was significantly shorter than that of older snakes. However, during their first year of life hatchling TL increased substantially. While TL of older snakes decreased with age, we did not observe any correlation between TL and age in cross-sectional sampling. In older snakes, female TL was longer than that of males. When using recapture as a proxy for survival, our results do not support that longer telomeres resulted in an increased water python survival/longevity. In fish high telomerase activity has been observed in somatic cells exhibiting high proliferation rates. Hatchling pythons show similar high somatic cell proliferation rates. Thus, the increase in TL of this group may have been caused by increased telomerase activity. In older humans female TL is longer than that of males. This has been suggested to be caused by high estrogen levels that stimulate increased telomerase activity. Thus, high estrogen levels may also have caused the longer telomeres in female pythons. The lack of correlation between TL and age among old snakes and the fact that longer telomeres did not appear to affect python survival do not support that erythrocyte telomere dynamics has a major impact on water python longevity.

Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom.

PubMed

Reyes-Velasco, Jacobo; Card, Daren C; Andrew, Audra L; Shaney, Kyle J; Adams, Richard H; Schield, Drew R; Casewell, Nicholas R; Mackessy, Stephen P; Castoe, Todd A

2015-01-01

Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete genome of the Burmese python, including information from tissue-specific patterns of gene expression. We identified the orthologs of snake venom genes in the python genome, and conducted detailed analysis of gene expression of these venom homologs to identify patterns that differ between snake venom gene families and all other genes. We found that venom gene homologs in the python are expressed in many different tissues outside of oral glands, which illustrates the pitfalls of using transcriptomic data alone to define "venom toxins." We hypothesize that the python may represent an ancestral state prior to major venom development, which is supported by our finding that the expansion of venom gene families is largely restricted to highly venomous caenophidian snakes. Therefore, the python provides insight into biases in which genes were recruited for snake venom systems. Python venom homologs are generally expressed at lower levels, have higher variance among tissues, and are expressed in fewer organs compared with all other python genes. We propose a model for the evolution of snake venoms in which venom genes are recruited preferentially from genes with particular expression profile characteristics, which facilitate a nearly neutral transition toward specialized venom system expression. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Unified EDGE

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

2007-06-18

UEDGE is an interactive suite of physics packages using the Python or BASIS scripting systems. The plasma is described by time-dependent 2D plasma fluid equations that include equations for density, velocity, ion temperature, electron temperature, electrostatic potential, and gas density in the edge region of a magnetic fusion energy confinement device. Slab, cylindrical, and toroidal geometries are allowed, and closed and open magnetic field-line regions are included. Classical transport is assumed along magnetic field lines, and anomalous transport is assumed across field lines. Multi-charge state impurities can be included with the corresponding line-radiation energy loss. Although UEDGE is written inmore » Fortran, for efficient execution and analysis of results, it utilizes either Python or BASIS scripting shells. Python is easily available for many platforms (http://www.Python.org/). The features and availability of BASIS are described in "Basis Manual Set" by P.F. Dubois, Z.C. Motteler, et al., Lawrence Livermore National Laboratory report UCRL-MA-1 18541, June, 2002 and http://basis.llnl.gov. BASIS has been reviewed and released by LLNL for unlimited distribution. The Python version utilizes PYBASIS scripts developed by D.P. Grote, LLNL. The Python version also uses MPPL code and MAC Perl script, available from the public-domain BASIS source above. The Forthon version of UEDGE uses the same source files, but utilizes Forthon to produce a Python-compatible source. Forthon has been developed by D.P. Grote at LBL (see http://hifweb.lbl.gov/Forthon/ and Grote et al. in the references below), and it is freely available. The graphics can be performed by any package importable to Python, such as PYGIST.« less

Python-Assisted MODFLOW Application and Code Development

NASA Astrophysics Data System (ADS)

Langevin, C.

2013-12-01

The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius).

PubMed

Uccellini, Lorenzo; Ossiboff, Robert J; de Matos, Ricardo E C; Morrisey, James K; Petrosov, Alexandra; Navarrete-Macias, Isamara; Jain, Komal; Hicks, Allison L; Buckles, Elizabeth L; Tokarz, Rafal; McAloose, Denise; Lipkin, Walter Ian

2014-08-08

Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses.

Pybus -- A Python Software Bus

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

Lavrijsen, Wim T.L.P.

2004-10-14

A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the conceptmore » of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user.« less

Saccular lung cannulation in a ball python (Python regius) to treat a tracheal obstruction.

PubMed

Myers, Debbie A; Wellehan, James F X; Isaza, Ramiro

2009-03-01

An adult male ball python (Python regius) presented in a state of severe dyspnea characterized by open-mouth breathing and vertical positioning of the head and neck. The animal had copious discharge in the tracheal lumen acting as an obstruction. A tube was placed through the body wall into the caudal saccular aspect of the lung to allow the animal to breathe while treatment was initiated. The ball python's dyspnea immediately improved. Diagnostics confirmed a bacterial respiratory infection with predominantly Providencia rettgeri. The saccular lung (air sac) tube was removed after 13 days. Pulmonary endoscopy before closure showed minimal damage with a small amount of hemorrhage in the surrounding muscle tissue. Respiratory disease is a common occurrence in captive snakes and can be associated with significant morbidity and mortality. Saccular lung cannulation is a relatively simple procedure that can alleviate tracheal narrowing or obstruction, similar to air sac cannulation in birds.

Nano-inclusions in diamond: Evidence of diamond genesis

NASA Astrophysics Data System (ADS)

Wirth, R.

2015-12-01

The use of Focused Ion Beam technology (FIB) for TEM sample preparation introduced approximately 15 years ago revolutionized the application of TEM in Geosciences. For the first time, FIB enabled cutting samples for TEM use from exactly the location we are interested in. Applied to diamond investigation, this technique revealed the presence of nanometre-sized inclusions in diamond that have been simply unknown before. Nanoinclusions in diamond from different location and origin such as diamonds from the Lower and Upper Mantle, metamorphic diamonds (Kazakhstan, Erzgebirge, Bohemia), diamonds from ophiolites (Tibet, Mongolia, Xinjiang, Ural Mountains), diamonds from igneous rocks (Hawaii, Kamchatka) and impact diamonds (Popigai Crater, Siberia) have been investigated during the last 15 years. The major conclusion of all these TEM studies is, that the nanoinclusions, their phases and phase composition together with the micro- and nanostructure evidence the origin of diamond and genesis of diamond. We can discriminate Five different mechanisms of diamond genesis in nature are observed: Diamond crystallized from a high-density fluid (Upper mantle and metamorphic diamond). Diamond crystallized from carbonatitic melt (Lower mantle diamond). Diamond precipitates from a metal alloy melt (Diamond from ophiolites). Diamond crystallized by gas phase condensation or chemical vapour condensation (CVD) (Lavas from Kamchatka, xenoliths in Hawaiian lavas). Direct transformation of graphite into diamond.

Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7

NASA Astrophysics Data System (ADS)

Petras, Vaclav; Petrasova, Anna; Chemin, Yann; Zambelli, Pietro; Landa, Martin; Gebbert, Sören; Neteler, Markus; Löwe, Peter

2015-04-01

GRASS GIS 7 is a free and open source GIS software developed and used by many scientists (Neteler et al., 2012). While some users of GRASS GIS prefer its graphical user interface, significant part of the scientific community takes advantage of various scripting and programing interfaces offered by GRASS GIS to develop new models and algorithms. Here we will present different interfaces added to GRASS GIS 7 and available in Python, a popular programming language and environment in geosciences. These Python interfaces are designed to satisfy the needs of scientists and programmers under various circumstances. PyGRASS (Zambelli et al., 2013) is a new object-oriented interface to GRASS GIS modules and libraries. The GRASS GIS libraries are implemented in C to ensure maximum performance and the PyGRASS interface provides an intuitive, pythonic access to their functionality. GRASS GIS Python scripting library is another way of accessing GRASS GIS modules. It combines the simplicity of Bash and the efficiency of the Python syntax. When full access to all low-level and advanced functions and structures from GRASS GIS library is required, Python programmers can use an interface based on the Python ctypes package. Ctypes interface provides complete, direct access to all functionality as it would be available to C programmers. GRASS GIS provides specialized Python library for managing and analyzing spatio-temporal data (Gebbert and Pebesma, 2014). The temporal library introduces space time datasets representing time series of raster, 3D raster or vector maps and allows users to combine various spatio-temporal operations including queries, aggregation, sampling or the analysis of spatio-temporal topology. We will also discuss the advantages of implementing scientific algorithm as a GRASS GIS module and we will show how to write such module in Python. To facilitate the development of the module, GRASS GIS provides a Python library for testing (Petras and Gebbert, 2014) which helps researchers to ensure the robustness of the algorithm, correctness of the results in edge cases as well as the detection of changes in results due to new development. For all modules GRASS GIS automatically creates standardized command line and graphical user interfaces and documentation. Finally, we will show how GRASS GIS can be used together with powerful Python tools such as the NumPy package and the IPython Notebook. References: Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environmental Modelling & Software 53, 1-12. Neteler, M., Bowman, M.H., Landa, M. and Metz, M., 2012. GRASS GIS: a multi-purpose Open Source GIS. Environmental Modelling & Software 31: 124-130. Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS International Journal of Geo-Information 2, 201-219.

Python based high-level synthesis compiler

NASA Astrophysics Data System (ADS)

Cieszewski, Radosław; Pozniak, Krzysztof; Romaniuk, Ryszard

2014-11-01

This paper presents a python based High-Level synthesis (HLS) compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and map it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the mapped circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs therefore have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. Creating parallel programs implemented in FPGAs is not trivial. This article describes design, implementation and first results of created Python based compiler.

Implementation of quantum game theory simulations using Python

NASA Astrophysics Data System (ADS)

Madrid S., A.

2013-05-01

This paper provides some examples about quantum games simulated in Python's programming language. The quantum games have been developed with the Sympy Python library, which permits solving quantum problems in a symbolic form. The application of these methods of quantum mechanics to game theory gives us more possibility to achieve results not possible before. To illustrate the results of these methods, in particular, there have been simulated the quantum battle of the sexes, the prisoner's dilemma and card games. These solutions are able to exceed the classic bottle neck and obtain optimal quantum strategies. In this form, python demonstrated that is possible to do more advanced and complicated quantum games algorithms.

Subspectacular nematodiasis caused by a novel Serpentirhabdias species in ball pythons (Python regius).

PubMed

Hausmann, J C; Mans, C; Dreyfus, J; Reavill, D R; Lucio-Forster, A; Bowman, D D

2015-01-01

Subspectacular nematodiasis was diagnosed in three captive-bred juvenile ball pythons (Python regius) from two unrelated facilities within a 6-month period. The snakes were presented with similar lesions, including swelling of facial, periocular and oral tissues. Bilaterally, the subspectacular spaces were distended and filled with an opaque fluid, which contained nematodes and eggs. Histopathology showed nematodes throughout the periocular tissue, subspectacular space and subcutaneous tissue of the head. The nematodes from both facilities were morphologically indistinguishable and most closely resembled Serpentirhabdias species. Morphological characterization and genetic sequencing indicate this is a previously undescribed rhabdiasid nematode. Copyright © 2014 Elsevier Ltd. All rights reserved.

Amebiasis in four ball pythons, Python reginus.

PubMed

Kojimoto, A; Uchida, K; Horii, Y; Okumura, S; Yamaguch, R; Tateyama, S

2001-12-01

Between September 13th and November 18th in 1999, four ball pythons, Python reginus kept in the same display, showed anorexia and died one after another. At necropsy, all four snakes had severe hemorrhagic colitis. Microscopically, all snakes had severe necrotizing hemorrhagic colitis, in association with ameba-like protozoa. Some of the protozoa had macrophage-like morphology and others formed protozoal cysts with thickened walls. These protozoa were distributed throughout the wall in the large intestine. Based on the pathological findings, these snakes were infested with a member of Entamoeba sp., presumably with infection by Entamoeba invadens, the most prevalent type of reptilian amoebae.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

PubMed

Smelter, Andrey; Moseley, Hunter N B

2018-01-01

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package. This Python package, named 'mwtab', is a parser for the domain-specific 'mwTab' flat file format, which provides facilities for reading, accessing, and writing 'mwTab' formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given 'mwTab' formatted file. In order to develop the 'mwtab' package we used the official 'mwTab' format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. The 'mwtab' package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating 'mwTab' formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, 'pythonic' access and manipulation of data and metadata. Also, the package provides facilities to convert 'mwTab' files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The 'mwtab' package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between 'mwTab' and JSONized formats in raw text and a variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

Industrial diamond

USGS Publications Warehouse

Olson, D.W.

2001-01-01

An overview of the industrial diamond industry is provided. More than 90 percent of the industrial diamond consumed in the U.S. and the rest of the world is manufactured diamond. Ireland, Japan, Russia, and the U.S. produce 75 percent of the global industrial diamond output. In 2000, the U.S. was the largest market for industrial diamond. Industrial diamond applications, prices for industrial diamonds, imports and exports of industrial diamonds, the National Defense Stockpile of industrial diamonds, and the outlook for the industrial diamond market are discussed.

Ecological correlates of invasion impact for Burmese pythons in Florida.

PubMed

Reed, Robert N; Willson, John D; Rodda, Gordon H; Dorcas, Michael E

2012-09-01

An invasive population of Burmese pythons (Python molurus bivittatus) is established across several thousand square kilometers of southern Florida and appears to have caused precipitous population declines among several species of native mammals. Why has this giant snake had such great success as an invasive species when many established reptiles have failed to spread? We scored the Burmese python for each of 15 literature-based attributes relative to predefined comparison groups from a diverse range of taxa and provide a review of the natural history and ecology of Burmese pythons relevant to each attribute. We focused on attributes linked to spread and magnitude of impacts rather than establishment success. Our results suggest that attributes related to body size and generalism appeared to be particularly applicable to the Burmese python's success in Florida. The attributes with the highest scores were: high reproductive potential, low vulnerability to predation, large adult body size, large offspring size and high dietary breadth. However, attributes of ectotherms in general and pythons in particular (including predatory mode, energetic efficiency and social interactions) might have also contributed to invasion success. Although establishment risk assessments are an important initial step in prevention of new establishments, evaluating species in terms of their potential for spreading widely and negatively impacting ecosystems might become part of the means by which resource managers prioritize control efforts in environments with large numbers of introduced species. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Pharmacokinetics of a long-acting ceftiofur formulation (ceftiofur crystalline free acid) in the ball python (Python regius).

PubMed

Adkesson, Michael J; Fernandez-Varon, Emilio; Cox, Sherry; Martín-Jiménez, Tomás

2011-09-01

The objective of this study was to determine the pharmacokinetics of a long-acting formulation of ceftiofur crystalline-free acid (CCFA) following intramuscular injection in ball pythons (Python regius). Six adult ball pythons received an injection of CCFA (15 mg/kg) in the epaxial muscles. Blood samples were collected by cardiocentesis immediately prior to and at 0.5, 1, 2, 4, 8, 12, 18, 24, 48, 72, 96, 144, 192, 240, 288, 384, 480, 576, 720, and 864 hr after CCFA administration. Plasma ceftiofur concentrations were determined by high-performance liquid chromatography. A noncompartmental pharmacokinetic analysis was applied to the data. Maximum plasma concentration (Cmax) was 7.096 +/- 1.95 microg/ml and occurred at (Tmax) 2.17 +/- 0.98 hr. The area under the curve (0 to infinity) for ceftiofur was 74.59 +/- 13.05 microg x h/ml and the elimination half-life associated with the terminal slope of the concentration-time curve was 64.31 +/- 14.2 hr. Mean residence time (0 to infinity) was 46.85 +/- 13.53 hr. CCFA at 15 mg/kg was well tolerated in all the pythons. Minimum inhibitory concentration (MIC) data for bacterial isolates from snakes are not well established. For MIC values of < or =0.1 microg/ml, a single dose of CCFA (15 mg/kg) provides adequate plasma concentrations for at least 5 days in the ball python. For MICs > or =0.5 microg/ml, more frequent dosing or a higher dosage may be required.

Development of a technique for contrast radiographic examination of the gastrointestinal tract in ball pythons (Python regius).

PubMed

Banzato, Tommaso; Russo, Elisa; Finotti, Luca; Zotti, Alessandro

2012-07-01

To develop a technique for radiographic evaluation of the gastrointestinal tract in ball pythons (Python regius). 10 ball python cadavers (5 males and 5 females) and 18 healthy adult ball pythons (10 males and 8 females). Live snakes were allocated to 3 groups (A, B, and C). A dose (25 mL/kg) of barium sulfate suspension at 3 concentrations (25%, 35%, and 45% [wt/vol]) was administered through an esophageal probe to snakes in groups A, B, and C, respectively. Each evaluation ended when all the contrast medium had reached the large intestine. Transit times through the esophagus, stomach, and small intestine were recorded. Imaging quality was evaluated by 3 investigators who assigned a grading score on the basis of predetermined criteria. Statistical analysis was conducted to evaluate differences in quality among the study groups. The esophagus and stomach had a consistent distribution pattern of contrast medium, whereas 3 distribution patterns of contrast medium were identified in the small intestine, regardless of barium concentration. Significant differences in imaging quality were detected among the 3 groups. Radiographic procedures were tolerated well by all snakes. The 35% concentration of contrast medium yielded the best imaging quality. Use of contrast medium for evaluation of the cranial portion of the gastrointestinal tract could be a reliable technique for the diagnosis of gastrointestinal diseases in ball pythons. However, results of this study may not translate to other snake species because of variables identified in this group of snakes.

Anatomy of the python heart.

PubMed

Jensen, Bjarke; Nyengaard, Jens R; Pedersen, Michael; Wang, Tobias

2010-12-01

The hearts of all snakes and lizards consist of two atria and a single incompletely divided ventricle. In general, the squamate ventricle is subdivided into three chambers: cavum arteriosum (left), cavum venosum (medial) and cavum pulmonale (right). Although a similar division also applies to the heart of pythons, this family of snakes is unique amongst snakes in having intracardiac pressure separation. Here we provide a detailed anatomical description of the cardiac structures that confer this functional division. We measured the masses and volumes of the ventricular chambers, and we describe the gross morphology based on dissections of the heart from 13 ball pythons (Python regius) and one Burmese python (P. molurus). The cavum venosum is much reduced in pythons and constitutes approximately 10% of the cavum arteriosum. We suggest that shunts will always be less than 20%, while other studies conclude up to 50%. The high-pressure cavum arteriosum accounted for approximately 75% of the total ventricular mass, and was twice as dense as the low-pressure cavum pulmonale. The reptile ventricle has a core of spongious myocardium, but the three ventricular septa that separate the pulmonary and systemic chambers--the muscular ridge, the bulbuslamelle and the vertical septum--all had layers of compact myocardium. Pythons, however, have unique pads of connective tissue on the site of pressure separation. Because the hearts of varanid lizards, which also are endowed with pressure separation, share many of these morphological specializations, we propose that intraventricular compact myocardium is an indicator of high-pressure systems and possibly pressure separation.

Large reptiles and cold temperatures: Do extreme cold spells set distributional limits for tropical reptiles in Florida?

USGS Publications Warehouse

Mazzotti, Frank J.; Cherkiss, Michael S.; Parry, Mark; Beauchamp, Jeff; Rochford, Mike; Smith, Brian J.; Hart, Kristen M.; Brandt, Laura A.

2016-01-01

Distributional limits of many tropical species in Florida are ultimately determined by tolerance to low temperature. An unprecedented cold spell during 2–11 January 2010, in South Florida provided an opportunity to compare the responses of tropical American crocodiles with warm-temperate American alligators and to compare the responses of nonnative Burmese pythons with native warm-temperate snakes exposed to prolonged cold temperatures. After the January 2010 cold spell, a record number of American crocodiles (n = 151) and Burmese pythons (n = 36) were found dead. In contrast, no American alligators and no native snakes were found dead. American alligators and American crocodiles behaved differently during the cold spell. American alligators stopped basking and retreated to warmer water. American crocodiles apparently continued to bask during extreme cold temperatures resulting in lethal body temperatures. The mortality of Burmese pythons compared to the absence of mortality for native snakes suggests that the current population of Burmese pythons in the Everglades is less tolerant of cold temperatures than native snakes. Burmese pythons introduced from other parts of their native range may be more tolerant of cold temperatures. We documented the direct effects of cold temperatures on crocodiles and pythons; however, evidence of long-term effects of cold temperature on their populations within their established ranges remains lacking. Mortality of crocodiles and pythons outside of their current established range may be more important in setting distributional limits.

Microstructural evolution of diamond growth during HFCVD

NASA Technical Reports Server (NTRS)

Singh, J.

1994-01-01

High resolution transmission electron microscopy (HRTEM) was used to study the nucleation and growth mechanism of diamond by hot filament chemical vapor deposition (HFCVD) process. A novel technique has shown a direct evidence for the formation of the diamond-like carbon layer 8-14 nm thick in which small diamond micro-crystallites were embedded. These diamond micro-crystallites were formed as a result of transformation of diamond-like carbon into diamond. The diamond micro-crystallites present in the amorphous diamond-like carbon layer provided nucleation sites for diamond growth. Large diamond crystallites were observed to grow from these micro-crystallites. The mechanism of diamond growth will be presented based on experimental findings.

Developing a Conceptual Architecture for a Generalized Agent-based Modeling Environment (GAME)

DTIC Science & Technology

2008-03-01

4. REPAST (Java, Python , C#, Open Source) ........28 5. MASON: Multi-Agent Modeling Language (Swarm Extension... Python , C#, Open Source) Repast (Recursive Porous Agent Simulation Toolkit) was designed for building agent-based models and simulations in the...Repast makes it easy for inexperienced users to build models by including a built-in simple model and provide interfaces through which menus and Python

Charming Users into Scripting CIAO with Python

NASA Astrophysics Data System (ADS)

Burke, D. J.

2011-07-01

The Science Data Systems group of the Chandra X-ray Center provides a number of scripts and Python modules that extend the capabilities of CIAO. Experience in converting the existing scripts—written in a variety of languages such as bash, csh/tcsh, Perl and S-Lang—to Python, and conversations with users, led to the development of the ciao_contrib.runtool module. This allows users to easily run CIAO tools from Python scripts, and utilizes the metadata provided by the parameter-file system to create an API that provides the flexibility and safety guarantees of the command-line. The module is provided to the user community and is being used within our group to create new scripts.

Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins

PubMed Central

Ruoppolo, Valeria; Schmidt, Annie; Lescroël, Amelie; Jongsomjit, Dennis; Elrod, Megan; Kraberger, Simona; Stainton, Daisy; Dugger, Katie M; Ballard, Grant; Ainley, David G

2017-01-01

Abstract The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adélie penguin (Pygoscelis adeliae) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares ∼64 per cent genome-wide identity to a previously described Adélie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota, associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins. PMID:29026649

Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins

USGS Publications Warehouse

Van Doorslaer, Koenraad; Ruoppolo, Valeria; Schmidt, Annie; Lescroël, Amelie; Jongsomjit, Dennis; Elrod, Megan; Kraberger, Simona; Stainton, Daisy; Dugger, Katie M.; Ballard, Grant; Ainley, David G.; Varsani, Arvind

2017-01-01

The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adélie penguin (Pygoscelis adeliae) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares ∼64 per cent genome-wide identity to a previously described Adélie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota, associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.

Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins.

PubMed

Van Doorslaer, Koenraad; Ruoppolo, Valeria; Schmidt, Annie; Lescroël, Amelie; Jongsomjit, Dennis; Elrod, Megan; Kraberger, Simona; Stainton, Daisy; Dugger, Katie M; Ballard, Grant; Ainley, David G; Varsani, Arvind

2017-07-01

The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds ( n  = 5), a fish ( n  = 1), a snake ( n  = 1), and turtles ( n  = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adélie penguin ( Pygoscelis adeliae ) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares ∼64 per cent genome-wide identity to a previously described Adélie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota , associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis ), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python

PubMed Central

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2008-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations. PMID:19543450

Imagining a Stata / Python Combination

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

There are occasions when a task is difficult in Stata, but fairly easy in a more general programming language. Python is a popular language for a range of uses. It is easy to use, has many high ]quality packages, and programs can be written relatively quickly. Is there any advantage in combining Stata and Python within a single interface? Stata already offers support for user-written programs, which allow extensive control over calculations, but somewhat less control over graphics. Also, except for specifying output, the user has minimal programmatic control over the user interface. Python can be used in a way that allows more control over the interface and graphics, and in so doing provide a roundabout method for satisfying some user requests (e.g., transparency levels in graphics and the ability to clear the results window). My talk will explore these ideas, present a possible method for combining Stata and Python, and give examples to demonstrate how this combination might be useful.

Status of parallel Python-based implementation of UEDGE

NASA Astrophysics Data System (ADS)

Umansky, M. V.; Pankin, A. Y.; Rognlien, T. D.; Dimits, A. M.; Friedman, A.; Joseph, I.

2017-10-01

The tokamak edge transport code UEDGE has long used the code-development and run-time framework Basis. However, with the support for Basis expected to terminate in the coming years, and with the advent of the modern numerical language Python, it has become desirable to move UEDGE to Python, to ensure its long-term viability. Our new Python-based UEDGE implementation takes advantage of the portable build system developed for FACETS. The new implementation gives access to Python's graphical libraries and numerical packages for pre- and post-processing, and support of HDF5 simplifies exchanging data. The older serial version of UEDGE has used for time-stepping the Newton-Krylov solver NKSOL. The renovated implementation uses backward Euler discretization with nonlinear solvers from PETSc, which has the promise to significantly improve the UEDGE parallel performance. We will report on assessment of some of the extended UEDGE capabilities emerging in the new implementation, and will discuss the future directions. Work performed for U.S. DOE by LLNL under contract DE-AC52-07NA27344.

PyMercury: Interactive Python for the Mercury Monte Carlo Particle Transport Code

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

Iandola, F N; O'Brien, M J; Procassini, R J

2010-11-29

Monte Carlo particle transport applications are often written in low-level languages (C/C++) for optimal performance on clusters and supercomputers. However, this development approach often sacrifices straightforward usability and testing in the interest of fast application performance. To improve usability, some high-performance computing applications employ mixed-language programming with high-level and low-level languages. In this study, we consider the benefits of incorporating an interactive Python interface into a Monte Carlo application. With PyMercury, a new Python extension to the Mercury general-purpose Monte Carlo particle transport code, we improve application usability without diminishing performance. In two case studies, we illustrate how PyMercury improvesmore » usability and simplifies testing and validation in a Monte Carlo application. In short, PyMercury demonstrates the value of interactive Python for Monte Carlo particle transport applications. In the future, we expect interactive Python to play an increasingly significant role in Monte Carlo usage and testing.« less

Record length, mass, and clutch size in the nonindigenous Burmese Python, Python bivittatus Kuhl 1820 (Squamata: Pythonidae), in Florida

USGS Publications Warehouse

Krysko, Kenneth L.; Hart, Kristen M.; Smith, Brian J.; Selby, Thomas H.; Cherkiss, Michael S.; Coutu, Nicholas T.; Reichart, Rebecca M.; Nuñez, Leroy P.; Mazzotti, Frank J.; Snow, Ray W.

2012-01-01

The Burmese Python, Python bivittatus Kuhl 1820 (Squamata: Pythonidae), is indigenous to northern India,east to southern China, and south to Vietnam and a few islands in Indonesia (Barker and Barker 2008, Reed and Rodda 2009). This species has been introduced since at least 1979 in southern Florida, USA, where it likely began reproducing and became established during the 1980s (Meshaka et al. 2000, Snowet al. 2007b,Kraus 2009, Krysko et al. 2011, Willson et al. 2011). Python bivittatus has been documented in Florida consuming a variety of mammals and birds, and the American Alligator(Alligator mississippiensis) (Snowet al. 2007a, 2007b; Harvey et al. 2008; Rochford et al. 2010b; Holbrook and Chesnes 2011), many of which are protected species. Herein, we provide details on two of the largest known wild P. bivittatus in Florida to date, including current records on length,mass,clutch size, and diet.

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

Veseli, S.

As the number of sites deploying and adopting EPICS Version 4 grows, so does the need to support PV Access from multiple languages. Especially important are the widely used scripting languages that tend to reduce both software development time and the learning curve for new users. In this paper we describe PvaPy, a Python API for the EPICS PV Access protocol and its accompanying structured data API. Rather than implementing the protocol itself in Python, PvaPy wraps the existing EPICS Version 4 C++ libraries using the Boost.Python framework. This approach allows us to benefit from the existing code base andmore » functionality, and to significantly reduce the Python API development effort. PvaPy objects are based on Python dictionaries and provide users with the ability to access even the most complex of PV Data structures in a relatively straightforward way. Its interfaces are easy to use, and include support for advanced EPICS Version 4 features such as implementation of client and server Remote Procedure Calls (RPC).« less

Lower pressure synthesis of diamond material

DOEpatents

Lueking, Angela; Gutierrez, Humberto; Narayanan, Deepa; Burgess Clifford, Caroline E.; Jain, Puja

2010-07-13

Methods of synthesizing a diamond material, particularly nanocrystalline diamond, diamond-like carbon and bucky diamond are provided. In particular embodiments, a composition including a carbon source, such as coal, is subjected to addition of energy, such as high energy reactive milling, producing a milling product enriched in hydrogenated tetrahedral amorphous diamond-like carbon compared to the coal. A milling product is treated with heat, acid and/or base to produce nanocrystalline diamond and/or crystalline diamond-like carbon. Energy is added to produced crystalline diamond-like carbon in particular embodiments to produce bucky diamonds.

Optimal Repair And Replacement Policy For A System With Multiple Components

DTIC Science & Technology

2016-06-17

Numerical Demonstration To implement the linear program, we use the Python Programming Language (PSF 2016) with the Pyomo optimization modeling language...opre.1040.0133. Hart, W.E., C. Laird, J. Watson, D.L. Woodruff. 2012. Pyomo–optimization modeling in python , vol. 67. Springer Science & Business...Media. Hart, W.E., J. Watson, D.L. Woodruff. 2011. Pyomo: modeling and solving mathematical programs in python . Mathematical Programming Computation 3(3

Sharma's Python Sign: A New Tubal Sign in Female Genital Tuberculosis.

PubMed

Sharma, Jai Bhagwan

2016-01-01

Female genital tuberculosis (FGTB) is an important cause of infertility in developing countries. Various type of TB salpingitis can be endosalpingitis, exosalpingitis, interstitial TB salpingitis, and salpingitis isthmica nodosa. The fallopian tubes are thickened enlarged and tortuous. Unilateral or bilateral hydrosalpinx or pyosalpinx may be formed. A new sign python sign is presented in which fallopian tube looks like a blue python on dye testing in FGTB.

Methods to Secure Databases Against Vulnerabilities

DTIC Science & Technology

2015-12-01

for several languages such as C, C++, PHP, Java and Python [16]. MySQL will work well with very large databases. The documentation references...using Eclipse and connected to each database management system using Python and Java drivers provided by MySQL , MongoDB, and Datastax (for Cassandra...tiers in Python and Java . Problem MySQL MongoDB Cassandra 1. Injection a. Tautologies Vulnerable Vulnerable Not Vulnerable b. Illegal query

Prevalence of Amblyomma gervaisi ticks on captive snakes in Tamil Nadu.

PubMed

Catherine, B R; Jayathangaraj, M G; Soundararajan, C; Bala Guru, C; Yogaraj, D

2017-12-01

Ticks are the important ectoparasites that occur on snakes and transmit rickettsiosis, anaplasmosis and ehrlichiosis. A total of 62 snakes (Reticulated python, Indian Rock Python, Rat snakes and Spectacled cobra) were examined for tick infestation at Chennai Snake Park Trust (Guindy), Arignar Anna Zoological Park (Vandalur) and Rescue centre (Velachery) in Tamil Nadu from September, 2015 to June, 2016. Ticks from infested snakes were collected and were identified as Amblyomma gervaisi (previously known as Aponomma gervaisi ). Overall occurrence of tick infestation on snakes was 66.13%. Highest prevalence of tick infestation was observed more on Reticulated Python ( Python reticulatus , 90.91%) followed by Indian Rock Python ( Python molurus , 88.89%), Spectacled cobra ( Naja naja, 33.33%) and Rat snake ( Ptyas mucosa, 21.05%). Highest prevalence of ticks were observed on snakes reared at Chennai Snake Park Trust, Guindy (83.33%), followed by Arignar Anna Zoological Park, Vandalur (60.00%) and low level prevalence of 37.50% on snakes at Rescue centre, Velachery. Among the system of management, the prevalence of ticks were more on captive snakes (70.37%) than the free ranging snakes (37.5%). The presences of ticks were more on the first quarter when compared to other three quarters and were highly significant ( P  ≤ 0.01).

Gist: A scientific graphics package for Python

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

Busby, L.E.

1996-05-08

{open_quotes}Gist{close_quotes} is a scientific graphics library written by David H. Munro of Lawrence Livermore National Laboratory (LLNL). It features support for three common graphics output devices: X Windows, (Color) PostScript, and ANSI/ISO Standard Computer Graphics Metafiles (CGM). The library is small (written directly to Xlib), portable, efficient, and full-featured. It produces X versus Y plots with {open_quotes}good{close_quotes} tick marks and tick labels, 2-dimensional quadrilateral mesh plots with contours, vector fields, or pseudo color maps on such meshes, with 3-dimensional plots on the way. The Python Gist module utilizes the new {open_quotes}Numeric{close_quotes} module due to J. Hugunin and others. It ismore » therefore fast and able to handle large datasets. The Gist module includes an X Windows event dispatcher which can be dynamically added (e.g., via importing a dynamically loaded module) to the Python interpreter after a simple two-line modification to the Python core. This makes fast mouse-controlled zoom, pan, and other graphic operations available to the researcher while maintaining the usual Python command-line interface. Munro`s Gist library is already freely available. The Python Gist module is currently under review and is also expected to qualify for unlimited release.« less

EMPIRE and pyenda: Two ensemble-based data assimilation systems written in Fortran and Python

NASA Astrophysics Data System (ADS)

Geppert, Gernot; Browne, Phil; van Leeuwen, Peter Jan; Merker, Claire

2017-04-01

We present and compare the features of two ensemble-based data assimilation frameworks, EMPIRE and pyenda. Both frameworks allow to couple models to the assimilation codes using the Message Passing Interface (MPI), leading to extremely efficient and fast coupling between models and the data-assimilation codes. The Fortran-based system EMPIRE (Employing Message Passing Interface for Researching Ensembles) is optimized for parallel, high-performance computing. It currently includes a suite of data assimilation algorithms including variants of the ensemble Kalman and several the particle filters. EMPIRE is targeted at models of all kinds of complexity and has been coupled to several geoscience models, eg. the Lorenz-63 model, a barotropic vorticity model, the general circulation model HadCM3, the ocean model NEMO, and the land-surface model JULES. The Python-based system pyenda (Python Ensemble Data Assimilation) allows Fortran- and Python-based models to be used for data assimilation. Models can be coupled either using MPI or by using a Python interface. Using Python allows quick prototyping and pyenda is aimed at small to medium scale models. pyenda currently includes variants of the ensemble Kalman filter and has been coupled to the Lorenz-63 model, an advection-based precipitation nowcasting scheme, and the dynamic global vegetation model JSBACH.

Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius

PubMed Central

Stenglein, Mark D.; Jacobson, Elliott R.; Wozniak, Edward J.; Wellehan, James F. X.; Kincaid, Anne; Gordon, Marcus; Porter, Brian F.; Baumgartner, Wes; Stahl, Scott; Kelley, Karen; Towner, Jonathan S.

2014-01-01

ABSTRACT A severe, sometimes fatal respiratory disease has been observed in captive ball pythons (Python regius) since the late 1990s. In order to better understand this disease and its etiology, we collected case and control samples and performed pathological and diagnostic analyses. Electron micrographs revealed filamentous virus-like particles in lung epithelial cells of sick animals. Diagnostic testing for known pathogens did not identify an etiologic agent, so unbiased metagenomic sequencing was performed. Abundant nidovirus-like sequences were identified in cases and were used to assemble the genome of a previously unknown virus in the order Nidovirales. The nidoviruses, which were not previously known to infect nonavian reptiles, are a diverse order that includes important human and veterinary pathogens. The presence of the viral RNA was confirmed in all diseased animals (n = 8) but was not detected in healthy pythons or other snakes (n = 57). Viral RNA levels were generally highest in the lung and other respiratory tract tissues. The 33.5-kb viral genome is the largest RNA genome yet described and shares canonical characteristics with other nidovirus genomes, although several features distinguish this from related viruses. This virus, which we named ball python nidovirus (BPNV), will likely establish a new genus in Torovirinae subfamily. The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease. PMID:25205093

Chained nuclei and python pattern in skeletal muscle cells as histological markers for electrical injury.

PubMed

Tanaka, Hiroki; Okuda, Katsuhiro; Ohtani, Seiji; Asari, Masaru; Horioka, Kie; Isozaki, Shotaro; Hayakawa, Akira; Ogawa, Katsuhiro; Hiroshi, Shiono; Shimizu, Keiko

2018-05-01

Electrical injury is damage caused by an electrical current passing through the body. We have previously reported that irregular stripes crossing skeletal muscle fibers (python pattern) and multiple small nuclei arranged in the longitudinal direction of the muscle fibers (chained nuclear change) are uniquely observed by histopathological analysis in the skeletal muscle tissues of patients with electrical injury. However, it remains unclear whether these phenomena are caused by the electrical current itself or by the joule heat generated by the electric current passing through the body. To clarify the causes underlying these changes, we applied electric and heat injury to the exteriorized rat soleus muscle in situ. Although both the python pattern and chained nuclear change were induced by electric injury, only the python pattern was induced by heat injury. Furthermore, a chained nuclear change was induced in the soleus muscle cells by electric current flow in physiological saline at 40 °C ex vivo, but a python pattern was not observed. When the skeletal muscle was exposed to electrical injury in cardiac-arrested rats, a python pattern was induced within 5 h after cardiac arrest, but no chained nuclear change was observed. Therefore, a chained nuclear change is induced by an electrical current alone in tissues in vital condition, whereas a python pattern is caused by joule heat, which may occur shortly after death. The degree and distribution of these skeletal muscle changes may be useful histological markers for analyzing cases of electrical injury in forensic medicine. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection and analysis of diamond fingerprinting feature and its application

NASA Astrophysics Data System (ADS)

Li, Xin; Huang, Guoliang; Li, Qiang; Chen, Shengyi

2011-01-01

Before becoming a jewelry diamonds need to be carved artistically with some special geometric features as the structure of the polyhedron. There are subtle differences in the structure of this polyhedron in each diamond. With the spatial frequency spectrum analysis of diamond surface structure, we can obtain the diamond fingerprint information which represents the "Diamond ID" and has good specificity. Based on the optical Fourier Transform spatial spectrum analysis, the fingerprinting identification of surface structure of diamond in spatial frequency domain was studied in this paper. We constructed both the completely coherent diamond fingerprinting detection system illuminated by laser and the partially coherent diamond fingerprinting detection system illuminated by led, and analyzed the effect of the coherence of light source to the diamond fingerprinting feature. We studied rotation invariance and translation invariance of the diamond fingerprinting and verified the feasibility of real-time and accurate identification of diamond fingerprint. With the profit of this work, we can provide customs, jewelers and consumers with a real-time and reliable diamonds identification instrument, which will curb diamond smuggling, theft and other crimes, and ensure the healthy development of the diamond industry.

Anisotropic diamond etching through thermochemical reaction between Ni and diamond in high-temperature water vapour.

PubMed

Nagai, Masatsugu; Nakanishi, Kazuhiro; Takahashi, Hiraku; Kato, Hiromitsu; Makino, Toshiharu; Yamasaki, Satoshi; Matsumoto, Tsubasa; Inokuma, Takao; Tokuda, Norio

2018-04-27

Diamond possesses excellent physical and electronic properties, and thus various applications that use diamond are under development. Additionally, the control of diamond geometry by etching technique is essential for such applications. However, conventional wet processes used for etching other materials are ineffective for diamond. Moreover, plasma processes currently employed for diamond etching are not selective, and plasma-induced damage to diamond deteriorates the device-performances. Here, we report a non-plasma etching process for single crystal diamond using thermochemical reaction between Ni and diamond in high-temperature water vapour. Diamond under Ni films was selectively etched, with no etching at other locations. A diamond-etching rate of approximately 8.7 μm/min (1000 °C) was successfully achieved. To the best of our knowledge, this rate is considerably greater than those reported so far for other diamond-etching processes, including plasma processes. The anisotropy observed for this diamond etching was considerably similar to that observed for Si etching using KOH.

Diamond fiber field emitters

DOEpatents

Blanchet-Fincher, Graciela B.; Coates, Don M.; Devlin, David J.; Eaton, David F.; Silzars, Aris K.; Valone, Steven M.

1996-01-01

A field emission electron emitter comprising an electrode formed of at least one diamond, diamond-like carbon or glassy carbon composite fiber, said composite fiber having a non-diamond core and a diamond, diamond-like carbon or glassy carbon coating on said non-diamond core, and electronic devices employing such a field emission electron emitter.

Sharma's Python Sign: A New Tubal Sign in Female Genital Tuberculosis

PubMed Central

Sharma, Jai Bhagwan

2016-01-01

Female genital tuberculosis (FGTB) is an important cause of infertility in developing countries. Various type of TB salpingitis can be endosalpingitis, exosalpingitis, interstitial TB salpingitis, and salpingitis isthmica nodosa. The fallopian tubes are thickened enlarged and tortuous. Unilateral or bilateral hydrosalpinx or pyosalpinx may be formed. A new sign python sign is presented in which fallopian tube looks like a blue python on dye testing in FGTB. PMID:27365923

C3I and Modelling and Simulation (M&S) Interoperability

DTIC Science & Technology

2004-03-01

customised Open Source products. The technical implementation is based on the use of the eXtendend Markup Language (XML) and Python . XML is developed...to structure, store and send information. The language is focus on the description of data. Python is a portable, interpreted, object-oriented...programming language. A huge variety of usable Open Source Projects were issued by the Python Community. 3.1 Phase 1: Feasibility Studies Phase 1 was

Lectin histochemical aspects of mucus function in the oesophagus of the reticulated python (Python reticulatus).

PubMed

Meyer, W; Luz, S; Schnapper, A

2009-08-01

Using lectin histochemistry, the study characterizes basic functional aspects of the mucus produced by the oesophageal epithelium of the Reticulated python (Python reticulatus). Reaction staining varied as related to the two epithelium types present, containing goblet cells and ciliary cells. Remarkable intensities were achieved especially in the luminal mucus layer and the fine mucus covering the epithelial ciliary border for Con A (alpha-D-Man; alpha-D-Glc) as part of neutral glycoproteins, Limax flavus agglutinin (NeuNac = NeuNgc), emphasizing that water binding hyaluronan provides a hydrated interface conductive to the passage of material and UEA-I (alpha-L-Fuc), corroborating the view that fucose-rich highly viscous mucus is helpful against mechanical stress during prey transport.

