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1

A tribute to Zachary Fisk  

NASA Astrophysics Data System (ADS)

We pay tribute to Zachary Fisk's contributions to materials physics on the occasion of his 60th birthday. His theme of ``new physics through new materials'' was made possible by a love of chemistry, a thorough grasp of physics, and a life-long association with the best researchers in the field.

Hecker, Siegfried S.

2002-05-01

2

Ball python  

NSDL National Science Digital Library

All reptiles are cold-blooded, meaning that they gather their warmth from the environment around them. Reptiles in captivity, like this ball python, need a sun lamp to stay warm. They could die if they get too cold.

Patrick Jean (muséum d'histoire naturelle de Nantes;)

2004-02-10

3

Extending Python  

Microsoft Academic Search

\\u000a You can implement anything in Python, really; it’s a powerful language, but sometimes it can get a bit too slow. For example,\\u000a if you’re writing a scientific simulation of some form of nuclear reaction, or you’re rendering the graphics for the next\\u000a Star Wars movie (wait—there won’t be any more now, will there?), writing the high-performance code in Python will

Magnus Lie Hetland

4

Teaching and Learning Python  

NSDL National Science Digital Library

Python is an introductory programming language considered ideal for learning the basic concepts of programming. This website offers examples of educational uses and lesson plans for Python. "LiveWires" is used to teach Python to children ages 12-15 at a summer camp in Britain. The lesson materials are free online and include a series of worksheets, reference sheets and game sheets for use with the LiveWires package (Python modules). Also on this website are a list of possible activities that will be offered in the 2004 summer session, interviews with current and former LiveWires people, and a typical timetable.

2007-07-24

5

The Distribution of the Burmese Python, Python bivittatus, in China  

Microsoft Academic Search

We here provide a revision of the distribution of the Burmese python, Python bivittatus, in China, as reported previously in Barker and Barker (2008). Information provided to us since the publication of that article allows a more detailed depiction of the natural distribution of the Burmese python in China. We dis- cuss the distribution of the Burmese python in each

David G. Barker; Tracy M. Barker

6

Extending Python with Fortran  

Microsoft Academic Search

Python is a great scripting language. It is portable, free, and has a powerful numerical facility, object oriented features, and a library of modules that enable a huge variety of applications: cryptography, image processing, special effects for movies, Web programming, Web site search engines, and so on. The authors have created a tool, Pyfort, for connecting Fortran routines to Python.

Paul F. Dubois; T.-Y. Yang

1999-01-01

7

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)....

8

Python fiber optic seal.  

National Technical Information Service (NTIS)

Sandia National Laboratories has developed a high security fiber optic seal that incorporates tamper resistance features that are not available in commercial fiber optic seals. The Python Seal is a passive fiber optic loop seal designed to give indication...

K. Ystesund J. Bartberger C. Brusseau P. Fleming K. Insch

1993-01-01

9

Monte Python: Monte Carlo Code for CLASS in Python  

NASA Astrophysics Data System (ADS)

Monte Python is a parameter inference code which combines the flexibility of the python language and the robustness of the cosmological code CLASS into a simple and easy to manipulate Monte Carlo Markov Chain code.

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

2013-07-01

10

Developing Sherpa with Python  

NASA Astrophysics Data System (ADS)

Sherpa is the general purpose fitting and modeling application for CIAO, the Chandra Interactive Analysis of Observations system. We have modified the original design and implemented a new version in Python. This version will be part of the upcoming CIAO4.0 release. We have previously presented a modular, flexible design for CIAO4.0 with the goal of packaging many models, fitting methods and statistics for analysis of astronomical data. The new design promised to be more robust than the previous Sherpa, and more easily extensible with user-written scripts. (We already see some sign of this, in that there were 50,000 lines of code in the CIAO3.0 implementation; with our new, cleaner design, implemented in Python, only half that number of lines were required.) We present the latest updates to our design, and our progress developing Sherpa. A major feature of this work has been the use of Python to implement the data structures from our design. Each part of Sherpa---models, fitting methods, statistics, and so on---has been implemented as a Python module. We have also developed application code to bind together data, models, statistics, and fitting methods for performing fits to data, as well as a high-level UI that makes it simple for users to read in data, define models, and perform fits. Working in Python has been a great aid in speeding development of Sherpa. We expect that Python will also simplify extending and maintaining the Sherpa code base, as well as making it possible to interoperate with other Python-based astronomy packages. To make Sherpa fully accessible to S--Lang users, we use PySL, a new package that is an interface between Python and S--Lang. Users are now able to import other Python or S--Lang modules to extend Sherpa; in addition, users may write and use scripts of their own, written in either Python or S--Lang.

Doe, S.; Nguyen, D.; Stawarz, C.; Refsdal, B.; Siemiginowska, A.; Burke, D.; Evans, I.; Evans, J.; McDowell, J.; Houck, J.; Nowak, M.

2007-10-01

11

Repast for Python Scripting.  

SciTech Connect

Repast for Python Scripting (RepastPy) is a rapid application development (RAD) tool for producing simulations from the Repast agent simulation framework. Using a point-and-click component based interface, users can easily construct a simulation and then use a special subset of the Python programming language to define agent behaviors. RepastPy is the next generation of Repast visual development tools superceding the older SimBuilder tool and incorporating a streamlined user interface, improved Python language support, and the latest improvements to Repast. RepastPy now provides the ability to export RepastPy models to Java, allowing users to then work in the traditional Repast for Java environment.

Collier, N.; North, M. J.; Decision and Information Sciences

2005-01-01

12

Python fiber optic seal  

Microsoft Academic Search

Sandia National Laboratories has developed a high security fiber optic seal that incorporates tamper resistance features that are not available in commercial fiber optic seals. The Python Seal is a passive fiber optic loop seal designed to give indication of unauthorized entry. The seal includes a fingerprint feature that provides seal identity information in addition to the unique fiber optic

K. Ystesund; J. Bartberger; C. Brusseau; P. Fleming; K. Insch; K. Tolk

1993-01-01

13

Thermoregulation in a Brooding Female Indian Python, Python molurus bivittatus  

Microsoft Academic Search

At varying environmental temperatures, measurements of body temperatures and gas exchange of a female Indian python (Python molurus bivittatus) show that during the brooding period this animal can regulate its body temperature by physiological means analogous to those in endotherms. Ambient temperatures below 33circC result in spasmodic contractions of the body musculature with a consequent increase in metabolism and body

Victor H. Hutchison; Herndon G. Dowling; Allen Vinegar

1966-01-01

14

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

USGS Publications Warehouse

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.

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

2011-01-01

15

Pyro Python Robotics  

NSDL National Science Digital Library

Pyro stands for Python Robotics. The goal of the project is to provide a programming environment for easily exploring advanced topics in artificial intelligence and robotics without having to worry about the low-level details of the underlying hardware. That is not to say that Pyro is just a toy. In fact, Pyro is used for real robotics research as well as courseware.This website is the 2005 recipient of Premier Award for Excellence in Engineering Education Courseware. It includes curriculum, tutorials, modules and documentations.

2012-03-26

16

Punishing the Lies on the Rio Grande: Catholic and Immigrant Volunteers in Zachary Taylor's Army and the Fight against Nativism  

Microsoft Academic Search

:In May 1846, in the midst of the largest wave of immigration up to that point in its history, the United States went to war with Mexico. The nation's attention became focused on northern Mexico as General Zachary Taylor's army marched up the Rio Grande and fought Mexican forces in the major battles of Monterrey and Buena Vista. Hundreds of

Tyler V. Johnson

2010-01-01

17

Punishing the Lies on the Rio Grande: Catholic and Immigrant Volunteers in Zachary Taylor's Army and the Fight against Nativism  

Microsoft Academic Search

In May 1846, in the midst of the largest wave of immigration up to that point in its history, the United States went to war with Mexico. The nation's attention became focused on northern Mexico as General Zachary Taylor's army marched up the Rio Grande and fought Mexican forces in the major battles of Monterrey and Buena Vista. Hundreds of

Tyler V. Johnson

2010-01-01

18

Notes on clotting in a Burmese python (Python molurus bivittatus).  

PubMed

Studies of the clotting mechanisms in the plasma of a Burmese python (Python molurus bivittatus) confirm earlier information that both extrinsic and intrinsic pathways of thrombin formation participate in reptilian hemostasis. Plasma fibrinogen was present at a concentration comparable to that in human plasma. Other assays were hampered by the need to use nonreptilian reagents. The activated partial thromboplastin time was shorter than was that of human plasma, thus implying the presence of prothrombin in python plasma; however, this protein could be demonstrated only in trace amounts. Similarly, only small amounts of Hageman factor (factor XII) and antihemophilic factor (factor VIII) were detected, and none of plasma prekallikrein, high-molecular-weight kininogen, and Christmas factor (factor IX). The prothrombin time was slower than that of human plasma. Factor VII was not detected, but both proaccelerin (factor V) and Stuart factor (factor X) were present. Python plasma inhibited bovine thrombin and human plasmin, but it was deficient in fibrinolytic capacity. PMID:2341766

Ratnoff, O D; Rosenberg, M J; Everson, B; Emanuelson, M; Tulodziecki, N

1990-05-01

19

Thermoregulation in a brooding female Indian python, Python molurus bivittatus.  

PubMed

At varying environmental temperatures, measurements of body temperatures and gas exchange of a female Indian python (Python molurus bivittatus) show that during the brooding period this animal can regulate its body temperature by physiological means analogous to those in endotherms. Ambient temperatures below 33 degrees C result in spasmodic contractions of the body musculature with a consequent increase in metabolism and body temperature. PMID:5908075

Hutchison, V H; Dowling, H G; Vinegar, A

1966-02-11

20

Computational Physics Education with Python  

NSDL National Science Digital Library

Educators at an institution in Germany have started using Python to teach computational physics. The author describes how graphical visualizations also play an important role, which he illustrates here with a few simple examples.

Bã¤cker, Arnd

2008-06-07

21

Pynamic: the Python Dynamic Benchmark  

SciTech Connect

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, we 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.

Lee, G L; Ahn, D H; de Supinksi, B R; Gyllenhaal, J C; Miller, P J

2007-07-10

22

Steering object-oriented computations with Python.  

National Technical Information Service (NTIS)

We have described current approaches and future plans for steering C++ application, running Python on parallel platforms, and combination of Tk interface and Python interpreter in steering computations. In addition, there has been significant enhancement ...

T. Y. B. Yang P. F. Dubois G. Furnish D. M. Beazley

1996-01-01

23

Anatomy of the python heart.  

PubMed

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. PMID:20376590

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

2010-04-08

24

Advanced Python Scripting Using Sherpa  

NASA Astrophysics Data System (ADS)

Sherpa is a general purpose modeling and fitting application written in Python. The dynamism of Python allows Sherpa to be a powerful and extensible software package ready for the modern challenges of data analysis. Primarily developed for the Chandra Interactive Analysis of Observations (CIAO) package, it provides a flexible environment for resolving spectral and image properties, analyzing time series, and modeling generic types of data. Complex model expressions are supported using Sherpa's general purpose definition syntax. Sherpa's parameterized data modeling is achieved using robust optimization methods implementing the forward fitting technique. Sherpa includes functions to calculate goodness-of-fit and parameter confidence limits. CPU intensive routines are written in C++/FORTRAN. But since all other data structures are contained in Python modules, users can easily add their own data structures, models, statistics or optimization methods to Sherpa. We will introduce a scripted example that highlights Sherpa's ability to estimate energy and photon flux errors using simulations. The draws from these simulations, accessible as NumPy ndarrays, can be sampled from uni-variate and multi-variate normal distributions and can be binned and visualized with simple high level functions. We will demonstrate how Sherpa can be extended with user-defined model and statistic classes written in Python. Sherpa's open design even allows users to incorporate prior statistics derived from the source model.

Refsdal, R.; Doe, S.; Nguyen, D.; Siemiginowska, A.; Burke, D.; Evans, J.; Evans, I.

2011-07-01

25

Geophysical data analysis using Python  

Microsoft Academic Search

A set of routines designed for geophysical data analysis that make extensive use of the numerical extensions to the computer language Python are presented. The routines perform some typical tasks during multivariate analysis of geophysical fields, such as principal component analysis and related tasks (truncation rules by means of analytical and Monte Carlo techniques). Other functions perform singular value decomposition

Jon Sáenz; Juan Zubillaga; Jesús Fernández

2002-01-01

26

Pybus -- A Python Software Bus  

SciTech Connect

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 concept 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.

Lavrijsen, Wim T.L.P.

2004-10-14

27

A Burmese Python and an Alligator Encounter in South Florida  

USGS Multimedia Gallery

A Burmese python (Python molurus) peeks over the head of an alligator that holds the python's body in its mouth in Everglades National Park. Photo courtesy of Lori Oberhofer, National Park Service....

2009-10-12

28

Steering object-oriented computations with Python  

SciTech Connect

We have described current approaches and future plans for steering C++ application, running Python on parallel platforms, and combination of Tk interface and Python interpreter in steering computations. In addition, there has been significant enhancement in the Gist module. Tk mega widgets has been implemented for a few physics applications. We have also written Python interface to SIJLO, a data storage package used as an interface to a visualization system named MeshTv. Python is being used to control large-scale simulations (molecular dynamics in particular) running on the CM-5 and T3D at LANL as well. A few other code development projects at LLNL are either using or considering Python as their steering shells. In summary, the merits of Python have been appreciated by more and more people in the scientific computation community.