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

Spotz, William F.

PyTrilinos is a set of Python interfaces to compiled Trilinos packages. This collection supports serial and parallel dense linear algebra, serial and parallel sparse linear algebra, direct and iterative linear solution techniques, algebraic and multilevel preconditioners, nonlinear solvers and continuation algorithms, eigensolvers and partitioning algorithms. Also included are a variety of related utility functions and classes, including distributed I/O, coloring algorithms and matrix generation. PyTrilinos vector objects are compatible with the popular NumPy Python package. As a Python front end to compiled libraries, PyTrilinos takes advantage of the flexibility and ease of use of Python, and the efficiency of themore » underlying C++, C and Fortran numerical kernels. This paper covers recent, previously unpublished advances in the PyTrilinos package.« less

Investigations on diamond nanostructuring of different morphologies by the reactive-ion etching process and their potential applications.

PubMed

Kunuku, Srinivasu; Sankaran, Kamatchi Jothiramalingam; Tsai, Cheng-Yen; Chang, Wen-Hao; Tai, Nyan-Hwa; Leou, Keh-Chyang; Lin, I-Nan

2013-08-14

We report the systematic studies on the fabrication of aligned, uniform, and highly dense diamond nanostructures from diamond films of various granular structures. Self-assembled Au nanodots are used as a mask in the self-biased reactive-ion etching (RIE) process, using an O2/CF4 process plasma. The morphology of diamond nanostructures is a close function of the initial phase composition of diamond. Cone-shaped and tip-shaped diamond nanostructures result for microcrystalline diamond (MCD) and nanocrystalline diamond (NCD) films, whereas pillarlike and grasslike diamond nanostructures are obtained for Ar-plasma-based and N2-plasma-based ultrananocrystalline diamond (UNCD) films, respectively. While the nitrogen-incorporated UNCD (N-UNCD) nanograss shows the most-superior electron-field-emission properties, the NCD nanotips exhibit the best photoluminescence properties, viz, different applications need different morphology of diamond nanostructures to optimize the respective characteristics. The optimum diamond nanostructure can be achieved by proper choice of granular structure of the initial diamond film. The etching mechanism is explained by in situ observation of optical emission spectrum of RIE plasma. The preferential etching of sp(2)-bonded carbon contained in the diamond films is the prime factor, which forms the unique diamond nanostructures from each type of diamond films. However, the excited oxygen atoms (O*) are the main etching species of diamond film.

Lateral overgrowth of diamond film on stripes patterned Ir/HPHT-diamond substrate

NASA Astrophysics Data System (ADS)

Wang, Yan-Feng; Chang, Xiaohui; Liu, Zhangcheng; Liu, Zongchen; Fu, Jiao; Zhao, Dan; Shao, Guoqing; Wang, Juan; Zhang, Shaopeng; Liang, Yan; Zhu, Tianfei; Wang, Wei; Wang, Hong-Xing

2018-05-01

Epitaxial lateral overgrowth (ELO) of diamond films on patterned Ir/(0 0 1)HPHT-diamond substrates have been carried out by microwave plasma CVD system. Ir/(0 0 1)HPHT-diamond substrates are fabricated by photolithographic and magnetron sputtering technique. The morphology of the as grown ELO diamond film is characterized by optical microscopy and scanning electronic microscopy. The quality and stress of the ELO diamond film are investigated by surface etching pit density and micro-Raman spectroscopy. Two ultraviolet photodetectors are fabricated on ELO diamond area and non-ELO diamond area prepared on same substrate, and that one on ELO diamond area indicates better photoelectric properties. All results indicate quality of ELO diamond film is improved.

Diamond Synthesis Employing Nanoparticle Seeds

NASA Technical Reports Server (NTRS)

Uppireddi, Kishore (Inventor); Morell, Gerardo (Inventor); Weiner, Brad R. (Inventor)

2014-01-01

Iron nanoparticles were employed to induce the synthesis of diamond on molybdenum, silicon, and quartz substrates. Diamond films were grown using conventional conditions for diamond synthesis by hot filament chemical vapor deposition, except that dispersed iron oxide nanoparticles replaced the seeding. This approach to diamond induction can be combined with dip pen nanolithography for the selective deposition of diamond and diamond patterning while avoiding surface damage associated to diamond-seeding methods.

Diamond tool machining of materials which react with diamond

DOEpatents

Lundin, Ralph L.; Stewart, Delbert D.; Evans, Christopher J.

1992-01-01

Apparatus for the diamond machining of materials which detrimentally react with diamond cutting tools in which the cutting tool and the workpiece are chilled to very low temperatures. This chilling halts or retards the chemical reaction between the workpiece and the diamond cutting tool so that wear rates of the diamond tool on previously detrimental materials are comparable with the diamond turning of materials which do not react with diamond.

All diamond self-aligned thin film transistor

DOEpatents

Gerbi, Jennifer [Champaign, IL

2008-07-01

A substantially all diamond transistor with an electrically insulating substrate, an electrically conductive diamond layer on the substrate, and a source and a drain contact on the electrically conductive diamond layer. An electrically insulating diamond layer is in contact with the electrically conductive diamond layer, and a gate contact is on the electrically insulating diamond layer. The diamond layers may be homoepitaxial, polycrystalline, nanocrystalline or ultrananocrystalline in various combinations.A method of making a substantially all diamond self-aligned gate transistor is disclosed in which seeding and patterning can be avoided or minimized, if desired.

Giant Constrictors: Biological and Management Profiles and an Establishment Risk Assessment for Nine Large Species of Pythons, Anacondas, and the Boa Constrictor

USGS Publications Warehouse

Reed, Robert N.; Rodda, Gordon H.

2009-01-01

Giant Constrictors: Biological and Management Profiles and an Establishment Risk Assessment for Nine Large Species of Pythons, Anacondas, and the Boa Constrictor, estimates the ecological risks associated with colonization of the United States by nine large constrictors. The nine include the world's four largest snake species (Green Anaconda, Eunectes murinus; Indian or Burmese Python, Python molurus; Northern African Python, Python sebae; and Reticulated Python, Broghammerus reticulatus), the Boa Constrictor (Boa constrictor), and four species that are ecologically or visually similar to one of the above (Southern African Python, Python natalensis; Yellow Anaconda, Eunectes notaeus; DeSchauensee's Anaconda, Eunectes deschauenseei; and Beni Anaconda, Eunectes beniensis). At present, the only probable pathway by which these species would become established in the United States is the pet trade. Although importation for the pet trade involves some risk that these animals could become established as exotic or invasive species, it does not guarantee such establishment. Federal regulators have the task of appraising the importation risks and balancing those risks against economic, social, and ecological benefits associated with the importation. The risk assessment quantifies only the ecological risks, recognizing that ecosystem processes are complex and only poorly understood. The risk assessment enumerates the types of economic impacts that may be experienced, but leaves quantification of economic costs to subsequent studies. Primary factors considered in judging the risk of establishment were: (1) history of establishment in other countries, (2) number of each species in commerce, (3) suitability of U.S. climates for each species, and (4) natural history traits, such as reproductive rate and dispersal ability, that influence the probability of establishment, spread, and impact. In addition, the risk assessment reviews all management tools for control of invasive giant constrictor populations. There is great uncertainty about many aspects of the risk assessment; the level of uncertainty is estimated separately for each risk component. Overall risk was judged to be high for five of the giant constrictors studied, and medium for the other four species. Because all nine species shared a large number of natural history traits that promote invasiveness or impede population control, none of the species was judged to be of low risk.

The role of python eggshell permeability dynamics in a respiration-hydration trade-off.

PubMed

Stahlschmidt, Zachary R; Heulin, Benoit; DeNardo, Dale F

2010-01-01

Parental care is taxonomically widespread because it improves developmental conditions and thus fitness of offspring. Although relatively simplistic compared with parental behaviors of other taxa, python egg-brooding behavior exemplifies parental care because it mediates a trade-off between embryonic respiration and hydration. However, because egg brooding increases gas-exchange resistance between embryonic and nest environments and because female pythons do not adjust their brooding behavior in response to the increasing metabolic requirements of developing offspring, python egg brooding imposes hypoxic costs on embryos during the late stages of incubation. We conducted a series of experiments to determine whether eggshells coadapted with brooding behavior to minimize the negative effects of developmental hypoxia. We tested the hypotheses that python eggshells (1) increase permeability over time to accommodate increasing embryonic respiration and (2) exhibit permeability plasticity in response to chronic hypoxia. Over incubation, we serially measured the atomic and structural components of Children's python (Antaresia childreni) eggshells as well as in vivo and in vitro gas exchange across eggshells. In support of our first hypothesis, A. childreni eggshells exhibited a reduced fibrous layer, became more permeable, and facilitated greater gas exchange as incubation progressed. Our second hypothesis was not supported, as incubation O(2) concentration did not affect the shells' permeabilities to O(2) and H(2)O vapor. Our results suggest that python eggshell permeability changes during incubation but that the alterations over time are fixed and independent of environmental conditions. These findings are of broad evolutionary interest because they demonstrate that, even in relatively simple parental-care models, successful parent-offspring relationships depend on adjustments made by both the parent (i.e., egg-brooding behavioral shifts) and the offspring (i.e., changes in eggshell permeability).

High performance Python for direct numerical simulations of turbulent flows

NASA Astrophysics Data System (ADS)

Mortensen, Mikael; Langtangen, Hans Petter

2016-06-01

Direct Numerical Simulations (DNS) of the Navier Stokes equations is an invaluable research tool in fluid dynamics. Still, there are few publicly available research codes and, due to the heavy number crunching implied, available codes are usually written in low-level languages such as C/C++ or Fortran. In this paper we describe a pure scientific Python pseudo-spectral DNS code that nearly matches the performance of C++ for thousands of processors and billions of unknowns. We also describe a version optimized through Cython, that is found to match the speed of C++. The solvers are written from scratch in Python, both the mesh, the MPI domain decomposition, and the temporal integrators. The solvers have been verified and benchmarked on the Shaheen supercomputer at the KAUST supercomputing laboratory, and we are able to show very good scaling up to several thousand cores. A very important part of the implementation is the mesh decomposition (we implement both slab and pencil decompositions) and 3D parallel Fast Fourier Transforms (FFT). The mesh decomposition and FFT routines have been implemented in Python using serial FFT routines (either NumPy, pyFFTW or any other serial FFT module), NumPy array manipulations and with MPI communications handled by MPI for Python (mpi4py). We show how we are able to execute a 3D parallel FFT in Python for a slab mesh decomposition using 4 lines of compact Python code, for which the parallel performance on Shaheen is found to be slightly better than similar routines provided through the FFTW library. For a pencil mesh decomposition 7 lines of code is required to execute a transform.

HOPE: A Python just-in-time compiler for astrophysical computations

NASA Astrophysics Data System (ADS)

Akeret, J.; Gamper, L.; Amara, A.; Refregier, A.

2015-04-01

The Python programming language is becoming increasingly popular for scientific applications due to its simplicity, versatility, and the broad range of its libraries. A drawback of this dynamic language, however, is its low runtime performance which limits its applicability for large simulations and for the analysis of large data sets, as is common in astrophysics and cosmology. While various frameworks have been developed to address this limitation, most focus on covering the complete language set, and either force the user to alter the code or are not able to reach the full speed of an optimised native compiled language. In order to combine the ease of Python and the speed of C++, we developed HOPE, a specialised Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimisation on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. We assess the performance of HOPE by performing a series of benchmarks and compare its execution speed with that of plain Python, C++ and the other existing frameworks. We find that HOPE improves the performance compared to plain Python by a factor of 2 to 120, achieves speeds comparable to that of C++, and often exceeds the speed of the existing solutions. We discuss the differences between HOPE and the other frameworks, as well as future extensions of its capabilities. The fully documented HOPE package is available at http://hope.phys.ethz.ch and is published under the GPLv3 license on PyPI and GitHub.

Impact resistance and energies of intermetallic bonded diamond composites and polycrystalline diamond compacts and their comparison

NASA Astrophysics Data System (ADS)

Gorla, Sai Prasanth

Chemistry of intermetallic bonded diamond is studied. The impact resistance and energies of intermetallic bonded diamond is compared to current poly crystalline diamond compacts. IBD's are found to have high standards of hardness and have more impact energies absorbed. Intermetallic bonded diamond composite comprises of diamond particles dispersed in Tungsten carbide using Nickel aluminide (Ni3Al) as binder. In previous research conducted on IBD's, diamonds are successfully dispersed in intermetallic alloy of nickel aluminide and processed at 1350°C such that diamond particles remain intact without forming graphite. Composites are formed by milling, pressing the intermetallic binder and diamond particles and sintering at high temperature conditions.

[Transfer of exotic tick Aponomma latum (Koch, 1844) (Acari: Ixodida: Ixodidae) on ball pythons (Python regius Shaw, 1802) brought to Poland].

PubMed

Siuda, Krzysztof; Nowak, Magdalena; Kedryna, Mariusz

2004-01-01

103 specimens of Python regius brought to Poland between October 2002 and March 2004 were examined. Occurrence of tick Aponomma latum was reported from 80.6% of the examined reptiles. 549 specimens of A. latum were collected including 341 males, 149 females and 59 nymphs at the various stage of engorgement. Tick A. latum is frequently transferred beyond its natural range of occurrence--Afrotropical region.

CVXPY: A Python-Embedded Modeling Language for Convex Optimization.

PubMed

Diamond, Steven; Boyd, Stephen

2016-04-01

CVXPY is a domain-specific language for convex optimization embedded in Python. It allows the user to express convex optimization problems in a natural syntax that follows the math, rather than in the restrictive standard form required by solvers. CVXPY makes it easy to combine convex optimization with high-level features of Python such as parallelism and object-oriented design. CVXPY is available at http://www.cvxpy.org/ under the GPL license, along with documentation and examples.

Introduction to Python for CMF Authority Users

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

Pritchett-Sheats, Lori A.

This talk is a very broad over view of Python that highlights key features in the language used in the Common Model Framework (CMF). I assume that the audience has some programming experience in a shell scripting language (C shell, Bash, PERL) or other high level language (C/C++/ Fortran). The talk will cover Python data types, classes (objects) and basic programming constructs. The talk concludes with slides describing how I developed the basic classes for a TITANS homework assignment.

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

Grote, D. P.

Forthon generates links between Fortran and Python. Python is a high level, object oriented, interactive and scripting language that allows a flexible and versatile interface to computational tools. The Forthon package generates the necessary wrapping code which allows access to the Fortran database and to the Fortran subroutines and functions. This provides a development package where the computationally intensive parts of a code can be written in efficient Fortran, and the high level controlling code can be written in the much more versatile Python language.

Trypanosoma cf. varani in an imported ball python (Python reginus) from Ghana.

PubMed

Sato, Hiroshi; Takano, Ai; Kawabata, Hiroki; Une, Yumi; Watanabe, Haruo; Mukhtar, Maowia M

2009-08-01

Peripheral blood from a ball python (Python reginus) imported from Ghana was cultured in Barbour-Stoenner-Kelly (BSK) medium for Borrelia spp. isolation, resulting in the prominent appearance of free, and clusters of, trypanosomes in a variety of morphological forms. The molecular phylogenetic characterization of these cultured trypanosomes, using the small subunit rDNA, indicated that this python was infected with a species closely related to Trypanosoma varani Wenyon, 1908, originally described in the Nile monitor lizard (Varanus niloticus) from Sudan. Furthermore, nucleotide sequences of glycosomal glyceraldehyde-3-phosphate dehydrogenase gene of both isolates showed few differences. Giemsa-stained blood smears, prepared from the infected python 8 mo after the initial observation of trypanosomes in hemoculture, contained trypomastigotes with a broad body and a short, free flagellum; these most closely resembled the original description of T. varani, or T. voltariae Macfie, 1919 recorded in a black-necked spitting cobra (Naja nigricollis) from Ghana. It is highly possible that lizards and snakes could naturally share an identical trypanosome species. Alternatively, lizards and snakes in the same region might have closely related, but distinct, Trypanosoma species as a result of sympatric speciation. From multiple viewpoints, including molecular phylogenetic analyses, reappraisal of trypanosome species from a wide range of reptiles in Africa is needed to clarify the relationship of recorded species, or to unmask unrecorded species.

Rapid microsatellite marker development using next generation pyrosequencing to inform invasive Burmese python -- Python molurus bivittatus -- management

USGS Publications Warehouse

Hunter, Margaret E.; Hart, Kristen M.

2013-01-01

Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae.

Diamond tool machining of materials which react with diamond

DOEpatents

Lundin, R.L.; Stewart, D.D.; Evans, C.J.

1992-04-14

An apparatus is described for the diamond machining of materials which detrimentally react with diamond cutting tools in which the cutting tool and the workpiece are chilled to very low temperatures. This chilling halts or retards the chemical reaction between the workpiece and the diamond cutting tool so that wear rates of the diamond tool on previously detrimental materials are comparable with the diamond turning of materials which do not react with diamond. 1 figs.

Self-composite comprised of nanocrystalline diamond and a non-diamond component useful for thermoelectric applications

DOEpatents

Gruen, Dieter M.

2012-09-04

One provides nanocrystalline diamond material that comprises a plurality of substantially ordered diamond crystallites that are sized no larger than about 10 nanometers. One then disposes a non-diamond component within the nanocrystalline diamond material. By one approach this non-diamond component comprises an electrical conductor that is formed at the grain boundaries that separate the diamond crystallites from one another. The resultant nanowire is then able to exhibit a desired increase with respect to its ability to conduct electricity while also preserving the thermal conductivity behavior of the nanocrystalline diamond material.

Self-composite comprised of nanocrystalline diamond and a non-diamond component useful for thermoelectric applications

DOEpatents

Gruen, Dieter M [Downers Grove, IL

2009-08-11

One provides nanocrystalline diamond material that comprises a plurality of substantially ordered diamond crystallites that are sized no larger than about 10 nanometers. One then disposes a non-diamond component within the nanocrystalline diamond material. By one approach this non-diamond component comprises an electrical conductor that is formed at the grain boundaries that separate the diamond crystallites from one another. The resultant nanowire is then able to exhibit a desired increase with respect to its ability to conduct electricity while also preserving the thermal conductivity behavior of the nanocrystalline diamond material.

PyXNAT: XNAT in Python.

PubMed

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line.

A high level interface to SCOP and ASTRAL implemented in python.

PubMed

Casbon, James A; Crooks, Gavin E; Saqi, Mansoor A S

2006-01-10

Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources. We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL. The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

PyPDB: a Python API for the Protein Data Bank.

PubMed

Gilpin, William

2016-01-01

We have created a Python programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval for a wide range of result types, including BLAST and sequence motif queries. The API relies on the existing XML-based API and operates by creating custom XML requests from native Python types, allowing extensibility and straightforward modification. The package has the ability to perform many types of advanced search of the PDB that are otherwise only available through the PDB website. PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibility. The most up-to-date version, including iPython notebooks containing usage tutorials, is available free-of-charge under an open-source MIT license via GitHub at https://github.com/williamgilpin/pypdb, and the full API reference is at http://williamgilpin.github.io/pypdb_docs/html/. The latest stable release is also available on PyPI. wgilpin@stanford.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

pypet: A Python Toolkit for Data Management of Parameter Explorations

PubMed Central

Meyer, Robert; Obermayer, Klaus

2016-01-01

pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines. PMID:27610080

p3d--Python module for structural bioinformatics.

PubMed

Fufezan, Christian; Specht, Michael

2009-08-21

High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

The big squeeze: scaling of constriction pressure in two of the world's largest snakes, Python reticulatus and Python molurus bivittatus.

PubMed

Penning, David A; Dartez, Schuyler F; Moon, Brad R

2015-11-01

Snakes are important predators that have radiated throughout many ecosystems, and constriction was important in their radiation. Constrictors immobilize and kill prey by using body loops to exert pressure on their prey. Despite its importance, little is known about constriction performance or its full effects on prey. We studied the scaling of constriction performance in two species of giant pythons (Python reticulatus and Python molurus bivittatus) and propose a new mechanism of prey death by constriction. In both species, peak constriction pressure increased significantly with snake diameter. These and other constrictors can exert pressures dramatically higher than their prey's blood pressure, suggesting that constriction can stop circulatory function and perhaps kill prey rapidly by over-pressurizing the brain and disrupting neural function. We propose the latter 'red-out effect' as another possible mechanism of prey death from constriction. These effects may be important to recognize and treat properly in rare cases when constrictors injure humans. © 2015. Published by The Company of Biologists Ltd.

Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation.

PubMed

Wall, Christopher E; Cozza, Steven; Riquelme, Cecilia A; McCombie, W Richard; Heimiller, Joseph K; Marr, Thomas G; Leinwand, Leslie A

2011-01-01

The infrequently feeding Burmese python (Python molurus) experiences significant and rapid postprandial cardiac hypertrophy followed by regression as digestion is completed. To begin to explore the molecular mechanisms of this response, we have sequenced and assembled the fasted and postfed Burmese python heart transcriptomes with Illumina technology using the chicken (Gallus gallus) genome as a reference. In addition, we have used RNA-seq analysis to identify differences in the expression of biological processes and signaling pathways between fasted, 1 day postfed (DPF), and 3 DPF hearts. Out of a combined transcriptome of ∼2,800 mRNAs, 464 genes were differentially expressed. Genes showing differential expression at 1 DPF compared with fasted were enriched for biological processes involved in metabolism and energetics, while genes showing differential expression at 3 DPF compared with fasted were enriched for processes involved in biogenesis, structural remodeling, and organization. Moreover, we present evidence for the activation of physiological and not pathological signaling pathways in this rapid, novel model of cardiac growth in pythons. Together, our data provide the first comprehensive gene expression profile for a reptile heart.

pypet: A Python Toolkit for Data Management of Parameter Explorations.

PubMed

Meyer, Robert; Obermayer, Klaus

2016-01-01

pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.

PyXNAT: XNAT in Python

PubMed Central

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S.; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line. PMID:22654752

Using Python Packages in 6D (Py)Ferret: EOF Analysis, OPeNDAP Sequence Data

NASA Astrophysics Data System (ADS)

Smith, K. M.; Manke, A.; Hankin, S. C.

2012-12-01

PyFerret was designed to provide the easy methods of access, analysis, and display of data found in the Ferret under the simple yet powerful Python scripting/programming language. This has enabled PyFerret to take advantage of a large and expanding collection of third-party scientific Python modules. Furthermore, ensemble and forecast axes have been added to Ferret and PyFerret for creating and working with collections of related data in Ferret's delayed-evaluation and minimal-data-access mode of operation. These axes simplify processing and visualization of these collections of related data. As one example, an empirical orthogonal function (EOF) analysis Python module was developed, taking advantage of the linear algebra module and other standard functionality in NumPy for efficient numerical array processing. This EOF analysis module is used in a Ferret function to provide an ensemble of levels of data explained by each EOF and Time Amplitude Function (TAF) product. Another example makes use of the PyDAP Python module to provide OPeNDAP sequence data for use in Ferret with minimal data access characteristic of Ferret.

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

modlAMP: Python for antimicrobial peptides.

PubMed

Müller, Alex T; Gabernet, Gisela; Hiss, Jan A; Schneider, Gisbert

2017-09-01

We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification and visual representation of peptide data. modlAMP offers functions for molecular descriptor calculation and the retrieval of amino acid sequences from public or local sequence databases, and provides instant access to precompiled datasets for machine learning. The package also contains methods for the analysis and representation of circular dichroism spectra. The modlAMP Python package is available under the BSD license from URL http://doi.org/10.5905/ethz-1007-72 or via pip from the Python Package Index (PyPI). gisbert.schneider@pharma.ethz.ch. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Py4CAtS - Python tools for line-by-line modelling of infrared atmospheric radiative transfer

NASA Astrophysics Data System (ADS)

Schreier, Franz; García, Sebastián Gimeno

2013-05-01

Py4CAtS — Python scripts for Computational ATmospheric Spectroscopy is a Python re-implementation of the Fortran infrared radiative transfer code GARLIC, where compute-intensive code sections utilize the Numeric/Scientific Python modules for highly optimized array-processing. The individual steps of an infrared or microwave radiative transfer computation are implemented in separate scripts to extract lines of relevant molecules in the spectral range of interest, to compute line-by-line cross sections for given pressure(s) and temperature(s), to combine cross sections to absorption coefficients and optical depths, and to integrate along the line-of-sight to transmission and radiance/intensity. The basic design of the package, numerical and computational aspects relevant for optimization, and a sketch of the typical workflow are presented.

Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

PubMed

Yesylevskyy, Semen O

2015-07-15

Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

n-Type diamond and method for producing same

DOEpatents

Anderson, Richard J.

2002-01-01

A new n-type semiconducting diamond is disclosed, which is doped with n-type dopant atoms. Such diamond is advantageously formed by chemical vapor deposition from a source gas mixture comprising a carbon source compound for the diamond, and a volatile hot wire filament for the n-type impurity species, so that the n-type impurity atoms are doped in the diamond during its formation. A corresponding chemical vapor deposition method of forming the n-type semiconducting diamond is disclosed. The n-type semiconducting diamond of the invention may be usefully employed in the formation of diamond-based transistor devices comprising pn diamond junctions, and in other microelectronic device applications.

Diamond anvil cells using boron-doped diamond electrodes covered with undoped diamond insulating layer

NASA Astrophysics Data System (ADS)

Matsumoto, Ryo; Yamashita, Aichi; Hara, Hiroshi; Irifune, Tetsuo; Adachi, Shintaro; Takeya, Hiroyuki; Takano, Yoshihiko

2018-05-01

Diamond anvil cells using boron-doped metallic diamond electrodes covered with undoped diamond insulating layers have been developed for electrical transport measurements under high pressure. These designed diamonds were grown on a bottom diamond anvil via a nanofabrication process combining microwave plasma-assisted chemical vapor deposition and electron beam lithography. The resistance measurements of a high-quality FeSe superconducting single crystal under high pressure were successfully demonstrated by just putting the sample and gasket on the bottom diamond anvil directly. The superconducting transition temperature of the FeSe single crystal was increased to up to 43 K by applying uniaxial-like pressure.

CSB: a Python framework for structural bioinformatics.

PubMed

Kalev, Ivan; Mechelke, Martin; Kopec, Klaus O; Holder, Thomas; Carstens, Simeon; Habeck, Michael

2012-11-15

Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. Stable release packages are available for download from the Python Package Index (PyPI) as well as from the project's website http://csb.codeplex.com. ivan.kalev@gmail.com or michael.habeck@tuebingen.mpg.de

Guided Tour of Pythonian Museum

NASA Technical Reports Server (NTRS)

Lee, H. Joe

2017-01-01

At http:hdfeos.orgzoo, we have a large collection of Python examples of dealing with NASA HDF (Hierarchical Data Format) products. During this hands-on Python tutorial session, we'll present a few common hacks to access and visualize local NASA HDF data. We'll also cover how to access remote data served by OPeNDAP (Open-source Project for a Network Data Access Protocol). As a glue language, we will demonstrate how you can use Python for your data workflow - from searching data to analyzing data with machine learning.

MontePython 3: Parameter inference code for cosmology

NASA Astrophysics Data System (ADS)

Brinckmann, Thejs; Lesgourgues, Julien; Audren, Benjamin; Benabed, Karim; Prunet, Simon

2018-05-01

MontePython 3 provides numerous ways to explore parameter space using Monte Carlo Markov Chain (MCMC) sampling, including Metropolis-Hastings, Nested Sampling, Cosmo Hammer, and a Fisher sampling method. This improved version of the Monte Python (ascl:1307.002) parameter inference code for cosmology offers new ingredients that improve the performance of Metropolis-Hastings sampling, speeding up convergence and offering significant time improvement in difficult runs. Additional likelihoods and plotting options are available, as are post-processing algorithms such as Importance Sampling and Adding Derived Parameter.

CVXPY: A Python-Embedded Modeling Language for Convex Optimization

PubMed Central

Diamond, Steven; Boyd, Stephen

2016-01-01

CVXPY is a domain-specific language for convex optimization embedded in Python. It allows the user to express convex optimization problems in a natural syntax that follows the math, rather than in the restrictive standard form required by solvers. CVXPY makes it easy to combine convex optimization with high-level features of Python such as parallelism and object-oriented design. CVXPY is available at http://www.cvxpy.org/ under the GPL license, along with documentation and examples. PMID:27375369

Obtaining and processing Daymet data using Python and ArcGIS

USGS Publications Warehouse

Bohms, Stefanie

2013-01-01

This set of scripts was developed to automate the process of downloading and mosaicking daily Daymet data to a user defined extent using ArcGIS and Python programming language. The three steps are downloading the needed Daymet tiles for the study area extent, converting the netcdf file to a tif raster format, and mosaicking those rasters to one file. The set of scripts is intended for all levels of experience with Python programming language and requires no scripting by the user.

High-density fluids and the growth of monocrystalline diamonds

NASA Astrophysics Data System (ADS)

Weiss, Y.; Kiflawi, I.; Davies, N.; Navon, O.

2014-09-01

The chemical nature and composition of the growth medium of monocrystalline (MC) diamonds is still a matter of debate, partially because carbonate-bearing high-density fluids (HDFs) that are common in fibrous diamonds have not been found in MC diamonds. Here we report the first finding of HDF microinclusions in a MC octahedral diamond from Finsch, South Africa and in the MC octahedral core of a coated diamond from Kankan, Guinea; both diamonds carry nitrogen in B-centers. Numerous microinclusions in diamond Finsch_2a_cap1 are restricted to two thin layers parallel to the (1 1 1) face, ∼20 and 200 μm from the diamond rim. Low-Mg carbonatitic HDFs are found along the inner layer while the outer layer trapped saline compositions. The major and trace element compositions of the inclusions and their infrared spectra are highly similar to those of microinclusions found in fibrous diamonds. A few isolated microinclusions of saline compositions are scattered around a sulfide inclusion in the center of the octahedral core of diamond ON-KAN-383. This evidence for the involvement of oxidized fluids in the formation of MC diamonds adds to previous reports on the antiquity of HDFs in fibrous diamonds, the presence of carbonate and halide phases in inclusions in MC diamonds and the similarity of trace element pattern of a MC diamond to those of low-Mg carbonatitic HDF in fibrous diamonds. In addition, we show that the interaction of HDFs with depleted garnets can produce sinusoidal REE patterns which are one of the primary features of lherzolitic and harzburgitic garnet inclusions in MC diamonds. Together, these observations suggest that HDFs are involved in the formation of many types of diamonds from the Archaean to the Phanerozoic. HDFs are trapped in large quantities during rapid, fibrous growth, but must also be present during the growth of many MC diamonds.

A new phase transformation path from nanodiamond to new-diamond via an intermediate carbon onion

NASA Astrophysics Data System (ADS)

Xiao, J.; Li, J. L.; Liu, P.; Yang, G. W.

2014-11-01

The investigation of carbon allotropes such as graphite, diamond, fullerenes, nanotubes and carbon onions and mechanisms that underlie their mutual phase transformation is a long-standing problem of great fundamental importance. New diamond (n-diamond) is a novel metastable phase of carbon with a face-centered cubic structure; it is called ``new diamond'' because many reflections in its electron diffraction pattern are similar to those of diamond. However, producing n-diamond from raw carbon materials has so far been challenging due to n-diamond's higher formation energy than that of diamond. Here, we, for the first time, demonstrate a new phase transformation path from nanodiamond to n-diamond via an intermediate carbon onion in the unique process of laser ablation in water, and establish that water plays a crucial role in the formation of n-diamond. When a laser irradiates colloidal suspensions of nanodiamonds at ambient pressure and room temperature, nanodiamonds are first transformed into carbon onions serving as an intermediate phase, and sequentially carbon onions are transformed into n-diamonds driven by the laser-induced high temperature and high pressure from the carbon onion as a nanoscaled temperature and pressure cell upon the process of laser irradiation in a liquid. This phase transformation not only provides new insight into the physical mechanism involved, but also offers one suitable opportunity for breaking controllable pathways between n-diamond and carbon allotropes such as diamond and carbon onions.The investigation of carbon allotropes such as graphite, diamond, fullerenes, nanotubes and carbon onions and mechanisms that underlie their mutual phase transformation is a long-standing problem of great fundamental importance. New diamond (n-diamond) is a novel metastable phase of carbon with a face-centered cubic structure; it is called ``new diamond'' because many reflections in its electron diffraction pattern are similar to those of diamond. However, producing n-diamond from raw carbon materials has so far been challenging due to n-diamond's higher formation energy than that of diamond. Here, we, for the first time, demonstrate a new phase transformation path from nanodiamond to n-diamond via an intermediate carbon onion in the unique process of laser ablation in water, and establish that water plays a crucial role in the formation of n-diamond. When a laser irradiates colloidal suspensions of nanodiamonds at ambient pressure and room temperature, nanodiamonds are first transformed into carbon onions serving as an intermediate phase, and sequentially carbon onions are transformed into n-diamonds driven by the laser-induced high temperature and high pressure from the carbon onion as a nanoscaled temperature and pressure cell upon the process of laser irradiation in a liquid. This phase transformation not only provides new insight into the physical mechanism involved, but also offers one suitable opportunity for breaking controllable pathways between n-diamond and carbon allotropes such as diamond and carbon onions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05246c

31 CFR 592.310 - Rough diamond.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Rough diamond. 592.310 Section 592.310... ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS General Definitions § 592.310 Rough diamond. The term rough diamond means any diamond that is unworked or simply sawn, cleaved...

31 CFR 592.310 - Rough diamond.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Rough diamond. 592.310 Section 592.310... ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS General Definitions § 592.310 Rough diamond. The term rough diamond means any diamond that is unworked or simply sawn, cleaved...

31 CFR 592.310 - Rough diamond.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Rough diamond. 592.310 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS General Definitions § 592.310 Rough diamond. The term rough diamond means any diamond that is unworked or simply sawn...

31 CFR 592.310 - Rough diamond.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Rough diamond. 592.310 Section 592.310... ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS General Definitions § 592.310 Rough diamond. The term rough diamond means any diamond that is unworked or simply sawn, cleaved...

31 CFR 592.310 - Rough diamond.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Rough diamond. 592.310 Section 592.310... ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS General Definitions § 592.310 Rough diamond. The term rough diamond means any diamond that is unworked or simply sawn, cleaved...

Diamond bio electronics.

PubMed

Linares, Robert; Doering, Patrick; Linares, Bryant

2009-01-01

The use of diamond for advanced applications has been the dream of mankind for centuries. Until recently this dream has been realized only in the use of diamond for gemstones and abrasive applications where tons of diamonds are used on an annual basis. Diamond is the material system of choice for many applications, but its use has historically been limited due to the small size, high cost, and inconsistent (and typically poor) quality of available diamond materials until recently. The recent development of high quality, single crystal diamond crystal growth via the Chemical Vapor Deposition (CVD) process has allowed physcists and increasingly scientists in the life science area to think beyond these limitations and envision how diamond may be used in advanced applications ranging from quantum computing, to power generation and molecular imaging, and eventually even diamond nano-bots. Because of diamond's unique properties as a bio-compatible material, better understanding of diamond's quantum effects and a convergence of mass production, semiconductor-like fabrication process, diamond now promises a unique and powerful key to the realization of the bio-electronic devices being envisioned for the new era of medical science. The combination of robust in-the-body diamond based sensors, coupled with smart bio-functionalized diamond devices may lead to diamond being the platform of choice for bio-electronics. This generation of diamond based bio-electronic devices would contribute substantially to ushering in a paradigm shift for medical science, leading to vastly improved patient diagnosis, decrease of drug development costs and risks, and improved effectiveness of drug delivery and gene therapy programs through better timed and more customized solutions.

Microstructure and thermal properties of copper–diamond composites with tungsten carbide coating on diamond particles

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

Kang, Qiping; He, Xinbo, E-mail: xb_he@163.com; Ren, Shubin

2015-07-15

An effective method for preparing tungsten carbide coating on diamond surfaces was proposed to improve the interface bonding between diamond and copper. The WC coating was formed on the diamond surfaces with a reaction medium of WO{sub 3} in mixed molten NaCl–KCl salts and the copper–diamond composites were obtained by vacuum pressure infiltration of WC-coated diamond particles with pure copper. The microstructure of interface bonding between diamond and copper was discussed. Thermal conductivity and thermal expansion behavior of the obtained copper–diamond composites were investigated. Results indicated that the thermal conductivity of as-fabricated composite reached 658 W m{sup −} {sup 1}more » K{sup −} {sup 1}. Significant reduction in coefficient of thermal expansion of the composite compared with that of pure copper was obtained. - Highlights: • WC coating was successfully synthesized on diamond particles in molten salts. • WC coating obviously promoted the wettability of diamond and copper matrix. • WC coating greatly enhanced the thermal conductivity of Cu–diamond composite. • The composites are suitable candidates for heat sink applications.« less

PyMC: Bayesian Stochastic Modelling in Python

PubMed Central

Patil, Anand; Huard, David; Fonnesbeck, Christopher J.

2010-01-01

This user guide describes a Python package, PyMC, that allows users to efficiently code a probabilistic model and draw samples from its posterior distribution using Markov chain Monte Carlo techniques. PMID:21603108

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator.

PubMed

Drewes, Rich; Zou, Quan; Goodman, Philip H

2009-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading "glue" tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS.

Python for large-scale electrophysiology.

PubMed

Spacek, Martin; Blanche, Tim; Swindale, Nicholas

2008-01-01

Electrophysiology is increasingly moving towards highly parallel recording techniques which generate large data sets. We record extracellularly in vivo in cat and rat visual cortex with 54-channel silicon polytrodes, under time-locked visual stimulation, from localized neuronal populations within a cortical column. To help deal with the complexity of generating and analysing these data, we used the Python programming language to develop three software projects: one for temporally precise visual stimulus generation ("dimstim"); one for electrophysiological waveform visualization and spike sorting ("spyke"); and one for spike train and stimulus analysis ("neuropy"). All three are open source and available for download (http://swindale.ecc.ubc.ca/code). The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three. Here we present our software as a showcase of the extensive capabilities of Python in neuroscience.

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator

PubMed Central

Drewes, Rich; Zou, Quan; Goodman, Philip H.

2008-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading “glue” tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS. PMID:19506707

The mechanical properties of the systemic and pulmonary arteries of Python regius correlate with blood pressures.

PubMed

van Soldt, Benjamin J; Danielsen, Carl Christian; Wang, Tobias

2015-12-01

Pythons are unique amongst snakes in having different pressures in the aortas and pulmonary arteries because of intraventricular pressure separation. In this study, we investigate whether this correlates with different blood vessel strength in the ball python Python regius. We excised segments from the left, right, and dorsal aortas, and from the two pulmonary arteries. These were subjected to tensile testing. We show that the aortic vessel wall is significantly stronger than the pulmonary artery wall in P. regius. Gross morphological characteristics (vessel wall thickness and correlated absolute amount of collagen content) are likely the most influential factors. Collagen fiber thickness and orientation are likely to have an effect, though the effect of collagen fiber type and cross-links between fibers will need further study. © 2015 Wiley Periodicals, Inc.

pysimm: A Python Package for Simulation of Molecular Systems

NASA Astrophysics Data System (ADS)

Fortunato, Michael; Colina, Coray

pysimm, short for python simulation interface for molecular modeling, is a python package designed to facilitate the structure generation and simulation of molecular systems through convenient and programmatic access to object-oriented representations of molecular system data. This poster presents core features of pysimm and design philosophies that highlight a generalized methodology for incorporation of third-party software packages through API interfaces. The integration with the LAMMPS simulation package is explained to demonstrate this methodology. pysimm began as a back-end python library that powered a cloud-based application on nanohub.org for amorphous polymer simulation. The extension from a specific application library to general purpose simulation interface is explained. Additionally, this poster highlights the rapid development of new applications to construct polymer chains capable of controlling chain morphology such as molecular weight distribution and monomer composition.

Algorithmic synthesis using Python compiler

NASA Astrophysics Data System (ADS)

Cieszewski, Radoslaw; Romaniuk, Ryszard; Pozniak, Krzysztof; Linczuk, Maciej

2015-09-01

This paper presents a python to VHDL compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and translate it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the programmed circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. This can be achieved by using many computational resources at the same time. Creating parallel programs implemented in FPGAs in pure HDL is difficult and time consuming. Using higher level of abstraction and High-Level Synthesis compiler implementation time can be reduced. The compiler has been implemented using the Python language. This article describes design, implementation and results of created tools.

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

Tomopy is a Python toolbox to perform x-ray data processing, image reconstruction and data exchange tasks at synchrotron facilities. The dependencies of the software are currently as follows: -Python related python standard library (http://docs.python.org/2/library/) numpy (http://www.numpy.org/) scipy (http://scipy.org/) matplotlib (http://matplotlip.org/) sphinx (http://sphinx-doc.org) pil (http://www.pythonware.com/products/pil/) pyhdf (http://pysclint.sourceforge.net/pyhdf/) h5py (http://www.h5py.org) pywt (http://www.pybytes.com/pywavelets/) file.py (https://pyspec.svn.sourceforge.net/svnroot/pyspec/trunk/pyspec/ccd/files.py) -C/C++ related: gridec (anonymous?? C-code written back in 1997 that uses standard C library) fftw (http://www.fftw.org/) tomoRecon (multi-threaded C++ verion of gridrec. Author: Mark Rivers from APS. http://cars9.uchicago.edu/software/epics/tomoRecon.html) epics (http://www.aps.anl.gov/epics/)

Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1, Introducing a Python Edition

NASA Astrophysics Data System (ADS)

Barron, Eric G.; Kaplan, G. H.; Bangert, J.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

2011-01-01

The Naval Observatory Vector Astrometry Software (NOVAS) is a source-code library that provides common astrometric quantities and transformations. NOVAS calculations are accurate at the sub-milliarcsecond level. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and, currently, mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to harness the object-oriented nature of the Python language, and will implement the ability to handle large quantities of objects or observers using the array functionality in NumPy (a third-party scientific package for Python). NOVAS 3.1 also adds a module to transform GCRS vectors to the ITRS; the ITRS to GCRS transformation was already provided in NOVAS 3.0. The module that corrects an ITRS vector for polar motion has been modified to undo that correction upon demand. In the C edition, the ephemeris-access functions have been revised for use on 64-bit systems and for improved performance in general. NOVAS, including documentation, is available from the USNO website (http://www.usno.navy.mil/USNO/astronomical-applications/software-products/novas).