Yang, T.-Y.B.; Dubois, P.F.; Furnish, G. [Lawrence Livermore National Lab., CA (United States); Beazley, D.M. [Utah Univ., Salt Lake City, UT (United States). Dept. of Computer Science

1996-10-01

29

Effect of feeding on circulating micronutrient concentrations in the Burmese python ( Python molurus)  

Microsoft Academic Search

Burmese pythons (Python molurus) regulate digestive performance and metabolism with the ingestion of each meal. To explore the python's postprandial responses, we monitored the concentrations of blood micronutrients and homocysteine during fasting and for 15 days after feeding. Plasma folate concentrations peaked with a 270% increase over fasting levels 3 days after feeding, whereas plasma B-12 peaked with a 66%

Stephen M Secor; Tim R Nagy; Kelley E Johnston; T Tamura

2001-01-01

30

Postprandial morphological response of the intestinal epithelium of the Burmese python ( Python molurus)  

Microsoft Academic Search

The postprandial morphological changes of the intestinal epithelium of Burmese pythons were examined using fasting pythons and at eight time points after feeding. In fasting pythons, tightly packed enterocytes possess very short microvilli and are arranged in a pseudostratified fashion. Enterocyte width increases by 23% within 24 h postfeeding, inducing significant increases in villus length and intestinal mass. By 6

Jean-Hervé Lignot; Cécile Helmstetter; Stephen M. Secor

2005-01-01

31

Postprandial morphological response of the intestinal epithelium of the Burmese python (Python molurus)  

Microsoft Academic Search

The postprandial morphological changes of the intestinal epithelium of Burmese pythons were examined using fasting pythons and at eight time points after feeding. In fasting pythons, tightly packed enterocytes possess very short microvilli and are arranged in a pseudostratified fashion. Enterocyte width increases by 23% within 24 h postfeeding, inducing significant increases in villus length and intestinal mass. By 6

Jean-Hervé Lignot; Cécile Helmstetter; Stephen M Secor

2006-01-01

32

Anatomy of the python heart  

Microsoft Academic Search

The hearts of all snakes and lizards consist of two atria and a single incompletely divided ventricle. In general, the squamate\\u000a ventricle is subdivided into three chambers: cavum arteriosum (left), cavum venosum (medial) and cavum pulmonale (right).\\u000a Although a similar division also applies to the heart of pythons, this family of snakes is unique amongst snakes in having\\u000a intracardiac pressure

Bjarke JensenJens; Jens R. Nyengaard; Michael Pedersen; Tobias Wang

2010-01-01

33

Pyomo : Python Optimization Modeling Objects.  

SciTech Connect

The Python Optimization Modeling Objects (Pyomo) package [1] is an open source tool for modeling optimization applications within Python. Pyomo provides an objected-oriented approach to optimization modeling, and it can be used to define symbolic problems, create concrete problem instances, and solve these instances with standard solvers. While Pyomo provides a capability that is commonly associated with algebraic modeling languages such as AMPL, AIMMS, and GAMS, Pyomo's modeling objects are embedded within a full-featured high-level programming language with a rich set of supporting libraries. Pyomo leverages the capabilities of the Coopr software library [2], which integrates Python packages (including Pyomo) for defining optimizers, modeling optimization applications, and managing computational experiments. A central design principle within Pyomo is extensibility. Pyomo is built upon a flexible component architecture [3] that allows users and developers to readily extend the core Pyomo functionality. Through these interface points, extensions and applications can have direct access to an optimization model's expression objects. This facilitates the rapid development and implementation of new modeling constructs and as well as high-level solution strategies (e.g. using decomposition- and reformulation-based techniques). In this presentation, we will give an overview of the Pyomo modeling environment and model syntax, and present several extensions to the core Pyomo environment, including support for Generalized Disjunctive Programming (Coopr GDP), Stochastic Programming (PySP), a generic Progressive Hedging solver [4], and a tailored implementation of Bender's Decomposition.

Siirola, John; Laird, Carl Damon (Texas A& M University, College Station, TX); Hart, William Eugene; Watson, Jean-Paul

2010-11-01

34

Biopython: Python tools for computational biology  

Microsoft Academic Search

The Biopython project was formed in August 1999 as a collaboration to collect and produce open source bioinformatics tools written in Python, an object-oriented scripting language. It is modeled on the highly successful Bioperl project, but has the goal of making libraries available for people doing computations in Python. The philosophy of all the Bio* projects is that part of

Brad Chapman; Jeffrey Chang

2000-01-01

35

Astropy: Community Python library for astronomy  

NASA Astrophysics Data System (ADS)

Astropy provides a common framework, core package of code, and affiliated packages for astronomy in Python. Development is actively ongoing, with major packages such as PyFITS, PyWCS, vo, and asciitable already merged in. Astropy is intended to contain much of the core functionality and some common tools needed for performing astronomy and astrophysics with Python.

Greenfield, Perry; Robitaille, Thomas; Tollerud, Erik; Aldcroft, Tom; Barbary, Kyle; Barrett, Paul; Bray, Erik; Crighton, Neil; Conley, Alex; Conseil, Simon; Davis, Matt; Deil, Christoph; Dencheva, Nadia; Droettboom, Michael; Ferguson, Henry; Ginsburg, Adam; Grollier, Frédéric; Moritz Günther, Hans; Hanley, Chris; Hsu, J. C.; Kerzendorf, Wolfgang; Kramer, Roban; Lian Lim, Pey; Muna, Demitri; Nair, Prasanth; Price-Whelan, Adrian; Shiga, David; Singer, Leo; Taylor, James; Turner, James; Woillez, Julien; Zabalza, Victor

2013-04-01

36

Facility for creating Python extensions in C++.  

National Technical Information Service (NTIS)

Python extensions are usually created by writing the glue that connects Python to the desired new functionality in the C language. While simple extensions do not require much effort, to do the job correctly with full error checking is tedious and prone to...

P. F. Dubois

1998-01-01

37

Physiology: Postprandial cardiac hypertrophy in pythons  

Microsoft Academic Search

Oxygen consumption by carnivorous reptiles increases enormously after they have eaten a large meal in order to meet metabolic demands, and this places an extra load on the cardiovascular system. Here we show that there is an extraordinarily rapid 40% increase in ventricular muscle mass in Burmese pythons (Python molurus) a mere 48 hours after feeding, which results from increased

Johnnie B. Andersen; Bryan C. Rourke; Vincent J. Caiozzo; Albert F. Bennett; James W. Hicks

2005-01-01

38

Retroviral particles in neoplasms of Burmese pythons (Python molurus bivittatus).  

PubMed

Neoplastic diseases associated with retroviruses were diagnosed in four Burmese pythons (Python molurus bivattatus) from a single collection. Snake No. 1 was a 7-year-old female with recurrent undifferentiated mesenchymal round cell tumor (lymphosarcoma) of the oral cavity. At necropsy, similar neoplastic masses were evident in the uterus and ovary, and there was diffuse involvement of the spleen. Snake No. 2 was a 4.5-year-old female that was euthanatized because of complications following resection of a segmental colonic adenocarcinoma. Snake No. 3 was a 5-year-old female that was euthanatized because of a large transitional cell carcinoma of the right kidney. Snake No. 4 was a 19-year-old female that was euthanatized following recurrence of an intermandibular fibrosarcoma. Ultrastructural examination revealed few to numerous extracellular and intracellular (intravacuolar) type C-like retroviral particles in all tumors. Tumors were about 90-95 nm in diameter, with an electron-dense core and bilaminar external membrane. The relationship of the intraneoplastic viral particles to the etiology of the tumors is uncertain. PMID:11572567

Chandra, A M; Jacobson, E R; Munn, R J

2001-09-01

39

Parallel, Distributed Scripting with Python  

SciTech Connect

Parallel computers used to be, for the most part, one-of-a-kind systems which were extremely difficult to program portably. With SMP architectures, the advent of the POSIX thread API and OpenMP gave developers ways to portably exploit on-the-box shared memory parallelism. Since these architectures didn't scale cost-effectively, distributed memory clusters were developed. The associated MPI message passing libraries gave these systems a portable paradigm too. Having programmers effectively use this paradigm is a somewhat different question. Distributed data has to be explicitly transported via the messaging system in order for it to be useful. In high level languages, the MPI library gives access to data distribution routines in C, C++, and FORTRAN. But we need more than that. Many reasonable and common tasks are best done in (or as extensions to) scripting languages. Consider sysadm tools such as password crackers, file purgers, etc ... These are simple to write in a scripting language such as Python (an open source, portable, and freely available interpreter). But these tasks beg to be done in parallel. Consider the a password checker that checks an encrypted password against a 25,000 word dictionary. This can take around 10 seconds in Python (6 seconds in C). It is trivial to parallelize if you can distribute the information and co-ordinate the work.

Miller, P J

2002-05-24

40

Retained Caseous Yolk Sac in a Burmese Python (Python molurus bivittatus)  

Microsoft Academic Search

Retained yolk sacs are common in the domestic chicken and account for consid- erable morbidity and mortality during late em- bryonic development and within the first 10 days of life. What is believed to be the first recorded instance of a retained caseous yolk sac and its successful surgical removal from a Bur- mese python (Python molurus Invittatus) is re-

M. S. Bodri; M. J. Hendrick; R. T. O'Brien; K. K. Sadanaga

41

Osteitis deformans (Paget’s disease) in a Burmese python ( Python molurus bivittatus) – A case report  

Microsoft Academic Search

Osteitis deformans (Paget’s disease of bone) is a chronic focal disorder of bone remodelling characterized by an initial increase in osteoclast-mediated bone resorption, with subsequent compensatory increase in new bone formation, resulting in a disorganized mosaic of woven and lamellar bone. In the Burmese python (Python molurus bivittatus) of this report, multifocal gross swellings involving the proximal third of the

Rosario Preziosi; Alessia Diana; Daniela Florio; Andrea Gustinelli; Giordano Nardini

2007-01-01

42

Why do female ball pythons (Python regius) coil so tightly around their eggs?  

Microsoft Academic Search

Question: What benefits does brooding confer to offspring viability that outweigh its costs to the nest-attending female? Organisms: Thirty captive Python regius females and their clutches. Site: Vicinity of Lomé, Togo. Background: It has previously been shown that brooding enhances ball python hatching success by reducing desiccation of eggs. Methods: We captured wild, gravid females just before the time of

Fabien Aubret; Xavier Bonnet; Richard Shine; Stéphanie Maumelat

2005-01-01

43

Python for Education: Computational Methods for Nonlinear Systems  

NSDL National Science Digital Library

The authors' interdisciplinary computational methods course uses Python and associated numerical and visualization libraries to enable students to implement simulations for several different course modules, which highlight the breadth and flexibility of Python-powered computational environments.

Myers, Christopher; Sethna, James

2008-07-23

44

Python and Java: The Best of Both Worlds  

Microsoft Academic Search

This paper describes a new working implementation ofthe Python language; built on top of the Java languageand run-time environment. This is in contrast to theexisting implementation of Python, which has been builton top of the C language and run-time environment.Implementing Python in Java has a number of limitationswhen compared to the current implementation ofPython in C. These include about 1.7X

Jim Hugunin

1997-01-01

45

Building a programmable interface for physics codes using numeric python  

SciTech Connect

With its portability, ease to add built-in functions and objects in C, and fast array facility among many other features, Python proved to be an excellent language for creating programmable scientific applications. In addition to the two modules presented, there are also other progresses at LLNL in using Python. For example, Python interfaces are being developed for at least three graphics packages, and Python interpreter and applications have been built on distributed platforms such as meiko and Cray T3D.

Yang, T.-Y.B.; Dubois, P.F.; Motteler, Z.C.

1996-04-16

46

Feeding a large-scale physics application to Python  

Microsoft Academic Search

The authors describe their experiences using Python with the SPaSM molecular dynamics code at Los Alamos National Laboratory. Originally developed as a large monolithic application for massive parallel processing systems, they have used Python to transform their application into a flexible, highly modular, and extremely powerful system for performing simulation, data analysis, and visualization. In addition, they describe how Python

David M. Beazley; Peter S. Lomdahl

1997-01-01

47

Consumption of bird eggs by invasive Burmese Pythons in Florida  

USGS Publications Warehouse

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.

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

2012-01-01

48

Implanting a Radio Transmitter in a Burmese Python  

USGS Multimedia Gallery

Researchers implant a radio transmitter in a 16-foot, 155-pound female Burmese python (Python molurus) at the South Florida Research Center, Everglades National Park. Radio-tracking builds understanding of where pythons spend their time and therefore where they can be controlled in practice. Photo c...

2009-10-12

49

Web development with python and django (abstract only)  

Microsoft Academic Search

Many instructors have already discovered the joy of teaching programming using the Python programming language. Now it's time to take Python to the next level. This workshop will introduce Django, an open source Python web framework that saves you time and makes web development fun. It's aimed at Computer Science instructors who want to teach how to build elegant web

Ariel Ortiz

2012-01-01

50

Pythons metabolize prey to fuel the response to feeding  

Microsoft Academic Search

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

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

2004-01-01

51

Gist: A scientific graphics package for Python  

SciTech Connect

{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 is 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.

Busby, L.E.

1996-05-08

52

The Python Interface to Antelope and Applications  

NASA Astrophysics Data System (ADS)

The Antelope Environmental Monitoring System from Boulder Real-Time Technologies, Inc. (http://www.brtt.com) is widely used for acquiring, processing, distributing, and archiving near-real-time monitoring data, especially in seismological networks. We have contributed a new Python interface to the Antelope toolkit, paralleling other commercial and open-source language interfaces in Matlab, PHP, TCL/Tk, and C. The Python programming language (http://www.python.org) is well suited both to scientific computing applications and to interactive web-based applications. In the latter, Python serves as the programming interface through which to connect to standardized open-source frameworks. Community development of these frameworks has advanced in parallel with cross-browser standardization and increasing broadband data transfer rates, making web-based applications the defacto standard for platform-agnostic access to large, heterogeneous datasets. These web-based solutions are starting to mirror some of the capabilities of standard desktop-based applications. We describe the functionality of the new Python interface to Antelope, applications of the interface to the interactive exploration of time-series data on the web using the Twisted open-source framework, and web-based prototype tools developed for the Earthscope Array Network Facility to provide community access to network monitoring and seismic event datasets.

Lindquist, K. G.; Clemesha, A.; Newman, R. L.; Vernon, F. L.

2008-12-01

53

Python: a language for computational physics  

NASA Astrophysics Data System (ADS)

Python is a relatively new computing language, created by Guido van Rossum [A.S. Tanenbaum, R. van Renesse, H. van Staveren, G.J. Sharp, S.J. Mullender, A.J. Jansen, G. van Rossum, Experiences with the Amoeba distributed operating system, Communications of the ACM 33 (1990) 46 63; also on-line at http://www.cs.vu.nl/pub/amoeba/. ], which is particularly suitable for teaching a course in computational physics. There are two questions to be considered: (i) For whom is the course intended? (ii) What are the criteria for a suitable language, and why choose Python? The criteria include the nature of the application. High performance computing requires a compiled language, e.g., FORTRAN. For some applications a computer algebra, e.g., Maple, is appropriate. For teaching, and for program development, an interpreted language has considerable advantages: Python appears particularly suitable. Python's attractions include (i) its system of modules which makes it easy to extend, (ii) its excellent graphics (VPython module), (iii) its excellent on line documentation, (iv) it is free and can be downloaded from the web. Python and VPython will be described briefly, and some programs demonstrated.

Borcherds, P. H.