Dr.LiTHO: a development and research lithography simulator

NASA Astrophysics Data System (ADS)

Fühner, Tim; Schnattinger, Thomas; Ardelean, Gheorghe; Erdmann, Andreas

2007-03-01

This paper introduces Dr.LiTHO, a research and development oriented lithography simulation environment developed at Fraunhofer IISB to flexibly integrate our simulation models into one coherent platform. We propose a light-weight approach to a lithography simulation environment: The use of a scripting (batch) language as an integration platform. Out of the great variety of different scripting languages, Python proved superior in many ways: It exhibits a good-natured learning-curve, it is efficient, available on virtually any platform, and provides sophisticated integration mechanisms for existing programs. In this paper, we will describe the steps, required to provide Python bindings for existing programs and to finally generate an integrated simulation environment. In addition, we will give a short introduction into selected software design demands associated with the development of such a framework. We will especially focus on testing and (both technical and user-oriented) documentation issues. Dr.LiTHO Python files contain not only all simulation parameter settings but also the simulation flow, providing maximum flexibility. In addition to relatively simple batch jobs, repetitive tasks can be pooled in libraries. And as Python is a full-blown programming language, users can add virtually any functionality, which is especially useful in the scope of simulation studies or optimization tasks, that often require masses of evaluations. Furthermore, we will give a short overview of the numerous existing Python packages. Several examples demonstrate the feasibility and productiveness of integrating Python packages into custom Dr.LiTHO scripts.

PESO - The Python Based Control System of the Ondrejov 2m Telescope

NASA Astrophysics Data System (ADS)

Skoda, P.; Fuchs, J.; Honsa, J.

2005-12-01

Python has been gaining a good reputation and respectability in many areas of software development. We have chosen Python after getting the new CCD detector for the coudé spectrograph of Ondřejov observatory 2m telescope. The VersArray detector from Roper Scientific came only with the closed source library PVCAM of low-level camera control functions for Linux, so we had to write the whole astronomical data acquisition system from scratch and integrate it with the current spectrograph and telescope control systems. The final result of our effort, PESO (Python Exposure System for Ondřejov) is a highly comfortable GUI-based environment allowing the observer to change the spectrograph configuration, choose the detector acquisition mode, select the exposure parameters, and monitor the exposure progress. All of the relevant information from the control computers is written into the FITS headers by the PyFITS module, and the acquired CCD frame is immediately displayed in an SAO DS9 window using XPA calls. The GTK-based front end design was drawn in the Glade visual development tool, giving the shape and position of all widgets in single XML file, which is used in Python by a simple call of the PyGlade module. We describe our experience with the design and implementation of PESO, stressing the easiness of quick changes of the GUI, together with the capability of separate testing of every module using the Python debugger, IPython.

Iron Oxide Nanoparticles Employed as Seeds for the Induction of Microcrystalline Diamond Synthesis

PubMed Central

2008-01-01

Iron nanoparticles were employed to induce the synthesis of diamond on molybdenum, silicon, and quartz substrates. Diamond films were grown using conventional conditions for diamond synthesis by hot filament chemical vapor deposition, except that dispersed iron oxide nanoparticles replaced the seeding. X-ray diffraction, visible, and ultraviolet Raman Spectroscopy, energy-filtered transmission electron microscopy , electron energy-loss spectroscopy, and X-ray photoelectron spectroscopy (XPS) were employed to study the carbon bonding nature of the films and to analyze the carbon clustering around the seed nanoparticles leading to diamond synthesis. The results indicate that iron oxide nanoparticles lose the O atoms, becoming thus active C traps that induce the formation of a dense region of trigonally and tetrahedrally bonded carbon around them with the ensuing precipitation of diamond-type bonds that develop into microcrystalline diamond films under chemical vapor deposition conditions. This approach to diamond induction can be combined with dip pen nanolithography for the selective deposition of diamond and diamond patterning while avoiding surface damage associated to diamond-seeding methods.

Episodic diamond growth beneath the Kaapvaal Craton at Jwaneng Mine, Botswana

NASA Astrophysics Data System (ADS)

Gress, Michael U.; Howell, Daniel; Chinn, Ingrid L.; Speich, Laura; Kohn, Simon C.; van den Heuvel, Quint; Schulten, Ellen; Pals, Anna S. M.; Davies, Gareth R.

2018-05-01

Important implications for the interior workings of the Earth can be drawn by studying diamonds and their inclusions. To better understand the timing and number of diamond forming events beneath the NW margin of the Kaapvaal Craton, a comprehensive reassessment of Jwaneng's diamond populations has been undertaken. We report new inclusion abundance data from the visual examination of 130,000 diamonds that validate the predominance of an eclogitic diamond suite (up to 88%) with on average 5% inclusion-bearing diamonds (with inclusions >10 μm in size). From this population, polished plates from 79 diamonds of eclogitic and peridotitic paragenesis have been studied with cathodoluminescence (CL) imaging and infrared spectroscopy (FTIR) traverses. The majority (80%) record major changes in N concentration and aggregation states, as well as sharp boundaries in the CL images of individual plates that are interpreted to demarcate discrete diamond growth events. In addition, bulk FTIR data have been acquired for 373 unpolished diamonds. Silicate inclusions sampled from distinct growth zones define 2 compositional groups of omphacites and pyrope-almandines associated with different N contents in their diamond hosts. These findings reinforce previous observations that at Jwaneng at least seven individual diamond forming events can be identified - 3 peridotitic and 4 eclogitic. The results demonstrate that detailed examination of diamond plates by CL imaging and FTIR traverses is necessary to unveil the complex history recorded in diamonds.

Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius.

PubMed

Stenglein, Mark D; Jacobson, Elliott R; Wozniak, Edward J; Wellehan, James F X; Kincaid, Anne; Gordon, Marcus; Porter, Brian F; Baumgartner, Wes; Stahl, Scott; Kelley, Karen; Towner, Jonathan S; DeRisi, Joseph L

2014-09-09

A severe, sometimes fatal respiratory disease has been observed in captive ball pythons (Python regius) since the late 1990s. In order to better understand this disease and its etiology, we collected case and control samples and performed pathological and diagnostic analyses. Electron micrographs revealed filamentous virus-like particles in lung epithelial cells of sick animals. Diagnostic testing for known pathogens did not identify an etiologic agent, so unbiased metagenomic sequencing was performed. Abundant nidovirus-like sequences were identified in cases and were used to assemble the genome of a previously unknown virus in the order Nidovirales. The nidoviruses, which were not previously known to infect nonavian reptiles, are a diverse order that includes important human and veterinary pathogens. The presence of the viral RNA was confirmed in all diseased animals (n = 8) but was not detected in healthy pythons or other snakes (n = 57). Viral RNA levels were generally highest in the lung and other respiratory tract tissues. The 33.5-kb viral genome is the largest RNA genome yet described and shares canonical characteristics with other nidovirus genomes, although several features distinguish this from related viruses. This virus, which we named ball python nidovirus (BPNV), will likely establish a new genus in Torovirinae subfamily. The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease. Ball pythons are popular pets because of their diverse coloration, generally nonaggressive behavior, and relatively small size. Since the 1990s, veterinarians have been aware of an infectious respiratory disease of unknown cause in ball pythons that can be fatal. We used unbiased shotgun sequencing to discover a novel virus in the order Nidovirales that was present in cases but not controls. While nidoviruses are known to infect a variety of animals, this is the first report of a nidovirus recovered from any reptile. This report will enable diagnostics that will assist in determining the role of this virus in the causation of disease, which would allow control of the disease in zoos and private collections. Given its evolutionary divergence from known nidoviruses and its unique host, the study of reptile nidoviruses may further our understanding of related diseases and the viruses that cause them in humans and other animals. Copyright © 2014 Stenglein et al.

Trace-element patterns of fibrous and monocrystalline diamonds: Insights into mantle fluids

NASA Astrophysics Data System (ADS)

Rege, S.; Griffin, W. L.; Pearson, N. J.; Araujo, D.; Zedgenizov, D.; O'Reilly, S. Y.

2010-08-01

During their growth diamonds may trap micron-scale inclusions of the fluids from which they grew, and these "time capsules" provide insights into the metasomatic processes that have modified the subcontinental lithospheric mantle. LAM-ICPMS analysis of trace elements in > 500 fibrous and monocrystalline diamonds worldwide has been used to understand the nature of these fluids. Analyses of fibrous diamonds define two general types of pattern, a "fibrous-high" (FH) one with high contents of LREE, Ba and K, and a "fibrous-low" (FL) pattern characterized by depletion in LREE/MREE, Ba and K, negative anomalies in Sr and Y, and subchondritic Zr/Hf and Nb/Ta. Both types may be found in fibrous diamonds from single deposits, and in three Yakutian pipes some diamonds show abrupt transitions from inclusion-rich cores with FH patterns to clearer rims with FL patterns. Most monocrystalline diamonds show FL-type patterns, but some have patterns that resemble those of FH fibrous diamonds. Peridotitic and eclogitic monocrystalline diamonds may show either patterns with relatively flat REE, or patterns with more strongly depleted LREE. Kimberlites that contain peridotitic diamonds with "high" patterns also contain eclogitic diamonds with "high" patterns. Strong similarities in the patterns of these two groups of diamonds may suggest high fluid/rock ratios. Many diamonds of the "superdeep" paragenesis have trace-element patterns similar to those of other monocrystalline diamonds. This may be evidence that the trace-element compositions of deep-seated fluids are generally similar to those that form diamonds in the subcontinental lithospheric mantle. The element fractionations observed between the FH and FL patterns are consistent with the immiscible separation of a silicic fluid from a carbonatite-silicate fluid, leaving a residual carbonatitic fluid strongly enriched in LREE, Ba and alkalies. This model would suggest that most monocrystalline diamonds crystallized from the more silicic fraction. Comparison with studies of single fluid inclusions in fibrous diamonds suggests that the FH patterns reflect trapped inclusions of high-Mg and low-Mg carbonatitic high-density fluids. In terms of the rock-forming elements, the fluids that precipitated the rims of some fibrous diamonds (FL pattern) and most monocrystalline diamonds are broadly similar to some hydro-silicic high-density fluids found in fibrous diamonds. However, there are still significant differences between the trace-element patterns of most monocrystalline diamonds and known high-density fluids, and further research is required to understand the formation and growth of these diamonds.

Fluid inclusions in Ebelyakh diamonds: Evidence of CO2 liberation in eclogite and the effect of H2O on diamond habit

NASA Astrophysics Data System (ADS)

Smith, Evan M.; Kopylova, Maya G.; Frezzotti, Maria Luce; Afanasiev, Valentin P.

2015-02-01

Fluid inclusions were studied in six octahedrally-grown, eclogitic diamonds from the Ebelyakh River mine, northern Russia, using microthermometry and Raman spectroscopy. The fluids are CO2-N2 mixtures with 40 ± 4 mol% N2, which are trapped along fractures that healed in the diamond stability field. The CO2-rich composition of the fluids provides the first empirical evidence that CO2 can be liberated as a free phase in eclogite in the diamond stability field of the lithospheric mantle, as has been previously predicted from theory. This finding means that the interpretation of carbon isotopes in eclogitic diamonds should not overlook isotopic fractionation due to CO2 liberation from carbonatitic diamond-forming media as it percolates through eclogites. Preferential nucleation of CO2 bubbles in eclogite compared to peridotite may lead to a rock type-specific fracturing mechanism and sampling bias that would help explain the overabundance of eclogite xenoliths in kimberlites. Fluid inclusions in octahedrally-grown, non-fibrous diamonds from both the studied Ebelyakh diamonds and those from other cratons do not show detectable amounts of water. In comparison, fibrous diamond fluid inclusions typically contain 10-25 wt.% water. The absence of "dry" fluids in fibrous diamonds and the presence of these in octahedrally-grown diamonds may indicate different compositions of fluids equilibrated with these two types of diamonds. If there is variability in the water content in diamond-forming fluids, it should affect diamond growth morphology. Water could be responsible for causing fibrous diamond growth, by inhibiting the advancement of growth steps within octahedral faces.

Nature of diamonds in Yakutian eclogites: views from eclogite tomography and mineral inclusions in diamonds

NASA Astrophysics Data System (ADS)

Anand, Mahesh; Taylor, Lawrence A.; Misra, Kula C.; Carlson, William D.; Sobolev, Nikolai V.

2004-09-01

We have performed dissections of two diamondiferous eclogites (UX-1 and U33/1) from the Udachnaya kimberlite, Yakutia in order to understand the nature of diamond formation and the relationship between the diamonds, their mineral inclusions, and host eclogite minerals. Diamonds were carefully recovered from each xenolith, based upon high-resolution X-ray tomography images and three-dimensional models. The nature and physical properties of minerals, in direct contact with diamonds, were investigated at the time of diamond extraction. Polished sections of the eclogites were made, containing the mould areas of the diamonds, to further investigate the chemical compositions of the host minerals and the phases that were in contact with diamonds. Major- and minor-element compositions of silicate and sulfide mineral inclusions in diamonds show variations among each other, and from those in the host eclogites. Oxygen isotope compositions of one garnet and five clinopyroxene inclusions in diamonds from another Udachnaya eclogite (U51) span the entire range recorded for eclogite xenoliths from Udachnaya. In addition, the reported compositions of almost all clinopyroxene inclusions in U51 diamonds exhibit positive Eu anomaly. This feature, together with the oxygen isotopic characteristics, is consistent with the well-established hypothesis of subduction origin for Udachnaya eclogite xenoliths. It is intuitive to expect that all eclogite xenoliths in a particular kimberlite should have common heritage, at least with respect to their included diamonds. However, the variation in the composition of multiple inclusions within diamonds, and among diamonds, from the same eclogite indicates the involvement of complex processes in diamond genesis, at least in the eclogite xenoliths from Yakutia that we have studied.

PyNEST: A Convenient Interface to the NEST Simulator.

PubMed

Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

2008-01-01

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10(4) neurons and 10(7) to 10(9) synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used.

PyNEST: A Convenient Interface to the NEST Simulator

PubMed Central

Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

2008-01-01

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 104 neurons and 107 to 109 synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used. PMID:19198667

GPAW - massively parallel electronic structure calculations with Python-based software.

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

Enkovaara, J.; Romero, N.; Shende, S.

2011-01-01

Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used thismore » approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.« less

Diagnostic Techniques Used to Study Chemical-Vapor-Deposited Diamond Films

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

2000-01-01

The advantages and utility of chemical-vapor-deposited (CVD) diamond as an industrial ceramic can only be realized if the price and quality are right. Until recently, this technology was of interest only to the academic and basic research community. However, interest has grown because of advances made by leading CVD diamond suppliers: 1) Reduction of the cost of CVD polycrystalline diamond deposition below $5/carat ($8/sq cm); 2) Installation of production capacity; 3) Epitaxial growth of CVD single-crystal diamond. Thus, CVD diamond applications and business are an industrial reality. At present, CVD diamond is produced in the form of coatings or wafers. CVD diamond film technology offers a broader technological potential than do natural and high-pressure synthetic diamonds because size, geometry, and eventually cost will not be as limiting. Now that they are cost effective, diamond coatings - with their extreme properties - can be used in a variety of applications. Diamond coatings can improve many of the surface properties of engineering substrate materials, including erosion, corrosion, and wear resistance. Examples of actual and potential applications, from microelectromechanical systems to the wear parts of diamond coatings and related superhard coatings are described. For example, diamond coatings can be used as a chemical and mechanical barrier for the space shuttles check valves, particularly on the guide pins and seat assemblies.

Voltammetric and impedance behaviours of surface-treated nano-crystalline diamond film electrodes

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

Liu, F. B.; Jing, B.; Cui, Y.

2015-04-15

The electrochemical performances of hydrogen- and oxygen-terminated nano-crystalline diamond film electrodes were investigated by cyclic voltammetry and AC impedance spectroscopy. In addition, the surface morphologies, phase structures, and chemical states of the two diamond films were analysed by scanning probe microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy, respectively. The results indicated that the potential window is narrower for the hydrogen-terminated nano-crystalline diamond film than for the oxygen-terminated one. The diamond film resistance and capacitance of oxygen-terminated diamond film are much larger than those of the hydrogen-terminated diamond film, and the polarization resistances and double-layer capacitance corresponding to oxygen-terminated diamond filmmore » are both one order of magnitude larger than those corresponding to the hydrogen-terminated diamond film. The electrochemical behaviours of the two diamond film electrodes are discussed.« less

Toward deep blue nano hope diamonds: heavily boron-doped diamond nanoparticles.

PubMed

Heyer, Steffen; Janssen, Wiebke; Turner, Stuart; Lu, Ying-Gang; Yeap, Weng Siang; Verbeeck, Jo; Haenen, Ken; Krueger, Anke

2014-06-24

The production of boron-doped diamond nanoparticles enables the application of this material for a broad range of fields, such as electrochemistry, thermal management, and fundamental superconductivity research. Here we present the production of highly boron-doped diamond nanoparticles using boron-doped CVD diamond films as a starting material. In a multistep milling process followed by purification and surface oxidation we obtained diamond nanoparticles of 10-60 nm with a boron content of approximately 2.3 × 10(21) cm(-3). Aberration-corrected HRTEM reveals the presence of defects within individual diamond grains, as well as a very thin nondiamond carbon layer at the particle surface. The boron K-edge electron energy-loss near-edge fine structure demonstrates that the B atoms are tetrahedrally embedded into the diamond lattice. The boron-doped diamond nanoparticles have been used to nucleate growth of a boron-doped diamond film by CVD that does not contain an insulating seeding layer.

Python/Lua Benchmarks

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

Busby, L.

This is an adaptation of the pre-existing Scimark benchmark code to a variety of Python and Lua implementations. It also measures performance of the Fparser expression parser and C and C++ code on a variety of simple scientific expressions.

Python-based geometry preparation and simulation visualization toolkits for STEPS

PubMed Central

Chen, Weiliang; De Schutter, Erik

2014-01-01

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations. PMID:24782754

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

Damiani, D.; Dubrovin, M.; Gaponenko, I.

Psana(Photon Science Analysis) is a software package that is used to analyze data produced by the Linac Coherent Light Source X-ray free-electron laser at the SLAC National Accelerator Laboratory. The project began in 2011, is written primarily in C++ with some Python, and provides user interfaces in both C++ and Python. Most users use the Python interface. The same code can be run in real time while data are being taken as well as offline, executing on many nodes/cores using MPI for parallelization. It is publicly available and installable on the RHEL5/6/7 operating systems.

Chemical-Vapor-Deposited Diamond Film

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1999-01-01

This chapter describes the nature of clean and contaminated diamond surfaces, Chemical-vapor-deposited (CVD) diamond film deposition technology, analytical techniques and the results of research on CVD diamond films, and the general properties of CVD diamond films. Further, it describes the friction and wear properties of CVD diamond films in the atmosphere, in a controlled nitrogen environment, and in an ultra-high-vacuum environment.

Electron energy loss spectrometry of interstellar diamonds

NASA Technical Reports Server (NTRS)

Bernatowicz, Thomas J.; Gibbons, Patrick C.; Lewis, Roy S.

1990-01-01

The results are reported of electron energy loss spectra (EELS) measurements on diamond residues from carbonaceous meteorites designed to elucidate the structure and composition of interstellar diamonds. Dynamic effective medium theory is used to model the dielectric properties of the diamonds and in particular to synthesize the observed spectra as mixtures of diamond and various pi-bonded carbons. The results are shown to be quantitatively consistent with the idea that diamonds and their surfaces are the only contributors to the electron energy loss spectra of the diamond residues and that these peculiar spectra are the result of the exceptionally small grain size and large specific surface area of the interstellar diamonds.

Diamond/diamond-like carbon coated nanotube structures for efficient electron field emission

NASA Technical Reports Server (NTRS)

Dimitrijevic, Steven (Inventor); Withers, James C. (Inventor); Loutfy, Raouf O. (Inventor)

2005-01-01

The present invention is directed to a nanotube coated with diamond or diamond-like carbon, a field emitter cathode comprising same, and a field emitter comprising the cathode. It is also directed to a method of preventing the evaporation of carbon from a field emitter comprising a cathode comprised of nanotubes by coating the nanotube with diamond or diamond-like carbon. In another aspect, the present invention is directed to a method of preventing the evaporation of carbon from an electron field emitter comprising a cathode comprised of nanotubes, which method comprises coating the nanotubes with diamond or diamond-like carbon.

Fabrication of microchannels in polycrystalline diamond using pre-fabricated Si substrates

NASA Astrophysics Data System (ADS)

Chandran, Maneesh; Elfimchev, Sergey; Michaelson, Shaul; Akhvlediani, Rozalia; Ternyak, Orna; Hoffman, Alon

2017-10-01

In this paper, we report on a simple, feasible method to fabricate microchannels in diamond. Polycrystalline diamond microchannels were produced by fabricating trenches in a Si wafer and subsequently depositing a thin layer of diamond onto this substrate using the hot filament vapor deposition technique. Fabrication of trenches in the Si substrate at different depths was carried out by standard photolithography, and the subsequent deposition of the diamond layer was performed by the hot filament chemical vapor deposition technique. The growth mechanism of diamond that leads to the formation of closed diamond microchannels is discussed in detail based on the Knudsen number and growth chemistry of diamond. Variations in the crystallite size, crystalline quality, and thickness of the diamond layer along the trench depths were systematically analyzed using cross-sectional scanning electron microscopy and Raman spectroscopy. Defect density and formation of non-diamond forms of carbon in the diamond layer were found to increase with the trench depth, which sets a limit of 5-45 μm trench depth (or an aspect ratio of 1-9) for the fabrication of diamond microchannels using this method under the present conditions.

Diamond For Optical Material

NASA Astrophysics Data System (ADS)

Clay, Robert D.; Clay, John P.

1984-12-01

Clay Engineering Inc. currently has a proposal before DARPA to manufacture large optical quality diamond for use as optical material. The manufactured diamond will be approximately 100 mm in diameter by 100 mm long. The cost of producing the diamond is expected to be three dollars per carat. It is expected that total impurities of a few parts per billion can readily be obtained. A study of diamond is a study of the effects of impurities. The elements boron and nitrogen can replace carbon atoms in the lattice structure, making diamond a "P" or "N" type semiconductor. Diamonds which are not semiconductors are classified as type IIa. The presence of B or N in the lattice causes diamond to photoconduct in ultraviolet light. All type I and III) and most type IIa diamonds photoconduct. The manufactured diamond will not photoconduct and will have an electrical resistivity greater than 1018 ohm*m. All non-lattice impurities are in the form of inclusions which dramatically affect the mechanical properties of diamond. High purity diamond has a coefficient of absorption of order 10-3 cm-1 at wavelengths of 8 to 12 micro metres, which makes it useful for infrared applications. It also has a low coefficient of absorption at wavelengths greater than 12 micro metres. For missile and aircraft applications, diamond is relatively immune to erosion or pitting damage by sand and rain. Diamond will readily withstand the stagnation temperature of Mach 3 flight and will go to Mach 4.8 with an anti-reflective coating to protect it from oxygen attack. Diamond is highly resistant to thermal shock, which makes it valuable for high energy laser applications. Using R = St (1-)) k/Ea as a measure of thermal shock resistance, diamond is 107 w/m vs "sapphire" and Zerodur at 104 and fused quartz at 1.45x103. Diamond does not perform well in the 2.5-7.5 micro metres and less than 0.4 micro metres wavelengths. Intense beams of less than 0.4 micro metres energy can create color centers in diamond. For laser pulses of such short duration that thermal shock is not a problem, diamond will take less peak power than some competing materials, such as quartz. One could take advantage of the superior strength of diamond and use a thinner slice to obtain equal peak power capacity.

Bases of the Mantle-Carbonatite Conception of Diamond Genesis

NASA Astrophysics Data System (ADS)

Litvin, Yuriy; Spivak, Anna; Kuzyura, Anastasia

2016-04-01

In the mantle-carbonatite conception of diamond genesis, the results of physic-chemical experiments are coordinated with the data of analytic mineralogy of primary inclusions in natural diamonds. Generalization of the solutions of principal genetic problems constitutes the bases of the conception. The solutions are following: (1) it is grounded that diamond-parental melts of the upper mantle have peridotite/eclogite - carbonatite - carbon compositions, of the transition zone - (wadsleite↔ringwoodite) - majorite - stishovite - carbonatite - carbon compositions, and of the lower mantle - periclase/wustite - bridgmanite - Ca-perovskite -stishovite - carbonatite - carbon compositions; (2) a construction of generalized diagrams for the diamond-parental media, which reveal changeable compositions of the growth melts of diamonds and associated phases, their genetic relations to the mantle substance, and classification connections of the primary inclusions in natural diamonds; (3) experimental equilibrium phase diagrams of syngenesis of diamonds and primary inclusions, which characterize the nucleation and growth conditions of diamonds and a capture of paragenetic and xenogenetic minerals by the growing diamonds; (4) a determination of the phase diagrams of diamonds and inclusions syngenesis under the regime of fractional crystallization, which discover the regularities of ultrabasic-basic evolution and paragenesis transitions in the diamond-forming systems of the upper and lower mantle. The evidence of the physic-chemically united mode of diamond genesis at the mantle depths with different mineralogy is obtained. References. Litvin Yu.A. (2007). High-pressure mineralogy of diamond genesis. In: Advances in High-Pressure Mineralogy (edited by Eiji Ohtani), Geological Society of America Special paper 421, 83-103. Litvin Yu.A. (2012). Experimental study of physic-chemical conditions of natural diamond formation on an example of the eclogite-carbonatite-sulphide-diamond system. Geology of Ore Deposits. 54(6), 523-539. Litvin Yu.A., Spivak A.V., Solopova N.A., Dubrovinsky L.S. (2014). On origin of lower-mantle diamonds and their primary inclusions. Physics of the Earth and Planetary Interiors, 228 (The Liebermann Volume), 176-185. http://dx.doi.org/10.1016/j/pepi/2013.12.007

Alluvial Diamond Resource Potential and Production Capacity Assessment of Ghana

USGS Publications Warehouse

Chirico, Peter G.; Malpeli, Katherine C.; Anum, Solomon; Phillips, Emily C.

2010-01-01

In May of 2000, a meeting was convened in Kimberley, South Africa, and attended by representatives of the diamond industry and leaders of African governments to develop a certification process intended to assure that rough, exported diamonds were free of conflictual concerns. This meeting was supported later in 2000 by the United Nations in a resolution adopted by the General Assembly. By 2002, the Kimberley Process Certification Scheme (KPCS) was ratified and signed by both diamond-producing and diamond-importing countries. Over 70 countries were included as members at the end of 2007. To prevent trade in 'conflict' diamonds while protecting legitimate trade, the KPCS requires that each country set up an internal system of controls to prevent conflict diamonds from entering any imported or exported shipments of rough diamonds. Every diamond or diamond shipment must be accompanied by a Kimberley Process (KP) certificate and be contained in tamper-proof packaging. The objective of this study was to assess the alluvial diamond resource endowment and current production capacity of the alluvial diamond-mining sector in Ghana. A modified volume and grade methodology was used to estimate the remaining diamond reserves within the Birim and Bonsa diamond fields. The production capacity of the sector was estimated using a formulaic expression of the number of workers reported in the sector, their productivity, and the average grade of deposits mined. This study estimates that there are approximately 91,600,000 carats of alluvial diamonds remaining in both the Birim and Bonsa diamond fields: 89,000,000 carats in the Birim and 2,600,000 carats in the Bonsa. Production capacity is calculated to be 765,000 carats per year, based on the formula used and available data on the number of workers and worker productivity. Annual production is highly dependent on the international diamond market and prices, the numbers of seasonal workers actively mining in the sector, and environmental conditions, which influence seasonal farming.

Absolute age Determinations on Diamond by Radioisotopic Methods: NOT the way to Accurately Identify Diamond Provenance

NASA Astrophysics Data System (ADS)

Shirey, S. B.

2002-05-01

Gem-quality diamond contains such low abundances of parent-daughter radionuclides that dating the diamond lattice directly by isotopic measurements has been and will be impossible. Absolute ages on diamonds typically are obtained through measurements of their syngenetic mineral inclusions: Rb-Sr in garnet; Sm-Nd in garnet and pyroxene; Re-Os and U-Th-Pb in sulfide; K-Ar in pyroxene; and U-Pb in zircon. The application of the first two isotope schemes in the list requires putting together many inclusions from many diamonds whereas the latter isotope schemes permit ages on single diamonds. The key limitations on the application of these decay pairs are the availability and size of the inclusions, the abundance levels of the radionuclides, and instrumental sensitivity. Practical complications of radioisotope dating of inclusions are fatal to the application of the technique for diamond provenance. In all mines, the ratio of gem-quality diamonds to stones with datable inclusions is very high. Thus there is no way to date the valuable, marketable stones that are part of the conflict diamond problem, just their rare, flawed cousins. Each analysis destroys the diamond host plus the inclusion and can only be carried out in research labs by highly trained scientists. Thus, these methods can not be automated or applied to the bulk of diamond production. The geological problems with age dating are equally fatal to its application to diamond provenance. From the geological perspective, for age determination to work as a tool for diamond provenance studies, diamond ages would have to be specific to particular kimberlites or kimberlite fields and different between fields. The southern African Kaapvaal-Zimbabwe Craton and Limpopo Mobile Belt is the only cratonic region where age determinations have been applied on a large enough scale to a number of kimberlites to illustrate the geological problems in age measurements for diamond provenance. However, this southern African example is seen as typical of other cratons. Here, the nearly universal occurrence of Archean or Proterozoic diamonds in much younger (often Cretaceous) kimberlites proves that diamonds are xenocrysts inherited from the ancient mantle lithospheric keel by the host kimberlite as it erupts. Differences in diamond ages are on the scale of the geological assembly of the mantle lithospheric keel and relate to geological terranes in the lithosphere; they have little to do with individual kimberlites. In southern Africa, two age groupings of diamonds exist: Archean (3.2 to 2.9 Ga) diamonds associated with initial creation/final stabilization of the mantle lithosphere and Proterozoic (1 to 2 Ga) diamonds associated with compositional changes to the mantle keel from magmatism and metasomatism. The distribution of these two age types is cratonwide, encompasses many kimberlites and both age groupings can occur in an individual kimberlite. One expects a recurrence of similar ages with a possible 2 Ga age spread from many different kimberlites across the craton. Similar old ages are seen on other cratons (e.g. Siberian, Slave); thus age can not even distinguish diamond source at the scale of a craton. A further complication is that both sampling of diamonds from their lithospheric host and the resting position of diamonds at the final solidification level of the kimberlite in the crust are accidental. This can produce significant variability in the diamond population which is further complicated if erosion and deposition of the diamonds to form alluvial deposits has obscured their host kimberlite.

Diamonds in an Archean greenstone belt: Diamond suites in unconventional rocks of Wawa, Northern Ontario (Canada)

NASA Astrophysics Data System (ADS)

Kopylova, Maya; Bruce, Loryn; Ryder, John

2010-05-01

Diamonds typically are found on Archean cratons entrained by younger Phanerozoic kimberlites. In contrast, Wawa diamonds are hosted in "unconventional", non-kimberlitic rocks that formed contemporaneously with the mafic and sedimentary rocks of the Archean Michipicoten Greenstone Belt (MGB). We studied two diamond suites that occur within the 2.9-2.7 Ga greenschist facies rocks of MGB located in the southwest portion of the Superior Craton (E. Canada). The first diamond suite henceforth referred to as the Wawa breccia diamonds (384 stones), are hosted in the 2618-2744 Ma calc-alkaline lamprophyres and volcaniclastic breccias, contemporaneous with pillow basalts and felsic volcanics of MGB. The second suite, the Wawa conglomerate diamonds (80 crystals), are hosted in the 2697-2700 Ma poorly sorted sedimentary polymictic conglomerate which is interpreted as a proximal alluvial fan debris flow in a fan-delta environment. The majority of the diamonds was found within the matrix of the conglomerate. The diamondiferous breccia occurs 20 km north of the town of Wawa, whereas the conglomerate is found 12 km northeast of Wawa. Diamonds from the 2 occurrences were characterized and described for provenance studies. Both the breccia and conglomerate diamonds show similar crystal habits, with the predominance of octahedral single crystals and ~ 10% of cubes. The conglomerate diamonds are significantly less resorbed (no resorbtion in 43% of the stones) than the breccia diamonds (8% non-resorbed stones). In both suites, only 21-24% show high degrees of resorption. The majority of crystals in both suites are colourless, with some yellow, brown and grey stones. Conglomerate diamonds had a wider variety of colours that were not seen in the breccia diamonds, including green and pink. The breccia diamonds contain 0-740 ppm N and show two modes of N aggregation at 0-30 and 60-95%. Among the breccia diamonds, Type IaA stones comprise 17%, whereas IaAB stones make up 49% of the population. Diamonds from the conglomerate have nitrogen contents below 400 ppm N, with 47% of the suite being Type IaA stones. Approximately one third of the conglomerate and breccia diamonds belongs to Type II having no measurable N. The two suites of Wawa diamonds, according to the morphology and nitrogen studies, are deemed to be different. The conglomerate diamonds are significantly less resorbed and contain less aggregated N. The diamonds that occur in the Wawa breccia and conglomerate have different primary volcanic sources. We suggest that the primary volcanic rock of the conglomerate diamonds may be a kimberlite, as kimberlitic indicator minerals are found in the matrix of the conglomerate. These indicator minerals garnet, Cr diopside and ilmenite are absent from the diamoniferous lamprophyric breccias. The hypothetical kimberlites may have occured in proximity to the conglomerates as suggested by low mechanical abrasion of the conglomerate diamonds and indicator minerals, and the preservation of garnet kelyphitic rims and Cr-diopside. Our study infers an episode of the Archean, pre-2.7 Ga kimberlite magmatism in MGB, which also experienced multiple emplacement episodes of the 2.7 Ga syn-orogenic diamondiferous calc-alkaline lamprophyres. Despite the distinct origins of the breccia and conglomerate diamonds, they all have similar red-orange-green cathodoluminescence colours controlled by the CL emission mainly at 520 nm. This contrasts with the prevalent CL emission at 415-440 nm commonly observed in kimberlitic and detrital diamonds. We ascribe the red-orange-green CL colours of the two diamond suites of Wawa to the late imprint of metamorphism.

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

Bahena, A.; Villasenor, L.

We describe a simple experimental setup to measure the rate of arrival of muons at the surface of the Earth by using a single water Cerenkov detector and home-made electronics. We find a strong anti-correlation between the muon rates averaged over one-hour periods and the atmospheric pressure, with a measured correlation coefficient of -0.67% per hPa. After applying this correction we achieve sufficient sensitivity to observe long term (hours) variations in the averaged muon rates which are greater than 2%. Forbush decreases as big as 4% have been observed with muon detectors located at similar magnetic rigidities compared to Morelia,more » therefore our experimental setup will detect Forbush decreases as soon as the Sun enters into a more active phase.« less

Effective thermal and mechanical properties of polycrystalline diamond films

NASA Astrophysics Data System (ADS)

Cheng, Hao-Yu; Yang, Chi-Yuan; Yang, Li-Chueh; Peng, Kun-Cheng; Chia, Chih-Ta; Liu, Shiu-Jen; Lin, I.-Nan; Lin, Kung-Hsuan

2018-04-01

Polycrystalline diamond films were demonstrated as good candidates for electron field emitters, and their mechanical/thermal properties should thus be considered for real devices. We utilized ultrafast optical techniques to investigate the phonon dynamics of several polycrystalline diamond films, prepared by microwave plasma enhanced chemical vapor deposition. The mechanical properties (longitudinal acoustic velocity) and thermal conductivities of diamond films were evaluated from the coherent and incoherent phonon dynamics, respectively. Ultrananocrystalline diamond films were grown using a CH4 (2%)/Ar plasma, while microcrystalline diamond films were grown using a CH4 (2%)/H2 plasma. The ultrananocrystalline diamond film (with a grain size of several nanometers) possesses low acoustic velocity (14.5 nm/ps) and low thermal conductivity (3.17 W/m K) compared with other kinds of diamond films. The acoustic velocity of diamond films increased abruptly to nearly the same as that of natural diamond and remained there when the rod-shaped diamond grains were induced due to the incorporation of H2 in the growth plasma (CH4/Ar). The thermal conductivities of the materials increased monotonously with increasing incorporation of H2 in the growth plasma (CH4/Ar). The thermal conductivity of 25.6 W/m K was attained for nanocrystalline diamond films containing spherical diamond grains (with a size of several tens of nanometers). Compared with single crystalline diamond, the low thermal conductivity of polycrystalline films results from phonon scattering at the interfaces of grains and amorphous carbon in the boundary phases.

Prioritizing blood flow: cardiovascular performance in response to the competing demands of locomotion and digestion for the Burmese python, Python molurus.

PubMed

Secor, Stephen M; White, Scott E

2010-01-01

Individually, the metabolic demands of digestion or movement can be fully supported by elevations in cardiovascular performance, but when occurring simultaneously, vascular perfusion may have to be prioritized to either the gut or skeletal muscles. Burmese pythons (Python molurus) experience similar increases in metabolic rate during the digestion of a meal as they do while crawling, hence each would have an equal demand for vascular supply when these two actions are combined. To determine, for the Burmese python, whether blood flow is prioritized when snakes are digesting and moving, we examined changes in cardiac performance and blood flow in response to digestion, movement, and the combination of digestion and movement. We used perivascular blood flow probes to measure blood flow through the left carotid artery, dorsal aorta, superior mesenteric artery and hepatic portal vein, and to calculate cardiac output, heart rate and stroke volume. Fasted pythons while crawling experienced a 2.7- and 3.3-fold increase, respectively, in heart rate and cardiac output, and a 66% decrease in superior mesenteric flow. During the digestion of a rodent meal equaling in mass to 24.7% of the snake's body mass, heart rate and cardiac output increased by 3.3- and 4.4-fold, respectively. Digestion also resulted in respective 11.6- and 14.1-fold increases in superior mesenteric and hepatic portal flow. When crawling while digesting, cardiac output and dorsal aorta flow increased by only 21% and 9%, respectively, a modest increase compared with that when they start to crawl on an empty stomach. Crawling did triggered a significant reduction in blood flow to the digesting gut, decreasing superior mesenteric and hepatic portal flow by 81% and 47%, respectively. When faced with the dual demands of digestion and crawling, Burmese pythons prioritize blood flow, apparently diverting visceral supply to the axial muscles.

Trace elements in Gem-Quality Diamonds - Origin and evolution of diamond-forming fluid inclusions

NASA Astrophysics Data System (ADS)

Pearson, Graham; Krebs, Mandy; Stachel, Thomas; Woodland, Sarah; Chinn, Ingrid; Kong, Julie

2017-04-01

In the same way that melt inclusions in phenocrysts have expanded our idea of melt formation and evolution in basalts, studying fluids trapped in diamonds is providing important new constraints on the nature of diamond-forming fluids. Fibrous and cloudy diamonds trap a high but variable density of fluid inclusions and so have been extensively studied using major and trace element compositions. In contrast, constraining the nature of the diamond-forming fluid for high purity gem-quality diamonds has been restricted by the rarity of available high quality trace element data. This is due to the extremely low concentrations of impurities that gem diamonds contain - often in the ppt range. The recent discovery of fluids in gem diamonds showing similar major element chemistry to fluid-rich diamonds suggest that many diamonds may share a common spectrum of parental fluids. Here we test this idea further. Recent advances in analytical techniques, in particular the development of the "off-line" laser ablation pre-concentration approach, have allowed fully quantitative trace element data to be recovered from "fluid-poor", high quality gem diamonds. We present trace element data for gem diamonds from a variety of locations from Canada, S. Africa and Russia, containing either silicate or sulphide inclusions to examine possible paragenetic or genetic differences between fluids. REE abundance in the "gem" diamonds vary from 0.1 to 0.0001 x chondrite. To a first order, we observe the same spectrum of trace element compositions in the gem diamonds as that seen in fluid-rich "fibrous" diamonds, supporting a common origin for the fluids. REE patterns range from extremely flat (Ce/Yb)n 2.5 to 5 (commonly in sulphide-bearing diamonds) to >70, the latter having significantly greater inter-element HFSE/LILE fractionation. In general, the fluids from the sulphide-bearing diamonds are less REE-enriched than the silicate-bearing diamonds, but the ranges overlap significantly. The very large range in REE fractionation mimics very closely that produced in high pressure (5-6 GPa) experimental melts of CO2-H2O fluxed peridotite. Hence, the elemental characteristics of the fluids could be reconciled by the diamonds growing from such melts over a range of T and hence F, with the sulphide-bearing diamonds generally being produced by larger fraction (higher T) melts that have reacted less with their wall rocks. It is also possible that the less REE enriched fluids are consistent with derivation from more reduced CH4-bearing fluids that have lower solute capacity than oxidised fluids. This option is being evaluated.

Isotopically Enriched C-13 Diamond Anvil as a Stress Sensor in High Pressure Experiments

NASA Astrophysics Data System (ADS)

Vohra, Yogesh; Qiu, Wei; Kondratyev, Andreiy; Velisavljevic, Nenad; Baker, Paul

2004-03-01

The conventional high pressure diamond anvils were modified by growing an isotopically pure C-13 diamond layer by microwave plasma chemical vapor deposition using methane/hydrogen/oxygen chemistry. The isotopically pure C-13 nature of the culet of the diamond anvil was confirmed by the Raman spectroscopy measurements. This isotopically engineered diamond anvil was used against a natural abundance diamond anvil for high pressure experiments in a diamond anvil cell. Spatial resolved Raman spectroscopy was used to measure the stress induced shift in the C-13 layer as well as the undelying C-12 layer to ultra high pressures. The observed shift and splitiing of the diamond first order Raman spectrum was correlated with the stress distribution in the diamond anvil cell. The experimental results will be compared with the finite element modeling results using NIKE-2D software in order to create a mathematical relationship between sets of the following parameters: vertical (z axis) distance; horizontal (r axis) distance; max shear stress, and pressure. The isotopically enriched diamond anvils offer unique opportunities to measure stress distribution in the diamond anvil cell devices.

interPopula: a Python API to access the HapMap Project dataset

PubMed Central

2010-01-01

Background The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. Results interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. Conclusions interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset. PMID:21210977

Python for Large-Scale Electrophysiology

PubMed Central

Spacek, Martin; Blanche, Tim; Swindale, Nicholas

2008-01-01

Electrophysiology is increasingly moving towards highly parallel recording techniques which generate large data sets. We record extracellularly in vivo in cat and rat visual cortex with 54-channel silicon polytrodes, under time-locked visual stimulation, from localized neuronal populations within a cortical column. To help deal with the complexity of generating and analysing these data, we used the Python programming language to develop three software projects: one for temporally precise visual stimulus generation (“dimstim”); one for electrophysiological waveform visualization and spike sorting (“spyke”); and one for spike train and stimulus analysis (“neuropy”). All three are open source and available for download (http://swindale.ecc.ubc.ca/code). The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three. Here we present our software as a showcase of the extensive capabilities of Python in neuroscience. PMID:19198646

[Not Available].

PubMed

Pecevski, Dejan; Natschläger, Thomas; Schuch, Klaus

2009-01-01

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.

DendroPy: a Python library for phylogenetic computing.

PubMed

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton.

PubMed

Nunez-Iglesias, Juan; Blanch, Adam J; Looker, Oliver; Dixon, Matthew W; Tilley, Leann

2018-01-01

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the "analyse skeletons" plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan's measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.

A Python-based interface to examine motions in time series of solar images

NASA Astrophysics Data System (ADS)

Campos-Rozo, J. I.; Vargas Domínguez, S.