2007-07-01

54

Tachykinins (Substance P, Neurokinin A and Neuropeptide ?) and Neurotensin from the Intestine of the Burmese Python, Python molurus  

Microsoft Academic Search

Conlon, J. M., T. E. Adrian and S. M. Secor. Tachykinins (substance P, neurokinin A and neuropeptide ?,) and neurotensin from the intestine of the burmese python, Python molurus. Peptides 18(10) 1505–1510, 1997.—Peptides with substance P-like immunoreactivity, neurokinin A-like immunoreactivity and neurotensin-like immunoreactivity were isolated in pure form from an extract of the intestine of the Burmese python (Python molurus).

J. Michael Conlon; Thomas E Adrian; Stephen M Secor

1997-01-01

55

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

Microsoft Academic Search

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

Christian L. Cox; Stephen M. Secor

2007-01-01

56

Acetaminophen as an Oral Toxicant for Nile Monitor Lizards (Varanus niloticus) and Burmese Pythons (Python molurus bivittatus)  

Microsoft Academic Search

Context. Invasive species are a growing global problem. Biological invasions can result in numerous harmful impacts on local ecologies, and non-native herpetofauna are frequently ignored. Nile monitor lizards (Varanus niloticus) and Burmese pythons (Python molurus bivittatus, recently reassessed as Python bivittatus bivittatus), have become established in southern Florida. Both are large, semi-aquatic predators that pose serious threats to a variety

Richard E. Mauldin; Peter J. Savarie

2010-01-01

57

Charming Users into Scripting CIAO with Python  

NASA Astrophysics Data System (ADS)

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.

Burke, D. J.

2011-07-01

58

Python for Large-Scale Electrophysiology  

PubMed Central

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.

Spacek, Martin; Blanche, Tim; Swindale, Nicholas

2008-01-01

59

A New Python Library for Spectroscopic Analysis with MIDAS Style  

NASA Astrophysics Data System (ADS)

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.

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

2013-10-01

60

THE PYTHON SHELL FOR THE ORBIT CODE  

SciTech Connect

A development of a Python driver shell for the ORBIT simulation code is presented. The original ORBIT code uses the SuperCode shell to organize accelerator-related simulations. It is outdated, unsupported, and it is an obstacle to future code development. The necessity and consequences of replacing the old shell language are discussed. A set of core modules and extensions that are currently in PyORBIT are presented. They include particle containers, parsers for MAD and SAD lattice files, a Python wrapper for MPI libraries, space charge calculators, TEAPOT trackers, and a laser stripping extension module.

Shishlo, Andrei P [ORNL; Gorlov, Timofey V [ORNL; Holmes, Jeffrey A [ORNL

2009-01-01

61

APLpy: Astronomical Plotting Library in Python  

NASA Astrophysics Data System (ADS)

APLpy (the Astronomical Plotting Library in Python) is a Python module for producing publication-quality plots of astronomical imaging data in FITS format. The module uses Matplotlib, a powerful and interactive plotting package. It is capable of creating output files in several graphical formats, including EPS, PDF, PS, PNG, and SVG. Plots can be made interactively or by using scripts, and can generate co-aligned FITS cubes to make three-color RGB images. It also offers different overlay capabilities, including contour sets, markers with customizable symbols, and coordinate grids, and a range of other useful features.

Robitaille, Thomas; Bressert, Eli

2012-08-01

62

Physiology: postprandial cardiac hypertrophy in pythons.  

PubMed

Oxygen consumption by carnivorous reptiles increases enormously after they have eaten a large meal in order to meet metabolic demands, and this places an extra load on the cardiovascular system. Here we show that there is an extraordinarily rapid 40% increase in ventricular muscle mass in Burmese pythons (Python molurus) a mere 48 hours after feeding, which results from increased gene expression of muscle-contractile proteins. As this fully reversible hypertrophy occurs naturally, it could provide a useful model for investigating the mechanisms that lead to cardiac growth in other animals. PMID:15744290

Andersen, Johnnie B; Rourke, Bryan C; Caiozzo, Vincent J; Bennett, Albert F; Hicks, James W

2005-03-01

63

Ecological divergence among sympatric colour morphs in blood pythons, Python brongersmai  

Microsoft Academic Search

Blood pythons in northeastern Sumatra display a series of discrete colour morphs, even among hatchlings within a single clutch.\\u000a The first step towards understanding the maintenance of this polymorphism is to test the null hypothesis that colour variation\\u000a in this species has no major biological correlates. Data on >2,000 blood pythons killed for the commercial leather industry\\u000a enabled us to

R. Shine; Ambariyanto; Peter S. Harlow; Mumpuni

1998-01-01

64

Identifying plausible scenarios for the establishment of invasive Burmese pythons ( Python molurus ) in Southern Florida  

Microsoft Academic Search

Successful invasions of secretive alien species often go unrecognized until spread has exceeded the point where control or\\u000a eradication is feasible. In such situations, understanding factors that contributed to establishment can be critical to preventing\\u000a subsequent introductions of previously-successful invaders or ecologically similar species. The Burmese python (Python molurus bivittatus), a native to Southeast Asia, is abundant in the pet

John D. WillsonMichael; Michael E. Dorcas; Raymond W. Snow

2011-01-01

65

Retained caseous yolk sac in a Burmese python (Python molurus bivittatus).  

PubMed

Retained yolk sacs are common in the domestic chicken and account for considerable morbidity and mortality during late embryonic development and within the first 10 days of life. What is believed to be the first recorded instance of a retained caseous yolk sac and its successful surgical removal from a Burmese python (Python molurus bivittatus) is reported. The snake experienced no post-operative complications and continues to be well 16 mo following surgery. PMID:2250338

Bodri, M S; Hendrick, M J; O'Brien, R T; Sadanaga, K K

1990-10-01

66

Postprandial increase of oleoylethanolamide mobilization in small intestine of the Burmese python (Python molurus)  

Microsoft Academic Search

ABSTRACT Oleoylethanolamide (OEA) is an,endogenous,lipid mediator that inhibits feeding in rats and mice by activating the nuclear receptor peroxisome ,proliferator-activated receptor- ? (PPAR-?). In rodents, intestinal OEA levels increase about 3-fold upon refeeding, a response,that may ,contribute to the ,induction of between-meal ,satiety. Here we examined,whether ,feeding-induced OEA mobilization also occurs in Burmese ,pythons (Python molurus), a species of ambush-hunting

Giuseppe Astarita; Bryan C. Rourke; Johnnie B. Andersen; Jin Fu; Janet H. Kim; Albert F. Bennett; James W. Hicks; Daniele Piomelli

2005-01-01

67

DEAP: a python framework for evolutionary algorithms  

Microsoft Academic Search

DEAP (Distributed Evolutionary Algorithms in Python) is a novel volutionary computation framework for rapid prototyping and testing of ideas. Its design departs from most other existing frameworks in that it seeks to make algorithms explicit and data structures transparent, as opposed to the more common black box type of frameworks. It also incorporates easy parallelism where users need not concern

François-Michel De Rainville; Félix-Antoine Fortin; Marc-André Gardner; Marc Parizeau; Christian Gagné

2012-01-01

68

Python Scripting in the Nengo Simulator  

PubMed Central

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.

Stewart, Terrence C.; Tripp, Bryan; Eliasmith, Chris

2008-01-01

69

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

USGS Publications Warehouse

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.

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

2012-01-01

70

Ventilatory and cardiovascular responses of a python (Python molurus) to exercise and digestion.  

PubMed

To investigate the potential limiting steps of peak metabolic rates, we examined gas exchange rates ( vdot (O2), vdot (CO2)), respiratory exchange ratio (RER), breathing frequency, tidal volume, minute ventilation volume (V.e) as well as the heart rate, systemic blood flow and stroke volume of Burmese pythons (Python molurus) while fasting at rest, exercising, digesting and exercising while digesting. All measured variables increased significantly during exercise (crawling at 0.4 km h(-)(1) and at vdot (O2max)), highlighted by a 17-fold increase in vdot (CO2) and a 24-fold increase in V.e. During the digestion of a meal equivalent to 25 % of the snake's body mass, pythons responded with increases in vdot (O2) and heart rate similar to those experienced during exercise, along with a 4.5-fold increase in systemic blood flow. Interestingly, pythons hyperventilated while exercising, whereas they hypoventilated during digestion. The combined demands of exercise and digestion resulted in significantly higher vdot (O2), vdot (CO2), breathing frequency and heart rate than during either exercise or digestion alone. Evidently, the capacities of the ventilatory and cardiovascular systems to transport oxygen to locomotor muscles are not a limiting factor in the attainment of peak metabolic rates during exercise in pythons PMID:10903159

Secor, S M; Hicks, J W; Bennett, A F

2000-08-01

71

Matched regulation of gastrointestinal performance in the Burmese python, Python molurus.  

PubMed

In Burmese pythons fasting and feeding cause dramatic regulation of gastric acid production and intestinal nutrient uptake. Predictably, other components of their gastrointestinal tract are similarly regulated with each meal. We therefore assessed the matched regulation of gastrointestinal performance by comparing the postprandial activities and capacities of gastric (pepsin), pancreatic (amylase and trypsin) and intestinal (aminopeptidase-N and maltase) enzymes, and intestinal nutrient uptake. Tissue samples were collected from pythons fasted and at 0.25, 0.5, 1, 2, 3, 4, 6, 10 and 15 days following their consumption of rodent meals equaling 25% of snake body mass. With feeding, pythons experience no significant change in stomach mass, whereas both the pancreas and small intestine doubled in mass. Feeding also triggered a depletion of gastric mucosal pepsinogen, a respective 5.7- and 20-fold increase in the peak activities of pancreatic trypsin and amylase, and a respective 2.3- and 5.5-fold increase in the peak activities of intestinal maltase and aminopeptidase-N. Enzyme activities peaked between 2 and 4 days postfeeding and returned to fasting levels by day 10. Independent of digestive stage, python intestine exhibited a proximal to distal decline in enzyme activity. For both sugars and proteins, intestinal capacities for enzyme activity were significantly correlated with nutrient uptake capacities. The concomitant postprandial upregulation of tissue morphology, intestinal nutrient transport rates and enzyme activities illustrate, for the python, the matched regulation of their gastrointestinal performance with each meal. PMID:18344488

Cox, Christian L; Secor, Stephen M

2008-04-01

72

Postprandial increase of oleoylethanolamide mobilization in small intestine of the Burmese python (Python molurus).  

PubMed

Oleoylethanolamide (OEA) is an endogenous lipid mediator that inhibits feeding in rats and mice by activating the nuclear receptor peroxisome proliferator-activated receptor-alpha (PPAR-alpha). In rodents, intestinal OEA levels increase about threefold upon refeeding, a response that may contribute to the induction of between-meal satiety. Here, we examined whether feeding-induced OEA mobilization also occurs in Burmese pythons (Python molurus), a species of ambush-hunting snakes that consume huge meals after months of fasting and undergo massive feeding-dependent changes in gastrointestinal hormonal release and gut morphology. Using liquid chromatography/mass spectrometry (LC/MS), we measured OEA levels in the gastrointestinal tract of fasted (28 days) and fed (48 h after feeding) pythons. We observed a nearly 300-fold increase in OEA levels in the small intestine of fed compared with fasted animals (322 +/- 121 vs. 1 +/- 1 pmol/mg protein, n = 3-4). In situ OEA biosynthesis was suggested by the concomitant increase of N-acyl phosphatidylethanolamine species that serve as potential biosynthetic precursors for OEA. Furthermore, we observed a concomitant increase in saturated, mono- and diunsaturated, but not polyunsaturated fatty-acid ethanolamides (FAE) in the small intestine of fed pythons. The identification of OEA and other FAEs in the gastrointestinal tract of Python molurus suggests that this class of lipid messengers may be widespread among vertebrate groups and may represent an evolutionarily ancient means of regulating energy intake. PMID:16373434

Astarita, Giuseppe; Rourke, Bryan C; Andersen, Johnnie B; Fu, Jin; Kim, Janet H; Bennett, Albert F; Hicks, James W; Piomelli, Daniele

2005-12-22

73

Effect of feeding on circulating micronutrient concentrations in the Burmese python (Python molurus).  

PubMed

Burmese pythons (Python molurus) regulate digestive performance and metabolism with the ingestion of each meal. To explore the python's postprandial responses, we monitored the concentrations of blood micronutrients and homocysteine during fasting and for 15 days after feeding. Plasma folate concentrations peaked with a 270% increase over fasting levels 3 days after feeding, whereas plasma B-12 peaked with a 66% increase within 1 day. Erythrocyte folate concentrations were highest 15 days after feeding with a 44% increase. The major plasma folate was 5-methyltetrahydrofolate during fasting and was non-5-methyltetrahydrofolate during digestion, whereas erythrocytes contained polyglutamyl forms of non-5-methyltetrahydrofolate. Plasma homocysteine concentrations peaked with a 56% increase 3 days after feeding, and were markedly greater than those of mammals. Plasma zinc and copper did not change significantly. Plasma zinc concentrations were 20 times greater than plasma copper and approximately 30 times higher than those of mammals. Pythons showed a significant postprandial decline of 25% in hematocrit. Plasma pyridoxal 5'-phosphate (coenzyme form of vitamin B-6) was not detected probably due to its tight protein binding. Most micronutrient concentrations appear to plateau 3 days after feeding, suggesting that pythons have relatively rapid homeostasis of micronutrients despite the ingestion of large meals. PMID:11423336

Secor, S M; Nagy, T R; Johnston, K E; Tamura, T

2001-06-01

74

Feeding a large-scale physics application to Python  

SciTech Connect

The authors describe their experiences using Python with the SPaSM molecular dynamics code at Los Alamos National Laboratory. Originally developed as a large monolithic application for massive parallel processing systems, they have used Python to transform their application into a flexible, highly modular, and extremely powerful system for performing simulation, data analysis, and visualization. In addition, they describe how Python has solved a number of important problems related to the development, debugging, deployment, and maintenance of scientific software.

Beazley, D.M. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Computer Science; Lomdahl, P.S. [Los Alamos National Lab., NM (United States). Theoretical Div.

1997-10-01

75

Leveraging Python Interoperability Tools to Improve Sapphire's Usability  

SciTech Connect

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.

Gezahegne, A; Love, N S

2007-12-10

76

matplotlib -- A Portable Python Plotting Package  

NASA Astrophysics Data System (ADS)

matplotlib is a portable 2D plotting and imaging package aimed primarily at visualization of scientific, engineering, and financial data. matplotlib can be used interactively from the Python shell, called from python scripts, or embedded in a GUI application (GTK, Wx, Tk, Windows). Many popular hardcopy outputs are supported including JPEG, PNG, PostScript and SVG. Features include the creation of multiple axes and figures per page, interactive navigation, many predefined line styles and symbols, images, antialiasing, alpha blending, date and financial plots, W3C compliant font management and FreeType2 support, legends and tables, pseudocolor plots, mathematical text and more. It works with both numarray and Numeric. The goals of the package, basic architecture, current features (illustrated with examples), and planned enhancements will be described.

Barrett, P.; Hunter, J.; Miller, J. T.; Hsu, J.-C.; Greenfield, P.

2005-12-01

77

An integrated optimization for hypersonic inlet design based on PYTHON  

Microsoft Academic Search

In this paper, an integrated optimization program, based on PYTHON script programming language, has been developed by integrating CFD software and optimization package for shape optimization of high speed flight vehicles. The program comprises four functions connected with PYTHON scripts: geometry module, flow grid generator, flow solver, and optimizer, and the data of each part can be exchanged and updated

Shizhen Li; Shuo Tang; Du Gao

2010-01-01

78

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

PubMed

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. PMID:20050011

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

2009-08-01

79

Molecular genetic evidence for parthenogenesis in the Burmese python, Python molurus bivittatus  

Microsoft Academic Search

Parthenogenesis among reptiles is rare. Only a few species have the ability to reproduce asexually. Most of these are obligate parthenogenetic species that consist (almost) entirely of females, which can reproduce solely through parthenogenesis. Rarer are sexual species that only sporadically reproduce through parthenogenesis. A female Python molurus bivittatus (Reptilia, Boidae) from the Artis Zoo, Amsterdam, produced eggs in five

T. V. M. Groot; E Bruins; J A J Breeuwer; TVM Groot

2003-01-01

80

A facility for creating Python extensions in C++  

SciTech Connect

Python extensions are usually created by writing the glue that connects Python to the desired new functionality in the C language. While simple extensions do not require much effort, to do the job correctly with full error checking is tedious and prone to errors in reference counting and to memory leaks, especially when errors occur. The resulting program is difficult to read and maintain. By designing suitable C++ classes to wrap the Python C API, we are able to produce extensions that are correct and which clean up after themselves correctly when errors occur. This facility also integrates the C++ and Python exception facilities. This paper briefly describes our package for this purpose, named CXX. The emphasis is on our design choices and the way these contribute to the construction of accurate Python extensions. We also briefly relate the way CXX's facilities for sequence classes allow use of C++'s Standard Template Library (STL) algorithms on C++ sequences.

Dubois, P F

1998-07-14

81

Gastric function and its contribution to the postprandial metabolic response of the Burmese python Python molurus.  

PubMed

The large intact prey ingested by Burmese pythons require considerable processing by the stomach before passage into the small intestine. To investigate the function and cost of gastric digestion and its contribution to postprandial metabolic response for the Burmese python, I examined the rate of gastric digestion, the postprandial profile of gastric pH and the effects of decreasing gastric workload on the metabolic cost of digestion, referred to as specific dynamic action (SDA). Ingested meal mass (equivalent to 25% of snake body mass) was reduced by 18% within 1 day postfeeding, by which time intragastric pH had decreased from 7.5 to 2. Gastric pH was maintained at 1.5 for the next 5-7 days, after which it returned to 7.5. The SDA generated by digesting an intact rat meal was reduced by 9.1%, 26.0%, 56.5% and 66.8%, respectively, when pythons were fed steak, ground rat, liquid diet or ground rat directly infused into the small intestine. The production of HCl and enzymes and other gastric functions represent an estimated 55% of the python's SDA generated from the digestion of an intact rodent meal. Additional contributors to SDA include protein synthesis (estimated 26%), gastrointestinal upregulation (estimated 5%) and the activities of the pancreas, gallbladder, liver, kidneys and intestines during digestion (estimated 14%). Operating on a 'pay before pumping' principle, pythons must expend endogenous energy in order to initiate acid production and other digestive processes before ingested nutrients can be absorbed and channeled into metabolic pathways. PMID:12682094

Secor, Stephen M

2003-05-01

82

Chiantipy - The Python Interface To Chianti  

NASA Astrophysics Data System (ADS)

Python is a free, modern, object-oriented programming language that is well suited to scientific data analysis. A command line version for use within the IPython shell is under development and significant progress has already been made. Programmatically, each ion in the CHIANTI database is treated as an object, providing a good match to the structure of the CHIANTI database. Currently, ChiantiPy is able to calculate and plot level populations, spectral line emissivities, contribution functions, G(n,T), and line intensity ratios as functions of temperature and electron and proton density. A GUI version is also planned. The current capabilities of ChiantiPy will be demonstrated.

Dere, Kenneth P.

2009-05-01

83

Responses of python gastrointestinal regulatory peptides to feeding.  

PubMed

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

Secor, S M; Fehsenfeld, D; Diamond, J; Adrian, T E

2001-11-13

84

Responses of python gastrointestinal regulatory peptides to feeding  

PubMed Central

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.

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

2001-01-01

85

Osteitis deformans (Paget's disease) in a Burmese python (Python molurus bivittatus)--a case report.  

PubMed

Osteitis deformans (Paget's disease of bone) is a chronic focal disorder of bone remodelling characterized by an initial increase in osteoclast-mediated bone resorption, with subsequent compensatory increase in new bone formation, resulting in a disorganized mosaic of woven and lamellar bone. In the Burmese python (Python molurus bivittatus) of this report, multifocal gross swellings involving the proximal third of the vertebral spine were observed and associated with anorexia, a relative inability to move or to fully extend the body, and to strike at prey. Serum biochemistry revealed elevated alkaline-phosphatase activity. Radiographic changes (irregular bone proliferation along the vertebral margins), computed tomography scan results (abnormal mineral density), and histopathological features (generalized thickening of the bony trabeculae at the expense of the intertrabecular spaces and irregular patches of lamellar bone with a characteristic "mosaic" pattern) indicated osteitis deformans. PMID:17222574

Preziosi, Rosario; Diana, Alessia; Florio, Daniela; Gustinelli, Andrea; Nardini, Giordano

2007-01-11

86

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

PubMed

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. PMID:21370657

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

2010-12-01

87

A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)  

PubMed Central

Background Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, including those related to development, metabolism, physiology, and venom. Despite their importance as research models, genomic resources for snakes are few. Among snakes, the Burmese python is the premier model for studying extremes of metabolic fluctuation and physiological remodelling. In this species, the consumption of large infrequent meals can induce a 40-fold increase in metabolic rate and more than a doubling in size of some organs. To provide a foundation for research utilizing the python, our aim was to assemble and annotate a transcriptome reference from the heart and liver. To accomplish this aim, we used the 454-FLX sequencing platform to collect sequence data from multiple cDNA libraries. Results We collected nearly 1 million 454 sequence reads, and assembled these into 37,245 contigs with a combined length of 13,409,006 bp. To identify known genes, these contigs were compared to chicken and lizard gene sets, and to all Genbank sequences. A total of 13,286 of these contigs were annotated based on similarity to known genes or Genbank sequences. We used gene ontology (GO) assignments to characterize the types of genes in this transcriptome resource. The raw data, transcript contig assembly, and transcript annotations are made available online for use by the broader research community. Conclusion These data should facilitate future studies using pythons and snakes in general, helping to further contribute to the utilization of snakes as a model evolutionary and physiological system. This sequence collection represents a major genomic resource for the Burmese python, and the large number of transcript sequences characterized should contribute to future research in this and other snake species.

2011-01-01

88

Postprandial morphological response of the intestinal epithelium of the Burmese python (Python molurus).  

PubMed

The postprandial morphological changes of the intestinal epithelium of Burmese pythons were examined using fasting pythons and at eight time points after feeding. In fasting pythons, tightly packed enterocytes possess very short microvilli and are arranged in a pseudostratified fashion. Enterocyte width increases by 23% within 24 h postfeeding, inducing significant increases in villus length and intestinal mass. By 6 days postfeeding, enterocyte volume had peaked, following as much as an 80% increase. Contributing to enterocyte hypertrophy is the cellular accumulation of lipid droplets at the tips and edges of the villi of the proximal and middle small intestine, but which were absent in the distal small intestine. At 3 days postfeeding, conventional and environmental scanning electron microscopy revealed cracks and lipid extrusion along the narrow edges of the villi and at the villus tips. Transmission electron microscopy demonstrated the rapid postprandial lengthening of enterocyte microvilli, increasing 4.8-fold in length within 24 h, and the maintaining of that length through digestion. Beginning at 24 h postfeeding, spherical particles were found embedded apically within enterocytes of the proximal and middle small intestine. These particles possessed an annular-like construction and were stained with the calcium-stain Alizarine red S suggesting that they were bone in origin. Following the completion of digestion, many of the postprandial responses were reversed, as observed by the atrophy of enterocytes, the shortening of villi, and the retraction of the microvilli. Further exploration of the python intestine will reveal the underlying mechanisms of these trophic responses and the origin and fate of the engulfed particles. PMID:16002308

Lignot, Jean-Hervé; Helmstetter, Cécile; Secor, Stephen M

2005-07-01

89

VENTILATORY AND CARDIOVASCULAR RESPONSES OF A PYTHON (PYTHON MOLURUS) TO EXERCISE AND DIGESTION  

Microsoft Academic Search

exercise (crawling at 0.4 km h -1 and at V. Omax), highlighted by a 17-fold increase in V. COand a 24-fold increase in V. E. During the digestion of a meal equivalent to 25 % of the snake's body mass, pythons responded with increases in V. Oand heart rate similar to those experienced during exercise, along with a 4.5-fold increase

STEPHEN M. SECOR; JAMES W. HICKS; ALBERT F. BENNETT

2000-01-01

90

Introduction to Python (A One-Hour Tour).  

National Technical Information Service (NTIS)

This tutorial highlights and goes over essential features of the Python programming language while it is still evolving, but sufficiently stable and mature for the development of diverse solutions to computational, networking, and visualization problems. ...

B. Q. Nguyen

2008-01-01

91

PyEphem: Astronomical Ephemeris for Python  

NASA Astrophysics Data System (ADS)

PyEphem provides scientific-grade astronomical computations for the Python programming language. Given a date and location on the Earth’s surface, it can compute the positions of the Sun and Moon, of the planets and their moons, and of any asteroids, comets, or earth satellites whose orbital elements the user can provide. Additional functions are provided to compute the angular separation between two objects in the sky, to determine the constellation in which an object lies, and to find the times at which an object rises, transits, and sets on a particular day.The numerical routines that lie behind PyEphem are those from the wonderful XEphem astronomy application, whose author, Elwood Downey, generously gave permission for us to use them as the basis for PyEphem.

Rhodes, Brandon Craig

2011-12-01

92

PySpecKit: Python Spectroscopic Toolkit  

NASA Astrophysics Data System (ADS)

PySpecKit is a Python spectroscopic analysis and reduction toolkit meant to be generally applicable to optical, infrared, and radio spectra. It is capable of reading FITS-standard and many non-standard file types including CLASS spectra. It contains procedures for line fitting including gaussian and voigt profile fitters, and baseline-subtraction routines. It is capable of more advanced line fitting using arbitrary model grids. Fitting can be done both in batch mode and interactively. PySpecKit also produces publication-quality plots with TeX axis labels and annotations. It is designed to be extensible, allowing user-written reader, writer, and fitting routines to be "plugged in." It is actively under development and currently in the 'alpha' phase, with plans for a beta release.

Ginsburg, Adam; Mirocha, Jordan

2011-09-01

93

Astropy: A community Python package for astronomy  

NASA Astrophysics Data System (ADS)

We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions. Significant functionality is under activedevelopment, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools. The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions.

Astropy Collaboration; Robitaille, Thomas P.; Tollerud, Erik J.; Greenfield, Perry; Droettboom, Michael; Bray, Erik; Aldcroft, Tom; Davis, Matt; Ginsburg, Adam; Price-Whelan, Adrian M.; Kerzendorf, Wolfgang E.; Conley, Alexander; Crighton, Neil; Barbary, Kyle; Muna, Demitri; Ferguson, Henry; Grollier, Frédéric; Parikh, Madhura M.; Nair, Prasanth H.; Unther, Hans M.; Deil, Christoph; Woillez, Julien; Conseil, Simon; Kramer, Roban; Turner, James E. H.; Singer, Leo; Fox, Ryan; Weaver, Benjamin A.; Zabalza, Victor; Edwards, Zachary I.; Azalee Bostroem, K.; Burke, D. J.; Casey, Andrew R.; Crawford, Steven M.; Dencheva, Nadia; Ely, Justin; Jenness, Tim; Labrie, Kathleen; Lian Lim, Pey; Pierfederici, Francesco; Pontzen, Andrew; Ptak, Andy; Refsdal, Brian; Servillat, Mathieu; Streicher, Ole

2013-10-01

94

Rapid Development of Interferometric Software Using MIRIAD and Python  

NASA Astrophysics Data System (ADS)

State-of-the-art radio interferometers are complex systems that unleash torrents of data. If current and planned instruments are to routinely meet their performance goals, standard analysis techniques must be significantly improved, becoming simultaneously more sophisticated, more automatic, and more scalable. While there is no shortage of ideas for next-generation algorithms, there is a shortage of development resources, so it is vital that programming environments for interferometric software allow for rapid, flexible development. We present an open-source software package, miriad-python, that provides access to the MIRIAD interferometric reduction system in the Python programming language. The modular design of MIRIAD and the high productivity and accessibility of Python provide an excellent foundation for rapid development of interferometric software. Several other projects with similar goals exist, and we describe them and compare miriad-python with them in detail. Along with an overview of the package design, we present sample code and applications, including the detection of millisecond astrophysical transients, determination and application of nonstandard calibration parameters, interactive data visualization, and a reduction pipeline using a directed acyclic graph dependency model analogous to that of the traditional UNIX tool make. The key aspects of the miriad-python software project are documented. We find that miriad-python provides an extremely effective environment for prototyping new interferometric software, though certain existing packages provide far more infrastructure for some applications. While equivalent software written in compiled languages can be much faster than Python, there are many situations in which execution time is profitably exchanged for speed of development, code readability, accessibility to nonexpert programmers, quick interlinking with foreign software packages, and other virtues of the Python language.

Williams, Peter K. G.; Law, Casey J.; Bower, Geoffrey C.