2017-10-01

Python is considered to be a mature programming language, besides of being widely accepted as an engaging option for scientific analysis in multiple areas, as will be presented in this work for the particular case of solar physics research. SunPy is an open-source library based on Python that has been recently developed to furnish software tools to solar data analysis and visualization. In this work we present a graphical user interface (GUI) based on Python and Qt to effectively compute proper motions for the analysis of time series of solar data. This user-friendly computing interface, that is intended to be incorporated to the Sunpy library, uses a local correlation tracking technique and some extra tools that allows the selection of different parameters to calculate, vizualize and analyze vector velocity fields of solar data, i.e. time series of solar filtergrams and magnetograms.

Ultrasonographic diagnosis of an endocarditis valvularis in a Burmese python (Python molurus bivittatus) with pneumonia.

PubMed

Schroff, Sandra; Schmidt, Volker; Kiefer, Ingmar; Krautwald-Junghanns, Maria-Elisabeth; Pees, Michael

2010-12-01

An 11-yr-old Burmese python (Python molurus bivittatus) was presented with a history of respiratory symptoms. Computed tomography and an endoscopic examination of the left lung were performed and revealed severe pneumonia. Microbiologic examination of a tracheal wash sample and an endoscopy-guided sample from the lung confirmed infection with Salmonella enterica ssp. IV, Enterobacter cloacae, and Klebsiella pneumoniae. Computed tomographic examination demonstrated a hyperattenuated structure within the heart. Echocardiographic examination revealed a hyperechoic mass at the pulmonic valve as well as a dilated truncus pulmonalis. As therapy for pneumonia was ineffective, the snake was euthanized. Postmortem examination confirmed pneumonia and infective endocarditis of the pulmonic valve caused by septicemia with Salmonella enterica ssp. IV. Focal arteriosclerosis of the pulmonary trunk was also diagnosed. The case presented here demonstrates the possible connection between respiratory and cardiovascular diseases in snakes.

Strike kinematics and performance in juvenile ball pythons (Python regius).

PubMed

Ryerson, William G; Tan, Weimin

2017-08-01

The rapid strike of snakes has interested researchers for decades. Although most work has focused on the strike performance of vipers, recent work has shown that other snakes outside of the Viperidae can strike with the same velocities and accelerations. However, to date all of these examples focus on performance in adult snakes. Here, we use high-speed video to measure the strike kinematics and performance of 10 juvenile (<6 months of age) ball pythons, Python regius. We find that juvenile P. regius strike at levels comparable to larger snakes, but with shorter durations and over shorter distances. We conclude that the juvenile P. regius maintain performance likely through manipulation of the axial musculature and accompanying elastic tissues, and that this is a first step to understanding ontogenetic changes in behavior and a potential avenue for understanding how captivity may also impact behavior. © 2017 Wiley Periodicals, Inc.

Food consumption increases cell proliferation in the python brain.

PubMed

Habroun, Stacy S; Schaffner, Andrew A; Taylor, Emily N; Strand, Christine R

2018-04-06

Pythons are model organisms for investigating physiological responses to food intake. While systemic growth in response to food consumption is well documented, what occurs in the brain is currently unexplored. In this study, male ball pythons ( Python regius ) were used to test the hypothesis that food consumption stimulates cell proliferation in the brain. We used 5-bromo-12'-deoxyuridine (BrdU) as a cell-birth marker to quantify and compare cell proliferation in the brain of fasted snakes and those at 2 and 6 days after a meal. Throughout the telencephalon, cell proliferation was significantly increased in the 6 day group, with no difference between the 2 day group and controls. Systemic postprandial plasticity occurs quickly after a meal is ingested, during the period of active digestion; however, the brain displays a surge of cell proliferation after most digestion and absorption is complete. © 2018. Published by The Company of Biologists Ltd.

A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton

PubMed Central

Looker, Oliver; Dixon, Matthew W.; Tilley, Leann

2018-01-01

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions. PMID:29472997

Charming the Snake: Student Experiences with Python Programming as a Data Analysis Tool

NASA Astrophysics Data System (ADS)

Booker, Melissa; Ivers, C. B.; Piper, M.; Powers, L.; Ali, B.

2014-01-01

During the past year, twelve high school students and one undergraduate student participated in the NASA/IPAC Teacher Archive Research Program (NITARP) alongside three high school educators and one informal educator, gaining experience in using Python as a tool for analyzing the vast amount of photometry data available from the Herschel and Spitzer telescopes in the NGC 281 region. Use of Python appeared to produce two main positive gains: (1) a gain in student ability to successfully write and execute Python programs for the bulk analysis of data, and (2) a change in their perceptions of the utility of computer programming and of the students’ abilities to use programming to solve problems. We outline the trials, tribulations, successes, and failures of the teachers and students through this learning exercise and provide some recommendations for incorporating programming in scientific learning.

Alluvial diamond resource potential and production capacity assessment of the Central African Republic

USGS Publications Warehouse

Chirico, Peter G.; Barthelemy, Francis; Ngbokoto, Francois A.

2010-01-01

In May of 2000, a meeting was convened in Kimberley, South Africa, and attended by representatives of the diamond industry and leaders of African governments to develop a certification process intended to assure that rough, exported diamonds were free of conflict concerns. This meeting was supported later in 2000 by the United Nations in a resolution adopted by the General Assembly. By 2002, the Kimberly Process Certification Scheme (KPCS) was ratified and signed by diamond-producing and diamond-importing countries. Over 70 countries were included as members of the KPCS at the end of 2007. To prevent trade in "conflict diamonds" while protecting legitimate trade, the KPCS requires that each country set up an internal system of controls to prevent conflict diamonds from entering any imported or exported shipments of rough diamonds. Every diamond or diamond shipment must be accompanied by a Kimberley Process (KP) certificate and be contained in tamper-proof packaging. The objective of this study was (1) to assess the naturally occurring endowment of diamonds in the Central African Republic (potential resources) based on geological evidence, previous studies, and recent field data and (2) to assess the diamond-production capacity and measure the intensity of mining activity. Several possible methods can be used to estimate the potential diamond resource. However, because there is generally a lack of sufficient and consistent data recording all diamond mining in the Central African Republic and because time to conduct fieldwork and accessibility to the diamond mining areas are limited, two different methodologies were used: the volume and grade approach and the content per kilometer approach. Estimates are that approximately 39,000,000 carats of alluvial diamonds remain in the eastern and western zones of the CAR combined. This amount is roughly twice the total amount of diamonds reportedly exported from the Central African Republic since 1931. Production capacity is calculated to be 840,000 carats per year, a number that is nearly twice the 450,000 carats per year reported annually by the Central African Republic. The difference in the two numbers reflects the lack of sufficient data on diamond resource grades, worker productivity, and the number and locations of sites being worked.

In-Situ Chemical Analyses of Mineral Inclusions in Diamonds in Kimberlitic Eclogites From Yakutia

NASA Astrophysics Data System (ADS)

ANAND, M.; MISRA, K. C.; TAYLOR, L. A.; SOBOLEV, N. V.

2001-12-01

Mineral inclusions in diamonds (DIs) are stated to provide P-T-X-t information regarding the formation of the diamonds and the nature of the upper mantle. In an endeavor to further understand the importance of diamonds and their DIs in relation to their host rocks, we have investigated several diamondiferous eclogites from Yakutia, first by HRXC tomography (Taylor et al., 2001, this meeting) and then by dissection of the eclogites into their individual minerals. The mineralogy of the host eclogite is presented by Misra et al. (2001, this meeting). Two of the diamondiferous eclogite xenoliths, although weighing but 66 g and 42 g, contain 74 and 47 macro-diamonds, resp. Based on HRXCT imaging, appropriate sections were selected in the eclogite to extract diamonds with minimum loss of material. In the majority of cases, diamonds occur as perfect octahedron with well developed crystal faces. In some cases, however, diamonds occur as macles (twinned xls). The size range of the diamonds is 1-6 mm. Optical examination reveals the sulfides as the most common DIs in these diamonds, followed by clinopyroxenes and garnets. Each diamond was cut and polished along relatively soft directions parallel to either (001) or (110) faces so as to expose DIs for in-situ analyses. Examination by cathodoluminescence (CL) on an EMP demonstrated that the majority of the diamonds have minute, optically invisible, cracks from the DIs to the surfaces of the diamonds - i.e., the possibility of an open system. These diamonds show complicated growth histories and contain DIs that are in some cases, found to be associated with secondary alteration. In addition, the DIs in each diamond, examined in-situ are of different composition from the host and different from DIs in other diamonds, a relationship reported earlier (Taylor et al., 2000, Int'l Geol Rev). These observations raise serious doubts about the significance of DIs and the pristinity and syngenesis of DIs removed by the typical diamond~crushing procedure. Therefore, extreme caution must be taken when interpreting any of the P-T-X-t conditions of diamond growth, based on DIs.

Genesis of diamond inclusions: An integrated cathodoluminescence (CL) and Electron backscatter diffraction (EBSD) study on eclogitic and peridotitic inclusions and their diamond host.

NASA Astrophysics Data System (ADS)

van den Heuvel, Quint; Matveev, Sergei; Drury, Martyn; Gress, Michael; Chinn, Ingrid; Davies, Gareth

2017-04-01

Diamond inclusions are potentially fundamental to understanding the formation conditions of diamond and the volatile cycles in the deep mantle. In order to fully understand the implications of the compositional information recorded by inclusions it is vital to know whether the inclusions are proto-, syn-, or epigenetic and the extent to which they have equilibrated with diamond forming fluids. In previous studies, the widespread assumption was made that the majority of diamond inclusions are syngenetic, based upon observation of cubo-octahedral morphology imposed on the inclusions. Recent work has reported the crystallographic relationship between inclusions and the host diamond to be highly complex and the lack of crystallographic relationships between inclusions and diamonds has led some to question the significance of imposed cubo-octahedral morphology. This study presents an integrated EBSD and CL study of 9 diamonds containing 20 pyropes, 2 diopsides, 1 forsterite and 1 rutile from the Jwaneng and Letlhakane kimberlite clusters, Botswana. A new method was developed to analyze the crystallographic orientation of the host diamond and the inclusions with EBSD. Diamonds plates were sequentially polished to expose inclusions at different levels in the diamond. CL imaging at different depths was performed in order to produce a 3D view of diamond growth zones around the inclusions. Standard diamond polishing techniques proved too aggressive for silicate inclusions as they were damaged to such a degree that EBSD measurements on the inclusions were impossible. The inclusions were milled with a Ga+ focused ion beam (FIB) at a 12° angle to clean the surface for EBSD measurements. Of the 24 inclusions, 9 have an imposed cubo-octahedral morphology. Of these inclusions, 6 have faces orientated parallel to diamond growth zones and/or appear to have nucleated on a diamond growth surface, implying syngenesis. In contrast, other diamonds record resorption events such that inclusions now cut diamond growth zones. In most cases, the growth zonation around inclusions is not well defined due to CL haloes but some inclusions clearly disrupt diamond growth. Crystallographic orientations of diamond and the inclusions, determined using EBSD, revealed that each inclusion has a homogeneous orientation and record no compositional zonation. The diamonds also showed no angular deviations despite many having multiple growth and resorption zones; implying epitaxial growth of diamond. Crystallographic alignment between diamond and inclusions was not recorded for the principle planes and limited to 3 possible coincidences on minor planes from the 24 inclusions studied. The CL data show no evidence of syngenesis for these 3 inclusions. Analyses of two diamonds with inclusion clusters in different growth zones, 400 µm apart, revealed the same chemical composition and orientation, potentially implying they originated from an original larger inclusion. Combined EBSD and CL data suggest that there is no direct orientational correlation (epitaxial growth) between silicate inclusions and the host diamond, even when the mineral phases are of the same symmetry group. The presentation will provide a detailed evaluation of the genesis of individual inclusions.

Industrial diamond

USGS Publications Warehouse

Olson, D.W.

2013-01-01

Estimated 2012 world production of natural and synthetic industrial diamond was about 4.45 billion carats. During 2012, natural industrial diamonds were produced in at least 20 countries, and synthetic industrial diamond was produced in at least 12 countries. About 99 percent of the combined natural and synthetic global output was produced in Belarus, China, Ireland, Japan, Russia, South Africa and the United States. During 2012, China was the world’s leading producer of synthetic industrial diamond followed by the United States and Russia. In 2012, the two U.S. synthetic producers, one in Pennsylvania and the other in Ohio, had an estimated output of 103 million carats, valued at about $70.6 million. This was an estimated 43.7 million carats of synthetic diamond bort, grit, and dust and powder with a value of $14.5 million combined with an estimated 59.7 million carats of synthetic diamond stone with a value of $56.1 million. Also in 2012, nine U.S. firms manufactured polycrystalline diamond (PCD) from synthetic diamond grit and powder. The United States government does not collect or maintain data for either domestic PCD producers or domestic chemical vapor deposition (CVD) diamond producers for quantity or value of annual production. Current trade and consumption quantity data are not available for PCD or for CVD diamond. For these reasons, PCD and CVD diamond are not included in the industrial diamond quantitative data reported here.

X-Ray Tomography of Diamondiferous Eclogites: Clues to the Origin of Diamonds.

NASA Astrophysics Data System (ADS)

Taylor, L. A.; Ketcham, R. A.

2009-05-01

During the last decade or so, considerable new and significant data have been gathered concerning the origin of diamonds. This has come from the mantle xenoliths that are the rocks in which the diamonds originated, namely eclogites and peridotites, the host rocks for diamonds in the mantle. Upon rising through the crust to the surface in their kimberlite magmatic carriers and subsequent weathering on the surface, the weak olivine commonly alters, thereby reducing the crushing strength of the peridotite xenoliths. However, the eclogite xenoliths often retain enough toughness to resist total shattering after initial crushing during diamond recovery process. Subjecting these eclogite nodules to X-rays (e.g., 1.54 Å Cu K) can reveal the bright-blue fluorescence of any diamonds exposed at the surface of the xenoliths. Slow and careful extraction can result in recovery of large diamonds. Many of these unique rocks are the ones upon which we have performed High- Resolution X-ray Computed Tomography (HRXCT) at UT Austin. These data have formed the basis for further eclogite dissections and diamond polishing at UT Knoxville. The size of the diamondiferous eclogites that were scanned by HRXCT are from 20 g to 8.8 kg, all with many diamonds ranging from <1 mm to >1 cm, most octahedral, several with mineral inclusions. These diamondiferous eclogites have both textures and fabrics that provide evidence indicating the secondary formation of the diamonds. These include lineations of diamonds along zones of metasomatic alteration, former zones of enhanced permeability; the non-association of sulfides (po, pn, cpy) with the diamonds, versus sulfide-immiscible melt for the diamond origin; lack of any diamonds in direct contact with the primary garnets or clinopyroxenes; and the presence of some dodecahedral diamonds, indicative of resorption processes, typically attributed to the kimberlite melt. Indeed, these eclogites are not igneous in origin, but metamorphic products of their subducted oceanic crustal protoliths. In addition, detailed studies of the extracted diamonds supply more unexpected results. Polished diamonds examined with cathodoluminescence show evidence for a torturous life of cubic nucleation, growth, resorption, octahedral growth, resorption, and even plastic deformation. These are anomalous observations of diamonds supposedly formed along with the primary minerals in their eclogite hosts. The mineral inclusions in the diamonds reveal additional compelling clues of their origin. Multiple clinopyroxene inclusions can have different compositions within a single diamond, different between diamonds, and even different from that of the host. It is proposed that diamonds present in mantle eclogite xenoliths are secondary, having little to do with their hosts, formed by metasomatic fluids penetrating the eclogites along zones of permeability, and causing extensive secondary alteration and even partial melting of the primary garnets and omphacites.

Equations of state and pressure dependence of bulk modulus for aggregated diamond nanorods

NASA Astrophysics Data System (ADS)

Patel, G. R.; Thakar, N. A.; Pandya, T. C.

2018-04-01

In the present paper study of the high pressure behaviour of aggregated diamond nanorods (ADNRs) and diamond have been carried out. A comparative study of different equations of state is discussed to understand the high pressure behaviour of diamond and the aggregated diamond nanorods. In the present study the usual Tait's equation of state has been modified to predict the high pressure behaviour of carbon material ADNRs and diamond. The results obtained in the present study are compared with available experimental evidences. Bulk moduli as a function of pressure are also computed for ADNRs and natural diamond in the light of recent investigations. Present study reveals that ADNRs are less compressible than diamond.

Electron emission from diamond films seeded using kitchen-wrap polyethylene

NASA Astrophysics Data System (ADS)

Varshney, D.; Makarov, V. I.; Saxena, P.; Guinel, M. J. F.; Kumar, A.; Scott, J. F.; Weiner, B. R.; Morell, G.

2011-03-01

Diamond has many potential electronic applications, but the diamond seeding methods are generally harsh on the substrates rendering them unsuitable for integration in electronics. We report a non-abrasive, scalable and economic process of diamond film seeding using kitchen-wrap polyethylene employing hot filament chemical vapour reaction of H2S/CH4/H2 gas mixtures on Cu substrates. The fabricated diamond films were characterized with scanning electron microscopy, transmission electron microscopy and Raman spectroscopy, which confirm that the deposited film consists of a microcrystalline diamond of size in the range 0.5-1.0 µm. The synthesized diamond films exhibit a turn-on field of about 8.5 V µm-1 and long-term stability. Diamond film synthesis using polyethylene will enable the integration of diamond heat sinks into high-power and high-temperature electronic devices.

Disposition of enrofloxacin and its metabolite ciprofloxacin after intramuscular injection in juvenile Burmese pythons (Python molurus bivittatus).

PubMed

Young, L A; Schumacher, J; Papich, M G; Jacobson, E R

1997-03-01

Eleven juvenile Burmese pythons (Python molurus bivittatus) weighing 0.75-1.75 kg were randomly divided into two groups. Blood samples were obtained through surgically placed anterior carotid artery cannulas. Six pythons received a single i.m. injection of enrofloxacin at 5 mg/kg. Blood samples were obtained at 0.5, 1, 3, 6, 12, 24, 48, 72, and 96 hr postinjection. A mean (+/- SD) maximal plasma concentration of 1.66 (+/- 0.42) micrograms/ml was measured at 5.75 hr postinjection. The harmonic mean half-life was calculated to be 6.37 hr. The second group of five snakes received enrofloxacin at 5 mg/kg i.m. s.i.d. for 5 days. Blood was collected immediately before each injection and at 6 hr after each injection. Over the 5-day period, there was a stepwise increase in mean trough plasma concentrations of enrofloxacin. Clinically effective peak plasma enrofloxacin concentrations were attained after the first injection but did not significantly increase during the sampling period. Pharmacokinetic data were assessed against minimum inhibitory concentrations of enrofloxacin for Pseudomonas ssp. isolates in snakes obtained from historical data at the Veterinary Medical Teaching Hospital, University of Florida. Enrofloxacin should be administered at 10 mg/kg i.m. every 48 hr when treating Pseudomonas ssp. infections in juvenile Burmese pythons. Treatment of infections of more enrofloxacin-sensitive gram-negative bacteria could be achieved with the administration of an initial i.m. dose of 10 mg/kg followed by 5 mg/kg every 48 hr.

Effects of preoperative administration of butorphanol or meloxicam on physiologic responses to surgery in ball pythons.

PubMed

Olesen, Mette G; Bertelsen, Mads F; Perry, Steve F; Wang, Tobias

2008-12-15

To characterize physiologic responses of ball pythons (Python regius) following a minor surgical procedure and investigate the effects of 2 commonly used analgesics on this response. 15 healthy ball pythons. Snakes were randomly assigned to receive 1 of 3 treatments: meloxicam (0.3 mg/kg [0.14 mg/lb]; n = 5), butorphanol (5 mg/kg [2.3 mg/lb]; 5), or saline (0.9% NaCl) solution (5) before catheterization of the vertebral artery. Plasma concentrations of catecholamines and cortisol, blood pressure, heart rate, and blood gas values were measured at various times for 72.5 hours after catheterization. The 72.5-hour point was defined as baseline. Heart rate of ball pythons increased significantly during the first hour following surgery. Mean plasma epinephrine concentration increased slightly at 2.5 hours after surgery, whereas mean plasma cortisol concentration increased beginning at 1.5 hours, reaching a maximum at 6.5 hours. Mean blood pressure increased within the first hour but returned to the baseline value at 2.5 hours after surgery. After 24.5 hours, blood pressure, heart rate, and plasma hormone concentrations remained stable at baseline values. There were no significant differences in values for physiologic variables between snakes that received saline solution and those that received meloxicam or butorphanol. Measurement of physiologic variables provides a means of assessing postoperative pain in snakes. Meloxicam and butorphanol at the dosages used did not decrease the physiologic stress response and did not appear to provide analgesic effects in ball pythons.

Postprandial remodeling of the gut microbiota in Burmese pythons

PubMed Central

Costello, Elizabeth K.; Gordon, Jeffrey I.; Secor, Stephen M.; Knight, Rob

2014-01-01

The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. Because many model species (e.g., mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We employed multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes, and Akkermansia, and reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 hours and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus, and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall ‘species’-level diversity increased significantly. Most lineages appeared to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships. PMID:20520652

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

PubMed

Vella, Michael; Cannon, Robert C; Crook, Sharon; Davison, Andrew P; Ganapathy, Gautham; Robinson, Hugh P C; Silver, R Angus; Gleeson, Padraig

2014-01-01

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment.

Python Winding Itself Around Datacubes: How to Access Massive Multi-Dimensional Arrays in a Pythonic Way

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Misev, Dimitar; Baumann, Peter

2017-04-01

While python has developed into the lingua franca in Data Science there is often a paradigm break when accessing specialized tools. In particular for one of the core data categories in science and engineering, massive multi-dimensional arrays, out-of-memory solutions typically employ their own, different models. We discuss this situation on the example of the scalable open-source array engine, rasdaman ("raster data manager") which offers access to and processing of Petascale multi-dimensional arrays through an SQL-style array query language, rasql. Such queries are executed in the server on a storage engine utilizing adaptive array partitioning and based on a processing engine implementing a "tile streaming" paradigm to allow processing of arrays massively larger than server RAM. The rasdaman QL has acted as blueprint for forthcoming ISO Array SQL and the Open Geospatial Consortium (OGC) geo analytics language, Web Coverage Processing Service, adopted in 2008. Not surprisingly, rasdaman is OGC and INSPIRE Reference Implementation for their "Big Earth Data" standards suite. Recently, rasdaman has been augmented with a python interface which allows to transparently interact with the database (credits go to Siddharth Shukla's Master Thesis at Jacobs University). Programmers do not need to know the rasdaman query language, as the operators are silently transformed, through lazy evaluation, into queries. Arrays delivered are likewise automatically transformed into their python representation. In the talk, the rasdaman concept will be illustrated with the help of large-scale real-life examples of operational satellite image and weather data services, and sample python code.

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience

PubMed Central

Vella, Michael; Cannon, Robert C.; Crook, Sharon; Davison, Andrew P.; Ganapathy, Gautham; Robinson, Hugh P. C.; Silver, R. Angus; Gleeson, Padraig

2014-01-01

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment. PMID:24795618

Drilling of optical glass with electroplated diamond tools

NASA Astrophysics Data System (ADS)

Wang, A. J.; Luan, C. G.; Yu, A. B.

2010-10-01

K9 optical glass drilling experiments were carried out. Bright nickel electroplated diamond tools with small slots and under heat treatment in different temperature were fabricated. Scan electro microscope was applied to analyze the wear of electroplated diamond tool. The material removal rate and grinding ratio were calculated. Machining quality was observed. Bond coating hardness was measured. The experimental results show that coolant is needed for the drilling processes of optical glasses. Heat treatment temperature of diamond tool has influence on wearability of diamond tool and grinding ratio. There were two wear types of electroplated diamond tool, diamond grit wear and bond wear. With the machining processes, wear of diamond grits included fracture, blunt and pull-out, and electroplated bond was gradually worn out. High material removal rates could be obtained by using diamond tool with suitable slot numbers. Bright nickel coating bond presents smallest grains and has better mechanical properties. Bright nickel electroplated diamond tool with slot structure and heat treatment under 200°C was suitable for optical glass drilling.

Microplasma device architectures with various diamond nanostructures

NASA Astrophysics Data System (ADS)

Kunuku, Srinivasu; Jothiramalingam Sankaran, Kamatchi; Leou, Keh-Chyang; Lin, I.-Nan

2017-02-01

Diamond nanostructures (DNSs) were fabricated from three different morphological diamonds, microcrystalline diamond (MCD), nanocrystalline diamond (NCD), and ultrananocrystalline diamond (UNCD) films, using a reactive ion etching method. The plasma illumination (PI) behavior of microplasma devices using the DNSs and the diamond films as cathode were investigated. The Paschen curve approach revealed that the secondary electron emission coefficient (γ value) of diamond materials is similar irrespective of the microstructure (MCD, NCD, and UNCD) and geometry of the materials (DNSs and diamond films). The diamond materials show markedly larger γ-coefficient than conventional metallic cathode materials such as Mo that resulted in markedly better PI behavior for the corresponding microplasma devices. Moreover, the PI behavior, i.e. the voltage dependence of plasma current density (J pl-V), plasma density (n e-V), and the robustness of the devices, varied markedly with the microstructure and geometry of the cathode materials that was closely correlated to the electron field emission (EFE) properties of the cathode materials. The UNCD nanopillars, possessing good EFE properties, resulted in superior PI behavior, whereas the MCD diamond films with insufficient EFE properties led to inferior PI behavior. Consequently, enhancement of plasma characteristics is the collective effects of EFE behavior and secondary electron emission characteristics of diamond-based cathode materials.

Enhancement of oxidation resistance via a self-healing boron carbide coating on diamond particles

PubMed Central

Sun, Youhong; Meng, Qingnan; Qian, Ming; Liu, Baochang; Gao, Ke; Ma, Yinlong; Wen, Mao; Zheng, Weitao

2016-01-01

A boron carbide coating was applied to diamond particles by heating the particles in a powder mixture consisting of H3BO3, B and Mg. The composition, bond state and coverage fraction of the boron carbide coating on the diamond particles were investigated. The boron carbide coating prefers to grow on the diamond (100) surface than on the diamond (111) surface. A stoichiometric B4C coating completely covered the diamond particle after maintaining the raw mixture at 1200 °C for 2 h. The contribution of the boron carbide coating to the oxidation resistance enhancement of the diamond particles was investigated. During annealing of the coated diamond in air, the priory formed B2O3, which exhibits a self-healing property, as an oxygen barrier layer, which protected the diamond from oxidation. The formation temperature of B2O3 is dependent on the amorphous boron carbide content. The coating on the diamond provided effective protection of the diamond against oxidation by heating in air at 1000 °C for 1 h. Furthermore, the presence of the boron carbide coating also contributed to the maintenance of the static compressive strength during the annealing of diamond in air. PMID:26831205

Enhancement of oxidation resistance via a self-healing boron carbide coating on diamond particles.

PubMed

Sun, Youhong; Meng, Qingnan; Qian, Ming; Liu, Baochang; Gao, Ke; Ma, Yinlong; Wen, Mao; Zheng, Weitao

2016-02-02

A boron carbide coating was applied to diamond particles by heating the particles in a powder mixture consisting of H3BO3, B and Mg. The composition, bond state and coverage fraction of the boron carbide coating on the diamond particles were investigated. The boron carbide coating prefers to grow on the diamond (100) surface than on the diamond (111) surface. A stoichiometric B4C coating completely covered the diamond particle after maintaining the raw mixture at 1200 °C for 2 h. The contribution of the boron carbide coating to the oxidation resistance enhancement of the diamond particles was investigated. During annealing of the coated diamond in air, the priory formed B2O3, which exhibits a self-healing property, as an oxygen barrier layer, which protected the diamond from oxidation. The formation temperature of B2O3 is dependent on the amorphous boron carbide content. The coating on the diamond provided effective protection of the diamond against oxidation by heating in air at 1000 °C for 1 h. Furthermore, the presence of the boron carbide coating also contributed to the maintenance of the static compressive strength during the annealing of diamond in air.

SPICE-Based Python Packages for ESA Solar System Exploration Mission's Geometry Exploitation

NASA Astrophysics Data System (ADS)

Costa, M.; Grass, M.

2018-04-01

This contribution outlines three Python packages to provide an enhanced and extended usage of SPICE Toolkit APIS providing higher-level functions and data quick-look capabilities focused on European Space Agency solar system exploration missions.

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2011 CFR

2011-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2012 CFR

2012-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2013 CFR

2013-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2014 CFR

2014-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Nanocrystalline diamond micro-anvil grown on single crystal diamond as a generator of ultra-high pressures

DOE PAGES

Samudrala, Gopi K.; Moore, Samuel L.; Velisavljevic, Nenad; ...

2016-09-29

By combining mask-less lithography and chemical vapor deposition (CVD) techniques, a novel two-stage diamond anvil has been fabricated. A nanocrystalline diamond (NCD) micro-anvil 30 μm in diameter was grown at the center of a [100]-oriented, diamond anvil by utilizing microwave plasma CVD method. The NCD micro-anvil has a diamond grain size of 115 nm and micro-focused Raman and X-ray Photoelectron spectroscopy analysis indicate sp3-bonded diamond content of 72%. Lastly, these CVD grown NCD micro-anvils were tested in an opposed anvil configuration and the transition metals osmium and tungsten were compressed to high pressures of 264 GPa in a diamond anvilmore » cell.« less

Surface Design and Engineering Toward Wear-Resistant, Self-Lubricant Diamond Films and Coatings. Chapter 10

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1999-01-01

This chapter describes three studies on the surface design, surface engineering, and tribology of chemical-vapor-deposited (CVD) diamond films and coatings toward wear-resistant, self-lubricating diamond films and coatings. Friction mechanisms and solid lubrication mechanisms of CVD diamond are stated. Effects of an amorphous hydrogenated carbon on CVD diamond, an amorphous, nondiamond carbon surface layer formed on CVD diamond by carbon and nitrogen ion implantation, and a materials combination of cubic boron nitride and CVD diamond on the adhesion, friction, and wear behaviors of CVD diamond in ultrahigh vacuum are described. How surface modification and the selected materials couple improved the tribological functionality of coatings, giving low coefficient of friction and good wear resistance, is explained.

Mechanical design of thin-film diamond crystal mounting apparatus with optimized thermal contact and crystal strain for coherence preservation x-ray optics

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

Shu, Deming; Shvydko, Yury; Stoupin, Stanislav

A method and mechanical design for a thin-film diamond crystal mounting apparatus for coherence preservation x-ray optics with optimized thermal contact and minimized crystal strain are provided. The novel thin-film diamond crystal mounting apparatus mounts a thin-film diamond crystal supported by a thick chemical vapor deposition (CVD) diamond film spacer with a thickness slightly thicker than the thin-film diamond crystal, and two groups of thin film thermal conductors, such as thin CVD diamond film thermal conductor groups separated by the thick CVD diamond spacer. The two groups of thin CVD film thermal conductors provide thermal conducting interface media with themore » thin-film diamond crystal. A piezoelectric actuator is integrated into a flexural clamping mechanism generating clamping force from zero to an optimal level.« less

Effect of TiO2/Al2O3 film coated diamond abrasive particles by sol-gel technique

NASA Astrophysics Data System (ADS)

Hu, Weida; Wan, Long; Liu, Xiaopan; Li, Qiang; Wang, Zhiqi

2011-04-01

The diamond abrasive particles were coated with the TiO2/Al2O3 film by the sol-gel technique. Compared with the uncoated diamonds, the TiO2/Al2O3 film was excellent material for the protection of the diamonds. The results showed that the incipient oxidation temperature of the TiO2/Al2O3 film coated diamonds in air atmosphere was 775 °C, which was higher 175 °C than that of the uncoated diamonds. And the coated diamonds also had better the diamond's single particle compressive strength and the impact toughness than that of uncoated diamonds after sintering at 750 °C. For the vitrified bond grinding wheels, replacing the uncoated diamonds with the TiO2/Al2O3 film coated diamonds, the volume expansion of the grinding wheels decreased from 6.2% to 3.4%, the porosity decreased from 35.7% to 25.7%, the hardness increased from 61.2HRC to 66.5HRC and the grinding ratio of the vitrified bond grinding wheels to carbide alloy (YG8) increased from 11.5 to 19.1.

Interfacial characteristics of diamond/aluminum composites with high thermal conductivity fabricated by squeeze-casting method

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

Jiang, Longtao, E-mail: longtaojiang@163.com; Wang, Pingping; Xiu, Ziyang

2015-08-15

In this work, aluminum matrix composites reinforced with diamond particles (diamond/aluminum composites) were fabricated by squeeze casting method. The material exhibited a thermal conductivity as high as 613 W / (m · K). The obtained composites were investigated by scanning electron microscope and transmission electron microscope in terms of the (100) and (111) facets of diamond particles. The diamond particles were observed to be homogeneously distributed in the aluminum matrix. The diamond{sub (111)}/Al interface was found to be devoid of reaction products. While at the diamond{sub (100)}/Al interface, large-sized aluminum carbides (Al{sub 4}C{sub 3}) with twin-crystal structure were identified. Themore » interfacial characteristics were believed to be responsible for the excellent thermal conductivity of the material. - Graphical abstract: Display Omitted - Highlights: • Squeeze casting method was introduced to fabricate diamond/Al composite. • Sound interfacial bonding with excellent thermal conductivity was produced. • Diamond{sub (111)}/ aluminum interface was firstly characterized by TEM/HRTEM. • Physical combination was the controlling bonding for diamond{sub (111)}/aluminum. • The growth mechanism of Al{sub 4}C{sub 3} was analyzed by crystallography theory.« less

Friction and Wear of Ion-Beam-Deposited Diamondlike Carbon on Chemical-Vapor-Deposited, Fine-Grain Diamond

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa; Wu, Richard L. C.; Lanter, William C.

1996-01-01

Friction and wear behavior of ion-beam-deposited diamondlike carbon (DLC) films coated on chemical-vapor-deposited (CVD), fine-grain diamond coatings were examined in ultrahigh vacuum, dry nitrogen, and humid air environments. The DLC films were produced by the direct impact of an ion beam (composed of a 3:17 mixture of Ar and CH4) at ion energies of 1500 and 700 eV and an RF power of 99 W. Sliding friction experiments were conducted with hemispherical CVD diamond pins sliding on four different carbon-base coating systems: DLC films on CVD diamond; DLC films on silicon; as-deposited, fine-grain CVD diamond; and carbon-ion-implanted, fine-grain CVD diamond on silicon. Results indicate that in ultrahigh vacuum the ion-beam-deposited DLC films on fine-grain CVD diamond (similar to the ion-implanted CVD diamond) greatly decrease both the friction and wear of fine-grain CVD diamond films and provide solid lubrication. In dry nitrogen and in humid air, ion-beam-deposited DLC films on fine-grain CVD diamond films also had a low steady-state coefficient of friction and a low wear rate. These tribological performance benefits, coupled with a wider range of coating thicknesses, led to longer endurance life and improved wear resistance for the DLC deposited on fine-grain CVD diamond in comparison to the ion-implanted diamond films. Thus, DLC deposited on fine-grain CVD diamond films can be an effective wear-resistant, lubricating coating regardless of environment.

Magnetically Orchestrated Formation of Diamond at Lower Temperatures and Pressures

NASA Astrophysics Data System (ADS)

Little, Reginald B.; Lochner, Eric; Goddard, Robert

2005-01-01

Man's curiosity and fascination with diamonds date back to ancient times. The knowledge of the many properties of diamond is recorded during Biblical times. Antoine Lavoisier determined the composition of diamond by burning in O2 to form CO2. With the then existing awareness of graphite as carbon, the race began to convert graphite to diamond. The selective chemical synthesis of diamond has been pursued by Cagniard, Hannay, Moisson and Parson. On the basis of the thermodynamically predicted equilibrium line of diamond and graphite, P W Bridgman attempted extraordinary conditions of high temperature (>2200°C) and pressure (>100,000 atm) for the allotropic conversion of graphite to diamond. H T Hall was the first to successfully form bulk diamond by realizing the kinetic restrictions to Bridgman's (thermodynamic) high pressure high temperature direct allotropic conversion. Moreover, Hall identified catalysts for the faster kinetics of diamond formation. H M Strong determined the import of the liquid catalyst during Hall's catalytic synthesis. W G Eversole discovered the slow metastable low pressure diamond formation by pyrolytic chemical vapor deposition with the molecular hydrogen etching of the rapidly forming stable graphitic carbon. J C Angus determined the import of atomic hydrogen for faster etching for faster diamond growth at low pressure. S Matsumoto has developed plasma and hot filament technology for faster hydrogen and carbon radical generations at low pressure for faster diamond formation. However the metastable low pressure chemical vapor depositions by plasma and hot filament are prone to polycrystalline films. From Bridgman to Hall to Eversole, Angus and Matsumoto, much knowledge has developed of the importance of pressure, temperature, transition metal catalyst, liquid state of metal (metal radicals atoms) and the carbon radical intermediates for diamond synthesis. Here we advance this understanding of diamond formation by demonstrating the external magnetic organization of carbon, metal and hydrogen radicals for lower temperature and pressure synthesis. Here we show that strong static external magnetic field (>15 T) enhances the formation of single crystal diamond at lower pressure and even atmospheric pressure with implications for much better, faster high quality diamond formation by magnetization of current high pressure and temperature technology.

Python in Astronomy 2016 Unproceedings

NASA Astrophysics Data System (ADS)

Robitaille, Thomas; Cruz, Kelle; Greenfield, Perry; Jeschke, Eric; Juric, Mario; Mumford, Stuart; Prescod-Weinstein, Chanda; Sosey, Megan; Tollerud, Erik; VanderPlas, Jake; Ford, Jes; Foreman-Mackey, Dan; Jenness, Tim; Aldcroft, Tom; Alexandersen, Mike; Bannister, Michele; Barbary, Kyle; Barentsen, Geert; Bennett, Samuel; Boquien, Médéric; Campos Rozo, Jose Ivan; Christe, Steven; Corrales, Lia; Craig, Matthew; Deil, Christoph; Dencheva, Nadia; Donath, Axel; Douglas, Stephanie; Ferreira, Leonardo; Ginsburg, Adam; Goldbaum, Nathan; Gordon, Karl; Hearin, Andrew; Hummels, Cameron; Huppenkothen, Daniela; Jennings, Elise; King, Johannes; Lawler, Samantha; Leonard, Andrew; Lim, Pey Lian; McBride, Lisa; Morris, Brett; Nunez, Carolina; Owen, Russell; Parejko, John; Patel, Ekta; Price-Whelan, Adrian; Ruggiero, Rafael; Sipocz, Brigitta; Stevens, Abigail; Turner, James; Tuttle, Sarah; Yanchulova Merica-Jones, Petia; Yoachim, Peter

2016-03-01

This document provides proceedings for unconference sessions as well as hacks/sprints which took place at the Python in Astronomy 2016 workshop, which was held at the University of Washington eScience Institute in Seattle from March 21st to 25th 2016.

Planetary Geologic Mapping Python Toolbox: A Suite of Tools to Support Mapping Workflows

NASA Astrophysics Data System (ADS)

Hunter, M. A.; Skinner, J. A.; Hare, T. M.; Fortezzo, C. M.

2017-06-01

The collective focus of the Planetary Geologic Mapping Python Toolbox is to provide researchers with additional means to migrate legacy GIS data, assess the quality of data and analysis results, and simplify common mapping tasks.

pyGeno: A Python package for precision medicine and proteogenomics.

PubMed

Daouda, Tariq; Perreault, Claude; Lemieux, Sébastien

2016-01-01

pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language. Its range of application therefore encompasses both short scripts and large scale genome-wide studies.

cloudPEST - A python module for cloud-computing deployment of PEST, a program for parameter estimation

USGS Publications Warehouse

Fienen, Michael N.; Kunicki, Thomas C.; Kester, Daniel E.

2011-01-01

This report documents cloudPEST-a Python module with functions to facilitate deployment of the model-independent parameter estimation code PEST on a cloud-computing environment. cloudPEST makes use of low-level, freely available command-line tools that interface with the Amazon Elastic Compute Cloud (EC2(TradeMark)) that are unlikely to change dramatically. This report describes the preliminary setup for both Python and EC2 tools and subsequently describes the functions themselves. The code and guidelines have been tested primarily on the Windows(Registered) operating system but are extensible to Linux(Registered).

Preliminary Work in Atmospheric Turbulence Profiles with the Differential Multi-image Motion Monitor

DTIC Science & Technology

2016-09-01

Center Pacific’s (SSC Pacific) Optical Channel Characterization in Maritime Atmospheres (OCCIMA) Python code is demonstrated with examples that match...OCCIMA) Python code, show how to model the DM3 and anisoplanitic jitter measurements, and finally demonstrate how the turbulence strength profile... python modules. 0.0 0.5 1.0 1.5 2.0 Separation at target plane (m) 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0 A ni so pl an at ic jit te r( λ /D ) Parallel

ModFossa: A library for modeling ion channels using Python.

PubMed

Ferneyhough, Gareth B; Thibealut, Corey M; Dascalu, Sergiu M; Harris, Frederick C

2016-06-01

The creation and simulation of ion channel models using continuous-time Markov processes is a powerful and well-used tool in the field of electrophysiology and ion channel research. While several software packages exist for the purpose of ion channel modeling, most are GUI based, and none are available as a Python library. In an attempt to provide an easy-to-use, yet powerful Markov model-based ion channel simulator, we have developed ModFossa, a Python library supporting easy model creation and stimulus definition, complete with a fast numerical solver, and attractive vector graphics plotting.

PyPanda: a Python package for gene regulatory network reconstruction

PubMed Central

van IJzendoorn, David G.P.; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L.

2016-01-01

Summary: PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. Availability and implementation: The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda. Contact: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl PMID:27402905

PyPanda: a Python package for gene regulatory network reconstruction.

PubMed

van IJzendoorn, David G P; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L

2016-11-01

PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda CONTACT: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl. © The Author 2016. Published by Oxford University Press.

pyGeno: A Python package for precision medicine and proteogenomics

PubMed Central

Daouda, Tariq; Perreault, Claude; Lemieux, Sébastien

2016-01-01

pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language. Its range of application therefore encompasses both short scripts and large scale genome-wide studies. PMID:27785359

An ecological risk assessment of nonnative boas and pythons as potentially invasive species in the United States.

PubMed

Reed, Robert N

2005-06-01

The growing international trade in live wildlife has the potential to result in continuing establishment of nonnative animal populations in the United States. Snakes may pose particularly high risks as potentially invasive species, as exemplified by the decimation of Guam's vertebrate fauna by the accidentally introduced brown tree snake. Herein, ecological and commercial predictors of the likelihood of establishment of invasive populations were used to model risk associated with legal commercial imports of 23 species of boas, pythons, and relatives into the United States during the period 1989-2000. Data on ecological variables were collected from multiple sources, while data on commercial variables were collated from import records maintained by the U.S. Fish and Wildlife Service. Results of the risk-assessment models indicate that species including boa constrictors (Boa constrictor), ball pythons (Python regius), and reticulated pythons (P. reticulatus) may pose particularly high risks as potentially invasive species. Recommendations for reducing risk of establishment of invasive populations of snakes and/or pathogens include temporary quarantine of imports to increase detection rates of nonnative pathogens, increasing research attention to reptile pathogens, reducing the risk that nonnative snakes will reach certain areas with high numbers of federally listed species (such as the Florida Keys), and attempting to better educate individuals purchasing reptiles.