2012-06-01

95

An Introduction to Python for UNIX\\/C Programmers  

Microsoft Academic Search

Python is an interpreted, object-oriented language suitable for many purposes. It has a clear, intuitive syntax, powerful high-level data structures, and a flexible dynamic type system. Python can be used interactively, in stand-alone scripts, for large programs, or as an extension language for existing applications. The language runs on UNIX, Macintosh, and DOS machines. Source and documentation are available by

Guido van Rossum

1993-01-01

96

Python Quick-Look Utilities for Ground WFC3 Images  

NASA Astrophysics Data System (ADS)

A Python module to process and manipulate ground WFC3 UVIS and IR images is presented. Several methods are defined to assemble and mosaic the images, calculate basic statistical quantities on the imaging areas and overscan regions, subtract the overscan and reference regions, trim the images, and calculate the UVIS dark current rate and IR noise. The module can be easily incorporated into Python scripts for more complex processing.

Martel, A. R.

2008-01-01

97

Cold weather and the potential range of invasive Burmese pythons  

Microsoft Academic Search

The Burmese python (Python molurus bivittatus) is established in Everglades National Park and neighboring areas in south Florida. Beyond its substantial ecological impacts\\u000a to native fauna in south Florida, concerns have been raised as to its potential to occupy other parts of the USA, even as\\u000a far north as Washington, DC. During a recent period of cold weather, seven of

Michael L. AveryRichard; Richard M. Engeman; Kandy L. Keacher; John S. Humphrey; William E. Bruce; Tom C. Mathies; Richard E. Mauldin

2010-01-01

98

Neutron Scattering Experiment Automation with Python  

SciTech Connect

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory currently holds the Guinness World Record as the world most powerful pulsed spallation neutron source. Neutrons scattered off atomic nuclei in a sample yield important information about the position, motions, and magnetic properties of atoms in materials. A neutron scattering experiment usually involves sample environment control (temperature, pressure, etc.), mechanical alignment (slits, sample and detector position), magnetic field controllers, neutron velocity selection (choppers) and neutron detectors. The SNS Data Acquisition System (DAS) consists of real-time sub-system (detector read-out with custom electronics, chopper interface), data preprocessing (soft real-time) and a cluster of control and ancillary PCs. The real-time system runs FPGA firmware and programs running on PCs (C++, LabView) typically perform one task such as motor control and communicate via TCP/IP networks. PyDas is a set of Python modules that are used to integrate various components of the SNS DAS system. It enables customized automation of neutron scattering experiments in a rapid and flexible manner. It provides wxPython GUIs for routine experiments as well as IPython command line scripting. Matplotlib and numpy are used for data presentation and simple analysis. We will present an overview of SNS Data Acquisition System and PyDas architectures and implementation along with the examples of use. We will also discuss plans for future development as well as the challenges that have to be met while maintaining PyDas for 20+ different scientific instruments.

Zolnierczuk, Piotr A [ORNL; Riedel, Richard A [ORNL

2010-01-01

99

Ecological correlates of invasion impact for Burmese pythons in Florida  

USGS Publications Warehouse

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.

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

2012-01-01

100

Ecological correlates of invasion impact for Burmese pythons in Florida.  

PubMed

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. PMID:22938523

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

2012-09-01

101

Pythons metabolize prey to fuel the response to feeding.  

PubMed Central

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.

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

2004-01-01

102

Tachykinins (substance P, neurokinin A and neuropeptide gamma) and neurotensin from the intestine of the Burmese python, Python molurus.  

PubMed

Peptides with substance P-like immunoreactivity, neurokinin A-like immunoreactivity and neurotensin-like immunoreactivity were isolated in pure form from an extract of the intestine of the Burmese python (Python molurus). The primary structure of python substance P (Arg-Pro-Arg-Pro-Gln-Gln-Phe-Tyr-Gly-Leu- Met-NH2) shows one amino acid substitution (Phe8-->Tyr) compared with chicken/alligator substance P and an additional substitution (Lys3-->Arg) as compared with mammalian substance P. The neurokinin A-like immunoreactivity was separated into two components. Python neuropeptide gamma (Asp-Ala-Gly-Tyr- Ser-Pro-Leu-Ser-His-Lys-Arg-His-Lys-Thr-Asp-Ser-Phe-Val-Gly-Leu-Met-NH2 shows three substitutions (Gly5-->Ser, Gln6-->Pro and Ile7-->Leu) compared with alligator neuropeptide gamma and an additional substitution (His4-->Tyr) compared with mammalian neuropeptide gamma. Python neurokinin A (His-Lys-Thr-Asp-Ser-Phe-Val-Gly- Leu-Met.NH2) is identical to human/chicken/alligator neurokinin A. Python neurotensin (pGlu-Leu-Val-His-Asn-Lys-Ala-Arg-Pro-Tyr-Ile-Leu) is identical to chicken/alligator neurotensin. The data are indicative of differential evolutionary pressure to conserve the amino acid sequences of reptilian gastrointestinal peptides. PMID:9437709

Conlon, J M; Adrian, T E; Secor, S M

1997-01-01

103

The effects of UV light on calcium metabolism in ball pythons (Python regius).  

PubMed

Despite the popularity of keeping snakes in captivity, there has been limited investigation into the effects of UV radiation on vitamin D levels in snakes. The aim of this study was to investigate the effects of UV-b radiation on plasma 25-hydroxyvitamin D3 levels and ionised calcium concentrations in ball pythons (Python regius). Blood samples were taken from 14 ball pythons, which had never been exposed to UV-b light, to obtain baseline 25-hydroxyvitamin D3 levels and ionised calcium concentrations. Blood samples were then taken again from the same snakes 70 days later after one group (Group 1, n=6 females) were exposed to UV-b radiation daily, and the other group (Group 2, n=5 males and 3 females) were exposed to no UV-b radiation. Mean±sd 25-hydroxyvitamin D3 levels on day 0 in Group 1 were 197±35 nmol/l, and on day 70 were 203.5±13.8 nmol/l. Mean±sd 25-hydroxyvitamin D3 levels in Group 2 on day 0 were 77.7±41.5 nmol/l, and on day 70 were 83.0±41.9 nmol/l. Mean±sd ionised calcium levels at day 0 were 1.84±0.05 mmol/l for Group 1, and on day 70 were 1.78±0.07 mmol/l. Mean±sd ionised calcium levels at day 0 were 1.79±0.07 mmol/l for Group 2, and on day 70 were 1.81±0.05 mmol/l. No association was demonstrated between exposure to UV-b radiation and plasma 25-hydroxyvitamin D3 and ionised calcium concentrations. These results may provide baseline parameters for future studies in this and other snake species to determine ability to utilise UV-b light for vitamin D production. PMID:24068697

Hedley, J; Eatwell, K

2013-09-25

104

Functional changes with feeding in the gastro-intestinal epithelia of the Burmese python (Python molurus).  

PubMed

The morphology of the digestive system in fasting and refed Burmese pythons was determined, as well as the localization of the proton (H(+), K(+)-ATPase) and sodium (Na(+), K(+)-ATPase) pumps. In fasting pythons, oxyntopeptic cells located within the fundic glands are typically non-active, with a thick apical tubulovesicular system and numerous zymogen granules. They become active Immediately after feeding but return to a non-active state 3 days after the Ingestion of the prey. The proton pump, expressed throughout the different fasting/feeding states, is either sequestered in the tubulovesicular system in non-active cells or located along the apical digitations extending within the crypt lumen in active cells. The sodium pump is rapidly upregulated in fed animals and is classically located along the baso-lateral membranes of the gastric oxyntopeptic cells. In the Intestine, it is only expressed along the lateral membranes of the enterocytes, i.e., above the lateral spaces and not along the basal side of the cells. Thus, solute transport within the Intestinal lining is mainly achieved through the apical part of the cells and across the lateral spaces while absorbed fat massively crosses the entire height of the cells and flows into the Intercellular spaces. Therefore, in the Burmese python, the gastrointestinal cellular system quickly upregulates after feeding, due to Inexpensive cellular changes, passive mechanisms, and the progressive activation and synthesis of key enzymes such as the sodium pump. This cell plasticity also allows anticipation of the next fasting and feeding periods. PMID:19799514

Helmstetter, Cécile; Reix, Nathalie; T'Flachebba, Mathieu; Pope, Robert K; Secor, Stephen M; Le Maho, Yvon; Lignot, Jean-Hervé

2009-09-01

105

Intracardiac flow separation in an in situ perfused heart from Burmese python Python molurus.  

PubMed

The heart of non-crocodilian reptiles has two separate atria that receive blood from the systemic and pulmonary circulations. The ventricle is not fully divided, but is compartmentalised into two chambers (cavum dorsale and cavum pulmonale) by a muscular ridge that runs from the apex to the base of the ventricle. The muscular ridge is small in turtles, but is well developed in varanid lizards and many species of snakes. These anatomical differences correlate with an effective blood flow separation in varanid lizards, whereas turtles can exhibit very large cardiac shunts. Very little is known about the cardiac shunt patterns in other groups of reptiles. Here we characterise cardiac performance and flow dynamics in the Burmese python (Python molurus) using an in situ perfused heart preparation. The pericardium remained intact and the two atria were perfused separately (Ringer solution), and the two systemic and the pulmonary outflows were independently cannulated. Right and left atrial filling pressures and ventricular outflow pressures of the pulmonary and systemic vessels could be manipulated independently, permitting the establishment of large experimental intraventricular pressure gradients across the muscular ridge. The maximal power output generated by the systemic side of the ventricle exceeded the maximal power output that was generated by the cavum pulmonale that perfuse the pulmonary circulation. Furthermore, systemic flow could be generated against a higher outflow pressure than pulmonary flow. Perfusate entering the right atrium was preferentially distributed into the pulmonary circulation, whereas perfusate into the left atrium was distributed to the systemic circulation. Our study indicates that the well-developed muscular ridge can separate the cavum systemic and pulmonary sides of the heart to prevent mixing of systemic and pulmonary flows. Therefore, the heart of Python appears to exhibit a large degree of ventricular flow separation as previously described for varanid lizards. We speculate that the ventricular separation has evolved in response to the need of maintaining high oxygen delivery while protecting the pulmonary circulation from oedema as result of high vascular pressures. PMID:12151377

Wang, Tobias; Altimiras, Jordi; Axelsson, Michael

2002-09-01

106

PyHelp-An Automatic Multi-Output Documentation Generator for Python.  

National Technical Information Service (NTIS)

The DRACO code creates geometry and meshes through a command-line Python interface consisting of hundreds of classes and modules which must be accompanied by current documentation. The standard Python utility pydoc performs introspection on objects and pr...

W. I. Nissen

2005-01-01

107

Cold-induced mortality of invasive Burmese pythons in south Florida  

Microsoft Academic Search

A recent record cold spell in southern Florida (2–11 January 2010) provided an opportunity to evaluate responses of an established\\u000a population of Burmese pythons (Python molurus bivittatus) to a prolonged period of unusually cold weather. We observed behavior, characterized thermal biology, determined fate of\\u000a radio-telemetered (n = 10) and non-telemetered (n = 104) Burmese pythons, and analyzed habitat and environmental conditions experienced by pythons

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

2011-01-01

108

Purification and characterization of islet hormones (insulin, glucagon, pancreatic, polypeptide and somatostatin) from the Burmese python, Python molurus.  

PubMed

Insulin was purified from an extract of the pancreas of the Burmese python, Python molurus (Squamata:Serpentes) and its primary structure established as: A Chain: Gly-Ile-Val-Glu-Gln-Cys-Cys-Glu-Asn-Thr10-Cys-Ser-Leu-Tyr-Glu-Leu- Glu-Asn-Tyr-Cys20-Asn. B-Chain: Ala-Pro-Asn-Gln-His-Leu-Cys-Gly-Ser-His10-Leu-Val-Glu-Ala-Leu-Tyr- Leu-Val-Cys-Gly20-Asp-Arg-Gly-Phe-Tyr-Tyr-Ser-Pro-Arg-Ser30. With the exception of the conservative substitution Phe --> Tyr at position B25, those residues in human insulin that comprise the receptor-binding and those residues involved in dimer and hexamer formation are fully conserved in python insulin. Python insulin was slightly more potent (1.8-fold) than human insulin in inhibiting the binding of [125I-Tyr-A14] insulin to the soluble full-length recombinant human insulin receptor but was slightly less potent (1.5-fold) than human insulin for inhibiting binding to the secreted extracellular domain of the receptor. The primary structure of python glucagon contains only one amino acid substitution (Ser28 --> Asn) compared with turtle/duck glucagon and python somatostatin is identical to that of mammalian somatostatin-14. In contrast, python pancreatic polypeptide (Arg-Ile-Ala-Pro-Val-Phe-Pro-Gly-Lys-Asp10-Glu-Leu-Ala-Lys-Phe- Tyr20-Thr-Glu-Leu-Gln-Gln-Tyr-Leu-Asn-Ser-Ile30-Asn-Arg-Pro-Arg -Phe.NH2) contains only 35 instead of the customary 36 residues and the amino acid sequence of this peptide has been poorly conserved between reptiles and birds (18 substitutions compared with alligator and 20 substitutions compared with chicken). PMID:9350978

Conlon, J M; Secor, S M; Adrian, T E; Mynarcik, D C; Whittaker, J

1997-08-29

109

Zur Taxonomie des Dunklen Tigerpythons, Python molurus bivittatus KUHL, 1820, speziell der Population von Sulawesi  

Microsoft Academic Search

The taxonomic status of the Burmese Python ( Python molurus bivittatus) is reassessed and elevated to specific rank again. The population from Sulawesi, Indonesia, is a dwarf form of this giant snake that is redefined as Python bivit- tatus progschai ssp. n.

Hans J. Jacobs; Mark Auliya; Wolfgang Böhme

2009-01-01

110

Python algorithms in particle tracking microrheology  

PubMed Central

Background Particle tracking passive microrheology relates recorded trajectories of microbeads, embedded in soft samples, to the local mechanical properties of the sample. The method requires intensive numerical data processing and tools allowing control of the calculation errors. Results We report the development of a software package collecting functions and scripts written in Python for automated and manual data processing, to extract viscoelastic information about the sample using recorded particle trajectories. The resulting program package analyzes the fundamental diffusion characteristics of particle trajectories and calculates the frequency dependent complex shear modulus using methods published in the literature. In order to increase conversion accuracy, segmentwise, double step, range-adaptive fitting and dynamic sampling algorithms are introduced to interpolate the data in a splinelike manner. Conclusions The presented set of algorithms allows for flexible data processing for particle tracking microrheology. The package presents improved algorithms for mean square displacement estimation, controlling effects of frame loss during recording, and a novel numerical conversion method using segmentwise interpolation, decreasing the conversion error from about 100% to the order of 1%.