OMPC: an Open-Source MATLAB®-to-Python Compiler

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

Assessing risks to humans from invasive Burmese pythons in Everglades National Park, Florida, USA

USGS Publications Warehouse

Reed, Robert N.; Snow, Ray W.

2014-01-01

Invasive Burmese pythons (Python molurus bivittatus) are now established across a large area of southern Florida, USA, including all of Everglades National Park (NP). The presence of these large-bodied snakes in the continental United States has attracted intense media attention, including regular reference to the possibility of these snakes preying on humans. Over the course of a decade (2003–2012), we solicited reports of apparently unprovoked strikes directed at humans in Everglades NP. We summarize the circumstances surrounding each of the 5 reported incidents, which occurred between 2006 and 2012. All strikes were directed toward biologists moving through flooded wetlands; 2 strikes resulted in minor injury and none resulted in constriction. We consider most of these strikes to be cases of “mistaken identity,” in which the python initiated a strike at a potential prey item but aborted its predatory behavior prior to constriction and ingestion. No strikes are known to have been directed at park visitors despite visitation rates averaging over one million per year during this period. We conclude that while risks to humans should not be completely discounted, the relative risk of a human being killed by a python in Everglades NP appears to be extremely low.

PyGOLD: a python based API for docking based virtual screening workflow generation.

PubMed

Patel, Hitesh; Brinkjost, Tobias; Koch, Oliver

2017-08-15

Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD. However, within an automated virtual screening workflow it is not feasible to use the GUI in between every step to change the GOLD configuration file. Thus, a python module called PyGOLD was developed, to parse, edit and write the GOLD configuration file and to automate docking based virtual screening workflows. The latest version of PyGOLD, its documentation and example scripts are available at: http://www.ccb.tu-dortmund.de/koch or http://www.agkoch.de. PyGOLD is implemented in Python and can be imported as a standard python module without any further dependencies. oliver.koch@agkoch.de, oliver.koch@tu-dortmund.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Python and computer vision

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

Doak, J. E.; Prasad, Lakshman

2002-01-01

This paper discusses the use of Python in a computer vision (CV) project. We begin by providing background information on the specific approach to CV employed by the project. This includes a brief discussion of Constrained Delaunay Triangulation (CDT), the Chordal Axis Transform (CAT), shape feature extraction and syntactic characterization, and normalization of strings representing objects. (The terms 'object' and 'blob' are used interchangeably, both referring to an entity extracted from an image.) The rest of the paper focuses on the use of Python in three critical areas: (1) interactions with a MySQL database, (2) rapid prototyping of algorithms, andmore » (3) gluing together all components of the project including existing C and C++ modules. For (l), we provide a schema definition and discuss how the various tables interact to represent objects in the database as tree structures. (2) focuses on an algorithm to create a hierarchical representation of an object, given its string representation, and an algorithm to match unknown objects against objects in a database. And finally, (3) discusses the use of Boost Python to interact with the pre-existing C and C++ code that creates the CDTs and CATS, performs shape feature extraction and syntactic characterization, and normalizes object strings. The paper concludes with a vision of the future use of Python for the CV project.« less

Wyrm: A Brain-Computer Interface Toolbox in Python.

PubMed

Venthur, Bastian; Dähne, Sven; Höhne, Johannes; Heller, Hendrik; Blankertz, Benjamin

2015-10-01

In the last years Python has gained more and more traction in the scientific community. Projects like NumPy, SciPy, and Matplotlib have created a strong foundation for scientific computing in Python and machine learning packages like scikit-learn or packages for data analysis like Pandas are building on top of it. In this paper we present Wyrm ( https://github.com/bbci/wyrm ), an open source BCI toolbox in Python. Wyrm is applicable to a broad range of neuroscientific problems. It can be used as a toolbox for analysis and visualization of neurophysiological data and in real-time settings, like an online BCI application. In order to prevent software defects, Wyrm makes extensive use of unit testing. We will explain the key aspects of Wyrm's software architecture and design decisions for its data structure, and demonstrate and validate the use of our toolbox by presenting our approach to the classification tasks of two different data sets from the BCI Competition III. Furthermore, we will give a brief analysis of the data sets using our toolbox, and demonstrate how we implemented an online experiment using Wyrm. With Wyrm we add the final piece to our ongoing effort to provide a complete, free and open source BCI system in Python.

An Overview of High-k Oxides on Hydrogenated-Diamond for Metal-Oxide-Semiconductor Capacitors and Field-Effect Transistors.

PubMed

Liu, Jiangwei; Koide, Yasuo

2018-06-04

Thanks to its excellent intrinsic properties, diamond is promising for applications of high-power electronic devices, ultraviolet detectors, biosensors, high-temperature tolerant gas sensors, etc. Here, an overview of high- k oxides on hydrogenated-diamond (H-diamond) for metal-oxide-semiconductor (MOS) capacitors and MOS field-effect transistors (MOSFETs) is demonstrated. Fabrication routines for the H-diamond MOS capacitors and MOSFETs, band configurations of oxide/H-diamond heterointerfaces, and electrical properties of the MOS and MOSFETs are summarized and discussed. High- k oxide insulators are deposited using atomic layer deposition (ALD) and sputtering deposition (SD) techniques. Electrical properties of the H-diamond MOS capacitors with high- k oxides of ALD-Al₂O₃, ALD-HfO₂, ALD-HfO₂/ALD-Al₂O₃ multilayer, SD-HfO₂/ALD-HfO₂ bilayer, SD-TiO₂/ALD-Al₂O₃ bilayer, and ALD-TiO₂/ALD-Al₂O₃ bilayer are discussed. Analyses for capacitance-voltage characteristics of them show that there are low fixed and trapped charge densities for the ALD-Al₂O₃/H-diamond and SD-HfO₂/ALD-HfO₂/H-diamond MOS capacitors. The k value of 27.2 for the ALD-TiO₂/ALD-Al₂O₃ bilayer is larger than those of the other oxide insulators. Drain-source current versus voltage curves show distinct pitch-off and p -type channel characteristics for the ALD-Al₂O₃/H-diamond, SD-HfO₂/ALD-HfO₂/H-diamond, and ALD-TiO₂/ALD-Al₂O₃/H-diamond MOSFETs. Understanding of fabrication routines and electrical properties for the high- k oxide/H-diamond MOS electronic devices is meaningful for the fabrication of high-performance H-diamond MOS capacitor and MOSFET gas sensors.

Diamonds from Orapa Mine show a clear subduction signature in SIMS stable isotope data

NASA Astrophysics Data System (ADS)

Chinn, Ingrid L.; Perritt, Samantha H.; Stiefenhofer, Johann; Stern, Richard A.

2018-05-01

Spatially resolved analyses reveal considerable isotopic heterogeneity within and among diamonds ranging in size from 0.15 to 4.75 mm from the Orapa Mine, Botswana. The isotopic data are interpreted in conjunction with nitrogen aggregation state data and growth zone relationships from cathodoluminescence images. The integrated information confirms that a distinct diamond growth event (with low IaAB nitrogen aggregation states, moderately high nitrogen contents and δ13C and δ15N values compatible with average mantle values) is younger than the dominant population(s) of Type IaAB diamonds and cores of composite diamonds with more negative and positive δ13C and δ15N values, respectively. A significant proportion of the older diamond generation has high nitrogen contents, well outside the limit sector relationship, and these diamonds are likely to reflect derivation from subducted organic matter. Diamonds with low δ13C values combined with high nitrogen contents and positive δ15N values have not been previously widely recognised, even in studies of diamonds from Orapa. This may have been caused by prior analytical bias towards inclusion-bearing diamonds that are not necessarily representative of the entire range of diamond populations, and because of average measurements from heterogeneous diamonds measured by bulk combustion methods. Two distinct low nitrogen/Type II microdiamond populations were recognised that do not appear to continue into the macrodiamond sizes in the samples studied. Other populations, e.g. those containing residual singly-substituted nitrogen defects, range in size from small microdiamonds to large macrodiamonds. The total diamond content of the Orapa kimberlite thus reflects a complex assortment of multiple diamond populations.

Triphasic Tooling with Small Oriented Diamond Tip for Turning and Smoothing Lightweight Mirrors

NASA Technical Reports Server (NTRS)

Voronov, O. A.; Tompa, G. S.; Kear, B. H.; Veress, V.

2004-01-01

We are developing a new method for the growth of small diamond crystals at very high temperatures and pressures directly from a carbon melt. A prototype "Supercell" has been developed for this purpose. This system is capable of high rate crystal growth in relatively large working volumes. The resulting high quality diamond crystals will be incorporated into a triphasic diamond/titanium carbide/titanium composite tool, with an oriented diamond crystal at its tip. High pressure is needed to prevent degradation of diamond at high temperature, and to ensure the formation of a crack & composite structure. After grinding and polishing, the composite material will be joined to a steel holder, thus forming a diamond-tipped tool for turning and smoothing of a mirror surface. A properly oriented single-crystal diamond cuts and smoothes much better than a conventional polycrystalline diamond crystal. This is because the hardness depends on crystallographic orientation-the difference corresponds to 60-100 GPa on the Knoop scale. Our goal is to achieve surface roughness of about 1 nm, which will be accomplished by precision cutting and smoothing. The hardness of the functionally-graded diamond/titanium carbide/titanium composite tool varies from 100 GPa at its tip to 15 GPa at its base. Previous work has shown that the mass of machined material using an oriented-diamond tool is much larger than that for a standard diamond-metal composite tool.

Diamond MEMS: wafer scale processing, devices, and technology insertion

NASA Astrophysics Data System (ADS)

Carlisle, J. A.

2009-05-01

Diamond has long held the promise of revolutionary new devices: impervious chemical barriers, smooth and reliable microscopic machines, and tough mechanical tools. Yet it's been an outsider. Laboratories have been effectively growing diamond crystals for at least 25 years, but the jump to market viability has always been blocked by the expense of diamond production and inability to integrate with other materials. Advances in chemical vapor deposition (CVD) processes have given rise to a hierarchy of carbon films ranging from diamond-like carbon (DLC) to vapor-deposited diamond coatings, however. All have pros and cons based on structure and cost, but they all share some of diamond's heralded attributes. The best performer, in theory, is the purest form of diamond film possible, one absent of graphitic phases. Such a material would capture the extreme hardness, high Young's modulus and chemical inertness of natural diamond. Advanced Diamond Technologies Inc., Romeoville, Ill., is the first company to develop a distinct chemical process to create a marketable phase-pure diamond film. The material, called UNCD® (for ultrananocrystalline diamond), features grain sizes from 3 to 300 nm in size, and layers just 1 to 2 microns thick. With significant advantages over other thin films, UNCD is designed to be inexpensive enough for use in atomic force microscopy (AFM) probes, microelectromechanical machines (MEMS), cell phone circuitry, radio frequency devices, and even biosensors.

Eclogitic inclusions in diamonds: Evidence of complex mantle processes over time

NASA Astrophysics Data System (ADS)

Taylor, Lawrence A.; Snyder, Gregory A.; Crozaz, Ghislaine; Sobolev, Vladimir N.; Yefimova, Emiliya S.; Sobolev, Nikolai V.

1996-08-01

The first ion-probe trace element analyses of clinopyroxene-garnet pairs both included within diamonds and from the eclogite host xenoliths are reported; these diamondiferous eclogites are from the Udachnaya and Mir kimberlite pipes, Yakutia, Russia. The major and trace element analyses of these diamond-inclusion and host-rock pairs are compared in order to determine the relative ages of the diamonds, confirm or deny genetic relationships between the diamonds and the eclogites, evaluate models of eclogite petrogenesis, and model igneous processes in the mantle before, during, and after diamond formation. The most striking aspect of the chemical compositions of the diamond inclusions is the diversity of relationships with their eclogite hosts. No single distinct pattern of variation from diamond inclusion minerals to host minerals is found for all four samples. Garnet and clinopyroxene inclusions in the diamonds from two samples (U-65/3 and U-66/3) have lower Mg#s, lower Mg, and higher Fe contents, and lower LREE than those in the host eclogite. We interpret such variations as due to metasomatism of the host eclogite after diamond formation. One sample, U-41/3 shows enrichment in diamond-inclusion MREE enrichment relative to the eclogite host and may indicate a metasomatic event prior to, or during, diamond formation. Bulanova [2] found striking differences between inclusions taken from within different portions of the very same diamond. Clinopyroxene inclusions taken from the central (early) portions of Yakutian diamonds were lower in Mg# and Mg contents (by up to 25%) than those later inclusions at the rims of diamonds. These trends are parallel to those between diamond inclusions and host eclogites determined for four of the five samples from the present study and may merely represent changing magmatic and/or P-T conditions in the mantle. Garnet trace element compositions are similar in relative proportions, but variable in abundances, between diamond inclusions and host eclogites. This is probably due to the rapid diffusion of trace elements in garnet under mantle temperatures and consequent alteration of the garnet, and not due to juvenile diamonds 'locking in' source heterogeneities (c.f., [3]). Trace element compositions of clinopyroxenes included in diamonds are generally similar to those in the host eclogite. However, one host clinopyroxene does show enrichment in the LREE compared to that in the inclusion and may be attributed to mantle metasomatism, not related to kimberlite transport. In another eclogite, M-46, the host clinopyroxene is depleted in the LREE and Fe, and enriched in the HREE and Mg, relative to the inclusion and is consistent with partial melting of the eclogite subsequent to diamond formation. Sm/Nd ratios in clinopyroxenes appear to be little affected by these processes for most samples, allowing SmNd isotopic studies to yield important information about ancient protoliths. Eclogitic mineral inclusions in Yakutian diamonds appear consanguineous with the diamonds, a contention supported by the observations of Bulanova [2]. Therefore, ReOs whole-rock and Sm/Nd clinopyroxene age determinations of the Udachnaya eclogites also yield the time of diamond formation, approximately 2.9 Ga [32,33].

16 CFR 23.13 - Disclosure of treatments to diamonds

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Disclosure of treatments to diamonds 23.13... JEWELRY, PRECIOUS METALS, AND PEWTER INDUSTRIES § 23.13 Disclosure of treatments to diamonds A diamond is a gemstone product. Treatments to diamonds should be disclosed in the manner prescribed in § 23.22...

16 CFR 23.13 - Disclosure of treatments to diamonds.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Disclosure of treatments to diamonds. 23.13... JEWELRY, PRECIOUS METALS, AND PEWTER INDUSTRIES § 23.13 Disclosure of treatments to diamonds. A diamond is a gemstone product. Treatments to diamonds should be disclosed in the manner prescribed in § 23.22...

15 CFR 30.70 - Violation of the Clean Diamond Trade Act.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Violation of the Clean Diamond Trade... Clean Diamond Trade Act. Public Law 108-19, the Clean Diamond Trade Act (the Act), section 8(c... diamonds, including those with respect to the validation of the Kimberley Process Certificate by the...

15 CFR 30.70 - Violation of the Clean Diamond Trade Act.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Violation of the Clean Diamond Trade... Clean Diamond Trade Act. Public Law 108-19, the Clean Diamond Trade Act (the Act), section 8(c... diamonds, including those with respect to the validation of the Kimberley Process Certificate by the...

15 CFR 30.70 - Violation of the Clean Diamond Trade Act.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Violation of the Clean Diamond Trade... Clean Diamond Trade Act. Public Law 108-19, the Clean Diamond Trade Act (the Act), section 8(c... diamonds, including those with respect to the validation of the Kimberley Process Certificate by the...

16 CFR 23.13 - Disclosure of treatments to diamonds

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Disclosure of treatments to diamonds 23.13... JEWELRY, PRECIOUS METALS, AND PEWTER INDUSTRIES § 23.13 Disclosure of treatments to diamonds A diamond is a gemstone product. Treatments to diamonds should be disclosed in the manner prescribed in § 23.22...

16 CFR 23.13 - Disclosure of treatments to diamonds.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Disclosure of treatments to diamonds. 23.13... JEWELRY, PRECIOUS METALS, AND PEWTER INDUSTRIES § 23.13 Disclosure of treatments to diamonds. A diamond is a gemstone product. Treatments to diamonds should be disclosed in the manner prescribed in § 23.22...

16 CFR 23.13 - Disclosure of treatments to diamonds.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Disclosure of treatments to diamonds. 23.13... JEWELRY, PRECIOUS METALS, AND PEWTER INDUSTRIES § 23.13 Disclosure of treatments to diamonds. A diamond is a gemstone product. Treatments to diamonds should be disclosed in the manner prescribed in § 23.22...

15 CFR 30.70 - Violation of the Clean Diamond Trade Act.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Violation of the Clean Diamond Trade... Clean Diamond Trade Act. Public Law 108-19, the Clean Diamond Trade Act (the Act), section 8(c... diamonds, including those with respect to the validation of the Kimberley Process Certificate by the...

Diamond nanostructures for drug delivery, bioimaging, and biosensing.

PubMed

Chen, Xianfeng; Zhang, Wenjun

2017-02-06

Diamond features an attractive combination of outstanding mechanical, optical, thermal and electrical properties; tunable surface characteristics; and unprecedented biocompatibility. Additionally, diamond can possess unique nitrogen-vacancy emission centers that are highly photostable and extremely sensitive to magnetic fields, temperatures, ion concentrations, and spin densities. With these inherent merits, diamond in various nanoscale configurations has demonstrated a variety of distinctive applications in a broad range of fields. In particular, research on diamond nanoparticles (0-dimensional structures) and arrays of diamond nanoneedles/nanowires (1-dimensional structures) has witnessed important and exciting progress in recent years. Here, we systematically review the superior properties of diamond nanomaterials and the nitrogen-vacancy centers they contain as well as their uses in biomedical applications, including biosensing, bioimaging and drug delivery. Moreover, systematic studies of the biocompatibility and toxicity of diamond nanostructures, which constitute an important issue for the biomedical applications of diamond that has not yet been thoroughly addressed in previous reviews, are also discussed. Finally, we present our insights into the key issues concerning these diamond nanomaterials and their future development for applications.

Diamond network: template-free fabrication and properties.

PubMed

Zhuang, Hao; Yang, Nianjun; Fu, Haiyuan; Zhang, Lei; Wang, Chun; Huang, Nan; Jiang, Xin

2015-03-11

A porous diamond network with three-dimensionally interconnected pores is of technical importance but difficult to be produced. In this contribution, we demonstrate a simple, controllable, and "template-free" approach to fabricate diamond networks. It combines the deposition of diamond/β-SiC nanocomposite film with a wet-chemical selective etching of the β-SiC phase. The porosity of these networks was tuned from 15 to 68%, determined by the ratio of the β-SiC phase in the composite films. The electrochemical working potential and the reactivity of redox probes on the diamond networks are similar to those of a flat nanocrystalline diamond film, while their surface areas are hundreds of times larger than that of a flat diamond film (e.g., 490-fold enhancement for a 3 μm thick diamond network). The marriage of the unprecedented physical/chemical features of diamond with inherent advantages of the porous structure makes the diamond network a potential candidate for various applications such as water treatment, energy conversion (batteries or fuel cells), and storage (capacitors), as well as electrochemical and biochemical sensing.

Effects of protein inter-layers on cell-diamond FET characteristics.

PubMed

Rezek, Bohuslav; Krátká, Marie; Kromka, Alexander; Kalbacova, Marie

2010-12-15

Diamond is recognized as an attractive material for merging solid-state and biological systems. The advantage of diamond field-effect transistors (FET) is that they are chemically resistant, bio-compatible, and can operate without gate oxides. Solution-gated FETs based on H-terminated nanocrystalline diamond films exhibiting surface conductivity are employed here for studying effects of fetal bovine serum (FBS) proteins and osteoblastic SAOS-2 cells on diamond electronic properties. FBS proteins adsorbed on the diamond FETs permanently decrease diamond conductivity as reflected by the -45 mV shift of the FET transfer characteristics. Cell cultivation for 2 days results in a further shift by another -78 mV. We attribute it to a change of diamond material properties rather than purely to the field-effect. Increase in gate leakage currents (by a factor of 4) indicates that the FBS proteins also decrease the diamond-electrolyte electronic barrier induced by C-H surface dipoles. We propose a model where the proteins replace ions in the very vicinity of the H-terminated diamond surface. Copyright © 2010 Elsevier B.V. All rights reserved.

Ultrafast transformation of graphite to diamond: an ab initio study of graphite under shock compression.

PubMed

Mundy, Christopher J; Curioni, Alessandro; Goldman, Nir; Will Kuo, I-F; Reed, Evan J; Fried, Laurence E; Ianuzzi, Marcella

2008-05-14

We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12 kms (longitudinal stress>130 GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.

In vitro assessment of cutting efficiency and durability of zirconia removal diamond rotary instruments.

PubMed

Kim, Joon-Soo; Bae, Ji-Hyeon; Yun, Mi-Jung; Huh, Jung-Bo

2017-06-01

Recently, zirconia removal diamond rotary instruments have become commercially available for efficient cutting of zirconia. However, research of cutting efficiency and the cutting characteristics of zirconia removal diamond rotary instruments is limited. The purpose of this in vitro study was to assess and compare the cutting efficiency, durability, and diamond rotary instrument wear pattern of zirconia diamond removal rotary instruments with those of conventional diamond rotary instruments. In addition, the surface characteristics of the cut zirconia were assessed. Block specimens of 3 mol% yttrium cation-doped tetragonal zirconia polycrystal were machined 10 times for 1 minute each using a high-speed handpiece with 6 types of diamond rotary instrument from 2 manufacturers at a constant force of 2 N (n=5). An electronic scale was used to measure the lost weight after each cut in order to evaluate the cutting efficiency. Field emission scanning electron microscopy was used to evaluate diamond rotary instrument wear patterns and machined zirconia block surface characteristics. Data were statistically analyzed using the Kruskal-Wallis test, followed by the Mann-Whitney U test (α=.05). Zirconia removal fine grit diamond rotary instruments showed cutting efficiency that was reduced compared with conventional fine grit diamond rotary instruments. Diamond grit fracture was the most dominant diamond rotary instrument wear pattern in all groups. All machined zirconia surfaces were primarily subjected to plastic deformation, which is evidence of ductile cutting. Zirconia blocks machined with zirconia removal fine grit diamond rotary instruments showed the least incidence of surface flaws. Although zirconia removal diamond rotary instruments did not show improved cutting efficiency compared with conventional diamond rotary instruments, the machined zirconia surface showed smoother furrows of plastic deformation and fewer surface flaws. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Physical and Tribological Characteristics of Ion-Implanted Diamond Films

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Heidger, S.; Korenyi-Both, A. L.; Jayne, D. T.; Herrera-Fierro, P.; Shogrin, B.; Wilbur, P. J.; Wu, R. L. C.; Garscadden, A.; Barnes, P. N.

1994-01-01

Unidirectional sliding friction experiments were conducted with a natural, polished diamond pin in contact with both as-deposited and carbon-ion-implanted diamond films in ultrahigh vacuum. Diamond films were deposited on silicon, silicon carbide, and silicon nitride by microwave-plasma-assisted chemical vapor deposition. The as-deposited diamond films were impacted with carbon ions at an accelerating energy of 60 keV and a current density of 50 micron A/cm(exp 2) for approximately 6 min, resulting in a dose of 1.2 x 10(exp 17) carbon ions/cm(exp 2). The results indicate that the carbon ion implantation produced a thin surface layer of amorphous, nondiamond carbon. The nondiamond carbon greatly decreased both friction and wear of the diamond films. The coefficients of friction for the carbon-ion-implanted, fine-grain diamond films were less than 0.1, factors of 20 to 30 lower than those for the as-deposited, fine-grain diamond films. The coefficients of friction for the carbon-ion-implanted, coarse-grain diamond films were approximately 0.35, a factor of five lower than those for the as-deposited, coarse-grain diamond films. The wear rates for the carbon-ion-implanted, diamond films were on the order of 10(exp -6) mm(exp 3)/Nm, factors of 30 to 80 lower than that for the as-deposited diamond films, regardless of grain size. The friction of the carbon-ion-implanted diamond films was greatly reduced because the amorphous, nondiamond carbon, which had a low shear strength, was restricted to the surface layers (less than 0.1 micron thick) and because the underlying diamond materials retained their high hardness. In conclusion, the carbon-ion-implanted, fine-grain diamond films can be used effectively as wear resistant, self-lubricating coatings for ceramics, such as silicon nitride and silicon carbide, in ultrahigh vacuum.

Using Python on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

was not designed for use in a shared computing environment. The following example creates a new Python is run. For example an environment.yml file can be created on the developer's laptop and used on the

PyGeoTess 0.2.0

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

Maccarthy, Jonathan K.

2016-07-28

PyGeoTess is a Python interface module to the GeoTess gridding and earth model library from Sandia National Laboratories. It provides simplified access to a subset of the GeoTess C++ library, and takes advantage of Python's interactive interpreter and inline documentation system.

Origins of diamond-forming fluids: An isotopic and trace element study of diamonds and silicates from diamondiferous xenoliths

NASA Astrophysics Data System (ADS)

Laiginhas, Fernando; Pearson, D. Graham; McNeill, John; Gurney, John; Nowell, Geoff; Ottley, Chris

2010-05-01

While there is increasing understanding of the age of formation and nature of "gem" diamonds, significant debate revolves around the nature of the fluids/melts from which they form. Stable C and N isotopes have been shown to be highly variable and yet the role of subduction-related fluids remains strongly debated. Recent studies on fibrous diamonds have yielded new trace and major element data (e.g., Weiss et al., 2009) that, together with new radiogenic isotope data (Klein BenDavid et al., 2010) indicate such diamonds grow from fluids that comprise mixtures of hydrous silicic, hydrous saline and carbonatitic fluids, derived from different source components of asthenospheric and lithospheric origin. However, until now such data has been lacking from gem diamonds. Using a new laser-based technique (McNeill et al., 2009), we have analysed a suite of diamonds plus co-existing host silicates from several diamondiferous xenoliths (6 harzburgites, 1 eclogite) from the Finsch and Newlands kimberlites in order to try to understand the fluid compositions that produce gem diamonds and better understand their effects of their mantle wall rocks. Diamonds from the xenoliths show a wide variety of trace element enrichment levels. While the eclogitic diamond shows similar trace element systematics to some of the harzburgitic diamonds there are significant differences within the harzburgitic diamonds from different xenoliths, with those from Finsch being significantly enriched in Ba, Sr and Pb relative to other elements. Nd isotope data on the host silicates is variable and dominantly unradiogenic, indicative of long-term enrichment typically associated with the source of some diamond-forming fluids. We will present Sr isotopic data on host silicates and diamond fluids to constrain whether the "gem" diamonds require the complex sources of fluids that characterise the growth of fibrous diamonds. 1) Y. Weiss, R. Kessel, W.L. Griffin, I. Kiflawi, O. Klein-BenDavid, D.R. Bell, J.W. Harris and O. Navon (2009). A new model for the evolution of diamond-forming fluids: Evidence from microinclusion-bearing diamonds from Kankan, Guinea. Lithos 112, Supp. 2: 660-674. 2) O. Klein-BenDavid, D.G. Pearson, G.M. Nowell, C. Ottley, J.C.R. McNeill, P. Cartigny (2010). Mixed fluid sources involved in diamond growth constrained by Sr-Nd-Pb-C-N isotopes and trace elements. EPSL 289, 1-2: 123-133. 3) J. McNeill, D.G. Pearson, O. Klein-BenDavid, G.M. Nowell, C.J. Ottley and I. Chinn (2009). Quantitative analysis of trace element concentrations in some gem-quality diamonds. J. Phys.: Condens. Matter 21: 364207 (13pp).

Study of diamond film growth and properties

NASA Technical Reports Server (NTRS)

Albin, Sacharial

1990-01-01

The objective was to study diamond film growth and its properties in order to enhance the laser damage threshold of substrate materials. Calculations were performed to evaluate laser induced thermal stress parameter, R(sub T) of diamond. It is found that diamond has several orders of magnitude higher in value for R(sub T) compared to other materials. Thus, the laser induced damage threshold (LIDT) of diamond is much higher. Diamond films were grown using a microwave plasma enhanced chemical vapor deposition (MPECVD) system at various conditions of gas composition, pressure, temperature, and substrate materials. A 0.5 percent CH4 in H2 at 20 torr were ideal conditions for growing of high quality diamond films on substrates maintained at 900 C. The diamond films were polycrystalline which were characterized by scanning electron microscopy (SEM) and Raman scattering spectroscopy. The top surface of the growing film is always rough due to the facets of polycrystalline film while the back surface of the film replicates the substrate surface. An analytical model based on two dimensional periodic heat flow was developed to calculate the effective in-plane (face parallel) diffusivity of a two layer system. The effective diffusivity of diamond/silicon samples was measured using a laser pulse technique. The thermal conductivity of the films was measured to be 13.5 W/cm K, which is better than that of a type Ia natural diamond. Laser induced damage experiments were performed on bare Si substrates, diamond film coated Si, and diamond film windows. Significant improvements in the LIDT were obtained for diamond film coated Si compared to the bare Si.

Enhancement of structure images of interstellar diamond microcrystals by image processing

NASA Technical Reports Server (NTRS)

O'Keefe, Michael A.; Hetherington, Crispin; Turner, John; Blake, David; Freund, Friedemann

1988-01-01

Image processed high resolution TEM images of diamond crystals found in oxidized acid residues of carbonaceous chondrites are presented. Two models of the origin of the diamonds are discussed. The model proposed by Lewis et al. (1987) supposes that the diamonds formed under low pressure conditions, whereas that of Blake et al (1988) suggests that the diamonds formed due to particle-particle collisions behind supernova shock waves. The TEM images of the diamond presented support the high pressure model.

The impact of diamond nanocrystallinity on osteoblast functions.

PubMed

Yang, Lei; Sheldon, Brian W; Webster, Thomas J

2009-07-01

Nanocrystalline diamond has been proposed as an anti-abrasive film on orthopedic implants. In this study, osteoblast (bone forming cells) functions including adhesion (up to 4h), proliferation (up to 5 days) and differentiation (up to 21 days) on different diamond film topographies were systematically investigated. In order to exclude interferences from changes in surface chemistry and wettability (energy), diamond films with nanometer and micron scale topographies were fabricated through microwave plasma enhanced chemical-vapor-deposition and hydrogen plasma treatment. Scanning electron microscopy (SEM), atomic force microscopy (AFM), Raman spectroscopy and water contact angle measurements verified the similar surface chemistry and wettability but varied topographies for all of the diamond films prepared on silicon in this study. Cytocompatibility assays demonstrated enhanced osteoblast functions (including adhesion, proliferation, intracellular protein synthesis, alkaline phosphatase activity and extracellular calcium deposition) on nanocrystalline diamond compared to submicron diamond grain size films for all time periods tested up to 21 days. An SEM study of osteoblast attachment helped to explain the topographical impact diamond had on osteoblast functions by showing altered filopodia extensions on the different diamond topographies. In summary, these results provided insights into understanding the role diamond nanotopography had on osteoblast interactions and more importantly, the application of diamond films to improve orthopedic implant lifetimes.

Friction and wear of plasma-deposited diamond films

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa; Wu, Richard L. C.; Garscadden, Alan; Barnes, Paul N.; Jackson, Howard E.

1993-01-01

Reciprocating sliding friction experiments in humid air and in dry nitrogen and unidirectional sliding friction experiments in ultrahigh vacuum were conducted with a natural diamond pin in contact with microwave-plasma-deposited diamond films. Diamond films with a surface roughness (R rms) ranging from 15 to 160 nm were produced by microwave-plasma-assisted chemical vapor deposition. In humid air and in dry nitrogen, abrasion occurred when the diamond pin made grooves in the surfaces of diamond films, and thus the initial coefficients of friction increased with increasing initial surface roughness. The equilibrium coefficients of friction were independent of the initial surface roughness of the diamond films. In vacuum the friction for diamond films contacting a diamond pin arose primarily from adhesion between the sliding surfaces. In these cases, the initial and equilibrium coefficients of friction were independent of the initial surface roughness of the diamond films. The equilibrium coefficients of friction were 0.02 to 0.04 in humid air and in dry nitrogen, but 1.5 to 1.8 in vacuum. The wear factor of the diamond films depended on the initial surface roughness, regardless of environment; it increased with increasing initial surface roughness. The wear factors were considerably higher in vacuum than in humid air and in dry nitrogen.

Hearing with an atympanic ear: good vibration and poor sound-pressure detection in the royal python, Python regius.

PubMed

Christensen, Christian Bech; Christensen-Dalsgaard, Jakob; Brandt, Christian; Madsen, Peter Teglberg

2012-01-15

Snakes lack both an outer ear and a tympanic middle ear, which in most tetrapods provide impedance matching between the air and inner ear fluids and hence improve pressure hearing in air. Snakes would therefore be expected to have very poor pressure hearing and generally be insensitive to airborne sound, whereas the connection of the middle ear bone to the jaw bones in snakes should confer acute sensitivity to substrate vibrations. Some studies have nevertheless claimed that snakes are quite sensitive to both vibration and sound pressure. Here we test the two hypotheses that: (1) snakes are sensitive to sound pressure and (2) snakes are sensitive to vibrations, but cannot hear the sound pressure per se. Vibration and sound-pressure sensitivities were quantified by measuring brainstem evoked potentials in 11 royal pythons, Python regius. Vibrograms and audiograms showed greatest sensitivity at low frequencies of 80-160 Hz, with sensitivities of -54 dB re. 1 m s(-2) and 78 dB re. 20 μPa, respectively. To investigate whether pythons detect sound pressure or sound-induced head vibrations, we measured the sound-induced head vibrations in three dimensions when snakes were exposed to sound pressure at threshold levels. In general, head vibrations induced by threshold-level sound pressure were equal to or greater than those induced by threshold-level vibrations, and therefore sound-pressure sensitivity can be explained by sound-induced head vibration. From this we conclude that pythons, and possibly all snakes, lost effective pressure hearing with the complete reduction of a functional outer and middle ear, but have an acute vibration sensitivity that may be used for communication and detection of predators and prey.

Evaluation of the role of the cyclooxygenase signaling pathway during inflammation in skin and muscle tissues of ball pythons (Python regius).

PubMed

Sadler, Ryan A; Schumacher, Juergen P; Rathore, Kusum; Newkirk, Kim M; Cole, Grayson; Seibert, Rachel; Cekanova, Maria

2016-05-01

OBJECTIVE To determine degrees of production of cyclooxygenase (COX)-1 and -2 and other mediators of inflammation in noninflamed and inflamed skin and muscle tissues in ball pythons (Python regius). ANIMALS 6 healthy adult male ball pythons. PROCEDURES Biopsy specimens of noninflamed skin and muscle tissue were collected from anesthetized snakes on day 0. A 2-cm skin and muscle incision was then made 5 cm distal to the biopsy sites with a CO2 laser to induce inflammation. On day 7, biopsy specimens of skin and muscle tissues were collected from the incision sites. Inflamed and noninflamed tissue specimens were evaluated for production of COX-1, COX-2, phosphorylated protein kinase B (AKT), total AKT, nuclear factor κ-light-chain-enhancer of activated B cells, phosphorylated extracellular receptor kinases (ERKs) 1 and 2, and total ERK proteins by western blot analysis. Histologic evaluation was performed on H&E-stained tissue sections. RESULTS All biopsy specimens of inflamed skin and muscle tissues had higher histologic inflammation scores than did specimens of noninflamed tissue. Inflamed skin specimens had significantly greater production of COX-1 and phosphorylated ERK than did noninflamed skin specimens. Inflamed muscle specimens had significantly greater production of phosphorylated ERK and phosphorylated AKT, significantly lower production of COX-1, and no difference in production of COX-2, compared with production in noninflamed muscle specimens. CONCLUSIONS AND CLINICAL RELEVANCE Production of COX-1, but not COX-2, was significantly greater in inflamed versus noninflamed skin specimens from ball pythons. Additional research into the reptilian COX signaling pathway is warranted.

Effect of water deprivation on baseline and stress-induced corticosterone levels in the Children's python (Antaresia childreni).

PubMed

Dupoué, Andréaz; Angelier, Frédéric; Lourdais, Olivier; Bonnet, Xavier; Brischoux, François

2014-02-01

Corticosterone (CORT) secretion is influenced by endogenous factors (e.g., physiological status) and environmental stressors (e.g., ambient temperature). Heretofore, the impact of water deprivation on CORT plasma levels has not been thoroughly investigated. However, both baseline CORT and stress-induced CORT are expected to respond to water deprivation not only because of hydric stress per se, but also because CORT is an important mineralocorticoid in vertebrates. We assessed the effects of water deprivation on baseline CORT and stress-induced CORT, in Children's pythons (Antaresia childreni), a species that experiences seasonal droughts in natural conditions. We imposed a 52-day water deprivation on a group of unfed Children's pythons (i.e., water-deprived treatment) and provided water ad libitum to another group (i.e., control treatment). We examined body mass variations throughout the experiment, and baseline CORT and stress-induced CORT at the end of the treatments. Relative body mass loss averaged ~10% in pythons without water, a value 2 to 4 times higher compared to control snakes. Following re-exposition to water, pythons from the water-deprived treatment drank readily and abundantly and attained a body mass similar to pythons from the control treatment. Together, these results suggest a substantial dehydration as a consequence of water deprivation. Interestingly, stress-induced but not baseline CORT level was significantly higher in water-deprived snakes, suggesting that baseline CORT might not respond to this degree of dehydration. Therefore, possible mineralocorticoid role of CORT needs to be clarified in snakes. Because dehydration usually induces adjustments (reduced movements, lowered body temperature) to limit water loss, and decreases locomotor performances, elevated stress-induced CORT in water-deprived snakes might therefore compensate for altered locomotor performances. Future studies should test this hypothesis. Copyright © 2013 Elsevier Inc. All rights reserved.

Emerge - A Python environment for the modeling of subsurface transfers

NASA Astrophysics Data System (ADS)

Lopez, S.; Smai, F.; Sochala, P.

2014-12-01

The simulation of subsurface mass and energy transfers often relies on specific codes that were mainly developed using compiled languages which usually ensure computational efficiency at the expense of relatively long development times and relatively rigid software. Even if a very detailed, possibly graphical, user-interface is developed the core numerical aspects are rarely accessible and the smallest modification will always need a compilation step. Thus, user-defined physical laws or alternative numerical schemes may be relatively difficult to use. Over the last decade, Python has emerged as a popular and widely used language in the scientific community. There already exist several libraries for the pre and post-treatment of input and output files for reservoir simulators (e.g. pytough). Development times in Python are considerably reduced compared to compiled languages, and programs can be easily interfaced with libraries written in compiled languages with several comprehensive numerical libraries that provide sequential and parallel solvers (e.g. PETSc, Trilinos…). The core objective of the Emerge project is to explore the possibility to develop a modeling environment in full Python. Consequently, we are developing an open python package with the classes/objects necessary to express, discretize and solve the physical problems encountered in the modeling of subsurface transfers. We heavily relied on Python to have a convenient and concise way of manipulating potentially complex concepts with a few lines of code and a high level of abstraction. Our result aims to be a friendly numerical environment targeting both numerical engineers and physicist or geoscientists with the possibility to quickly specify and handle geometries, arbitrary meshes, spatially or temporally varying properties, PDE formulations, boundary conditions…

Comparison of cyclic correlation algorithm implemented in matlab and python

NASA Astrophysics Data System (ADS)

Carr, Richard; Whitney, James

Simulation is a necessary step for all engineering projects. Simulation gives the engineers an approximation of how their devices will perform under different circumstances, without hav-ing to build, or before building a physical prototype. This is especially true for space bound devices, i.e., space communication systems, where the impact of system malfunction or failure is several orders of magnitude over that of terrestrial applications. Therefore having a reliable simulation tool is key in developing these devices and systems. Math Works Matrix Laboratory (MATLAB) is a matrix based software used by scientists and engineers to solve problems and perform complex simulations. MATLAB has a number of applications in a wide variety of fields which include communications, signal processing, image processing, mathematics, eco-nomics and physics. Because of its many uses MATLAB has become the preferred software for many engineers; it is also very expensive, especially for students and startups. One alternative to MATLAB is Python. The Python is a powerful, easy to use, open source programming environment that can be used to perform many of the same functions as MATLAB. Python programming environment has been steadily gaining popularity in niche programming circles. While there are not as many function included in the software as MATLAB, there are many open source functions that have been developed that are available to be downloaded for free. This paper illustrates how Python can implement the cyclic correlation algorithm and com-pares the results to the cyclic correlation algorithm implemented in the MATLAB environment. Some of the characteristics to be compared are the accuracy and precision of the results, and the length of the programs. The paper will demonstrate that Python is capable of performing simulations of complex algorithms such cyclic correlation.

19 CFR 12.152 - Prohibitions and conditions on the importation and exportation of rough diamonds.

Code of Federal Regulations, 2014 CFR

2014-04-01

... exportation of rough diamonds. 12.152 Section 12.152 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION... rough diamonds. (a) General. The Clean Diamond Trade Act (Pub. L. 108-19) requires the President... States, of any rough diamond, from whatever source, that has not been controlled through the Kimberley...

Electrical Conductivity Of Diamond Up To 1,200 Degrees C

NASA Technical Reports Server (NTRS)

Vandersande, Jan W.; Zoltan, Leslie D.

1993-01-01

Report discusses measurements of electrical conductivities of two synthetic diamond films, three synthetic diamondlike films, and two natural type IIa diamonds at temperatures from ambient to 1,200 degrees C. Measurements performed to compare electrical conductivities of state-of-the-art diamond films with those of natural insulating diamond, particularly at temperatures above 700 degrees C.

Fabrication of diamond based sensors for use in extreme environments

DOE PAGES

Samudrala, Gopi K.; Moore, Samuel L.; Vohra, Yogesh K.

2015-04-23

Electrical and magnetic sensors can be lithographically fabricated on top of diamond substrates and encapsulated in a protective layer of chemical vapor deposited single crystalline diamond. This process when carried out on single crystal diamond anvils employed in high pressure research is termed as designer diamond anvil fabrication. These designer diamond anvils allow researchers to study electrical and magnetic properties of materials under extreme conditions without any possibility of damaging the sensing elements. We describe a novel method for the fabrication of designer diamond anvils with the use of maskless lithography and chemical vapor deposition in this paper. This methodmore » can be utilized to produce diamond based sensors which can function in extreme environments of high pressures, high and low temperatures, corrosive and high radiation conditions. Here, we demonstrate applicability of these diamonds under extreme environments by performing electrical resistance measurements during superconducting transition in rare earth doped iron-based compounds under high pressures to 12 GPa and low temperatures to 10 K.« less

Fabrication of diamond based sensors for use in extreme environments

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

Samudrala, Gopi K.; Moore, Samuel L.; Vohra, Yogesh K.

Electrical and magnetic sensors can be lithographically fabricated on top of diamond substrates and encapsulated in a protective layer of chemical vapor deposited single crystalline diamond. This process when carried out on single crystal diamond anvils employed in high pressure research is termed as designer diamond anvil fabrication. These designer diamond anvils allow researchers to study electrical and magnetic properties of materials under extreme conditions without any possibility of damaging the sensing elements. We describe a novel method for the fabrication of designer diamond anvils with the use of maskless lithography and chemical vapor deposition in this paper. This methodmore » can be utilized to produce diamond based sensors which can function in extreme environments of high pressures, high and low temperatures, corrosive and high radiation conditions. Here, we demonstrate applicability of these diamonds under extreme environments by performing electrical resistance measurements during superconducting transition in rare earth doped iron-based compounds under high pressures to 12 GPa and low temperatures to 10 K.« less

Laser patterning of diamond films

NASA Astrophysics Data System (ADS)

Narayan, J.; Chen, X.

1992-04-01

Selective deposition and fine-scale patterning of hot filament deposited diamond films by the use of pulsed laser irradiation on silicon and copper substrates are reported. The substrates were abraded with diamond and alumina powders before hot-filament chemical vapor deposition. A drastic enhancement in diamond nucleation (using hot-filament chemical vapor deposition) was observed on specimens treated with diamond powder, whereas enhancement on specimens pretreated with alumina powder was relatively insignificant. It is found that the seeding of diamond crystals was substantially reduced by pulsed laser annealing/melting which removes the plastic damage as well as the seed crystals introduced by diamond powder pretreatment. The selective deposition or fine-scale patterning of diamond films was achieved either by a shadow masking or by scanning a focused laser beam to generate desired patterns. The nucleation can also be enhanced by laser deposition of thin films, such as diamond-like carbon and tungsten carbide (WC), and selective deposition and patterning achieved by controlled removal or deposition of the above films.

Effect of Minor Titanium Addition on Copper/Diamond Composites Prepared by Hot Forging

NASA Astrophysics Data System (ADS)

Yang, Fei; Sun, Wei; Singh, Ajit; Bolzoni, Leandro

2018-03-01

Copper/diamond composites have great potential to lead the next generation of advanced heat sink materials for use in high-power electronic devices and high-density integrated circuits because of their potential excellent properties of high thermal conductivity and close thermal expansion to the chip materials (e.g., Si, InP, GaAs). However, the poor wettability between copper and diamond presents a challenge for synthesizing copper/diamond composites with effective metallurgical bonding and satisfied thermal performance. In this article, copper/diamond composites were successfully prepared by hot forging of elemental copper and artificial diamond powders with small amounts (0 vol.%, 3 vol.% and 5 vol.%) of titanium additives. Microstructure observation and mechanical tests showed that adding minor titanium additions in the copper/diamond composite resulted in fewer cracks in the composites' microstructure and significantly improved the bonding between the copper and diamond. The strongest bonding strength was achieved for the copper/diamond composite with 3 vol.% titanium addition, and the possible reasons were discussed.

Cathodoluminescence of diamond as an indicator of its metamorphic history

NASA Astrophysics Data System (ADS)

Kopylova, Maya; Bruce, Loryn; Longo, Micaela; Ryder, John; Dobrzhinetskaya, Larissa

2010-05-01

Diamond displays a supreme resistance to chemical and mechanical weathering, ensuring its survival through complex and prolonged crustal processes, including metamorphism and exhumation. For these reasons, volcanic sources and secondary and tertiary collectors for detrital placer diamonds, like Ural or Bingara diamonds, may be difficult to determine. If metamorphic processes leave their marks on diamond, they can be used to reconstruct crustal geologic processes and ages of primary diamondiferous volcanics. Four diamond suites extracted from metamorphic rocks have been characterized using optical CL, infrared and CL spectroscopy, and photoluminescence at the liquid nitrogen temperature. The studied diamonds are from the ~2.7 Ga sedimentary conglomerate and lamprophyric breccia metamorphosed in the greenschist facies (Wawa, Northern Ontario, Canada) during the 2.67 Ga Kenoran orogeny, and from the ultra-high pressure (UHP) terranes of Kokchetav (Kazakhstan) and Erzgebirge (Germany) exhumated in the Paleozoic. Wawa diamonds (Type IaAB and Type II) displayed green, yellow, orange, and red CL colours controlled by the CL emittance at 520, 576 nm, and between 586 and 664 nm. The UHP terranes diamonds show much weaker CL; few luminescent stones display CL peaks at 395, 498, 528 nm and a broad band at 580-668 nm. In contrast, most common diamonds found in unmetamorphosed rocks, i.e. octahedrally grown Type IaAB stones, luminescence blue emitting light at ~415-440 nm and 480-490 nm. There is a noticeable difference between cathodoluminescence of these diamonds and diamonds in metamorphic rocks. The studied diamonds that experienced metamorphism show a shift of CL emission to longer wavelengths (above 520 nm) and to green, yellow and red CL colours. Photoluminescence has the high resolution necessary to assign luminescence to specific optical centers of diamond. Diamonds in metamorphic rocks contain H3 (pairs of substitutional nitrogen atoms separated by a vacancy) and NVo optical centers (neutrally charged complexes of a vacancy and a single nitrogen). We ascribe the effect of metamorphism on the diamond CL to low-T, low-P deformation that creates lattice dislocations and vacancies. These combine with substitutional N to make and enhance optical centers. The metamorphism-induced CL anneals when diamonds are stored at high-T mantle conditions, as the mobility of dislocations at T>750oC quenches the luminescence. Indeed, all studied diamonds that displayed unusual green, yellow and red CL were found in low and medium grade metamorphic rocks, i.e. Wawa greenschists (T<350oC and P< 3 kb) and Kokchetav and Erzgebirge UHP terranes retrograded in the amphibolite facies (T<750oC, P<14 kb) Our study suggest that a low abundance of octahedrally grown Type IaAB diamonds with blue CL colours among detrital diamonds may indicate that the stones may have once been a part of a low- or medium-grade metamorphic terrane. The CL characteristics superimposed by metamorphism could survive through billions of years of the geological history if not annealed by a high -T process. The discovered record of metamorphism in the diamond crystal lattice provides an opportunity for a better reconstruction of the crustal history and provenance studies of diamond.

Alluvial diamond resource potential and production capacity assessment of Mali

USGS Publications Warehouse

Chirico, Peter G.; Barthelemy, Francis; Kone, Fatiaga

2010-01-01

In May of 2000, a meeting was convened in Kimberley, South Africa, and attended by representatives of the diamond industry and leaders of African governments to develop a certification process intended to assure that rough, exported diamonds were free of conflictual concerns. This meeting was supported later in 2000 by the United Nations in a resolution adopted by the General Assembly. By 2002, the Kimberley Process Certification Scheme (KPCS) was ratified and signed by diamond-producing and diamond-importing countries. Over 70 countries were included as members of the KPCS at the end of 2007. To prevent trade in "conflict diamonds" while protecting legitimate trade, the KPCS requires that each country set up an internal system of controls to prevent conflict diamonds from entering any imported or exported shipments of rough diamonds. Every diamond or diamond shipment must be accompanied by a Kimberley Process (KP) certificate and be contained in tamper-proof packaging. The objective of this study was (1) to assess the naturally occurring endowment of diamonds in Mali (potential resources) based on geological evidence, previous studies, and recent field data and (2) to assess the diamond-production capacity and measure the intensity of mining activity. Several possible methods can be used to estimate the potential diamond resource. However, because there is generally a lack of sufficient and consistent data recording all diamond mining in Mali and because time to conduct fieldwork and accessibility to the diamond mining areas are limited, four different methodologies were used: the cylindrical calculation of the primary kimberlitic deposits, the surface area methodology, the volume and grade approach, and the content per kilometer approach. Approximately 700,000 carats are estimated to be in the alluvial deposits of the Kenieba region, with 540,000 carats calculated to lie within the concentration grade deposits. Additionally, 580,000 carats are estimated to have been released from the primary kimberlites in the region. Therefore, the total estimated diamond resources in the Kenieba region are thought to be nearly 1,300,000 carats. The Bougouni zones are estimated to have 1,000,000 carats with more than half, 630,000 carats, contained in concentrated deposits. When combined, the Kenieba and Bougouni regions of Mali are estimated to be host to 2,300,000 carats of diamonds.

Diamonds in ophiolites: Contamination or a new diamond growth environment?

NASA Astrophysics Data System (ADS)

Howell, D.; Griffin, W. L.; Yang, J.; Gain, S.; Stern, R. A.; Huang, J.-X.; Jacob, D. E.; Xu, X.; Stokes, A. J.; O'Reilly, S. Y.; Pearson, N. J.

2015-11-01

For more than 20 years, the reported occurrence of diamonds in the chromites and peridotites of the Luobusa massif in Tibet (a complex described as an ophiolite) has been widely ignored by the diamond research community. This skepticism has persisted because the diamonds are similar in many respects to high-pressure high-temperature (HPHT) synthetic/industrial diamonds (grown from metal solvents), and the finding previously has not been independently replicated. We present a detailed examination of the Luobusa diamonds (recovered from both peridotites and chromitites), including morphology, size, color, impurity characteristics (by infrared spectroscopy), internal growth structures, trace-element patterns, and C and N isotopes. A detailed comparison with synthetic industrial diamonds shows many similarities. Cubo-octahedral morphology, yellow color due to unaggregated nitrogen (C centres only, Type Ib), metal-alloy inclusions and highly negative δ13C values are present in both sets of diamonds. The Tibetan diamonds (n = 3) show an exceptionally large range in δ15N (-5.6 to + 28.7 ‰) within individual crystals, and inconsistent fractionation between {111} and {100} growth sectors. This in contrast to large synthetic HPHT diamonds grown by the temperature gradient method, which have with δ15N = 0 ‰ in {111} sectors and + 30 ‰ in {100} sectors, as reported in the literature. This comparison is limited by the small sample set combined with the fact the diamonds probably grew by different processes. However, the Tibetan diamonds do have generally higher concentrations and different ratios of trace elements; most inclusions are a NiMnCo alloy, but there are also some small REE-rich phases never seen in HPHT synthetics. These characteristics indicate that the Tibetan diamonds grew in contact with a C-saturated Ni-Mn-Co-rich melt in a highly reduced environment. The stable isotopes indicate a major subduction-related contribution to the chemical environment. The unaggregated nitrogen, combined with the lack of evidence for resorption or plastic deformation, suggests a short (geologically speaking) residence in the mantle. Previously published models to explain the occurrence of the diamonds, and other phases indicative of highly reduced conditions and very high pressures, have failed to take into account the characteristics of the diamonds and the implications for their formation. For these diamonds to be seriously considered as the result of a natural growth environment requires a new understanding of mantle conditions that could produce them.

Theoretical analysis of SAW propagation characteristics in (100) oriented AlN/diamond structure.

PubMed

Ro, Ruyen; Chiang, Yuan-Feng; Sung, Chia-Chi; Lee, Ruyue; Wu, Sean

2010-01-01

In this study, the finite element method is employed to calculate SAW characteristics in (100) AlN/diamond based structures with different electrical interfaces; i.e., IDT/ AlN/diamond, AlN/IDT/diamond, IDT/AlN/thin metal film/ diamond, and thin metal film/AlN/IDT/diamond. The effects of Cu and Al electrodes as well as the thickness of electrode on phase velocity, coupling coefficient, and reflectivity of SAWs are illustrated. Propagation characteristics of SAWs in (002) AlN/diamond-based structures are also presented for comparison. Simulation results show that to retain a large reflectivity for the design of RF filters and duplexers, the Cu IDT/(100) AlN/diamond structure possesses the highest phase velocity and largest coupling coefficient at the smallest AlN film thickness- to-wavelength ratio.

Hydrogen-terminated diamond vertical-type metal oxide semiconductor field-effect transistors with a trench gate

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

Inaba, Masafumi, E-mail: inaba-ma@ruri.waseda.jp; Muta, Tsubasa; Kobayashi, Mikinori

2016-07-18

The hydrogen-terminated diamond surface (C-H diamond) has a two-dimensional hole gas (2DHG) layer independent of the crystal orientation. A 2DHG layer is ubiquitously formed on the C-H diamond surface covered by atomic-layer-deposited-Al{sub 2}O{sub 3}. Using Al{sub 2}O{sub 3} as a gate oxide, C-H diamond metal oxide semiconductor field-effect transistors (MOSFETs) operate in a trench gate structure where the diamond side-wall acts as a channel. MOSFETs with a side-wall channel exhibit equivalent performance to the lateral C-H diamond MOSFET without a side-wall channel. Here, a vertical-type MOSFET with a drain on the bottom is demonstrated in diamond with channel current modulationmore » by the gate and pinch off.« less

Grain-size-dependent diamond-nondiamond composite films: characterization and field-emission properties.

PubMed

Pradhan, Debabrata; Lin, I Nan

2009-07-01

Diamond films with grain sizes in the range of 5-1000 nm and grain boundaries containing nondiamond carbon are deposited on a silicon substrate by varying the deposition parameters. The overall morphologies of the as-deposited diamond-nondiamond composite films are examined by scanning electron microscopy and atomic force microscopy, which show a decrease in the surface roughness with a decrease in the diamond grain size. Although the Raman spectra show predominately nondiamond carbon features in the diamond films with smaller grain sizes, glancing-angle X-ray diffraction spectra show the absence of graphitic carbon features and the presence of very small amorphous carbon diffraction features. The CH4 percentage (%) in Ar and H2 plasma during deposition plays a crucial role in the formation of diamond films with different grain sizes and nondiamond carbon contents, which, in turn, determines the field-emission behavior of the corresponding diamond films. The smaller the grain size of the diamond, the lower is the turn-on field for electron emission. A lower turn-on field is obtained from the diamond films deposited with 2-5% CH4 than from the films deposited with either 1% or 7.5% CH4 in the Ar medium. A current density greater than 1 mA/cm2 (at 50 V/microm) is obtained from diamond films deposited with a higher percentage of CH4. A model is suggested for the field-emission mechanism from the diamond-nondiamond composite films with different diamond grain sizes and nondiamond contents.

Teaching CS1 with Python GUI Game Programming

NASA Astrophysics Data System (ADS)

Wang, Hong

2010-06-01

Python is becoming a popular programming language in teaching freshman programming courses. The author designed a sequence of game programming labs using Pygame to further help engage students and to improve their programming skills. The class survey showed that the adoption of Pygame is successful.

Detecting Moving Sources in Astronomical Images (Abstract)

NASA Astrophysics Data System (ADS)

Block, A.

2018-06-01

(Abstract only) Source detection in images is an important part of analyzing astronomical data. This project discusses an implementation of image detection in python, as well as processes for performing photometry in python. Application of these tools to looking for moving sources is also discussed.

SWMM5 Application Programming Interface and PySWMM: A Python Interfacing Wrapper

EPA Science Inventory

In support of the OpenWaterAnalytics open source initiative, the PySWMM project encompasses the development of a Python interfacing wrapper to SWMM5 with parallel ongoing development of the USEPA Stormwater Management Model (SWMM5) application programming interface (API). ...

HTSeq--a Python framework to work with high-throughput sequencing data.

PubMed

Anders, Simon; Pyl, Paul Theodor; Huber, Wolfgang

2015-01-15

A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. © The Author 2014. Published by Oxford University Press.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

PubMed

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

BioC implementations in Go, Perl, Python and Ruby

PubMed Central

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W. John; Comeau, Donald C.

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ PMID:24961236

graphkernels: R and Python packages for graph comparison

PubMed Central

Ghisu, M Elisabetta; Llinares-López, Felipe; Borgwardt, Karsten

2018-01-01

Abstract Summary Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel. The core of all graph kernels is implemented in C ++ for efficiency. Using the kernel matrices computed by the package, we can easily perform tasks such as classification, regression and clustering on graph-structured samples. Availability and implementation The R and Python packages including source code are available at https://CRAN.R-project.org/package=graphkernels and https://pypi.python.org/pypi/graphkernels. Contact mahito@nii.ac.jp or elisabetta.ghisu@bsse.ethz.ch Supplementary information Supplementary data are available online at Bioinformatics. PMID:29028902

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

PubMed Central

Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

2015-01-01

Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas.

PubMed

Esquerré, Damien; Scott Keogh, J

2016-07-01

Pythons and boas are globally distributed and distantly related radiations with remarkable phenotypic and ecological diversity. We tested whether pythons, boas and their relatives have evolved convergent phenotypes when they display similar ecology. We collected geometric morphometric data on head shape for 1073 specimens representing over 80% of species. We show that these two groups display strong and widespread convergence when they occupy equivalent ecological niches and that the history of phenotypic evolution strongly matches the history of ecological diversification, suggesting that both processes are strongly coupled. These results are consistent with replicated adaptive radiation in both groups. We argue that strong selective pressures related to habitat-use have driven this convergence. Pythons and boas provide a new model system for the study of macro-evolutionary patterns of morphological and ecological evolution and they do so at a deeper level of divergence and global scale than any well-established adaptive radiation model systems. © 2016 John Wiley & Sons Ltd/CNRS.

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

TESP combines existing domain simulators in the electric power grid, with new transactive agents, growth models and evaluation scripts. The existing domain simulators include GridLAB-D for the distribution grid and single-family residential buildings, MATPOWER for transmission and bulk generation, and EnergyPlus for large buildings. More are planned for subsequent versions of TESP. The new elements are: TEAgents - simulate market participants and transactive systems for market clearing. Some of this functionality was extracted from GridLAB-D and implemented in Python for customization by PNNL and others; Growth Model - a means for simulating system changes over a multiyear period, including bothmore » normal load growth and specific investment decisions. Customizable in Python code; and Evaluation Script - a means of evaluating different transactive systems through customizable post-processing in Python code. TESP provides a method for other researchers and vendors to design transactive systems, and test them in a virtual environment. It allows customization of the key components by modifying Python code.« less

graphkernels: R and Python packages for graph comparison.

PubMed

Sugiyama, Mahito; Ghisu, M Elisabetta; Llinares-López, Felipe; Borgwardt, Karsten

2018-02-01

Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel. The core of all graph kernels is implemented in C ++ for efficiency. Using the kernel matrices computed by the package, we can easily perform tasks such as classification, regression and clustering on graph-structured samples. The R and Python packages including source code are available at https://CRAN.R-project.org/package=graphkernels and https://pypi.python.org/pypi/graphkernels. mahito@nii.ac.jp or elisabetta.ghisu@bsse.ethz.ch. Supplementary data are available online at Bioinformatics. © The Author(s) 2017. Published by Oxford University Press.

ChemoPy: freely available python package for computational biology and chemoinformatics.

PubMed

Cao, Dong-Sheng; Xu, Qing-Song; Hu, Qian-Nan; Liang, Yi-Zeng

2013-04-15

Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.

3-D X-ray tomography of diamondiferous mantle eclogite xenoliths, Siberia: A review

NASA Astrophysics Data System (ADS)

Howarth, Geoffrey H.; Sobolev, Nikolay V.; Pernet-Fisher, John F.; Ketcham, Richard A.; Maisano, Jessica A.; Pokhilenko, Lyudmila N.; Taylor, Dawn; Taylor, Lawrence A.

2015-04-01

Diamonds form over billions of years, hundreds of kilometers beneath the Earth's surface, and in combination with inclusions trapped within, provide important constraints on the evolution of the mantle over geological time. Diamonds are generally studied as individual crystals sourced from highly explosive kimberlite pipes, which entrain and subsequently disaggregate mantle fragments (xenoliths) en route to the surface. This has resulted in a general absence of robust textural descriptions of diamonds relative to their hosting mantle protolith. The textural associations of diamonds within their mantle host rocks are reviewed here on the basis of a compilation of X-ray tomographic data for 17 diamondiferous eclogite xenoliths from Siberian kimberlites. This review represents a comprehensive description of diamonds relative to their host silicates. The lack of such descriptions in previous studies is largely due to the rarity of these xenoliths, the difficulty in preparing petrographic thin sections containing diamonds, and their high-monetary value. High-resolution computed X-ray tomography (HRCXT) produces up to 1200 sequential 2-D slices through individual xenoliths, each of which represents a 'pseudo thin-section' with a resolution on the order of 5-20 μm. The improved resolution of X-ray imaging in recent studies allows for the identification of not only primary minerals, but metasomatic minerals assemblages, including: 'spongy' textured clinopyroxene, phlogopite/K-richterite, and hercynitic spinel, allowing for the delineation of distinct metasomatic pathways through the xenoliths and their relationship to diamonds. Diamonds are observed in three distinct textural settings, potentially representing several temporally distinct diamond growth events, these setting includes: (1) diamonds completely enclosed in garnet; (2) diamonds associated with highly embayed silicate grain boundaries; and (3) diamonds contained within distinct metasomatic 'plumbing-systems'. Diamonds observed completely enclosed in garnets suggest an early diamond-forming event prior to major re-crystallization and eclogite formation during subduction. The occurrence of diamond in association with embayed garnets suggests that diamond grew at the expense of the hosting silicate protolith. In addition, the spatial relationships of diamonds with metasomatic pathways, which are generally interpreted to result from late-stage proto-kimberlitic fluid percolation, indicate a period of diamond growth occurring close to, but prior to, the time of kimberlite emplacement. Furthermore, the paragenesis of sulfides within eclogite xenoliths are described using 3-D models for entire xenoliths volumes, providing important constraints of the timing of sulfide mobilization within the mantle. Three-D animations created using X-ray tomography data for ten of the xenoliths can be viewed at the following link: http://eps.utk.edu/faculty/taylor/tomography.php

Diamond growth from oxidized carbon sources beneath the Northern Slave Craton, Canada: A δ 13C-N study of eclogite-hosted diamonds from the Jericho kimberlite

NASA Astrophysics Data System (ADS)

Smart, Katie A.; Chacko, Thomas; Stachel, Thomas; Muehlenbachs, Karlis; Stern, Richard A.; Heaman, Larry M.

2011-10-01

Diamonds from high- and low-MgO groups of eclogite xenoliths from the Jericho kimberlite, Slave Craton, Canada were analyzed for carbon isotope compositions and nitrogen contents. Diamonds extracted from the two groups show remarkably different nitrogen abundances and δ 13C values. While diamonds from high-MgO eclogites have low nitrogen contents (5-82 ppm) and extremely low δ 13C values clustering at ˜-40‰, diamonds from the low-MgO eclogites have high nitrogen contents (>1200 ppm) and δ 13C values from -3.5‰ to -5.3‰. Coupled cathodoluminescence (CL) imaging and SIMS analysis of the Jericho diamonds provides insight into diamond growth processes. Diamonds from the high-MgO eclogites display little CL structure and generally have constant δ 13C values and nitrogen contents. Some of these diamonds have secondary rims with increasing δ 13C values from -40‰ to ˜-34‰, which suggests secondary diamond growth occurred from an oxidized growth medium. The extreme negative δ 13C values of the high-MgO eclogite diamonds cannot be produced by Rayleigh isotopic fractionation of average mantle-derived carbon (-5‰) or carbon derived from typical organic matter (˜-25‰). However, excursions in δ 13C values to -60‰ are known in the organic sedimentary record at ca. 2.7 and 2.0 Ga, such that diamonds from the high-MgO eclogites could have formed from similar organic matter brought into the Slave lithospheric mantle by subduction. SIMS analyses of a diamond from a low-MgO eclogite show an outer core with systematic rimwards increases in δ 13C values coupled with decreases in nitrogen contents, and a rim with pronounced alternating growth zones. The coupled δ 13C-nitrogen data suggest that the diamond precipitated during fractional crystallization from an oxidized fluid/melt from which nitrogen was progressively depleted during growth. Model calculations of the co-variation of δ 13C-N yielded a partition coefficient ( KN) value of 5, indicating that nitrogen is strongly compatible in diamond relative to the growth medium. δ 13C values of diamond cores (-4‰) dictate the growth medium had higher δ 13C values than primary mantle-derived carbon. Therefore, possible carbon sources for the low-MgO eclogite diamonds include oxidized mantle-derived (e.g. protokimberlite or carbonatite) fluids/melts that underwent some fractionation during migration or, devolatilized subducted carbonates.

Near-ultraviolet micro-Raman study of diamond grown on GaN

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

Nazari, M., E-mail: m-n79@txstate.edu; Hancock, B. L.; Anderson, J.

2016-01-18

Ultraviolet (UV) micro-Raman measurements are reported of diamond grown on GaN using chemical vapor deposition. UV excitation permits simultaneous investigation of the diamond (D) and disordered carbon (DC) comprising the polycrystalline layer. From line scans of a cross-section along the diamond growth direction, the DC component of the diamond layer is found to be highest near the GaN-on-diamond interface and diminish with characteristic length scale of ∼3.5 μm. Transmission electron microscopy (TEM) of the diamond near the interface confirms the presence of DC. Combined micro-Raman and TEM are used to develop an optical method for estimating the DC volume fraction.

Study on effect of plasma surface treatments for diamond deposition by DC arc plasmatron.

PubMed

Kang, In-Je; Joa, Sang-Beom; Lee, Heon-Ju

2013-11-01

To improve the thermal conductivity and wear resistance of ceramic materials in the field of renewable energy technologies, diamond coating by plasma processing has been carried out in recent years. This study's goal is to improve diamond deposition on Al2O3 ceramic substrates by plasma surface treatments. Before diamond deposition was carried out in a vacuum, plasma surface treatments using Ar gas were conducted to improve conditions for deposition. We also conducted plasma processing for diamond deposition on Al2O3 ceramic substrates using a DC arc Plasmatron. The Al2O3 ceramic substrates with diamond film (5 x 15 mm2), were investigated by SEM (Scanning Electron Microscopy), AFM (Atomic Force Microscopy) and XRD (X-ray Diffractometer). Then, the C-H stretching of synthetic diamond films by FTIR (Fourier Transform Infrared Spectroscopy) was studied. We identified nanocrystalline diamond films on the Al2O3 ceramic substrates. The results showed us that the deposition rate of diamond films was 2.3 microm/h after plasma surface treatments. Comparing the above result with untreated ceramic substrates, the deposition rate improved with the surface roughness of the deposited diamond films.

Diamond Smoothing Tools

NASA Technical Reports Server (NTRS)

Voronov, Oleg

2007-01-01

Diamond smoothing tools have been proposed for use in conjunction with diamond cutting tools that are used in many finish-machining operations. Diamond machining (including finishing) is often used, for example, in fabrication of precise metal mirrors. A diamond smoothing tool according to the proposal would have a smooth spherical surface. For a given finish machining operation, the smoothing tool would be mounted next to the cutting tool. The smoothing tool would slide on the machined surface left behind by the cutting tool, plastically deforming the surface material and thereby reducing the roughness of the surface, closing microcracks and otherwise generally reducing or eliminating microscopic surface and subsurface defects, and increasing the microhardness of the surface layer. It has been estimated that if smoothing tools of this type were used in conjunction with cutting tools on sufficiently precise lathes, it would be possible to reduce the roughness of machined surfaces to as little as 3 nm. A tool according to the proposal would consist of a smoothing insert in a metal holder. The smoothing insert would be made from a diamond/metal functionally graded composite rod preform, which, in turn, would be made by sintering together a bulk single-crystal or polycrystalline diamond, a diamond powder, and a metallic alloy at high pressure. To form the spherical smoothing tip, the diamond end of the preform would be subjected to flat grinding, conical grinding, spherical grinding using diamond wheels, and finally spherical polishing and/or buffing using diamond powders. If the diamond were a single crystal, then it would be crystallographically oriented, relative to the machining motion, to minimize its wear and maximize its hardness. Spherically polished diamonds could also be useful for purposes other than smoothing in finish machining: They would likely also be suitable for use as heat-resistant, wear-resistant, unlubricated sliding-fit bearing inserts.

Comparison of cutting efficiency with different diamond burs and water flow rates in cutting lithium disilicate glass ceramic.

PubMed

Siegel, Sharon C; Patel, Tejas

2016-10-01

This study compared different diamond burs and different water flow rates on the cutting efficiency of sectioning through lithium disilicate glass ceramic. The authors used a standardized cutting regimen with 4 brands of diamond burs to section through lithium disilicate glass ceramic blocks. Twelve diamonds of each brand cut through the blocks in randomized order. In the first part of the study, the authors recorded sectioning rates in millimeters per minute for each diamond bur as a measure of cutting efficiency. In the second part of the study, the authors compared sectioning rates using only 1 brand of diamond bur, with 3 different water flow rates. The authors averaged and compared cutting rates of each brand of diamond bur and the cutting rates for each flow rate using an analysis of variance and determined the differences with a Tukey honest significant difference test. One diamond bur cut significantly slower than the other 3, and one diamond bur cut significantly faster than 2 of the others. The diamond bur cutting efficiency through lithium disilicate glass ceramic with a 20 mL/min water flow rate was significantly higher than 15 mL/min. There are differences in cutting efficiency between diamond burs when sectioning lithium disilicate glass ceramic. Use a minimum of 20 mL/min of water coolant flow when sectioning lithium disilicate glass ceramic with dental diamond burs to maximize cutting efficiency. Recommendations for specific diamond burs with a coarse grit and water flow rate of 20 mL/min can be made when removing or adjusting restorations made from lithium disilicate glass ceramic. Copyright © 2016 American Dental Association. Published by Elsevier Inc. All rights reserved.

Industrial diamond

USGS Publications Warehouse

Olson, D.W.

2011-01-01

Estimated world production of natural and synthetic industrial diamond was about 4.44 billion carats in 2010. Natural industrial diamond deposits have been found in more than 35 countries, and synthetic industrial diamond is produced in at least 15 countries.

Diamond formation through isochemical cooling of CHO fluids vs redox buffering: examples from Marange peridotitic and Zimmi eclogitic diamonds

NASA Astrophysics Data System (ADS)

Smit, Karen V.; Stachel, Thomas; Stern, Richard A.; Shirey, Steven B.; Steele, Andrew

2017-04-01

Traditional models for diamond formation within the lithospheric mantle invoke either carbonate reduction or methane oxidation. Both these mechanisms require some oxygen exchange with the surrounding wall-rock at the site of diamond precipitation. However, peridotite does not have sufficient buffering capacity to allow for diamond formation via these traditional models and instead peridotitic diamonds may form through isochemical cooling of H2O-rich CHO fluids [1]. Marange mixed-habit diamonds from eastern Zimbabwe provide the first natural confirmation of this new diamond growth model [2]. Although Marange diamonds do not contain any silicate or sulphide inclusions, they contain Ni-N-vacancy complexes detected through photoluminescence (PL) spectroscopy that suggest the source fluids equilibrated in the Ni-rich depleted peridotitic lithosphere. Cuboid sectors also contain abundant micro-inclusions of CH4, the first direct observation of reduced CH4-rich fluids that are thought to percolate through the lithospheric mantle [2]. In fluid inclusion-free diamonds, core-to-rim trends in δ13C and N content are used to infer the speciation of the diamond-forming fluid. Core to rim trends of increasing δ13C with decreasing N content are interpreted as diamond growth from oxidized CO2- or carbonate-bearing fluids. Diamond growth from reduced species should show the opposite trends - decreasing δ13C from core to rim with decreasing N content. Within the CH4-bearing growth sectors of Marange diamonds, however, such a 'reduced' trend is not observed. Rather, δ13C increases from core to rim within a homogeneously grown zone [2]. These contradictory observations can be explained through either mixing between CH4- and CO2-rich end-members of hydrous fluids [2] or through closed system precipitation from an already mixed CH4-CO2 H2O-maximum fluid with XCO2 (CO2/[CO2+CH4]) between 0.3 and 0.7 [3]. These results demonstrate that Marange diamonds precipitated from cooling CH4-CO2-bearing hydrous fluids rather than through redox buffering. As this growth mechanism applies to both the fluid-rich cuboid and gem-like octahedral sectors of Marange diamonds, a non-redox model for diamond formation from mixed CH4-CO2 fluids is indicated for a wider range of gem-quality peridotitic diamonds. Indeed, at the redox conditions of global diamond-bearing lithospheric mantle (FMQ -2 to -4; [4]), CHO fluids are strongly water-dominated and contain both CH4 and CO2 as dominant carbon species [5]. By contrast diamond formation in eclogitic assemblages, through either redox buffering or cooling of carbon-bearing fluids, is not as well constrained. Zimmi diamonds from the West African craton have eclogitic sulphide inclusions (with low Ni and high Re/Os) and formed at 650 Ma, overlapping with the timing of subduction [6]. In one Zimmi diamond, a core to rim trend of decreasing δ13C (-23.4 to -24.5 ) and N content is indicative of formation from reduced C2H6/CH4-rich fluids, likely derived from oceanic crust recycled during Neoproterozoic subduction. Unlike mixed CH4-CO2 fluids near the water maximum, isochemical cooling or ascent of such reduced CHO fluids is not effficient at diamond precipitation. Furthermore, measurable carbon isotopic variations in diamond are not predicted in this model and therefore cannot be reconciled with the ˜1 ‰ internal variation seen. Consequently, this Zimmi eclogitic diamond likely formed through redox buffering of reduced subduction-related fluids, infiltrating into sulphide-bearing eclogite. References 1. Luth and Stachel, 2014. CMP, 168, 1083 2. Smit et al., 2016. Lithos, 265, 68-81 3. Stachel et al., in review 4. Stagno et al., 2013. Nature, 493, 84-88 5. Zhang and Duan, 2009. GCA 73, 2089-2102 6. Smit et al., 2016. Precamb Res, 286, 152-166

Note: Novel diamond anvil cell for electrical measurements using boron-doped metallic diamond electrodes

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

Matsumoto, R.; Sasama, Y.; Yamaguchi, T.

2016-07-15

A novel diamond anvil cell suitable for electrical transport measurements under high pressure has been developed. A boron-doped metallic diamond film was deposited as an electrode on a nano-polycrystalline diamond anvil using a microwave plasma-assisted chemical vapor deposition technique combined with electron beam lithography. The maximum pressure that can be achieved by this assembly is above 30 GPa. We report electrical transport measurements of Pb up to 8 GPa. The boron-doped metallic diamond electrodes showed no signs of degradation after repeated compression.

Industrial diamond

USGS Publications Warehouse

Olson, D.W.

2000-01-01

Part of the 1999 Industrial Minerals Review. A review of the state of the global industrial diamond industry in 1999 is presented. World consumption of industrial diamond has increased annually in recent years, with an estimated 500 million carats valued between $650 million and $800 million consumed in 1999. In 1999, the U.S. was the world's largest market for industrial diamond and was also one of the world's main producers; the others were Ireland, Russia, and South Africa. Uses of industrial diamonds are discussed, and prices of natural and synthetic industrial diamond are reported.

Materials Research Society Symposium Proceedings on Diamond, SiC and Nitride Wide Bandgap Semiconductors Held at San Francisco, California on 4-8 April 1994. Volume 339.

DTIC Science & Technology

1994-04-08

demonstrated that there existed no graphite phase at the surface of the as-deposited and 02 plasma treated polycrystalline diamond films. W 3- uO 2.5...diamond, highly ordered pyrolitic graphite ( HOPG ), and an amorphous carbon surface created by 1 keV ion bombardment of diamond. The diamond surface was...Library of Congress Cataloging in Publication Data Materials Research Society. Meeting (1994 : San Francisco, Calif.). Symposium D. Diamond, SiC and nitride

Fluidized bed deposition of diamond

DOEpatents

Laia, Jr., Joseph R.; Carroll, David W.; Trkula, Mitchell; Anderson, Wallace E.; Valone, Steven M.

1998-01-01

A process for coating a substrate with diamond or diamond-like material including maintaining a substrate within a bed of particles capable of being fluidized, the particles having substantially uniform dimensions and the substrate characterized as having different dimensions than the bed particles, fluidizing the bed of particles, and depositing a coating of diamond or diamond-like material upon the substrate by chemical vapor deposition of a carbon-containing precursor gas mixture, the precursor gas mixture introduced into the fluidized bed under conditions resulting in excitation mechanisms sufficient to form the diamond coating.

Diamond heteroepitaxial lateral overgrowth

DOE PAGES

Tang, Y. -H.; Bi, B.; Golding, B.

2015-02-24

A method of diamond heteroepitaxial lateral overgrowth is demonstrated which utilizes a photolithographic metal mask to pattern a thin (001) epitaxial diamond surface. Significant structural improvement was found, with a threading dislocation density reduced by two orders of magnitude at the top surface of a thick overgrown diamond layer. In the initial stage of overgrowth, a reduction of diamond Raman linewidth in the overgrown area was also realized. Thermally-induced stress and internal stress were determined by Raman spectroscopy of adhering and delaminated diamond films. As a result, the internal stress is found to decrease as sample thickness increases.

Recent results on CVD diamond radiation sensors

NASA Astrophysics Data System (ADS)

Weilhammer, P.; Adam, W.; Bauer, C.; Berdermann, E.; Bogani, F.; Borchi, E.; Bruzzi, M.; Colledani, C.; Conway, J.; Dabrowski, W.; Delpierre, P.; Deneuville, A.; Dulinski, W.; v. d. Eijk, R.; van Eijk, B.; Fallou, A.; Fish, D.; Fried, M.; Gan, K. K.; Gheeraert, E.; Grigoriev, E.; Hallewell, G.; Hall-Wilton, R.; Han, S.; Hartjes, F.; Hrubec, J.; Husson, D.; Kagan, H.; Kania, D.; Kaplon, J.; Kass, R.; Knopfle, K. T.; Krammer, M.; Manfredi, P. F.; Meier, D.; LeNormand; Pan, L. S.; Pernegger, H.; Pernicka, M.; Plano, R.; Re, V.; Riester, J. L.; Roe, S.; Roff; Rudge, A.; Schieber, M.; Schnetzer, S.; Sciortino, S.; Speziali, V.; Stelzer, H.; Stone, R.; Tapper, R. J.; Tesarek, R.; Thomson, G. B.; Trawick, M.; Trischuk, W.; Turchetta, R.; RD 42 Collaboration

1998-02-01

CVD diamond radiation sensors are being developed for possible use in trackers in the LHC experiments. The diamond promises to be radiation hard well beyond particle fluences that can be tolerated by Si sensors. Recent results from the RD 42 collaboration on charge collection distance and on radiation hardness of CVD diamond samples will be reported. Measurements with diamond tracking devices, both strip detectors and pixel detectors, will be discussed. Results from beam tests using a diamond strip detector which was read out with fast, 25 ns shaping time, radiation-hard pipeline electronics will be presented.

ConKit: a python interface to contact predictions.

PubMed

Simkovic, Felix; Thomas, Jens M H; Rigden, Daniel J

2017-07-15

Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

In situ analysis of carbon isotopes in North American diamonds

NASA Astrophysics Data System (ADS)

van Rythoven, A. D.; Hauri, E. H.; Wang, J.; McCandless, T.; Shirey, S. B.; Schulze, D. J.

2010-12-01

Diamonds from three North American kimberlite occurrences were investigated with cathodoluminescence (CL) and secondary ion mass spectrometry (SIMS) to determine their growth history and carbon isotope composition. Diamonds analyzed include fourteen from Lynx (Quebec), twelve from Kelsey Lake (Colorado) and eleven from A154 South (Diavik mine, Northwest Territories). Growth histories for the diamonds vary from simple to highly complex based on their CL images and depending on the individual stone. Deformation laminae are evident in CL images of the Lynx diamonds that typically are brownish in color. Two to five points per diamond were analyzed by SIMS for carbon isotope composition. Sample heterogeneity is minimal in terms of δ13C (vs. PDB) values. Points within single diamond had a maximum range of approximately 1 ‰. The results for the A154 South (-6.4 to -3 ‰) and Kelsey Lake (-11.2 to -2.6 ‰) stones were in accordance with earlier reported values. The Lynx kimberlite stones have anomalously high ratios and range from -3.5 to +0.2 ‰ (average: -1.4 ‰). No previous carbon isotope analyses on diamonds from Lynx or any other eastern Superior craton occurrence have been published. The diamonds possess carbon isotope ratios higher than those for the only other reported analyses of Superior craton diamonds at Wawa, Ontario (-5.5 to -1.1 ‰). In global terms, the only published analyses of diamonds that consistently contain even higher values are those from New South Wales (Australia). However, these diamonds are alluvial and contain eclogitic and/or exotic mineral inclusions. The Lynx diamonds are entirely peridotitic and from a primary deposit. The unusually low (i.e. >-5‰) δ13C values of the Lynx (and Wawa) diamonds may indicate a different carbon reservoir for the Superior craton mantle as compared to other cratons.

Quantitative analysis of trace element concentrations in some gem-quality diamonds

NASA Astrophysics Data System (ADS)

McNeill, J.; Pearson, D. G.; Klein-Ben David, O.; Nowell, G. M.; Ottley, C. J.; Chinn, I.

2009-09-01

The geochemical signature of diamond-forming fluids can be used to unravel diamond-forming processes and is of potential use in the detection of so-called 'conflict' diamonds. While fluid-rich fibrous diamonds can be analyzed by a variety of techniques, very few data have been published for fluid-poor, gem-quality diamonds because of their very low impurity levels. Here we present a new ICPMS-based (ICPMS: inductively coupled plasma mass spectrometry) method for the analysis of trace element concentrations within fluid-poor, gem-quality diamonds. The method employs a closed-system laser ablation cell. Diamonds are ablated and the products trapped for later pre-concentration into solutions that are analyzed by sector-field ICPMS. We show that our limits of quantification for a wide range of elements are at the sub-pg to low pg level. The method is applied to a suite of 10 diamonds from the Cullinan Mine (previously known as Premier), South Africa, along with other diamonds from Siberia (Mir and Udachnaya) and Venezuela. The concentrations of a wide range of elements for all the samples (expressed by weight in the solid) are very low, with rare earth elements along with Y, Nb, Cs ranging from 0.01 to 2 ppb. Large ion lithophile elements (LILE) such as Rb and Ba vary from 1 to 30 ppb. Ti ranges from ppb levels up to 2 ppm. From the combined, currently small data set we observe two kinds of diamond-forming fluids within gem diamonds. One group has enrichments in LILE over Nb, whereas a second group has normalized LILE abundances more similar to those of Nb. These two groups bear some similarity to different groups of fluid-rich diamonds, providing some supporting evidence of a link between the parental fluids for both fluid-inclusion-rich and gem diamonds.

North American Fuzzy Logic Processing Society (NAFIPS 1992), volume 1

NASA Technical Reports Server (NTRS)

Villarreal, James A. (Compiler)

1992-01-01

This document contains papers presented at the NAFIPS '92 North American Fuzzy Information Processing Society Conference. More than 75 papers were presented at this Conference, which was sponsored by NAFIPS in cooperation with NASA, the Instituto Tecnologico de Morelia, the Indian Society for Fuzzy Mathematics and Information Processing (ISFUMIP), the Instituto Tecnologico de Estudios Superiores de Monterrey (ITESM), the International Fuzzy Systems Association (IFSA), the Japan Society for Fuzzy Theory and Systems, and the Microelectronics and Computer Technology Corporation (MCC). The fuzzy set theory has led to a large number of diverse applications. Recently, interesting applications have been developed which involve the integration of fuzzy systems with adaptive processes such as neural networks and genetic algorithms. NAFIPS '92 was directed toward the advancement, commercialization, and engineering development of these technologies.