2012-01-01

111

The effect of meal composition on specific dynamic action in burmese pythons (Python molurus).  

PubMed

We quantified the specific dynamic action (SDA) resulting from the ingestion of various meal types in Burmese pythons (Python molurus) at 30 degrees C. Each snake was fed a series of experimental meals consisting of amino acid mixtures, simple proteins, simple or complex carbohydrates, or lipids as well as meals of whole animal tissue (chicken breast, beef suet, and mouse). Rates of oxygen consumption were measured for approximately 4 d after feeding, and the increment above standard metabolic rate was determined and compared to energy content of the meals. While food type (protein, carbohydrate, and lipid) had a general influence, SDA was highly dependent on meal composition (i.e., amino acid composition and carbohydrate structure). For chicken breast and simple carbohydrates, the SDA coefficient was approximately one-third the energetic content of the meal. Lard, suet, cellulose, and starch were not digested and did not produce measurable SDA. We conclude that the cost of de novo protein synthesis is an important component of SDA after ingestion of protein meals because (1) simple proteins, such as gelatin and collagen, did not stimulate levels of SDA attained after consumption of complete protein, (2) incomplete mixtures of amino acids failed to elicit the SDA of a complete mixture, and (3) the inhibition of de novo protein synthesis with the drug cycloheximide caused a more than 70% decrease in SDA. Stomach distension and mechanical digestion of intact prey did not cause measurable SDA. PMID:15778938

McCue, M D; Bennett, A F; Hicks, J W

2005-02-25

112

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

PubMed

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. PMID:17913527

Cox, Christian L; Secor, Stephen M

2007-09-04

113

Chapter 23: Programmatic Interfaces - VOLib/VOAgent (Python)  

NASA Astrophysics Data System (ADS)

This section describes the Python VO client library, VOLib. First an overview of the requirements and capabilities of the library is given, followed by a description of the general class hierarchy. Then each of the classes implementing VO protocols (Cone Search and SIAP) and the web services (Registry, SkyNode, and SkyPortal) is explained. Examples showing how to use these classes individually and in combination are given. VOAgent is presented as a more elaborate example of using these classes to create new functionality. We assume that the reader is already acquainted with VO protocols, web services, the Python programming language and object-oriented programming in general.

Kwok, S. H.

114

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

USGS Publications Warehouse

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.

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

115

A Python interface with Narcisse graphics  

SciTech Connect

Narcisse is a graphics package developed by our French colleagues at Centre d`Etudes de Limeil Valenton of the Commissariat d`Energie Atomique. Narcisse is quite comprehensive; it can do two-, three-, and four-dimensional plots (the latter meaning that the surface is colored according to the values of an arbitrary function). One can open and send plots to a Narcisse window on a distant machine. Narcisse has a user-friendly graphical user interface (GUI) which, once a graph has appeared, allows the user to change its characteristics interactively. This enables one to find the best appearance for a particular plot without having to graph it repeatedly from the user program. Previously created files in various formats can also be imported directly into the Narcisse GUI and manipulated from there. Narcisse runs independently, as a graphics server. The user program communicates with Narcisse via Unix sockets. This communication is quite low level and very complex. The appearance of a plot is controlled by nearly 150 parameters for determining such things as the color palette, type of shading, axis scales, curve and surface labels, titles, angle and distance of view (for three- and four-dimensional graphs), hidden line removal, etc. Most end users do not wish to spend time learning the tedious details of such interfaces; they would just like to specify data and ask to have it plotted. This paper describes a high level, easy to use graphics interface which hides (as much as possible) the low level details of whatever graphics system is actually being used, so that the low level can be essentially ``plug-and-play.`` Then, whenever a better system becomes available, it should only be necessary to change low level interface routines not normally accessed by ordinary users. Python, with its easy extendability, was ideally suited for this job.

Motteler, Z.C.

1996-04-15

116

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

PubMed

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. PMID:21370663

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

2010-12-01

117

A novel Mycoplasma sp. associated with proliferative tracheitis and pneumonia in a Burmese python (Python molurus bivittatus).  

PubMed

Proliferative lymphocytic tracheitis and pneumonia were observed histologically in the respiratory tract of a captive Burmese python (Python molurus bivittatus). A mycoplasma species was isolated from the respiratory tissue. Polymerase chain reaction analysis of the 16S rRNA gene sequence of the isolate showed 0.90 similarity to Mycoplasma agassizii, an organism previously shown to cause respiratory disease in reptiles. Based on these findings, a novel Mycoplasma species was suspected to be the causative agent of respiratory disease in this snake. PMID:9447490

Penner, J D; Jacobson, E R; Brown, D R; Adams, H P; Besch-Williford, C L

1997-10-01

118

Determinants of the postfeeding metabolic response of Burmese pythons, Python molurus.  

PubMed

The relatively large meal sizes consumed by sit-and-wait-foraging snake species make them favorable for investigating specific dynamic action, the rise in metabolic rate associated with digestion. Hence, we measured O2 consumption rates (VO2) before and up to 20 d after Burmese pythons (Python molurus) either had only constricted and killed rodent meals or had also been allowed to consume meals ranging in size from 5% to 111% of their body mass. Postprandial VO2 peaked within 2 d at a value that increased with meal size, up to 44 times standard metabolic rate for the largest meals. In addition to being the largest known magnitude of postprandial metabolic response, this also exceeds the factorial increase in VO2 during peak physical activity for all studied animals except perhaps racehorses. Specific dynamic action, calculated from the extra VO2 above standard metabolic rate over the duration of digestion, increased with meal size and equaled 32% of ingested meal energy. The allometric exponent for body mass was 0.68 for standard metabolic rate, 0.90 for peak postprandial VO2, and 1.01 for specific dynamic action. Specific dynamic action is higher, and standard metabolic rate is lower, in sit-and-wait-foraging snake species than in actively foraging snake species. This suggests that sit-and-wait-foraging snakes, which consume large meals at long and unpredictable intervals, reduce standard metabolic rate by allowing the energetically expensive small intestine and other associated organs to atrophy between meals but thereby incur a large specific dynamic action while rebuilding those organs upon feeding. PMID:9231393

Secor, S M; Diamond, J

119

Effects of meal size on postprandial responses in juvenile Burmese pythons (Python molurus).  

PubMed

Pythons were reported previously to exhibit large changes in intestinal mass and transporter activities on consuming meals equal to 25% of the snake's body mass. This paper examines how those and other adaptive responses to feeding vary with meal size (5, 25, or 65% of body mass). Larger meals took longer to pass through the stomach and small intestine. After ingestion of a meal, O2 consumption rates rose to up to 32 times fasting levels and remained significantly elevated for up to 13 days. This specific dynamic action equaled 29-36% of ingested energy. After 25 and 65% size meals, plasma Cl- significantly dropped, whereas plasma CO2, glucose, creatinine, and urea nitrogen increased as much as a factor of 2.3-4.2. Within 1 day the intestinal mucosal mass more than doubled, and masses of the intestinal serosa, liver, stomach, pancreas, and kidneys also increased. Intestinal uptake rates of amino acids and of D-glucose increased by up to 43 times fasting levels, whereas uptake capacities increased by up to 59 times fasting levels. Magnitudes of many of these responses (O2 consumption rate, kidney hypertrophy, and D-glucose and L-lysine uptake) increased with meal size up to the largest meals studied; other responses (Na+-independent L-leucine uptake, plasma Cl-, and organ masses) plateaued at meals equal to 25% of the snake's body mass; and still other responses (nutrient uptake at day 1, passive glucose uptake, and plasma protein and alkaline phosphatase) were all-or-nothing, being independent of meal size between 5 and 65% of body mass. Pythons undergo a wide array of postprandial responses, many of which differ in their sensitivity to meal size. PMID:9087654

Secor, S M; Diamond, J

1997-03-01

120

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

PubMed Central

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.

Jurica, Peter; van Leeuwen, Cees

2008-01-01

121

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

PubMed

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. PMID:19225577

Jurica, Peter; van Leeuwen, Cees

2009-02-10

122

FIRST IDENTIFICATION OF A RANAVIRUS FROM GREEN PYTHONS (CHONDROPYTHON VIRIDIS)  

Microsoft Academic Search

Ten juvenile green pythons (Chondropython viridis) died or were euthanized shortly after having been illegally imported into Australia from Indonesia in 1998. Histologic examination of two of the three snakes that died revealed moderately severe chronic ulceration of the nasal mucosa and focal or periacinar degeneration and necrosis of the liver. In addition there was severe necrotizing inflammation of the

A. D. Hyatt; M. Williamson; B. E. H. Coupar; D. Middleton; S. G. Hengstberger; A. R. Gould; P. Selleck; T. G. Wise; J. Kattenbelt; A. A. Cunningham; J. Lee

2002-01-01

123

Building a programmable interface for physics codes using numeric python.  

National Technical Information Service (NTIS)

With its portability, ease to add built-in functions and objects in C, and fast array facility among many other features, Python proved to be an excellent language for creating programmable scientific applications. In addition to the two modules presented...

T. Y. B. Yang P. F. Dubois Z. C. Motteler

1996-01-01

124

Python robotics: an environment for exploring robotics beyond LEGOs  

Microsoft Academic Search

This paper describes Pyro, a robotics programming environment designed to allow inexperienced undergraduates to explore topics in advanced robotics. Pyro, which stands for Python Robotics, runs on a number of advanced robotics platforms. In addition, programs in Pyro can abstract away low-level details such that individual programs can work unchanged across very different robotics hardware. Results of using Pyro in

Douglas S. Blank; Lisa Meeden; Deepak Kumar

2003-01-01

125

Another breadth-first approach to CS I using python  

Microsoft Academic Search

In an effort to serve the needs of both majors and non-majors, the Computer Science Department at Centre College has restructured the CS I course so that it uses the language Python, devotes more attention to the Internet and the World Wide Web, addresses ethical and societal issues, and introduces students to programmable robots and an SQL database. This diverse

Christine Shannon

2003-01-01

126

Deep Integration of Python with Web Ontology Language  

Microsoft Academic Search

The Semantic Web is a vision for the future of the Web in which information is given explicit meaning, making it easier for ma- chines to automatically process and integrate information available on the Web. Semantic Web will build on the well known Semantic Web language stack, part of which is the Web Ontology Language (OWL). Python is an interpreted,

Marian Babik; Ladislav Hluchy

127

A python graphics package for the first day and beyond  

Microsoft Academic Search

We demonstrate the use of a new Python graphics package named cs1graphics, while discussing its impact on peda- gogy and showcasing the recent work of our students. Our package was originally developed with two goals in mind. First, we insisted that it be intuitive enough that students can sit down and make use of it from the very first day

Michael H. Goldwasser; David Letscher

2008-01-01

128

Comparison of cyclic correlation algorithm implemented in matlab and python  

NASA Astrophysics Data System (ADS)

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.

Carr, Richard; Whitney, James

129

Postprandial remodeling of the gut microbiota in Burmese pythons.  

PubMed

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. As many model species (for example, 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 used 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 with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12?h 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 seemed 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

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

2010-06-03

130

Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python--Python molurus bivittatus--Management  

PubMed Central

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.

Hunter, Margaret E.; Hart, Kristen M.

2013-01-01

131

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

PubMed

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. PMID:21801464

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

132

Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python-Python molurus bivittatus-Management.  

PubMed

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

Hunter, Margaret E; Hart, Kristen M

2013-02-28

133

Molecular genetic evidence for parthenogenesis in the Burmese python, Python molurus bivittatus.  

PubMed

Parthenogenesis among reptiles is rare. Only a few species have the ability to reproduce asexually. Most of these are obligate parthenogenetic species that consist (almost) entirely of females, which can reproduce solely through parthenogenesis. Rarer are sexual species that only sporadically reproduce through parthenogenesis. A female Python molurus bivittatus (Reptilia, Boidae) from the Artis Zoo, Amsterdam, produced eggs in five consecutive years that contained embryos while she was isolated from males. These eggs might be fertilized with stored sperm, or might be the product of parthenogenesis. Parthenogenesis has not been shown for the Boidae family before. We performed parentship analyses on the snake and seven of her embryos using microsatellites and AFLP. Four microsatellite loci developed for this species combined with three loci developed previously for different snake species revealed too little variation to discriminate between sperm retention and parthenogenesis. With AFLP we were able to confirm that the Artis Zoo female reproduced parthenogenetically. Because the offspring are genetically identical to their mother, whereas in previous studies on sporadic parthenogenesis in snakes a loss of genetic information was reported, we conclude that the meiotic pathways that produce the diploid egg cells are different. PMID:12634818

Groot, T V M; Bruins, E; Breeuwer, J A J

2003-02-01

134

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

PubMed Central

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.

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

2011-01-01

135

Interactive, Extensible PIC Simulations with a Python Interface  

NASA Astrophysics Data System (ADS)

Particle-in-Cell (PIC) simulations of plasmas are used for a wide variety of systems, and can range significantly in scale. There are many informative simulations that can be run at interactive speeds, and good tools for interacting with simulations are important for facilitating science. By wrapping simulation code in Python, we gain the use of a full programming language as the simulation interface. This quickly gives us the tools for defining new diagnostics in-flight, enabling more natural investigation of the system. The Python interface also allows very powerful interaction between codes, facilitating iterative approaches for finding target simulation parameters, and working with other simulation codes. The toolset is also developed with parallel simulations in mind, allowing for aggregation of subdomain diagnostics from different nodes.

Ragan-Kelley, Benjamin; Verboncoeur, John

2011-11-01

136

The Crates Library: The Redesigned Python Interface for Scripting Languages  

NASA Astrophysics Data System (ADS)

Crates is a Python module produced by the Chandra X-ray Center (CXC) that provides a convenient high-level user interface for accessing and manipulating data stored in a variety of formats. Crates is currently utilized by Chandra's plotting, modeling and fitting tools. This paper will highlight the design changes and improvements made to Crates. This version of Crates has been completely rewritten in Python and has been optimized to conserve time and memory resources through lazy initialization. It provides increased functionality for data and metadata manipulation along with better memory management. In addition, Crates will be able to interface with several different backend modules, allowing the user to effortlessly switch between the CXC Data Model (DM), Virtual Observatory (VO), and pyFITS formats.

Lyn, J.; Burke, D.; Cresitello-Dittmar, M.; Evans, I.; Evans, J. D.