North American Fuzzy Logic Processing Society (NAFIPS 1992), volume 2

NASA Technical Reports Server (NTRS)

Villarreal, James A. (Compiler)

1992-01-01

This document contains papers presented at the NAFIPS '92 North American Fuzzy Information Processing Society Conference. More than 75 papers were presented at this Conference, which was sponsored by NAFIPS in cooperation with NASA, the Instituto Tecnologico de Morelia, the Indian Society for Fuzzy Mathematics and Information Processing (ISFUMIP), the Instituto Tecnologico de Estudios Superiores de Monterrey (ITESM), the International Fuzzy Systems Association (IFSA), the Japan Society for Fuzzy Theory and Systems, and the Microelectronics and Computer Technology Corporation (MCC). The fuzzy set theory has led to a large number of diverse applications. Recently, interesting applications have been developed which involve the integration of fuzzy systems with adaptive processes such a neural networks and genetic algorithms. NAFIPS '92 was directed toward the advancement, commercialization, and engineering development of these technologies.

Boron-doped diamond electrode: synthesis, characterization, functionalization and analytical applications.

PubMed

Luong, John H T; Male, Keith B; Glennon, Jeremy D

2009-10-01

In recent years, conductive diamond electrodes for electrochemical applications have been a major focus of research and development. The impetus behind such endeavors could be attributed to their wide potential window, low background current, chemical inertness, and mechanical durability. Several analytes can be oxidized by conducting diamond compared to other carbon-based materials before the breakdown of water in aqueous electrolytes. This is important for detecting and/or identifying species in solution since oxygen and hydrogen evolution do not interfere with the analysis. Thus, conductive diamond electrodes take electrochemical detection into new areas and extend their usefulness to analytes which are not feasible with conventional electrode materials. Different types of diamond electrodes, polycrystalline, microcrystalline, nanocrystalline and ultrananocrystalline, have been synthesized and characterized. Of particular interest is the synthesis of boron-doped diamond (BDD) films by chemical vapor deposition on various substrates. In the tetrahedral diamond lattice, each carbon atom is covalently bonded to its neighbors forming an extremely robust crystalline structure. Some carbon atoms in the lattice are substituted with boron to provide electrical conductivity. Modification strategies of doped diamond electrodes with metallic nanoparticles and/or electropolymerized films are of importance to impart novel characteristics or to improve the performance of diamond electrodes. Biofunctionalization of diamond films is also feasible to foster several useful bioanalytical applications. A plethora of opportunities for nanoscale analytical devices based on conducting diamond is anticipated in the very near future.

Development of Designer Diamond Anvils for High Pressure-High-Temperature Experiments in Support of the Stockpile Stewardship Program

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

Yogesh K. Vohra

The focus of this program at the University of Alabama at Birmingham (UAB) is to develop the next generation of designer diamond anvils that can perform simultaneous joule heating and temperature profile measurements in a diamond anvil cell. A series of tungsten-rhenium thermocouples will be fabricated onto to the anvil and encapsulated by a chemical vapor deposited diamond layer to allow for a complete temperature profile measurement across the anvil. The tip of the diamond anvil will be engineered to reduce the thermal conductivity so that the tungsten-heating coils can be deposited on top of this layer. Several different approachesmore » will be investigated to engineer the tip of the diamond anvil for reduction in thermal conductivity (a) isotopic mixture of 12C and 13C in the diamond layer, (b) doping of diamond with impurities (nitrogen and/or boron), and (c) growing diamond in a higher concentration of methane in hydrogen plasma. Under this academic alliance with Lawrence Livermore National Laboratory (LLNL), PI and his graduate students will use the lithographic and diamond polishing facility at LLNL. This proposed next generation of designer diamond anvils will allow multi-tasking capability with the ability to measure electrical, magnetic, structural and thermal data on actinide materials with unparallel sensitivity in support of the stockpile stewardship program.« less

Magnitude and extent of land subsidence in central Mexico revealed by regional InSAR ALOS time-series survey

NASA Astrophysics Data System (ADS)

Chaussard, E.; Wdowinski, S.; Amelung, F.; Cabral-Cano, E.

2013-05-01

Massive groundwater extraction is very common in Mexico and is well known to result in land subsidence. However, most surveys dedicated to land subsidence focus on one single city, mainly Mexico City, and thus fail to provide a comprehensive picture of the problem. Here we use a space-based radar remote sensing technique, known as Interferometric Synthetic Aperture Radar (InSAR) to detect land subsidence in the entire central Mexico area. We used data from the Japanese satellite ALOS, processed over 600 SAR images acquired between 2007-2011 and produced over 3000 interferograms to cover and area of 200,000 km2 in central Mexico. We identify land subsidence in twenty-one areas, including seventeen cities, namely from east to west, Puebla, Mexico city, Toluca de Lerdo, Queretaro, San Luis de la Paz, south of San Luis de la Paz, Celaya, south of Villa de Reyes, San Luis Potosi, west of Villa de Arista, Morelia, Salamanca, Irapuato, Silao, Leon, Aguascalientes, north of Aguascalientes, Zamora de Hidalgo, Guadalajara, Ahuacatlan, and Tepic. Subsidence rates of 30 cm/yr are observed in Mexico City, while in the other locations typical rates of 5-10 cm/yr are noticed. Regional surveys of this type are necessary for the development of hazard mitigation plans and efficient use of ground-based monitoring. We additionally correlate subsidence with land use, surface geology, and faults distribution and suggest that groundwater extraction for agricultural, urban, and industrial uses are the main causes of land subsidence. We also reveal that the limits of the subsiding areas often correlate with existing faults, motion on these faults being driven by water extraction rather than by tectonic activity. In all the subsiding locations we observe high ground velocity gradients emphasizing the significant risks associated with land subsidence in central Mexico. Averaged 2007-2011 ground velocity map from ALOS InSAR time-series in central Mexico, revealing land subsidence in 21 locations. The color scale shows red colors as subsidence and blue colors as uplift. The emplacement of subsiding cities are shown by black diamonds and labeled for reference, the ones included in the UNESCO World Heritage list are shown with an asterisk.

Inhibiting the oxidation of diamond during preparing the vitrified dental grinding tools by depositing a ZnO coating using direct urea precipitation method.

PubMed

Wang, Yanhui; Yuan, Yungang; Cheng, Xiaozhe; Li, Xiaohu; Zang, Jianbing; Lu, Jing; Yu, Yiqing; Xu, Xipeng

2015-08-01

Oxidation of diamond during the manufacturing of vitrified dental grinding tools would reduce the strength and sharpness of tools. Zinc oxide (ZnO) coating was deposited on diamond particles by urea precipitation method to protect diamond in borosilicate glass. The FESEM results showed that the ZnO coating was formed by plate-shaped particles. According to the TG results, the onset oxidation temperature of the ZnO-coated diamond was about 70 °C higher than the pristine diamond. The EDS results showed that ZnO diffused into the borosilicate glass during sintering. As the result, the bending strength of the composites containing ZnO-coated diamond was increased by 24% compared to that of the composites containing pristine diamond. Copyright © 2015 Elsevier B.V. All rights reserved.

Thermally stable diamond brazing

DOEpatents

Radtke, Robert P [Kingwood, TX

2009-02-10

A cutting element and a method for forming a cutting element is described and shown. The cutting element includes a substrate, a TSP diamond layer, a metal interlayer between the substrate and the diamond layer, and a braze joint securing the diamond layer to the substrate. The thickness of the metal interlayer is determined according to a formula. The formula takes into account the thickness and modulus of elasticity of the metal interlayer and the thickness of the TSP diamond. This prevents the use of a too thin or too thick metal interlayer. A metal interlayer that is too thin is not capable of absorbing enough energy to prevent the TSP diamond from fracturing. A metal interlayer that is too thick may allow the TSP diamond to fracture by reason of bending stress. A coating may be provided between the TSP diamond layer and the metal interlayer. This coating serves as a thermal barrier and to control residual thermal stress.

Single crystal diamond membranes for nanoelectronics.

PubMed

Bray, Kerem; Kato, Hiromitsu; Previdi, Rodolfo; Sandstrom, Russell; Ganesan, Kumaravelu; Ogura, Masahiko; Makino, Toshiharu; Yamasaki, Satoshi; Magyar, Andrew P; Toth, Milos; Aharonovich, Igor

2018-02-22

Single crystal, nanoscale diamond membranes are highly sought after for a variety of applications including nanophotonics, nanoelectronics and quantum information science. However, so far, the availability of conductive diamond membranes has remained an unreachable goal. In this work we present a complete nanofabrication methodology for engineering high aspect ratio, electrically active single crystal diamond membranes. The membranes have large lateral directions, exceeding ∼500 × 500 μm 2 and are only several hundreds of nanometers thick. We further realize vertical single crystal p-n junctions made from the diamond membranes that exhibit onset voltages of ∼10 V and a current of several mA. Moreover, we deterministically introduce optically active color centers into the membranes, and demonstrate for the first time a single crystal nanoscale diamond LED. The robust and scalable approach to engineer the electrically active single crystal diamond membranes offers new pathways for advanced nanophotonic, nanoelectronic and optomechanical devices employing diamond.

Carbon isotope fractionation during diamond growth in depleted peridotite: Counterintuitive insights from modelling water-maximum CHO fluids as multi-component systems

NASA Astrophysics Data System (ADS)

Stachel, T.; Chacko, T.; Luth, R. W.

2017-09-01

Because of the inability of depleted cratonic peridotites to effectively buffer oxygen fugacities when infiltrated by CHO or carbonatitic fluids, it has been proposed recently (Luth and Stachel, 2014) that diamond formation in peridotites typically does not occur by rock-buffered redox reactions as previously thought but by an oxygen-conserving reaction in which minor coexisting CH4 and CO2 components in a water-rich fluid react to form diamond (CO2 + CH4 = 2C + 2H2O). In such fluid-buffered systems, carbon isotope fractionation during diamond precipitation occurs in the presence of two dominant fluid carbon species. Carbon isotope modelling of diamond precipitation from mixed CH4- and CO2-bearing fluids reveals unexpected fundamental differences relative to diamond crystallization from a single carbon fluid species: (1) irrespective of which carbon fluid species (CH4 or CO2) is dominant in the initial fluid, diamond formation is invariably associated with progressive minor (<1‰) enrichment of diamond in 13C as crystallization proceeds. This is in contrast to diamond precipitation by rock-buffered redox processes from a fluid containing only a single carbon species, which can result in either progressive 13C enrichment (CO2 or carbonate fluids) or 13C depletion (CH4 fluids) in the diamond. (2) Fluid speciation is the key factor controlling diamond δ13 C values; as XCO2 (XCO2 = CO2/[CO2 + CH4]) in the initial fluid increases from 0.1 to 0.9 (corresponding to an increase in fO2 of 0.8 log units), the carbon isotope composition of the first-precipitated diamond decreases by 3.7‰. The tight mode in δ13C of - 5 ± 1 ‰ for diamonds worldwide places strict constraints on the dominant range of XCO2 in water-rich fluids responsible for diamond formation. Specifically, precipitation of diamonds with δ13C values in the range -4 to -6‰ from mantle-derived fluids with an average δ13C value of -5‰ (derived from evidence not related to diamonds) requires that diamond-forming fluids were relatively reduced and had methane as the dominant carbon species (XCO2 = 0.1-0.5). Application of our model to a recently published set of in-situ carbon isotope analyses for peridotitic diamonds from Marange, Zimbabwe (Smit et al., 2016), which contain CH4 fluid inclusions, allows us to perfectly match the observed co-variations in δ13 C, δ15 N and N content and at the same time explain the previously counter-intuitive observation of progressive 13C enrichment in diamonds that appear to have grown from a fluid with methane as the dominant carbon species. Similarly, the almost complete absence in the published record of progressive 13C depletion trends within diamonds likely reflects ubiquitous precipitation from CH4- and CO2-bearing water-rich fluids, rather than diamond formation exclusively by carbonate-bearing and CH4-free oxidized fluids or melts.

First reports of ectoparasites collected from wild-caught exotic reptiles in Florida.

PubMed

Corn, Joseph L; Mertins, James W; Hanson, Britta; Snow, Skip

2011-01-01

We collected ectoparasites from 27 of 51 wild-caught, free-ranging exotic reptiles examined in Florida from 2003 to 2008. Sampled animals represented eight species, five of which yielded ectoparasites. Reported new parasite distribution records for the United States include the following: the first collection of the African tick Amblyomma latum (Koch) from a wild-caught animal [ball python, Python regius (Shaw)] in the United States; the first collection of the lizard scale mite Hirstiella stamii (Jack) from any wild-caught animal [green iguana, Iguana iguana (L.)]; and the first collection of the lizard scale mite Geckobia hemidactyli (Lawrence) in the continental United States from a wild-caught tropical house gecko, Hemidactylus mabouia (Moreau de Jonnès). We also report the first collections of the Neotropical ticks Amblyomma rotundatum (Koch) and Amblyomma dissimile (Koch) from wild-caught Burmese pythons, Python molurus bivittatus (Kuhl); the first collections of A. dissimile from a wild-caught African savannah monitor, Varanus exanthematicus (Bosc); and from wild-caught green iguanas in the United States; and the first collections of the native chiggers Eutrombicula splendens (Ewing) and Eutrombicula cinnabaris (Ewing) from wild-caught Burmese pythons. These reports may only suggest the diversity of reptile ectoparasites introduced and established in Florida and the new host-parasite relationships that have developed among exotic and native ectoparasites and established exotic reptiles.

Python scripting in the nengo simulator.

PubMed

Stewart, Terrence C; Tripp, Bryan; Eliasmith, Chris

2009-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models.

Data management routines for reproducible research using the G-Node Python Client library

PubMed Central

Sobolev, Andrey; Stoewer, Adrian; Pereira, Michael; Kellner, Christian J.; Garbers, Christian; Rautenberg, Philipp L.; Wachtler, Thomas

2014-01-01

Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology. The G-Node Python Library exposes these services to the Python environment, enabling researchers to organize and access their experimental data using their familiar tools while gaining the advantages that a centralized storage entails. The library provides powerful query features, including data slicing and selection by metadata, as well as fine-grained permission control for collaboration and data sharing. Here we demonstrate key actions in working with experimental neuroscience data, such as building a metadata structure, organizing recorded data in datasets, annotating data, or selecting data regions of interest, that can be automated to large degree using the library. Compliant with existing de-facto standards, the G-Node Python Library is compatible with many Python tools in the field of neurophysiology and thus enables seamless integration of data organization into the scientific data workflow. PMID:24634654

Reduction of blood oxygen levels enhances postprandial cardiac hypertrophy in Burmese python (Python bivittatus).

PubMed

Slay, Christopher E; Enok, Sanne; Hicks, James W; Wang, Tobias

2014-05-15

Physiological cardiac hypertrophy is characterized by reversible enlargement of cardiomyocytes and changes in chamber architecture, which increase stroke volume and via augmented convective oxygen transport. Cardiac hypertrophy is known to occur in response to repeated elevations of O2 demand and/or reduced O2 supply in several species of vertebrate ectotherms, including postprandial Burmese pythons (Python bivittatus). Recent data suggest postprandial cardiac hypertrophy in P. bivittatus is a facultative rather than obligatory response to digestion, though the triggers of this response are unknown. Here, we hypothesized that an O2 supply-demand mismatch stimulates postprandial cardiac enlargement in Burmese pythons. To test this hypothesis, we rendered animals anemic prior to feeding, essentially halving blood oxygen content during the postprandial period. Fed anemic animals had heart rates 126% higher than those of fasted controls, which, coupled with a 71% increase in mean arterial pressure, suggests fed anemic animals were experiencing significantly elevated cardiac work. We found significant cardiac hypertrophy in fed anemic animals, which exhibited ventricles 39% larger than those of fasted controls and 28% larger than in fed controls. These findings support our hypothesis that those animals with a greater magnitude of O2 supply-demand mismatch exhibit the largest hearts. The 'low O2 signal' stimulating postprandial cardiac hypertrophy is likely mediated by elevated ventricular wall stress associated with postprandial hemodynamics. © 2014. Published by The Company of Biologists Ltd.

Python Scripting in the Nengo Simulator

PubMed Central

Stewart, Terrence C.; Tripp, Bryan; Eliasmith, Chris

2008-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models. PMID:19352442

The Clawpack Community of Codes

NASA Astrophysics Data System (ADS)

Mandli, K. T.; LeVeque, R. J.; Ketcheson, D.; Ahmadia, A. J.

2014-12-01

Clawpack, the Conservation Laws Package, has long been one of the standards for solving hyperbolic conservation laws but over the years has extended well beyond this role. Today a community of open-source codes have been developed that address a multitude of different needs including non-conservative balance laws, high-order accurate methods, and parallelism while remaining extensible and easy to use, largely by the judicious use of Python and the original Fortran codes that it wraps. This talk will present some of the recent developments in projects under the Clawpack umbrella, notably the GeoClaw and PyClaw projects. GeoClaw was originally developed as a tool for simulating tsunamis using adaptive mesh refinement but has since encompassed a large number of other geophysically relevant flows including storm surge and debris-flows. PyClaw originated as a Python version of the original Clawpack algorithms but has since been both a testing ground for new algorithmic advances in the Clawpack framework but also an easily extensible framework for solving hyperbolic balance laws. Some of these extensions include the addition of WENO high-order methods, massively parallel capabilities, and adaptive mesh refinement technologies, made possible largely by the flexibility of the Python language and community libraries such as NumPy and PETSc. Because of the tight integration with Python tecnologies, both packages have benefited also from the focus on reproducibility in the Python community, notably IPython notebooks.

HyDe: a Python Package for Genome-Scale Hybridization Detection.

PubMed

Blischak, Paul D; Chifman, Julia; Wolfe, Andrea D; Kubatko, Laura S

2018-03-19

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this paper we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python, and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).

Data management routines for reproducible research using the G-Node Python Client library.

PubMed

Sobolev, Andrey; Stoewer, Adrian; Pereira, Michael; Kellner, Christian J; Garbers, Christian; Rautenberg, Philipp L; Wachtler, Thomas

2014-01-01

Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology. The G-Node Python Library exposes these services to the Python environment, enabling researchers to organize and access their experimental data using their familiar tools while gaining the advantages that a centralized storage entails. The library provides powerful query features, including data slicing and selection by metadata, as well as fine-grained permission control for collaboration and data sharing. Here we demonstrate key actions in working with experimental neuroscience data, such as building a metadata structure, organizing recorded data in datasets, annotating data, or selecting data regions of interest, that can be automated to large degree using the library. Compliant with existing de-facto standards, the G-Node Python Library is compatible with many Python tools in the field of neurophysiology and thus enables seamless integration of data organization into the scientific data workflow.

OMPC: an Open-Source MATLAB-to-Python Compiler.

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python—Python molurus bivittatus—Management

PubMed Central

Hunter, Margaret E.; Hart, Kristen M.

2013-01-01

Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae. PMID:23449030

Replacing the IRAF/PyRAF Code-base at STScI: The Advanced Camera for Surveys (ACS)

NASA Astrophysics Data System (ADS)

Lucas, Ray A.; Desjardins, Tyler D.; STScI ACS (Advanced Camera for Surveys) Team

2018-06-01

IRAF/PyRAF are no longer viable on the latest hardware often used by HST observers, therefore STScI no longer actively supports IRAF or PyRAF for most purposes. STScI instrument teams are in the process of converting all of our data processing and analysis code from IRAF/PyRAF to Python, including our calibration reference file pipelines and data reduction software. This is exemplified by our latest ACS Data Handbook, version 9.0, which was recently published in February 2018. Examples of IRAF and PyRAF commands have now been replaced by code blocks in Python, with references linked to documentation on how to download and install the latest Python software via Conda and AstroConda. With the temporary exception of the ACS slitless spectroscopy tool aXe, all ACS-related software is now independent of IRAF/PyRAF. A concerted effort has been made across STScI divisions to help the astronomical community transition from IRAF/PyRAF to Python, with tools such as Python Jupyter notebooks being made to give users workable examples. In addition to our code changes, the new ACS data handbook discusses the latest developments in charge transfer efficiency (CTE) correction, bias de-striping, and updates to the creation and format of calibration reference files among other topics.

Why diamond dimensions and electrode geometry are crucial for small photon beam dosimetry

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

Marsolat, F.; Tromson, D.; Tranchant, N.

2015-12-21

Recent use of very small photon beams (down to 4 mm) in stereotactic radiotherapy requires new detectors to accurately determine the delivered dose. Diamond detectors have been presented in the literature as an attractive candidate for this application, due to their small detection volume and the diamond atomic number (Z = 6) which is close to water effective atomic number (Zeff ∼ 7.42). However, diamond exhibits a density 3.51 times greater than that of water and recent studies using Monte Carlo simulations have demonstrated the drawback of a high-density detector on small beam output factors. The current study focuses on geometrical parameters of diamond detector,more » namely, the diamond dimensions and the electrode geometry, in order to solve the dosimetric issues still observed in small photon beams with diamond detectors. To give better insights to these open questions, we have used both computational method and experimental analysis. This study highlighted that reducing diamond dimensions is crucial for small beam output factor measurements and to limit the influence of its high density. Furthermore, electrodes covering the whole diamond surface were essential for a dose rate independence of the diamond detector. The optimal dosimeter derived from this work presented small diamond dimensions of approximately 1 × 1 × 0.15 mm{sup 3}, with diamond-like-carbon electrodes covering the whole diamond surface. A dose rate independence of this diamond detector (better than 0.5% over a wide range of dose rates available on a stereotactic dedicated facility) was obtained due to the electrode geometry. Concerning the output factor measurements, a good agreement (better than 1.1%) was observed between this carbon material detector and two types of passive dosimeters (LiF microcubes and EBT2 radiochromic films) for all beam sizes except the smallest field of 0.6 × 0.6 cm{sup 2} with a deviation of 2.6%. This new study showed the high performance of this diamond detector in small photon beams, in comparison with various commercially available passive and active dosimeters.« less

Kankan diamonds (Guinea) III: δ13C and nitrogen characteristics of deep diamonds

NASA Astrophysics Data System (ADS)

Stachel, T.; Harris, J. W.; Aulbach, S.; Deines, P.

Diamonds from the Kankan area in Guinea formed over a large depth profile beginning within the cratonic mantle lithosphere and extending through the asthenosphere and transition zone into the lower mantle. The carbon isotopic composition, the concentration of nitrogen impurities and the nitrogen aggregation level of diamonds representing this entire depth range have been determined. Peridotitic and eclogitic diamonds of lithospheric origin from Kankan have carbon isotopic compositions (δ13C: peridotitic -5.4 to -2.2‰ eclogitic -19.7 to -0.7‰) and nitrogen characteristics (N: peridotitic 17-648 atomic ppm; eclogitic 0-1,313 atomic ppm; aggregation from IaA to IaB) which are generally typical for diamonds of these two suites worldwide. Geothermobarometry of peridotitic and eclogitic inclusion parageneses (worldwide sources) indicates that both suites formed under very similar conditions within the cratonic lithosphere, which is not consistent with a derivation of diamonds with light carbon isotopic composition from subducted organic matter within subducting oceanic slabs. Diamonds containing majorite garnet inclusions fall to the isotopically heavy side (δ13C: -3.1‰ to +0.9‰) of the worldwide diamond population. Nitrogen contents are low (0-126 atomic ppm) and one of the two nitrogen-bearing diamonds shows such a low level of nitrogen aggregation (30% B-centre) that it cannot have been exposed to ambient temperatures of the transition zone (>=1,400 °C) for more than 0.2 Ma. This suggests rapid upward transport and formation of some Kankan diamonds pene-contemporaneous to Cretaceous kimberlite activity. Similar to these diamonds from the asthenosphere and the transition zone, lower mantle diamonds show a small shift towards isotopic heavy compositions (-6.6 to -0.5‰, mode at -3.5‰). As already observed for other mines, the nitrogen contents of lower mantle diamonds were below detection (using FTIRS). The mutual shift of sublithospheric diamonds towards isotopic heavier compositions suggests a common carbon source, which may have inherited an isotopic heavy composition from a component consisting of subducted carbonates.

Kankan diamonds (Guinea) III: δ13C and nitrogen characteristics of deep diamonds

NASA Astrophysics Data System (ADS)

Stachel, T.; Harris, J. W.; Aulbach, S.; Deines, P.

2001-08-01

Diamonds from the Kankan area in Guinea formed over a large depth profile beginning within the cratonic mantle lithosphere and extending through the asthenosphere and transition zone into the lower mantle. The carbon isotopic composition, the concentration of nitrogen impurities and the nitrogen aggregation level of diamonds representing this entire depth range have been determined. Peridotitic and eclogitic diamonds of lithospheric origin from Kankan have carbon isotopic compositions (δ13C: peridotitic -5.4 to -2.2‰ eclogitic -19.7 to -0.7‰) and nitrogen characteristics (N: peridotitic 17-648 atomic ppm; eclogitic 0-1,313 atomic ppm; aggregation from IaA to IaB) which are generally typical for diamonds of these two suites worldwide. Geothermobarometry of peridotitic and eclogitic inclusion parageneses (worldwide sources) indicates that both suites formed under very similar conditions within the cratonic lithosphere, which is not consistent with a derivation of diamonds with light carbon isotopic composition from subducted organic matter within subducting oceanic slabs. Diamonds containing majorite garnet inclusions fall to the isotopically heavy side (δ13C: -3.1‰ to +0.9‰) of the worldwide diamond population. Nitrogen contents are low (0-126 atomic ppm) and one of the two nitrogen-bearing diamonds shows such a low level of nitrogen aggregation (30% B-centre) that it cannot have been exposed to ambient temperatures of the transition zone (>=1,400 °C) for more than 0.2 Ma. This suggests rapid upward transport and formation of some Kankan diamonds pene-contemporaneous to Cretaceous kimberlite activity. Similar to these diamonds from the asthenosphere and the transition zone, lower mantle diamonds show a small shift towards isotopic heavy compositions (-6.6 to -0.5‰, mode at -3.5‰). As already observed for other mines, the nitrogen contents of lower mantle diamonds were below detection (using FTIRS). The mutual shift of sublithospheric diamonds towards isotopic heavier compositions suggests a common carbon source, which may have inherited an isotopic heavy composition from a component consisting of subducted carbonates.

Study on Platinum Coating Depth in Focused Ion Beam Diamond Cutting Tool Milling and Methods for Removing Platinum Layer.

PubMed

Choi, Woong Kirl; Baek, Seung Yub

2015-09-22

In recent years, nanomachining has attracted increasing attention in advanced manufacturing science and technologies as a value-added processes to control material structures, components, devices, and nanoscale systems. To make sub-micro patterns on these products, micro/nanoscale single-crystal diamond cutting tools are essential. Popular non-contact methods for the macro/micro processing of diamond composites are pulsed laser ablation (PLA) and electric discharge machining (EDM). However, for manufacturing nanoscale diamond tools, these machining methods are not appropriate. Despite diamond's extreme physical properties, diamond can be micro/nano machined relatively easily using a focused ion beam (FIB) technique. In the FIB milling process, the surface properties of the diamond cutting tool is affected by the amorphous damage layer caused by the FIB gallium ion collision and implantation and these influence the diamond cutting tool edge sharpness and increase the processing procedures. To protect the diamond substrate, a protection layer-platinum (Pt) coating is essential in diamond FIB milling. In this study, the depth of Pt coating layer which could decrease process-induced damage during FIB fabrication is investigated, along with methods for removing the Pt coating layer on diamond tools. The optimum Pt coating depth has been confirmed, which is very important for maintaining cutting tool edge sharpness and decreasing processing procedures. The ultra-precision grinding method and etching with aqua regia method have been investigated for removing the Pt coating layer. Experimental results show that when the diamond cutting tool width is bigger than 500 nm, ultra-precision grinding method is appropriate for removing Pt coating layer on diamond tool. However, the ultra-precision grinding method is not recommended for removing the Pt coating layer when the cutting tool width is smaller than 500 nm, because the possibility that the diamond cutting tool is damaged by the grinding process will be increased. Despite the etching method requiring more procedures to remove the Pt coating layer after FIB milling, it is a feasible method for diamond tools with under 500 nm width.

Regional patterns in the paragenesis and age of inclusions in diamond, diamond composition, and the lithospheric seismic structure of Southern Africa

NASA Astrophysics Data System (ADS)

Shirey, Steven B.; Harris, Jeffrey W.; Richardson, Stephen H.; Fouch, Matthew; James, David E.; Cartigny, Pierre; Deines, Peter; Viljoen, Fanus

2003-12-01

The Archean lithospheric mantle beneath the Kaapvaal-Zimbabwe craton of Southern Africa shows ±1% variations in seismic P-wave velocity at depths within the diamond stability field (150-250 km) that correlate regionally with differences in the composition of diamonds and their syngenetic inclusions. Seismically slower mantle trends from the mantle below Swaziland to that below southeastern Botswana, roughly following the surface outcrop pattern of the Bushveld-Molopo Farms Complex. Seismically slower mantle also is evident under the southwestern side of the Zimbabwe craton below crust metamorphosed around 2 Ga. Individual eclogitic sulfide inclusions in diamonds from the Kimberley area kimberlites, Koffiefontein, Orapa, and Jwaneng have Re-Os isotopic ages that range from circa 2.9 Ga to the Proterozoic and show little correspondence with these lithospheric variations. However, silicate inclusions in diamonds and their host diamond compositions for the above kimberlites, Finsch, Jagersfontein, Roberts Victor, Premier, Venetia, and Letlhakane do show some regional relationship to the seismic velocity of the lithosphere. Mantle lithosphere with slower P-wave velocity correlates with a greater proportion of eclogitic versus peridotitic silicate inclusions in diamond, a greater incidence of younger Sm-Nd ages of silicate inclusions, a greater proportion of diamonds with lighter C isotopic composition, and a lower percentage of low-N diamonds whereas the converse is true for diamonds from higher velocity mantle. The oldest formation ages of diamonds indicate that the mantle keels which became continental nuclei were created by middle Archean (3.2-3.3 Ga) mantle depletion events with high degrees of melting and early harzburgite formation. The predominance of sulfide inclusions that are eclogitic in the 2.9 Ga age population links late Archean (2.9 Ga) subduction-accretion events involving an oceanic lithosphere component to craton stabilization. These events resulted in a widely distributed younger Archean generation of eclogitic diamonds in the lithospheric mantle. Subsequent Proterozoic tectonic and magmatic events altered the composition of the continental lithosphere and added new lherzolitic and eclogitic diamonds to the already extensive Archean diamond suite.

On the Fabrication and Behavior of Diamond Microelectromechanical Sensors (DMEMS)

NASA Technical Reports Server (NTRS)

Holmes, K.; Davidson, J. L.; Kang, W. P.; Howell, M.

2001-01-01

CVD (chemically vapor deposited) diamond films can be processed similar to "conventional" semiconductor device fabrication and as such can be used to achieve microelectromechanical structures (MEMS) also similar to, for example, silicon technology. Very small cantilever beams, membranes, stripes, tips, etc. can be constructed in doped and undoped diamond films and offer an array of choices in diamond with its known superior properties such as elastic modulus, high temperature semiconduction, high thermal conductivity, very low coefficient of expansion and numerous other diamond parameters. This paper will review the construction and behavior of the second generation DMEMS devices comprised as an accelerometer with a diamond diaphragm for use in very high G applications and a diamond pressure sensor for very high temperature and frequency response.

Diamond nanowires: fabrication, structure, properties, and applications.

PubMed

Yu, Yuan; Wu, Liangzhuan; Zhi, Jinfang

2014-12-22

C(sp(3) )C-bonded diamond nanowires are wide band gap semiconductors that exhibit a combination of superior properties such as negative electron affinity, chemical inertness, high Young's modulus, the highest hardness, and room-temperature thermal conductivity. The creation of 1D diamond nanowires with their giant surface-to-volume ratio enhancements makes it possible to control and enhance the fundamental properties of diamond. Although theoretical comparisons with carbon nanotubes have shown that diamond nanowires are energetically and mechanically viable structures, reproducibly synthesizing the crystalline diamond nanowires has remained challenging. We present a comprehensive, up-to-date review of diamond nanowires, including a discussion of their synthesis along with their structures, properties, and applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gas-phase kinetics during diamond growth: CH4 as-growth species

NASA Astrophysics Data System (ADS)

Harris, Stephen J.

1989-04-01

We have used a one-dimensional kinetic analysis to model the gas-phase chemistry that occurred during the diamond growth experiments of Chauhan, Angus, and Gardner [J. Appl. Phys. 47, 4746 (1976)]. In those experiments the weight of diamond seed crystals heated by lamps in a CH4/H2 environment was monitored by a microbalance. No filament or electric discharge was present. Our analysis shows that diamond growth occurred in this system by direct reaction of CH4 on the diamond surface. C2H2 and CH3, which have been proposed as diamond growth species, played no significant role there, although our results do not address their possible contributions in other systems such as filament- or plasma-assisted diamond growth.

Metal films on the surfaces and within diamond crystals from Arkhangelskaya and Yakutian diamond provinces

NASA Astrophysics Data System (ADS)

Makeev, A. B.; Kriulina, G. Yu.

2012-12-01

Representative samples of diamonds from five kimberlite pipes (Lomonosovskaya, Archangel'sk, Snegurochka, XXIII Congress of the Communist Party of the Soviet Union (CPSU), and Internationalnaya) of the Arkhangelskaya and Yakutian diamond provinces in Russia have been studied. Thirty-three varieties of metal films have been identified as syngenetic associated minerals. The films consist of 15 chemical elements that occur in the form of native metals and their natural alloys. Remnants of metal films were detected within diamond crystals. The metal films coating diamonds are a worldwide phenomenon. To date, these films have been described from Europe, Asia, South America, and Africa. Native metals, their alloys, and intermetallides are actual companion minerals of diamond.

Ultrananocrystalline diamond contacts for electronic devices

DOEpatents

Sumant, Anirudha V.; Smedley, John; Muller, Erik

2016-11-01

A method of forming electrical contacts on a diamond substrate comprises producing a plasma ball using a microwave plasma source in the presence of a mixture of gases. The mixture of gases include a source of a p-type or an n-type dopant. The plasma ball is disposed at a first distance from the diamond substrate. The diamond substrate is maintained at a first temperature. The plasma ball is maintained at the first distance from the diamond substrate for a first time, and a UNCD film, which is doped with at least one of a p-type dopant and an n-type dopant, is disposed on the diamond substrate. The doped UNCD film is patterned to define UNCD electrical contacts on the diamond substrate.

Ultrananocrystalline diamond contacts for electronic devices

DOEpatents

Sumant, Anirudha V.; Smedley, John; Muller, Erik

2017-12-12

A method of forming electrical contacts on a diamond substrate comprises producing a plasma ball using a microwave plasma source in the presence of a mixture of gases. The mixture of gases include a source of a p-type or an n-type dopant. The plasma ball is disposed at a first distance from the diamond substrate. The diamond substrate is maintained at a first temperature. The plasma ball is maintained at the first distance from the diamond substrate for a first time, and a UNCD film, which is doped with at least one of a p-type dopant and an n-type dopant, is disposed on the diamond substrate. The doped UNCD film is patterned to define UNCD electrical contacts on the diamond substrate.

Diamond based adsorbents and their application in chromatography.

PubMed

Peristyy, Anton A; Fedyanina, Olga N; Paull, Brett; Nesterenko, Pavel N

2014-08-29

The idea of using diamond and diamond containing materials in separation sciences has attracted a strong interest in the past decade. The combination of a unique range of properties, such as chemical inertness, mechanical, thermal and hydrolytic stability, excellent thermal conductivity with minimal thermal expansion and intriguing adsorption properties makes diamond a promising material for use in various modes of chromatography. This review summarises the recent research on the preparation of diamond and diamond based stationary phases, their properties and chromatographic performance. Special attention is devoted to the dominant retention mechanisms evident for particular diamond containing phases, and their subsequent applicability to various modes of chromatography, including chromatography carried out under conditions of high temperature and pressure. Copyright © 2014 Elsevier B.V. All rights reserved.

Process for making a cesiated diamond film field emitter and field emitter formed therefrom

DOEpatents

Anderson, D.F.; Kwan, S.W.

1999-03-30

A process for making a cesiated diamond film comprises (a) depositing a quantity of cesium iodide on the diamond film in a vacuum of between about 10{sup {minus}4} Torr and about 10{sup {minus}7} Torr, (b) increasing the vacuum to at least about 10{sup {minus}8} Torr, and (c) imposing an electron beam upon the diamond film, said electron beam having an energy sufficient to dissociate said cesium iodide and to incorporate cesium into interstices of the diamond film. The cesiated diamond film prepared according to the process has an operating voltage that is reduced by a factor of at least approximately 2.5 relative to conventional, non-cesiated diamond film field emitters. 2 figs.

Process for making a cesiated diamond film field emitter and field emitter formed therefrom

DOEpatents

Anderson, David F.; Kwan, Simon W.

1999-01-01

A process for making a cesiated diamond film comprises (a) depositing a quantity of cesium iodide on the diamond film in a vacuum of between about 10.sup.-4 Torr and about 10.sup.-7 Torr, (b) increasing the vacuum to at least about 10.sup.-8 Torr, and (c) imposing an electron beam upon the diamond film, said electron beam having an energy sufficient to dissociate said cesium iodide and to incorporate cesium into interstices of the diamond film. The cesiated diamond film prepared according to the process has an operating voltage that is reduced by a factor of at least approximately 2.5 relative to conventional, non-cesiated diamond film field emitters.

Structures and Mechanical Properties of Natural and Synthetic Diamonds

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1998-01-01

A revolution in the diamond technology is in progress, as the low-pressure process becomes an industrial reality. It will soon be possible to take advantage of the demanding properties of diamond to develop a myriad of new applications, particularly for self-lubricating, wear-resistant, and superhard coatings. The production of large diamond films or sheets at low cost, a distinct possibility in the not-too-distant future, may drastically change tribology technology, particularly regarding solid lubricants and lubricating materials and systems. This paper reviews the structures and properties of natural and synthetic diamonds to gain a better understanding of the tribological properties of diamond and related materials. Atomic and crystal structure, impurities, mechanical properties, and indentation hardness of diamond are described.

Making Diamond in the Laboratory

ERIC Educational Resources Information Center

Strong, Herbert

1975-01-01

Discusses the graphite to diamond transformation and a phase diagram for carbon. Describes high temperature-higher pressure experimental apparatus and growth of diamonds from seed crystals. Reviews properties of the diamond which suggest uses for the synthetic product. Illustrations with text. (GH)

Studies of Diamonds Using Electron Paramagnetic Resonance and Other Techniques

NASA Astrophysics Data System (ADS)

Zhang, Shigang

Studies of impurities/defects in diamonds grown with the high-temperature high-pressure technique (HTHP) and B- and P-doped diamond films using fast ion implantation and chemical evaporation have been carried out. The main technique employed in the study is electron paramagnetic resonance (EPR). Raman, laser and X-ray fluorescence are also used to characterize the samples. While other commonly used techniques such as infrared (IR) spectroscopy detect no nitrogen in an isotopically enriched ^ {12}C diamond, the clear EPR spectrum consistently measures a nitrogen concentration of about 0.05ppm by calibration against a few standards. The ^{12}C diamond is evaluated to be ideal for optical window application and studies of diamond properties. Neither the EPR lineshape nor the second moment supports a random nitrogen distribution in the ^{12}C diamond. Instead, the average nitrogen distance is found to be larger than the of the random nitrogen distribution. The g-tensor for substitutional nitrogen is found to be axially symmetric along the (111) direction with g_| - g_| = 0.00002(5). In the study of a HTHP IIb blue semiconducting diamond, neutral N is measured with a concentration of 0.02ppm. The result is not well understood since neutral nitrogen is expected to lose its extra electron to boron due to electron-hole recombination. Further studies are suggested to better understand this result. EPR studies of two sets of P-doped diamond films grown using fast ion implantation and chemical incorporation reveal that defect levels caused by diamond doping are still too high for semiconductor applications. As expected, P doping causes a defect level two orders of magnitude higher than B doping, which can be explained by the relatively larger size of P than B. The theoretical analysis based on EPR hyperfine interaction suggest that P forms a shallow donor in diamond and that the electron density at the P site is |psi(0)|^2 = 0.27 times 10^{24} cm^ {-3}. This is consistent with the temperature dependent EPR experimental results. The EPR spectra for all diamond samples I have studied are compared, revealing that the HTHP diamonds show no defect related spectrum, which are commonly observed in natural IIa and IIb diamonds. This result indicates that HTHP diamond has superior quality compared to other diamonds.

Friction and Wear Properties of As-Deposited and Carbon Ion-Implanted Diamond Films

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1996-01-01

Recent work on the friction and wear properties of as-deposited and carbon ion-implanted diamond films was reviewed. Diamond films were produced by the microwave plasma chemical vapor deposition (CVD) technique. Diamond films with various grain sizes and surface roughnesses were implanted with carbon ions at 60 keV ion energy, resulting in a dose of 1.2 x 10(exp 17) carbon ions per cm(exp 2). Various analytical techniques, including Raman spectroscopy, proton recoil analysis, Rutherford backscattering, transmission and scanning electron microscopy, X-ray photoelectron spectroscopy, and X-ray diffraction, were utilized to characterize the diamond films. Sliding friction experiments were conducted with a polished natural diamond pin in contact with diamond films in the three environments: humid air (40% relative humidity), dry nitrogen (less than 1 percent relative humidity), and ultrahigh vacuum (10(exp -7) Pa). The CVD diamond films indeed have friction and wear properties similar to those of natural diamond in the three environments. The as-deposited, fine-grain diamond films can be effectively used as self-lubricating, wear-resistant coatings that have low coefficients of friction (0.02 to 0.04) and low wear rates (10(exp -7) to lO(exp -8) mm(exp 3) N(exp -1) m(exp -1)) in both humid air and dry nitrogen. However, they have high coefficients of friction (1.5 to 1.7) and a high wear rate (10(exp -4) mm(exp 7) N(exp -1) m(exp -1)) in ultrahigh vacuum. The carbon ion implantation produced a thin surficial layer (less than 0.1 micron thick) of amorphous, non-diamond carbon on the diamond films. In humid air and dry nitrogen, the ion-implanted, fine and coarse-grain diamond films have a low coefficient of friction (around 0.1) and a low wear rate (10(exp -7) mm(exp 3) N(exp -1) m(exp-1)). Even in ultrahigh vacuum, the presence of the non-diamond carbon layer reduced the coefficient of friction of fine-grain diamond films to 0.1 or lower and the wear rate to 10(exp -6) mm(exp 3) N(exp -1) m(exp -1). Thus, the carbon ion-implanted, fine-grain diamond films can be effectively used as wear-resistant, self-lubricating coatings not only in air and dry nitrogen, but also in ultrahigh vacuum.

Diamond thin films: giving biomedical applications a new shine

PubMed Central

Nistor, P. A.

2017-01-01

Progress made in the last two decades in chemical vapour deposition technology has enabled the production of inexpensive, high-quality coatings made from diamond to become a scientific and commercial reality. Two properties of diamond make it a highly desirable candidate material for biomedical applications: first, it is bioinert, meaning that there is minimal immune response when diamond is implanted into the body, and second, its electrical conductivity can be altered in a controlled manner, from insulating to near-metallic. In vitro, diamond can be used as a substrate upon which a range of biological cells can be cultured. In vivo, diamond thin films have been proposed as coatings for implants and prostheses. Here, we review a large body of data regarding the use of diamond substrates for in vitro cell culture. We also detail more recent work exploring diamond-coated implants with the main targets being bone and neural tissue. We conclude that diamond emerges as one of the major new biomaterials of the twenty-first century that could shape the way medical treatment will be performed, especially when invasive procedures are required. PMID:28931637

Diamond- cBN alloy: A universal cutting material

DOE PAGES

Wang, Pei; He, Duanwei; Wang, Liping; ...

2015-09-08

Diamond and cubic boron nitride ( cBN) as conventional superhard materials have found widespread industrial applications, but both have inherent limitations. Diamond is not suitable for high-speed cutting of ferrous materials due to its poor chemical inertness, while cBN is only about half as hard as diamond. Because of their affinity in structural lattices and covalent bonding character, diamond and cBN could form alloys that can potentially fill the performance gap. However, the idea has never been demonstrated because samples obtained in the previous studies were too small to be tested for their practical performance. Here, we report the synthesismore » and characterization of transparent bulk diamond- cBN alloy compacts whose diameters (3 mm) are sufficiently large for them to be processed into cutting tools. The testing results show that the diamond- cBN alloy has superior chemical inertness over polycrystalline diamond and higher hardness than single crystal cBN. In conclusion, high-speed cutting tests on hardened steel and granite suggest that diamond- cBN alloy is indeed a universal cutting material.« less

Diamond-cBN alloy: A universal cutting material

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

Wang, Pei; High Pressure Science and Engineering Center and Department of Physics and Astronomy, University of Nevada Las Vegas, Las Vegas, Nevada 89154; He, Duanwei, E-mail: duanweihe@scu.edu.cn

Diamond and cubic boron nitride (cBN) as conventional superhard materials have found widespread industrial applications, but both have inherent limitations. Diamond is not suitable for high-speed cutting of ferrous materials due to its poor chemical inertness, while cBN is only about half as hard as diamond. Because of their affinity in structural lattices and covalent bonding character, diamond and cBN could form alloys that can potentially fill the performance gap. However, the idea has never been demonstrated because samples obtained in the previous studies were too small to be tested for their practical performance. Here, we report the synthesis andmore » characterization of transparent bulk diamond-cBN alloy compacts whose diameters (3 mm) are sufficiently large for them to be processed into cutting tools. The testing results show that the diamond-cBN alloy has superior chemical inertness over polycrystalline diamond and higher hardness than single crystal cBN. High-speed cutting tests on hardened steel and granite suggest that diamond-cBN alloy is indeed a universal cutting material.« less

Diamond- cBN alloy: A universal cutting material

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

Wang, Pei; He, Duanwei; Wang, Liping

Diamond and cubic boron nitride ( cBN) as conventional superhard materials have found widespread industrial applications, but both have inherent limitations. Diamond is not suitable for high-speed cutting of ferrous materials due to its poor chemical inertness, while cBN is only about half as hard as diamond. Because of their affinity in structural lattices and covalent bonding character, diamond and cBN could form alloys that can potentially fill the performance gap. However, the idea has never been demonstrated because samples obtained in the previous studies were too small to be tested for their practical performance. Here, we report the synthesismore » and characterization of transparent bulk diamond- cBN alloy compacts whose diameters (3 mm) are sufficiently large for them to be processed into cutting tools. The testing results show that the diamond- cBN alloy has superior chemical inertness over polycrystalline diamond and higher hardness than single crystal cBN. In conclusion, high-speed cutting tests on hardened steel and granite suggest that diamond- cBN alloy is indeed a universal cutting material.« less

High pressure studies using two-stage diamond micro-anvils grown by chemical vapor deposition

DOE PAGES

Vohra, Yogesh K.; Samudrala, Gopi K.; Moore, Samuel L.; ...

2015-06-10

Ultra-high static pressures have been achieved in the laboratory using a two-stage micro-ball nanodiamond anvils as well as a two-stage micro-paired diamond anvils machined using a focused ion-beam system. The two-stage diamond anvils’ designs implemented thus far suffer from a limitation of one diamond anvil sliding past another anvil at extreme conditions. We describe a new method of fabricating two-stage diamond micro-anvils using a tungsten mask on a standard diamond anvil followed by microwave plasma chemical vapor deposition (CVD) homoepitaxial diamond growth. A prototype two stage diamond anvil with 300 μm culet and with a CVD diamond second stage ofmore » 50 μm in diameter was fabricated. We have carried out preliminary high pressure X-ray diffraction studies on a sample of rare-earth metal lutetium sample with a copper pressure standard to 86 GPa. Furthermore, the micro-anvil grown by CVD remained intact during indentation of gasket as well as on decompression from the highest pressure of 86 GPa.« less

Direct observation of inversion capacitance in p-type diamond MOS capacitors with an electron injection layer

NASA Astrophysics Data System (ADS)

Matsumoto, Tsubasa; Kato, Hiromitsu; Makino, Toshiharu; Ogura, Masahiko; Takeuchi, Daisuke; Yamasaki, Satoshi; Imura, Masataka; Ueda, Akihiro; Inokuma, Takao; Tokuda, Norio

2018-04-01

The electrical properties of Al2O3/p-type diamond (111) MOS capacitors were studied with the goal of furthering diamond-based semiconductor research. To confirm the formation of an inversion layer in the p-type diamond body, an n-type layer for use as a minority carrier injection layer was selectively deposited onto p-type diamond. To form the diamond MOS capacitors, Al2O3 was deposited onto OH-terminated diamond using atomic layer deposition. The MOS capacitor showed clear inversion capacitance at 10 Hz. The minority carrier injection from the n-type layer reached the inversion n-channel diamond MOS field-effect transistor (MOSFET). Using the high-low frequency capacitance method, the interface state density, D it, within an energy range of 0.1-0.5 eV from the valence band edge energy, E v, was estimated at (4-9) × 1012 cm-2 eV-1. However, the high D it near E v remains an obstacle to improving the field effect mobility for the inversion p-channel diamond MOSFET.

Superconductivity in diamond.

PubMed

Ekimov, E A; Sidorov, V A; Bauer, E D; Mel'nik, N N; Curro, N J; Thompson, J D; Stishov, S M

2004-04-01

Diamond is an electrical insulator well known for its exceptional hardness. It also conducts heat even more effectively than copper, and can withstand very high electric fields. With these physical properties, diamond is attractive for electronic applications, particularly when charge carriers are introduced (by chemical doping) into the system. Boron has one less electron than carbon and, because of its small atomic radius, boron is relatively easily incorporated into diamond; as boron acts as a charge acceptor, the resulting diamond is effectively hole-doped. Here we report the discovery of superconductivity in boron-doped diamond synthesized at high pressure (nearly 100,000 atmospheres) and temperature (2,500-2,800 K). Electrical resistivity, magnetic susceptibility, specific heat and field-dependent resistance measurements show that boron-doped diamond is a bulk, type-II superconductor below the superconducting transition temperature T(c) approximately 4 K; superconductivity survives in a magnetic field up to Hc2(0) > or = 3.5 T. The discovery of superconductivity in diamond-structured carbon suggests that Si and Ge, which also form in the diamond structure, may similarly exhibit superconductivity under the appropriate conditions.

Geometry and Grid Modeling for Numerical Simulation

DTIC Science & Technology

2005-06-01

which makes them particularly vexing to beginners . In addition, they are expensive in terms of memory requirements and compile times. 3.1.4 TSTT The...F77, Python , or Fortran90 (beta). It supports drivers written in C, C++, F77, Python , Java or Fortran90 (beta). It is supported currently on

A Gene Ontology Tutorial in Python.

PubMed

Vesztrocy, Alex Warwick; Dessimoz, Christophe

2017-01-01

This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic similarity between GO terms. An interactive version of the tutorial, including solutions, is available at http://gohandbook.org .

Python Source Code Plagiarism Attacks on Introductory Programming Course Assignments

ERIC Educational Resources Information Center

Karnalim, Oscar

2017-01-01

This paper empirically enlists Python plagiarism attacks that have been found on Introductory Programming course assignments for undergraduate students. According to our observation toward 400 plagiarism-suspected cases, there are 35 plagiarism attacks that have been conducted by students. It starts with comment & whitespace modification as…

Python Spectral Analysis Tool (PySAT) for Preprocessing, Multivariate Analysis, and Machine Learning with Point Spectra

NASA Astrophysics Data System (ADS)

Anderson, R. B.; Finch, N.; Clegg, S.; Graff, T.; Morris, R. V.; Laura, J.

2017-06-01

We present a Python-based library and graphical interface for the analysis of point spectra. The tool is being developed with a focus on methods used for ChemCam data, but is flexible enough to handle spectra from other instruments.

Method of improving field emission characteristics of diamond thin films

DOEpatents

Krauss, A.R.; Gruen, D.M.

1999-05-11

A method of preparing diamond thin films with improved field emission properties is disclosed. The method includes preparing a diamond thin film on a substrate, such as Mo, W, Si and Ni. An atmosphere of hydrogen (molecular or atomic) can be provided above the already deposited film to form absorbed hydrogen to reduce the work function and enhance field emission properties of the diamond film. In addition, hydrogen can be absorbed on intergranular surfaces to enhance electrical conductivity of the diamond film. The treated diamond film can be part of a microtip array in a flat panel display. 3 figs.

Method of improving field emission characteristics of diamond thin films

DOEpatents

Krauss, Alan R.; Gruen, Dieter M.

1999-01-01

A method of preparing diamond thin films with improved field emission properties. The method includes preparing a diamond thin film on a substrate, such as Mo, W, Si and Ni. An atmosphere of hydrogen (molecular or atomic) can be provided above the already deposited film to form absorbed hydrogen to reduce the work function and enhance field emission properties of the diamond film. In addition, hydrogen can be absorbed on intergranular surfaces to enhance electrical conductivity of the diamond film. The treated diamond film can be part of a microtip array in a flat panel display.

Synthesis of n-type semiconductor diamond single crystal under high pressure and high temperature

NASA Astrophysics Data System (ADS)

Li, Yong; Li, Shangsheng; Song, Mousheng; She, Yanchao; Wang, Qiang; Guan, Xuemao

2017-12-01

In this paper, diamond single crystal co-doped with sulfur and boron was successfully synthesized at the fixed pressure of 6.0 GPa and temperature range of 1535 K. Sulfur was detected in the co-doped diamond by Fourier Transform Infrared Spectroscopy (FTIR) and the corresponding characteristic peak located at 848 cm-1. Interestingly, Hall effect measurements indicated that the diamond co-doped with sulfur and boron exhibited n-type semiconductor behaviour. Furthermore, the Hall mobility and carrier concentration of the co-doped diamond higher than those of the boron-doping diamond.

Method for machining steel with diamond tools

DOEpatents

Casstevens, J.M.

1984-01-01

The present invention is directed to a method for machine optical quality finishes and contour accuracies of workpieces of carbon-containing metals such as steel with diamond tooling. The wear rate of the diamond tooling is significantly reduced by saturating the atmosphere at the interface of the workpiece and the diamond tool with a gaseous hydrocarbon during the machining operation. The presence of the gaseous hydrocarbon effectively eliminates the deterioration of the diamond tool by inhibiting or preventing the conversion of the diamond carbon to graphite carbon at the point of contact between the cutting tool and the workpiece.

Method for machining steel with diamond tools

DOEpatents

Casstevens, John M.

1986-01-01

The present invention is directed to a method for machining optical quality inishes and contour accuracies of workpieces of carbon-containing metals such as steel with diamond tooling. The wear rate of the diamond tooling is significantly reduced by saturating the atmosphere at the interface of the workpiece and the diamond tool with a gaseous hydrocarbon during the machining operation. The presence of the gaseous hydrocarbon effectively eliminates the deterioration of the diamond tool by inhibiting or preventing the conversion of the diamond carbon to graphite carbon at the point of contact between the cutting tool and the workpiece.

A density functional study of the effect of hydrogen on electronic properties and band discontinuity at anatase TiO2/diamond interface

NASA Astrophysics Data System (ADS)

Wu, Kongping; Liao, Meiyong; Sang, Liwen; Liu, Jiangwei; Imura, Masataka; Ye, Haitao; Koide, Yasuo

2018-04-01

Tailoring the electronic states of the dielectric oxide/diamond interface is critical to the development of next generation semiconductor devices like high-power high-frequency field-effect transistors. In this work, we investigate the electronic states of the TiO2/diamond 2 × 1-(100) interface by using first principles total energy calculations. Based on the calculation of the chemical potentials for the TiO2/diamond interface, it is observed that the hetero-interfaces with the C-OTi configuration or with two O vacancies are the most energetically favorable structures under the O-rich condition and under Ti-rich condition, respectively. The band structure and density of states of both TiO2/diamond and TiO2/H-diamond hetero-structures are calculated. It is revealed that there are considerable interface states at the interface of the anatase TiO2/diamond hetero-structure. By introducing H on the diamond surface, the interface states are significantly suppressed. A type-II alignment band structure is disclosed at the interface of the TiO2/diamond hetero-structure. The valence band offset increases from 0.6 to 1.7 eV when H is introduced at the TiO2/diamond interface.

A perforated diamond anvil cell for high-energy x-ray diffraction of liquids and amorphous solids at high pressure.

PubMed

Soignard, Emmanuel; Benmore, Chris J; Yarger, Jeffery L

2010-03-01

Diamond anvil cells (DACs) are widely used for the study of materials at high pressure. The typical diamonds used are between 1 and 3 mm thick, while the sample contained within the opposing diamonds is often just a few microns in thickness. Hence, any absorbance or scattering from diamond can cause a significant background or interference when probing a sample in a DAC. By perforating the diamond to within 50-100 microm of the sample, the amount of diamond and the resulting background or interference can be dramatically reduced. The DAC presented in this article is designed to study amorphous materials at high pressure using high-energy x-ray scattering (>60 keV) using laser-perforated diamonds. A small diameter perforation maintains structural integrity and has allowed us to reach pressures >50 GPa, while dramatically decreasing the intensity of the x-ray diffraction background (primarily Compton scattering) when compared to studies using solid diamonds. This cell design allows us for the first time measurement of x-ray scattering from light (low Z) amorphous materials. Here, we present data for two examples using the described DAC with one and two perforated diamond geometries for the high-pressure structural studies of SiO(2) glass and B(2)O(3) glass.

Identifying the Source of Gem Diamonds: Requirements for a Certification System

NASA Astrophysics Data System (ADS)

Shigley, J. E.

2002-05-01

Recent civil conflicts in several countries, in which profits from the sales of gem diamonds have supported the rival factions, have forced the jewelry industry to confront the need to certify the geographic sources of gem diamonds. The goals of this program are to prohibit the sale of so-called "conflict diamonds", and to prevent the loss of consumer confidence. Efforts to identify unique characteristics of gem diamonds have been hampered so far by the absence of chemical or physical features that are diagnostic of particular sources, and the lack of a representative collection of diamonds from major producing areas that would be required for a rigorous scientific study. The jewelry industry has therefore adopted plans to track gem diamonds from the mine through the manufacturing process to the consumer. Practical requirements for implementation of such a certification system will be summarized. Any proposed solutions for determining the sources of gem diamonds by some analytical technique, or for following diamonds from the mine, must take into account the annual production of several tens of millions of carats of rough diamonds, which are transformed during manufacturing into several hundreds of millions of polished gemstones (with an average weight of only about 0.03 carat, or 0.006 gram).

Tailoring nanocrystalline diamond coated on titanium for osteoblast adhesion.

PubMed

Pareta, Rajesh; Yang, Lei; Kothari, Abhishek; Sirinrath, Sirivisoot; Xiao, Xingcheng; Sheldon, Brian W; Webster, Thomas J

2010-10-01

Diamond coatings with superior chemical stability, antiwear, and cytocompatibility properties have been considered for lengthening the lifetime of metallic orthopedic implants for over a decade. In this study, an attempt to tailor the surface properties of diamond films on titanium to promote osteoblast (bone forming cell) adhesion was reported. The surface properties investigated here included the size of diamond surface features, topography, wettability, and surface chemistry, all of which were controlled during microwave plasma enhanced chemical-vapor-deposition (MPCVD) processes using CH4-Ar-H2 gas mixtures. The hardness and elastic modulus of the diamond films were also determined. H2 concentration in the plasma was altered to control the crystallinity, grain size, and topography of the diamond coatings, and specific plasma gases (O2 and NH3) were introduced to change the surface chemistry of the diamond coatings. To understand the impact of the altered surface properties on osteoblast responses, cell adhesion tests were performed on the various diamond-coated titanium. The results revealed that nanocrystalline diamond (grain sizes <100 nm) coated titanium dramatically increased surface hardness, and the introduction of O2 and NH3 during the MPCVD process promoted osteoblast adhesion on diamond and, thus, should be further studied for improving orthopedic applications. Copyright 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2010.

Homoepitaxial Boron Doped Diamond Anvils as Heating Elements in a Diamond Anvil Cell

NASA Astrophysics Data System (ADS)

Montgomery, Jeffrey; Samudrala, Gopi; Smith, Spencer; Tsoi, Georgiy; Vohra, Yogesh; Weir, Samuel

2013-03-01

Recent advances in designer-diamond technology have allowed for the use of electrically and thermally conducting homoepitaxially-grown layers of boron-doped diamond (grown at 1200 °C with a 2% mixture of CH4 in H, resulting in extremely high doping levels ~ 1020/cm3) to be used as heating elements in a diamond anvil cell (DAC). These diamonds allow for precise control of the temperature inside of the diamond anvil itself, particularly when coupled with a cryostat. Furthermore, the unmatched thermally conducting nature of diamond ensures that no significant lateral gradient in temperature occurs across the culet area. Since a thermocouple can easily be attached anywhere on the diamond surface, we can also measure diamond temperatures directly. With two such heaters, one can raise sample temperatures uniformly, or with any desired gradient along the pressure axis while preserving optical access. In our continuing set of benchmark experiments, we use two newly created matching heater anvils with 500 μm culets to analyze the various fluorescence emission lines of ruby microspheres, which show more complicated behavior than traditional ruby chips. We also report on the temperature dependence of the high-pressure Raman modes of paracetamol (C8H9NO2) up to 20 GPa.

Diamonds, a resource curse? The case of Kono District in Sierra Leone

NASA Astrophysics Data System (ADS)

Wilson, Sigismond Ayodele

Using an actor-oriented approach to political ecology integrated with theory on the social production of scale, this dissertation examines the extent to which diamond exploitation constitutes a resource curse in Sierra Leone, with Kono District as a case-study. It uses social survey methods and remote sensing analysis of Landsat images to (1) evaluate the role of Sierra Leone's diamonds in economic development from a historical lens, (2) examine the extent to which a weak regulatory state apparatus makes a rich diamond endowment more of a curse than a blessing, (3) determine whether geographically diffuse and remotely-located diamonds are more a liability than an asset, and (4) assess whether environmental conditions are worse in diamond than in non-diamond chiefdoms. Results of the study showed that the contribution of diamonds to national economic growth declined precipitously following the politicization of diamonds and growing informalization of mining under the leadership of Siaka Stevens. Growing disenchantment combined with grievances over access to diamond resources and rights, culminating in a civil war fuelled by conflict diamonds. Findings indicated that actors capitalized on a weak regulatory state to fulfill their agendas. Illicit diamond exploitation was mainly driven by corruption, economic constraints and perverse economic incentives. Preferential land allocation to industrial mining following World Bank Group-directed national mining policy reforms and the weakness of the state in ensuring companies' adherence to mining clauses precipitated corporation-community conflicts. Study findings showed that the resource curse was acute on diggers who received less than 1 a day unlike their South American counterparts who made at least 7 daily. Results from the study demonstrate that the spatiality of diamonds also contributed to the resource curse. Illicit diamond mining was more acute in remotely located mining sites than in extractive sites closer to towns, and spatial proximity to Guinea and Liberia facilitated diamond smuggling. Remote sensing analysis and social surveys revealed that negative environmental impacts were more manifested in the diamond mining chiefdoms than in non-mining areas, confirming the environment as major dimensions of the resource curse. The environmental impacts of diamond mining had broader implications as the forest, land, and water were affected. Transformation of fertile lands (wetlands) to mining lands, and without required reclamation, had negative consequences on the agricultural productivity of local residents in mining areas. Examination of power relations constituted the pros and cons of managing diamond exploitation. Policy makers should employ broad-based strategies to empower mining communities so that they can elect credible local governments. Clearly demarcated industrial and artisanal mining zones and equity and transparency in the distribution of mineral revenues could minimize potential conflicts between corporations and mining companies.

Super-deep diamond genesis at Redox conditions of slab-mantle boundary

NASA Astrophysics Data System (ADS)

Gao, J.; Chen, B.; Wu, X.

2017-12-01

Diamond genesis is an intriguing issue for diamond resources and the deep carbon cycle of the Earth's interiors. Super-deep diamonds, representing only 6% of the global diamond population, often host inclusions with phase assemblages requiring a sublithospheric origin (>300 km). Being the windows for probing the deep Earth, super-deep diamonds with their distinctive micro-inclusions not only record a history of oceanic lithosphere subduction and upward transport at a depth of >250 km to even 1000 km, but indicate their genesis pertinent to mantle-carbonate melts in a Fe0-bufferred reduced condition. Our pilot experiments have evidenced the formation of diamonds from MgCO3-Fe0 system in a diamond anvil cell device at 25 GPa and 1800 K. Detailed experimental investigations of redox mechanism of MgCO3-Fe0 and CaCO3-Fe0 coupling have been conducted using multi-anvil apparatus. The conditions are set along the oceanic lithosphere subduction paths in the pressure-temperature range of 10-24 GPa and 1200-2000 K, covering the formation region of most super-deep diamonds. The clear reaction zones strongly support the redox reaction between carbonatitic slab and Fe0-bearing metals under mantle conditions. Our study has experimentally documented the possibility of super-deep diamond genesis at redox conditions of carbonateitic slab and Fe0-bearings. The kinetics of diamond formation as a function of pressure-temperature conditions are also discussed.

Designer Diamonds: Applications in Iron-based Superconductors and Lanthanides

NASA Astrophysics Data System (ADS)

Vohra, Yogesh

2013-06-01

This talk will focus on the recent progress in the fabrication of designer diamond anvils as well as scientific applications of these diamonds in static high pressure research. The two critical parameters that have emerged in the microwave plasma chemical vapor deposition of designer diamond anvils are (1) the precise [100] alignment of the starting diamond substrate and (2) balancing the competing roles of parts per million levels of nitrogen and oxygen in the diamond growth plasma. The control of these parameters results in the fabrication of high quality designer diamonds with culet size in excess of 300 microns in diameter. The three different applications of designer diamond anvils will be discussed (1) simultaneous electrical resistance and crystal structure measurements using a synchrotron source on Iron-based superconductors with data on both electron and hole doped BaFe2As2 materials and other novel superconducting materials (2) high-pressure high-temperature melting studies on metals using eight-probe Ohmic heating designer diamonds and (3) high pressure low temperature studies on magnetic behavior of 4f-lanthanide metals using four-probe electrical resistance measurements and complementary neutron diffraction studies on a spallation neutron source. Future opportunities in boron-doped conducting designer diamond anvils as well as fabrication of two-stage designer diamonds for ultra high pressure experiments will also be presented. This work was supported by the Department of Energy (DOE) - National Nuclear Security Administration (NNSA) under Grant No. DE-FG52-10NA29660.

Structures and Mechanical Properties of Natural and Synthetic Diamonds. Chapter 8

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1998-01-01

A revolution in diamond technology is in progress as the low-pressure process becomes an industrial reality. It will soon be possible to take advantage of the demanding properties of diamond to develop a myriad of new applications, particularly for self-lubricating, wear, and superhard coatings. The production of large diamond films or sheets at low cost, a distinct possibility in the not-too-distant future, may drastically change tribology technology, particularly solid lubricants and lubricating materials and systems. This chapter reviews the structures and properties of natural and synthetic diamond to gain a better understanding of the tribological properties of diamond and related materials to be described in the following chapters. Atomic and crystal structure, impurities, mechanical properties, and indentation hardness of diamond are described.

[Spectroscopic studies on transition metal ions in colored diamonds].

PubMed

Meng, Yu-Fei; Peng, Ming-Sheng

2004-07-01

Transition metals like nickel, cobalt and iron have been often used as solvent catalysts in high pressure high temperature (HPHT) synthesis of diamond, and nickel and cobalt ions have been found in diamond lattice. Available studies indicated that nickel and cobalt ions could enter the lattice as interstitial or substitutional impurities and form complexes with nitrogen. Polarized microscopy, SEM-EDS, EPR, PL and FTIR have been used in this study to investigate six fancy color natural and synthetic diamonds in order to determine the spectroscopic characteristics and the existing forms of transition metal ions in colored diamond lattice. Cobalt-related optical centers were first found in natural chameleon diamonds, and some new nickel and cobalt-related optical and EPR centers have also been detected in these diamond samples.

New diamond cell for single-crystal x-ray diffraction

NASA Astrophysics Data System (ADS)

Boehler, Reinhard

2006-11-01

A new design for a high-precision diamond cell is described. Two kinematically mounted steel disks are elastically deflected to generate pressure. This principle provides higher precision in the diamond anvil alignment than most sliding piston-cylinder or guide-pin devices at significantly lower cost. With this new diamond cell conical diamond anvils with an x-ray aperture of 85° were successfully tested to over 50GPa using helium as a pressure medium. Anvil thickness of less than 1.4mm provides high x-ray transmission and low background, a significant improvement compared to beryllium or diamond-disk backing plates. Because the diamond anvils are supported by tungsten carbide seats, samples and pressure media can be annealed by external or laser heating to provide hydrostatic pressure conditions.

A methodology for conducting national-scale alluvial diamond resource potential and production capacity assessments, with a focus on artisanal mining

USGS Publications Warehouse

Chirico, Peter G.; Malpeli, Katherine C.

2012-01-01

In May of 2000, a meeting was convened in Kimberley, South Africa, by representatives of the diamond industry and leaders of African governments to develop a certification process intended to assure that export shipments of rough diamonds were free of conflict concerns. Outcomes of the meeting were formally supported later in December of 2000 by the United Nations in a resolution adopted by the General Assembly. By 2002, the Kimberley Process Certification Scheme was ratified and signed by diamond-producing and diamond-importing countries. As of August 2012, the Kimberley Process (KP) had 51 participants representing 77 countries. It is often difficult to obtain independent verification of the diamond production statistics that are provided to the KP. However, some degree of independent verification can be obtained through an understanding of a country’s naturally occurring endowment of diamonds and the intensity of mining activities. Studies that integrate these two components can produce a range of estimated values for a country’s diamond production, and these estimates can then be compared to the production statistics released by that country. This methodology is used to calculate (1) the diamond resource potential of a country, which refers to the total number of carats estimated to be remaining in the country, and (2) the diamond production capacity of a country, which is the current volume of diamonds that may realistically be produced per year utilizing current human and physical resources. The following sections outline the methodology used by the U.S. Geological Survey (USGS) to perform diamond assessments in Mali, the Central African Republic, Ghana, and Guinea.

Rhenium Alloys as Ductile Substrates for Diamond Thin-Film Electrodes.

PubMed

Halpern, Jeffrey M; Martin, Heidi B

2014-02-01

Molybdenum-rhenium (Mo/Re) and tungsten-rhenium (W/Re) alloys were investigated as substrates for thin-film, polycrystalline boron-doped diamond electrodes. Traditional, carbide-forming metal substrates adhere strongly to diamond but lose their ductility during exposure to the high-temperature (1000°C) diamond, chemical vapor deposition environment. Boron-doped semi-metallic diamond was selectively deposited for up to 20 hours on one end of Mo/Re (47.5/52.5 wt.%) and W/Re (75/25 wt.%) alloy wires. Conformal diamond films on the alloys displayed grain sizes and Raman signatures similar to films grown on tungsten; in all cases, the morphology and Raman spectra were consistent with well-faceted, microcrystalline diamond with minimal sp 2 carbon content. Cyclic voltammograms of dopamine in phosphate-buffered saline (PBS) showed the wide window and low baseline current of high-quality diamond electrodes. In addition, the films showed consistently well-defined, dopamine electrochemical redox activity. The Mo/Re substrate regions that were uncoated but still exposed to the diamond-growth environment remained substantially more flexible than tungsten in a bend-to-fracture rotation test, bending to the test maximum of 90° and not fracturing. The W/Re substrates fractured after a 27° bend, and the tungsten fractured after a 21° bend. Brittle, transgranular cleavage fracture surfaces were observed for tungsten and W/Re. A tension-induced fracture of the Mo/Re after the prior bend test showed a dimple fracture with a visible ductile core. Overall, the Mo/Re and W/Re alloys were suitable substrates for diamond growth. The Mo/Re alloy remained significantly more ductile than traditional tungsten substrates after diamond growth, and thus may be an attractive metal substrate for more ductile, thin-film diamond electrodes.

Rhenium Alloys as Ductile Substrates for Diamond Thin-Film Electrodes

PubMed Central

Halpern, Jeffrey M.; Martin, Heidi B.

2014-01-01

Molybdenum-rhenium (Mo/Re) and tungsten-rhenium (W/Re) alloys were investigated as substrates for thin-film, polycrystalline boron-doped diamond electrodes. Traditional, carbide-forming metal substrates adhere strongly to diamond but lose their ductility during exposure to the high-temperature (1000°C) diamond, chemical vapor deposition environment. Boron-doped semi-metallic diamond was selectively deposited for up to 20 hours on one end of Mo/Re (47.5/52.5 wt.%) and W/Re (75/25 wt.%) alloy wires. Conformal diamond films on the alloys displayed grain sizes and Raman signatures similar to films grown on tungsten; in all cases, the morphology and Raman spectra were consistent with well-faceted, microcrystalline diamond with minimal sp2 carbon content. Cyclic voltammograms of dopamine in phosphate-buffered saline (PBS) showed the wide window and low baseline current of high-quality diamond electrodes. In addition, the films showed consistently well-defined, dopamine electrochemical redox activity. The Mo/Re substrate regions that were uncoated but still exposed to the diamond-growth environment remained substantially more flexible than tungsten in a bend-to-fracture rotation test, bending to the test maximum of 90° and not fracturing. The W/Re substrates fractured after a 27° bend, and the tungsten fractured after a 21° bend. Brittle, transgranular cleavage fracture surfaces were observed for tungsten and W/Re. A tension-induced fracture of the Mo/Re after the prior bend test showed a dimple fracture with a visible ductile core. Overall, the Mo/Re and W/Re alloys were suitable substrates for diamond growth. The Mo/Re alloy remained significantly more ductile than traditional tungsten substrates after diamond growth, and thus may be an attractive metal substrate for more ductile, thin-film diamond electrodes. PMID:25404788

Contract W911NF-12-C-0102 (Advanced Diamond Technologies, Inc.)

DTIC Science & Technology

2013-06-24

resistivity, residual stress and Raman spectra measurement is finished. Raman spectra shows basically regular nanocrystalline diamond signature as expected...diamond films including thickness, resistivity, residual stress and Raman spectra measurement is finished. Raman spectra shows basically regular...15743 WF600B05 3000 0.02 0.03 0.0018 4 Fig. 2 Raman spectra (λ=532 nm) of (a) all diamond with different doping level and (b) diamond only with

Industrial diamond

USGS Publications Warehouse

Olson, D.W.

2012-01-01

Estimated 2011 world production of natural and synthetic industrial diamond was about 4.45 billion carats. During 2011, natural industrial diamonds were produced in more than 20 countries, and synthetic industrial diamond was produced in at least 13 countries. About 98 percent of the combined natural and synthetic global output was produced in China, Ireland, Japan, Russia, South Africa and the United States. China is the world's leading producer of synthetic industrial diamond followed by Russia and the United States.

Uncovering the Physical Basis Connecting Environment and Tribological Performance of Ultrananocrystalline Diamond

DTIC Science & Technology

2014-04-17

measured with an infrared pyrometer (550-3200°C). The substrates were coated with diamond nanoparticles (ITC Inc.) which serve as nucleation sites...wafers were seeded with nano-diamond particles prior to film growth to provide nucleation sites for diamond growth. To study the effect of surface...wafers are appropriate to generate uniform seeding. AFM tips were seeded with nano-diamond particles prior to coating with NCD to provide nucleation

Mechanism-Based FE Simulation of Tool Wear in Diamond Drilling of SiCp/Al Composites.

PubMed

Xiang, Junfeng; Pang, Siqin; Xie, Lijing; Gao, Feinong; Hu, Xin; Yi, Jie; Hu, Fang

2018-02-07

The aim of this work is to analyze the micro mechanisms underlying the wear of macroscale tools during diamond machining of SiC p /Al6063 composites and to develop the mechanism-based diamond wear model in relation to the dominant wear behaviors. During drilling, high volume fraction SiC p /Al6063 composites containing Cu, the dominant wear mechanisms of diamond tool involve thermodynamically activated physicochemical wear due to diamond-graphite transformation catalyzed by Cu in air atmosphere and mechanically driven abrasive wear due to high-frequency scrape of hard SiC reinforcement on tool surface. An analytical diamond wear model, coupling Usui abrasive wear model and Arrhenius extended graphitization wear model was proposed and implemented through a user-defined subroutine for tool wear estimates. Tool wear estimate in diamond drilling of SiC p /Al6063 composites was achieved by incorporating the combined abrasive-chemical tool wear subroutine into the coupled thermomechanical FE model of 3D drilling. The developed drilling FE model for reproducing diamond tool wear was validated for feasibility and reliability by comparing numerically simulated tool wear morphology and experimentally observed results after drilling a hole using brazed polycrystalline diamond (PCD) and chemical vapor deposition (CVD) diamond coated tools. A fairly good agreement of experimental and simulated results in cutting forces, chip and tool wear morphologies demonstrates that the developed 3D drilling FE model, combined with a subroutine for diamond tool wear estimate can provide a more accurate analysis not only in cutting forces and chip shape but also in tool wear behavior during drilling SiC p /Al6063 composites. Once validated and calibrated, the developed diamond tool wear model in conjunction with other machining FE models can be easily extended to the investigation of tool wear evolution with various diamond tool geometries and other machining processes in cutting different workpiece materials.

Mechanism-Based FE Simulation of Tool Wear in Diamond Drilling of SiCp/Al Composites

PubMed Central

Xiang, Junfeng; Pang, Siqin; Xie, Lijing; Gao, Feinong; Hu, Xin; Yi, Jie; Hu, Fang

2018-01-01

The aim of this work is to analyze the micro mechanisms underlying the wear of macroscale tools during diamond machining of SiCp/Al6063 composites and to develop the mechanism-based diamond wear model in relation to the dominant wear behaviors. During drilling, high volume fraction SiCp/Al6063 composites containing Cu, the dominant wear mechanisms of diamond tool involve thermodynamically activated physicochemical wear due to diamond-graphite transformation catalyzed by Cu in air atmosphere and mechanically driven abrasive wear due to high-frequency scrape of hard SiC reinforcement on tool surface. An analytical diamond wear model, coupling Usui abrasive wear model and Arrhenius extended graphitization wear model was proposed and implemented through a user-defined subroutine for tool wear estimates. Tool wear estimate in diamond drilling of SiCp/Al6063 composites was achieved by incorporating the combined abrasive-chemical tool wear subroutine into the coupled thermomechanical FE model of 3D drilling. The developed drilling FE model for reproducing diamond tool wear was validated for feasibility and reliability by comparing numerically simulated tool wear morphology and experimentally observed results after drilling a hole using brazed polycrystalline diamond (PCD) and chemical vapor deposition (CVD) diamond coated tools. A fairly good agreement of experimental and simulated results in cutting forces, chip and tool wear morphologies demonstrates that the developed 3D drilling FE model, combined with a subroutine for diamond tool wear estimate can provide a more accurate analysis not only in cutting forces and chip shape but also in tool wear behavior during drilling SiCp/Al6063 composites. Once validated and calibrated, the developed diamond tool wear model in conjunction with other machining FE models can be easily extended to the investigation of tool wear evolution with various diamond tool geometries and other machining processes in cutting different workpiece materials. PMID:29414839

The Effect of ZrO₂ Nanoparticles on the Microstructure and Properties of Sintered WC-Bronze-Based Diamond Composites.

PubMed

Sun, Youhong; Wu, Haidong; Li, Meng; Meng, Qingnan; Gao, Ke; Lü, Xiaoshu; Liu, Baochang

2016-05-06

Metal matrix-impregnated diamond composites are widely used in diamond tool manufacturing. In order to satisfy the increasing engineering requirements, researchers have paid more and more attention to enhancing conventional metal matrices by applying novel methods. In this work, ZrO₂ nanoparticles were introduced into the WC-bronze matrix with and without diamond grits via hot pressing to improve the performance of conventional diamond composites. The effects of ZrO₂ nanoparticles on the microstructure, density, hardness, bending strength, and wear resistance of diamond composites were investigated. The results indicated that the hardness and relative density increased, while the bending strength decreased when the content of ZrO₂ nanoparticles increased. The grinding ratio of diamond composites increased significantly by 60% as a result of nano-ZrO₂ addition. The enhancement mechanism was discussed. Diamond composites showed the best overall properties with the addition of 1 wt % ZrO₂ nanoparticles, thus paving the way for further applications.

The Effect of ZrO2 Nanoparticles on the Microstructure and Properties of Sintered WC–Bronze-Based Diamond Composites

PubMed Central

Sun, Youhong; Wu, Haidong; Li, Meng; Meng, Qingnan; Gao, Ke; Lü, Xiaoshu; Liu, Baochang

2016-01-01

Metal matrix-impregnated diamond composites are widely used in diamond tool manufacturing. In order to satisfy the increasing engineering requirements, researchers have paid more and more attention to enhancing conventional metal matrices by applying novel methods. In this work, ZrO2 nanoparticles were introduced into the WC–bronze matrix with and without diamond grits via hot pressing to improve the performance of conventional diamond composites. The effects of ZrO2 nanoparticles on the microstructure, density, hardness, bending strength, and wear resistance of diamond composites were investigated. The results indicated that the hardness and relative density increased, while the bending strength decreased when the content of ZrO2 nanoparticles increased. The grinding ratio of diamond composites increased significantly by 60% as a result of nano-ZrO2 addition. The enhancement mechanism was discussed. Diamond composites showed the best overall properties with the addition of 1 wt % ZrO2 nanoparticles, thus paving the way for further applications. PMID:28773469

Fabrication of Fe-Based Diamond Composites by Pressureless Infiltration

PubMed Central

Li, Meng; Sun, Youhong; Meng, Qingnan; Wu, Haidong; Gao, Ke; Liu, Baochang

2016-01-01

A metal-based matrix is usually used for the fabrication of diamond bits in order to achieve favorable properties and easy processing. In the effort to reduce the cost and to attain the desired bit properties, researchers have brought more attention to diamond composites. In this paper, Fe-based impregnated diamond composites for drill bits were fabricated by using a pressureless infiltration sintering method at 970 °C for 5 min. In addition, boron was introduced into Fe-based diamond composites. The influence of boron on the density, hardness, bending strength, grinding ratio, and microstructure was investigated. An Fe-based diamond composite with 1 wt % B has an optimal overall performance, the grinding ratio especially improving by 80%. After comparing with tungsten carbide (WC)-based diamond composites with and without 1 wt % B, results showed that the Fe-based diamond composite with 1 wt % B exhibits higher bending strength and wear resistance, being satisfactory to bit needs. PMID:28774124

Thermal conductivity of ultrathin nano-crystalline diamond films determined by Raman thermography assisted by silicon nanowires

NASA Astrophysics Data System (ADS)

Anaya, Julian; Rossi, Stefano; Alomari, Mohammed; Kohn, Erhard; Tóth, Lajos; Pécz, Béla; Kuball, Martin

2015-06-01

The thermal transport in polycrystalline diamond films near its nucleation region is still not well understood. Here, a steady-state technique to determine the thermal transport within the nano-crystalline diamond present at their nucleation site has been demonstrated. Taking advantage of silicon nanowires as surface temperature nano-sensors, and using Raman Thermography, the in-plane and cross-plane components of the thermal conductivity of ultra-thin diamond layers and their thermal barrier to the Si substrate were determined. Both components of the thermal conductivity of the nano-crystalline diamond were found to be well below the values of polycrystalline bulk diamond, with a cross-plane thermal conductivity larger than the in-plane thermal conductivity. Also a depth dependence of the lateral thermal conductivity through the diamond layer was determined. The results impact the design and integration of diamond for thermal management of AlGaN/GaN high power transistors and also show the usefulness of the nanowires as accurate nano-thermometers.

Effect of electronic structure of the diamond surface on the strength of the diamond-metal interface

NASA Technical Reports Server (NTRS)

Pepper, S. V.

1981-01-01

A diamond surface undergoes a transformation in its electronic structure by a vacuum anneal at approximately 900 C. The polished surface has no electronic states in the band gap, whereas the annealed surface has both occupied and unoccupied states in the and gap and exhibits some electrical conductivity. The effect of this transformation on the strength of the diamond metal interface was investigated by measuring the static friction force of an atomically clean meta sphere on a diamond flat in ultrahigh vacuum. It was found that low friction (weak bonding) is associated with the diamond surface devoid of gap states whereas high friction (strong bonding) is associated with the diamond surface with gap states. Exposure of the annealed surface to excited hydrogen also leads to weak bonding. The interfacial bond is discussed in terms of interaction of the metal conduction band electrons with the band gap states on the diamond surface. Effects of surface electrical conductivity on the interfacial bond are also be considered.

Effect of added dispersants on diamond particles in Ni-diamond composites fabricated with electrodeposition

NASA Astrophysics Data System (ADS)

Choi, Yongje; Kim, Donghyun; Son, Kyungsik; Lee, Sanghyuk; Chung, Wonsub

2015-11-01

The electrodeposition of Ni-diamond composites was investigated to improve the dispersion and adhesion of the diamond particles, and thus, increase the performance of cutting tools. The additives, so called firstclass brighteners, benzoic sulfimide, benzene sulfonamide, and benzene sulfonic acid were used as dispersants to enhance the dispersivity of diamond particles. The dispersivity was analyzed with Image-Pro software, which was used to asses optical microscopy images, and the number of individual diamond particles and area fraction were calculated. In addition, electrochemical tests were performed, including zeta potential and galvanostatic measurements, and the adhesion strengths was tested by evaluating the wear resistance using ball-on-disk tester. The dispersion and adhesion of the diamond particles were improved when benzoic sulfimide was added to the composite plating bath at a concentration of 0.06 g/L. The number of individual diamond particles was 56 EA/mm2, and the weight loss of alumina ball and specimen was 2.88 mg and 0.80 mg, respectively.