2011-07-01

137

Brian: A Simulator for Spiking Neural Networks in Python  

PubMed Central

“Brian” is a new simulator for spiking neural networks, written in Python (http://brian. di.ens.fr). It is an intuitive and highly flexible tool for rapidly developing new models, especially networks of single-compartment neurons. In addition to using standard types of neuron models, users can define models by writing arbitrary differential equations in ordinary mathematical notation. Python scientific libraries can also be used for defining models and analysing data. Vectorisation techniques allow efficient simulations despite the overheads of an interpreted language. Brian will be especially valuable for working on non-standard neuron models not easily covered by existing software, and as an alternative to using Matlab or C for simulations. With its easy and intuitive syntax, Brian is also very well suited for teaching computational neuroscience.

Goodman, Dan; Brette, Romain

2008-01-01

138

Python as a Federation Tool for GENESIS 3.0  

PubMed Central

The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be ‘glued’ together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience.

Cornelis, Hugo; Rodriguez, Armando L.; Coop, Allan D.; Bower, James M.

2012-01-01

139

PyRAT - python radiography analysis tool (u)  

SciTech Connect

PyRAT is a radiography analysis tool used to reconstruction images of unknown 1-0 objects. The tool is written in Python and developed for use on LINUX and Windows platforms. The tool is capable of performing nonlinear inversions of the images with minimal manual interaction in the optimization process. The tool utilizes the NOMAD mixed variable optimization tool to perform the optimization.

Temple, Brian A [Los Alamos National Laboratory; Buescher, Kevin L [Los Alamos National Laboratory; Armstrong, Jerawan C [Los Alamos National Laboratory

2011-01-14

140

ViPEr, a Visual Programming Environment for Python  

Microsoft Academic Search

In this paper we describe a Python-and Tkinter-based visual-programming environment called ViPEr. This tool enables non-programmers to build computational and visualization networks interactively. Computational nodes can be placed onto a canvas and their input and output ports can be connected using the mouse. The connections between the nodes define a directed graph that will be used to propagate data and

Michel F. Sanner; Daniel. Stoffler; Arthur J. Olson

141

Extensible Message Passing Application Development and Debugging with Python  

Microsoft Academic Search

We describe how we have parallelized Python, an in- terpreted object oriented scripting language, and used it to build an extensible message-passing molecular dynam- ics application for the CM-5, Cray T3D, and Sun multi- processor servers running MPI. This allows us to interact with large-scale message-passing applications, rapidly pro- totype new features, and perform application specific de- bugging. It is

David M. Beazley; Peter S. Lomdahl

1997-01-01

142

PySAL: A Python Library of Spatial Analytical Methods  

Microsoft Academic Search

This chapter describes PySAL, an open source library for spatial analysis written in the object oriented language Python.\\u000a PySAL grew out of the software development activities that were part of the Center for Spatially Integrated Social Sciences\\u000a Tools Project (Goodchild et al. 2000). This National Science Foundation infrastructure project had as its goals to facilitate\\u000a dissemination of spatial analysis software

Sergio J. Rey; Luc Anselin

2007-01-01

143

VPython: Python plus Animations in Stereo 3D  

NASA Astrophysics Data System (ADS)

Python is a modern object-oriented programming language. VPython (http://vpython.org) is a combination of Python (http://python.org), the Numeric module from LLNL (http://www.pfdubois.com/numpy), and the Visual module created by David Scherer, all of which have been under continuous development as open source projects. VPython makes it easy to write programs that generate real-time, navigable 3D animations. The Visual module includes a set of 3D objects (sphere, cylinder, arrow, etc.), tools for creating other shapes, and support for vector algebra. The 3D renderer runs in a parallel thread, and animations are produced as a side effect of computations, freeing the programmer to concentrate on the physics. Applications include educational and research visualization. In the Fall of 2003 Hugh Fisher at the Australian National University, John Zelle at Wartburg College, and I contributed to a new stereo capability of VPython. By adding a single statement to an existing VPython program, animations can be viewed in true stereo 3D. One can choose several modes: active shutter glasses, passive polarized glasses, or colored glasses (e.g. red-cyan). The talk will demonstrate the new stereo capability and discuss the pros and cons of various schemes for display of stereo 3D for a large audience. Supported in part by NSF grant DUE-0237132.

Sherwood, Bruce

2004-03-01

144

GAiN: Distributed Array Computation with Python  

SciTech Connect

Scientific computing makes use of very large, multidimensional numerical arrays - typically, gigabytes to terabytes in size - much larger than can fit on even the largest single compute node. Such arrays must be distributed across a "cluster" of nodes. Global Arrays is a cluster-based software system from Battelle Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate these arrays. Written in and for the C and FORTRAN programming languages, it takes advantage of high-performance cluster interconnections to allow any node in the cluster to access data on any other node very rapidly. The "numpy" module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. numpy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, numpy is inherently serial. Our system, GAiN (Global Arrays in NumPy), is a parallel extension to Python that accesses Global Arrays through numpy. This allows parallel processing and/or larger problem sizes to be harnessed almost transparently within new or existing numpy programs.

Daily, Jeffrey A.

2009-04-24

145

Computational modeling of multiphase flow and transport with Python  

NASA Astrophysics Data System (ADS)

Computational flow and transport models play an important role in many hydrological investigations. Unfortunately, developing simulators that are efficient, widely applicable, and robust is a challenge. This is particularly true if the target applications include complications like multiple fluid phases with multiple components and material heterogeneity. To be specific, these problems often involve physical phenomena at multiple spatial and temporal scales. The appropriate formulation may evolve, and the systems of partial differential equations (PDEs) that arise from traditional formulations can be hard to solve efficiently at the desired resolution. Here, we discuss the development of a Python-based modeling framework for finite element approximation of systems of nonlinear PDEs with an emphasis on multiphase, multicomponent systems relevant for surface and subsurface hydrology. In addition to the overall approach and application, we consider the role of Python in managing code complexity, providing user interfaces, developing solution algorithms, and implementing numerical methods for execution on serial and parallel platforms. We evaluate trade-offs and design choices that follow from our use of Python versus other languages like C++ or Fortran and consider the impact on performance measured in terms of metrics like memory usage, execution time, and developer time.

Kees, C. E.; Farthing, M. W.; Hines, A. M.; Howington, S. E.

2008-12-01

146

ACPYPE - AnteChamber PYthon Parser interfacE  

PubMed Central

Background ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. Findings We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB. Conclusions ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

2012-01-01

147

Purification and characterization of islet hormones (insulin, glucagon, pancreatic polypeptide and somatostatin) from the Burmese python, Python molurus  

Microsoft Academic Search

Insulin was purified from an extract of the pancreas of the Burmese python, Python molurus (Squamata:Serpentes) and its primary structure established as: A Chain: Gly-Ile-Val-Glu-Gln-Cys-Cys-Glu-Asn-Thr10-Cys-Ser-Leu-Tyr-Glu-Leu-Glu-Asn-Tyr-Cys20-Asn. B-Chain: Ala-Pro-Asn-Gln-His-Leu-Cys-Gly-Ser-His10-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly20-Asp-Arg-Gly-Phe-Tyr-Tyr-Ser-Pro-Arg-Ser30. With the exception of the conservative substitution Phe?Tyr at position B25, those residues in human insulin that comprise the receptor-binding and those residues involved in dimer and hexamer formation are fully conserved in

J Michael Conlon; Stephen M Secor; Thomas E Adrian; Dennis C Mynarcik; Jonathan Whittaker

1997-01-01

148

What Parts of the U.S. Mainland Are Climatically Suitable for Invasive Alien Pythons Spreading from Everglades National Park.  

National Technical Information Service (NTIS)

The Burmese Python (Python molurus bivittatus) is now well established in southern Florida and spreading northward. The factors likely to limit this spread are unknown, but presumably include climate or are correlated with climate. We compiled monthly rai...

C. S. Jarnevich G. H. Rodda R. N. Reed

2008-01-01

149

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

PubMed

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. PMID:9226619

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

1997-03-01

150

What parts of the US mainland are climatically suitable for invasive alien pythons spreading from Everglades National Park?  

Microsoft Academic Search

The Burmese Python (Python molurus bivittatus) is now well established in southern Florida and spreading northward. The factors likely to limit this spread are unknown,\\u000a but presumably include climate or are correlated with climate. We compiled monthly rainfall and temperature statistics from\\u000a 149 stations located near the edge of the python’s native range in Asia (Pakistan east to China and

Gordon H. Rodda; Catherine S. Jarnevich; Robert N. Reed

2009-01-01

151

Life History Consequences of Nest-Site Variation in Tropical Pythons (Liasis fuscus)  

Microsoft Academic Search

We document and interpret microgeographic variation in life history traits of water pythons (Liasis fuscus) on the Adelaide River floodplain in tropical Australia. Subpopulations of pythons separated by ,2 km differ in reproductive timing, in survival rates at three different life history stages (adults, embryos, and hatchlings), in costs of reproduction, and in reproductive frequencies. Remarkably, these differences all seem

Thomas Madsen; Richard Shine

1999-01-01

152

The Molecular Modeling Toolkit: a case study of a large scientific application in Python  

Microsoft Academic Search

The Molecular Modeling Toolkit is a library of Python modules and C extension modules that provides an object-oriented description of molecular systems and an implementation of the most common modeling tech- niques. It is one of the first large scientific applica- tions implemented in Python. This article presents some aspects of its design and implementation that are typi- cal for

Konrad Hinsen

1997-01-01

153

Climate Map for Northern African Python: Areas Potentially Suitable for Invasion  

USGS Multimedia Gallery

The Northern African Python ( Python sebae ) occurs naturally in a diverse collection of localities in central Africa. The climate-matched portions of the U.S. include peninsular Florida, extreme south Texas, Puerto Rico (right inset), Hawaii (left inset), and the other island territories (not shown...

2009-10-12

154

Increased blood oxygen affinity during digestion in the snake Python molurus  

Microsoft Academic Search

Many snakes exhibit large increases in metabolic rate during digestion that place extensive demands on efficient oxygen transport. In the present study, we describe blood oxygen affinity following three weeks of fasting and 48 h after feeding in the Burmese python (Python molurus). We also report simultaneous measurements of arterial blood gases and haematological parameters. Arterial blood was obtained from

Johannes Overgaard; Tobias Wang

155

Effects of temperature on the metabolic response to feeding in Python molurus  

Microsoft Academic Search

As ectothermic vertebrates, reptiles undergo diurnal and seasonal changes in body temperature, which affect many biological functions. In conjunction with a general review regarding the effects of temperature on digestion in reptiles, we describe the effects of various temperatures (20–35 °C) on the metabolic response to digestion in the Burmese python (Python molurus). The snakes were fed mice amounting to

Tobias Wang; Morten Zaar; Sine Arvedsen; Christina Vedel-Smith; Johannes Overgaard

2002-01-01

156

Reptilian Pathogens of the Florida Everglades: The Associated Costs of Burmese Pythons  

Microsoft Academic Search

The predation activity of the invasive Burmese python (Python molurus bivi- tattus ) was evaluated using probability and the economic costs associated with current federal and state values for endangered species. The objective was to provide a realistic valuation of the associated costs of Burmese py- thon predation in southern Florida ecosystems for use as both a policy and management

Henry T. Smith; Arthur Sementelli; Walter E. Meshaka; Richard M. Engeman

2007-01-01

157

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

PubMed

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. PMID:22034436

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

2011-10-28

158

Fatty Acids Identified in the Burmese Python Promote Beneficial Cardiac Growth  

PubMed Central

Burmese pythons display a dramatic 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 PI3K/Akt/mTor signaling 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 the cardioprotective enzyme, superoxide dismutase. Finally, we identified a combination of fatty acids in python plasma that promotes physiological heart growth when injected into either pythons or mice.

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

2012-01-01

159

A Flexible Python Design for Analytic Modeling of Groundwater Flow  

NASA Astrophysics Data System (ADS)

We present a simple and flexible, object-oriented design for the modeling of groundwater flow using analytic elements in Python. The primary feature is that new analytic elements may be added to the code without the need to make any changes in the existing part of the code. The code consists of a Model class and an Element base class. Each new element is derived from the Element base class (or a derived class) and added to the model. Boundary conditions are implemented by each element itself, because they generate their own equations. Significant speed-up may be obtained through the use of FORTRAN extensions of the computationally intensive functions. Another way to increase performance is by grouping elements with same-type boundary conditions, although that requires changes to the existing code when elements with new boundary conditions are implemented. The described design has been applied successfully to three types of flow: steady multi-aquifer flow, transient periodic flow, and steady unsaturated flow. All systems include wells (point-sinks), line-sinks and circular inhomogeneities. Heads and velocities can be computed analytically at any point; path lines may be computed through numerical integration of the velocity field. The multi-aquifer code is the most extensive and includes many other features such as polygonal inhomogeneities and impermeable walls. Additional Python features make it very easy to create models; input scripts can be generated from GIS coverages of elements; high-quality and interactive graphical output is generated with the matplotlib package.

Bakker, M.

2008-12-01

160

New Python-based methods for data processing.  

PubMed

Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2?TB?h(-1)) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units. PMID:23793153

Sauter, Nicholas K; Hattne, Johan; Grosse-Kunstleve, Ralf W; Echols, Nathaniel

2013-06-18

161

PyFACT: Python and FITS analysis for Cherenkov telescopes  

NASA Astrophysics Data System (ADS)

Ground-based very-high energy (VHE; E>100 GeV) gamma-ray astronomy is growing from being conducted by small teams in closed collaborations into a full-fledged branch of astronomy with open observatories. This is best illustrated by the number of known sources: it increased by one order of magnitude in the past ten years, from 10 in the year 2000 to more than 100 in 2010. It is expected that this trend will continue with the next-generation instrument Cherenkov Telescope Array (CTA). This transformation has a profound impact on the data format and analysis of Imaging Atmospheric Cherenkov Telescopes (IACTs). Up to now, IACT data analysis was an internal task performed by specialists with no public access to the data or software. In the future, a large community of VHE astronomers from different scientific topics should be enabled to work with the data. Ease of use, compatibility, and integration with existing astronomy standards and tools will be key. In this contribution, a collection of Python tools for the analysis of data in FITS format (PyFACT; Python and FITS Analysis for Cherenkov Telescopes) is presented, which connects with existing tools like xspec, sherpa, and ds9. The package is available as open source (https://github.com/mraue/pyfact, comments and contributions welcome). Advantages of the chosen ansatz are discussed and implications for future observatories and data archival are presented.

Raue, Martin; Deil, Christoph

2012-12-01

162

Programming biological models in Python using PySB.  

PubMed

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis. PMID:23423320

Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

2013-01-01

163

Adaptive responses to feeding in Burmese pythons: pay before pumping.  

PubMed

Burmese pythons normally consume large meals after long intervals. We measured gut contents, O2 consumption rates, small intestinal brush-border uptake rates of amino acids and glucose, organ masses and blood chemistry in pythons during the 30 days following ingestion of meals equivalent to 25% of their body mass. Within 1-3 days after ingestion, O2 consumption rates, intestinal nutrient uptake rates and uptake capacities peaked at 17, 6-26 and 11-24 times fasting levels, respectively. Small intestinal mass doubled, and other organs also increased in mass. Changes in blood chemistry included a 78% decline in PO2 and a large 'alkaline tide' associated with gastric acid section (i.e. a rise in blood pH and HCO3- concentrations and a fall in Cl- concentration). All of these values returned to fasting levels by the time of defecation at 8-14 days. The response of O2 consumption (referred to as specific dynamic action, SDA) is the largest, and the upregulation of intestinal nutrient transporters the second largest, response reported for any vertebrate upon feeding. The SDA is a large as the factorial rise in O2 consumption measured in mammalian sprinters and is sustained for much longer. The extra energy expended for digestion is equivalent to 32% of the meal's energy yield, with much of it being measured before the prey energy was absorbed. PMID:7782719

Secor, S M; Diamond, J

1995-06-01

164

Programming biological models in Python using PySB  

PubMed Central

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.

Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

2013-01-01

165

OPUS: A CORBA Pipeline for Java, Python, and Perl Applications  

NASA Astrophysics Data System (ADS)

With the introduction of the OPUS CORBA mode, a limited subset of OPUS Applications Programming Interface (OAPI) functionality was cast into CORBA IDL so that both OPUS applications and the Java-based OPUS pipeline managers were able to use the same CORBA infrastructure to access information on blackboards. Exposing even more of the OAPI through CORBA interfaces benefits OPUS applications in similar ways. Those applications not developed in C++ could use CORBA to interact with OPUS facilities directly, providing that a CORBA binding exists for the programming language of choice. Other applications might benefit from running `outside' of the traditional file system-based OPUS environment like the Java managers and, in particular, on platforms not supported by OPUS. The enhancements to OPUS discussed in this paper have been exercised in both Java and Python, and the code for these examples are available on the web.

Miller, W. W., III; Sontag, C.; Rose, J. F.

166

PyRAT (python radiography analysis tool): overview  

SciTech Connect

PyRAT was developed as a quantitative tool for robustly characterizing objects from radiographs to solve problems such as the hybrid nonlinear inverse problem. The optimization software library that was used is the nonsmooth optimization by MADS algorithm (NOMAD). Some of PyRAT's features are: (1) hybrid nonlinear inverse problem with calculated x-ray spectrum and detector response; (2) optimization based inversion approach with goal of identifying unknown object configurations - MVO problem; (3) using functionalities of Python libraries for radiographic image processing and analysis; (4) using the Tikhonov regularization method of linear inverse problem to recover partial information of object configurations; (5) using a priori knowledge of problem solutions to define feasible region and discrete neighbor for the MVO problem - initial data analysis + material library {yields} a priori knowledge; and (6) using the NOMAD (C++ version) software in the object.

Armstrong, Jerawan C [Los Alamos National Laboratory; Temple, Brian A [Los Alamos National Laboratory; Buescher, Kevin L [Los Alamos National Laboratory

2011-01-14

167

PyORBIT: A Python Shell For ORBIT  

SciTech Connect

ORBIT is code developed at SNS to simulate beam dynamics in accumulation rings and synchrotrons. The code is structured as a collection of external C++ modules for SuperCode, a high level interpreter shell developed at LLNL in the early 1990s. SuperCode is no longer actively supported and there has for some time been interest in replacing it by a modern scripting language, while preserving the feel of the original ORBIT program. In this paper, we describe a new version of ORBIT where the role of SuperCode is assumed by Python, a free, well-documented and widely supported object-oriented scripting language. We also compare PyORBIT to ORBIT from the standpoint of features, performance and future expandability.

Jean-Francois Ostiguy; Jeffrey Holmes

2003-07-01

168

Multiple papillomas in a diamond python, Morelia spilota spilota.  

PubMed

A 4-yr-old male diamond python (Morelia spilota spilota) was evaluated for multiple black papillated exophytic skin proliferations and signs of pneumonia. The histopathologic structure of the skin biopsy specimens led to the diagnosis of a benign papilloma-like neoplasia. In this case, papillomavirus DNA could be amplified from a biopsy sample with a broad range polymerase chain reaction. Nested pan-herpes polymerase chain reaction was negative, and herpesvirus inclusion bodies were not found. Because of the histologically benign nature of the papilloma, the skin proliferations were left untreated. Ten mo after the first presentation, the skin lesions had regressed almost completely; 34 mo later, only scars from the biopsies were left. PMID:23272369

Gull, Jessica M; Lange, Christian E; Favrot, Claude; Dorrestein, Gerry M; Hatt, Jean-Michel

2012-12-01

169

PyMidas--A Python Interface to ESO-MIDAS  

NASA Astrophysics Data System (ADS)

Finland joined the European Southern Observatory in 2004, providing a contribution in kind of software expertise as part of its joining fee. This significant resource, called the Sampo project, will be devoted to exploring the options for the future of data reduction and analysis in an ESO context, to understanding user requirements and to performing a series of major pilot projects to investigate different technologies, approaches and architectures. The Sampo project {http://www.eso.org/sampo} will run for three years and aims to prepare the ESO community for the data analysis and reduction challenges of the next decades. The first major Sampo project is PyMidas, an interface from Python to the ESO-MIDAS data analysis and reduction system. This paper describes the motivation for this project, how it has been implemented and gives some examples of PyMidas in action.

Hook, R. N.; Maisala, S.; Oittinen, T.; Ullgren, M.; Vasko, K.; Savolainen, V.; Lindroos, J.; Anttila, M.; Solin, O.; Møller, P. M.; Banse, K.; Peron, M.

2006-07-01

170

Obtaining and processing Daymet data using Python and ArcGIS  

USGS Publications Warehouse

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.

Bohms, Stefanie

2013-01-01

171

Can invasive Burmese pythons inhabit temperate regions of the southeastern United States?  

Microsoft Academic Search

Understanding potential for range expansion is critical when evaluating the risk posed by invasive species. Burmese pythons\\u000a (Python molurus bivittatus) are established in southern Florida and pose a significant threat to native ecosystems. Recent studies indicate that climate\\u000a suitable for the species P. molurus exists throughout much of the southern United States. We examined survivorship, thermal biology, and behavior of

Michael E. Dorcas; John D. Willson; J. Whitfield Gibbons

2011-01-01

172

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

PubMed Central

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.

Dorcas, Michael E.; Willson, 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

173

Environmental temperatures, physiology and behavior limit the range expansion of invasive Burmese pythons in southeastern USA.  

PubMed

A well-established population of Burmese pythons resides in the Everglades of southern Florida. Prompted in part by a report that identified much of southern USA as suitable habitat for expansion or establishment of the Burmese python, we examined the plausibility of this snake to survive winters at sites north of the Everglades. We integrated daily low and high temperatures recorded from October to February from 2005-2011 at Homestead, Orlando and Gainesville, Florida; and Aiken, South Carolina, with minimum temperatures projected for python digestion (16 °C), activity (5 °C) and survival (0 °C). Mean low and high temperatures decreased northward from Homestead to Aiken and the number of days of freezing temperatures increased northward. Digestion was impaired or inhibited for 2 months in the Everglades and up to at least 5 months in Aiken, and activity was increasingly limited northward during these months. Reports of overwinter survivorship document that a single bout of low and freezing temperatures results in python death. The capacity for Burmese pythons to successfully overwinter in more temperate regions of the USA is seemingly prohibited because they lack the behaviors to seek refuge from, and the physiology to tolerate, cold temperatures. As tropical Southeast Asia is the source of the Everglades Burmese pythons, we predict it is unlikely that they will be able to successfully expand to or colonize more temperate areas of Florida and adjoining states due to their lack of behavioral and physiological traits to seek refuge from cold temperatures. PMID:22938524

Jacobson, Elliott R; Barker, David G; Barker, Tracy M; Mauldin, Richard; Avery, Michael L; Engeman, Richard; Secor, Stephen

2012-09-01

174

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

PubMed

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. PMID:22308381

Dorcas, Michael E; Willson, 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

2012-01-30

175

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

PubMed

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. PMID:20008365

Secor, Stephen M; White, Scott E

2010-01-01

176

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

NASA Astrophysics Data System (ADS)

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).

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

2011-01-01

177

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

NASA Astrophysics Data System (ADS)

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 Ond?ejov 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 Ond?ejov) 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.

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

2005-12-01

178

Python framework for kinetic modeling of electronically excited reaction pathways  

NASA Astrophysics Data System (ADS)

The use of plasma energy to enhance and control the chemical reactions during combustion, a technology referred to as ``plasma assisted combustion'' (PAC), can result in a variety of beneficial effects: e.g. stable lean operation, pollution reduction, and wider range of p-T operating conditions. While experimental evidence abounds, theoretical understanding of PAC is at best incomplete, and numerical tools still lack in reliable predictive capabilities. In the context of a joint experimental-numerical effort at Michigan State University, we present here an open-source modular Python framework dedicated to the dynamic optimization of non-equilibrium PAC systems. Multiple sources of experimental reaction data, e.g. reaction rates, cross-sections and oscillator strengths, are used in order to quantify the effect of data uncertainty and limiting assumptions. A collisional-radiative model (CRM) is implemented to organize reactions by importance and as a potential means of measuring a non-Maxwellian electron energy distribution function (EEDF), when coupled to optical emission spectroscopy data. Finally, we explore scaling laws in PAC parameter space using a kinetic global model (KGM) accelerated with CRM optimized reaction sequences and sparse stiff integrators.

Verboncoeur, John; Parsey, Guy; Guclu, Yaman; Christlieb, Andrew

2012-10-01

179

Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models  

Microsoft Academic Search

BackgroundRecent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are

R. Alexander Pyron; Frank T. Burbrink; Timothy J. Guiher; Andy Hector

2008-01-01

180

Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models  

Microsoft Academic Search

Background: Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python

R. Alexander Pyron; Frank T. Burbrink; Timothy J. Guiher

2008-01-01

181

PeptideBuilder: A simple Python library to generate model peptides.  

PubMed

We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default. PMID:23717802

Tien, Matthew Z; Sydykova, Dariya K; Meyer, Austin G; Wilke, Claus O

2013-05-21

182

PeptideBuilder: A simple Python library to generate model peptides  

PubMed Central

We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default.

Tien, Matthew Z.; Sydykova, Dariya K.; Meyer, Austin G.

2013-01-01

183

ESCRIPT-RT: Reactive transport simulation in PYTHON using ESCRIPT  

NASA Astrophysics Data System (ADS)

We present ESCRIPT-RT, a new reactive transport simulation code for fully saturated porous media which is based on a finite element method (FEM) combined with three other components: (i) a Gibbs minimisation solver for equilibrium modelling of fluid–rock interactions, (ii) an equation of state for pure water to calculate fluid properties and (iii) a thermodynamically consistent material database to determine rocks' material properties. Using decoupling of most of the standard governing equations, this code solves sequentially for temperature, pressure, mass transport and chemical equilibrium. In contrast, pressure and Darcy flow velocities are solved as a coupled system. The reactive transport itself is performed using the masses of chemical elements instead of chemical species. In such way it requires less computing memory and time than the majority of other packages. The code is based on ESCRIPT, a parallelised platform which supports efficient stepwise simulation of realistic geodynamic scenarios at multiple scales. It is particularly suitable to analyse hydrothermal systems involving geometrically complex geological structures with strong permeability contrasts and subject to complex fluid–rock chemical interactions. The modular architecture of the code and its high level Python interface also provide flexibility for modellers who can easily modify or add new feedbacks between the different physical processes. In addition, the implemented abstract user interface allows geologists to run the code without knowledge of the underlying numerical implementation. As an example we show the simulation of hydrothermal gold precipitation in a granite–greenstone geological sequence, which illustrates the important coupling between thermal response and mass transfer to the localisation of gold.

Poulet, T.; Gross, L.; Georgiev, D.; Cleverley, J.

2012-08-01

184

Python and Roles of Variables in Introductory Programming: Experiences from Three Educational Institutions  

ERIC Educational Resources Information Center

Students often find that learning to program is hard. Introductory programming courses have high drop-out rates and students do not learn to program well. This paper presents experiences from three educational institutions where introductory programming courses were improved by adopting Python as the first programming language and roles of…

Nikula, Uolevi; Sajaniemi, Jorma; Tedre, Matti; Wray, Stuart

2007-01-01

185

History Revenged: Monty Python Translates Chretien de Troyes's "Perceval, or the Story of the Grail" (Again).  

ERIC Educational Resources Information Center

Finds "Monty Python and the Holy Grail" functions as a "surprisingly accurate cultural translation" of de Troyes's "Perceval" text. Suggests that using such films helps students open a door upon film studies and discursive studies that will serve them well as they adapt to their own historical moment. (PA)

Murrell, Elizabeth

1998-01-01

186

PyHelp - An automatic multi-output documentation generator for Python  

SciTech Connect

The DRACO code creates geometry and meshes through a command-line Python interface consisting of hundreds of classes and modules which must be accompanied by current documentation. The standard Python utility pydoc performs introspection on objects and prints their associated documentation strings verbatim. However, pydoc supports only very rudimentary formatting and cannot produce printable documentation. We decided to modify pydoc to process formatted ''docstrings'' and use the Doxygen tool to generate the needed forms of documentation. Codes with complex interfaces often require substantial effort to keep user documentation current with interface changes. The DRACO code creates geometry and meshes through a command-line Python interface consisting of hundreds of classes and thousands of functions. A previous attempt to write documentation manually quickly fell out of date, so the development team needed to find an alternative. The existing tools did not provide the flexibility we needed, and the team was already conversant in Doxygen, a C++ code-documenting utility with a simple tag-based markup. Python comes with a utility, pydoc, that performs introspection on objects and prints their docstrings verbatim. However, pydoc supports only very rudimentary formatting and cannot produce printable documentation. Thus we decided to create ''docstrings'' written in Doxygen syntax for each object and process them with a modified pydoc to generate the needed forms of documentation.

Nissen, W I

2005-02-10

187

Biopython: freely available Python tools for computational molecular biology and bioinformatics  

Microsoft Academic Search

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW, and EMBOSS, accessing key online databases, as well

Peter J. A. Cock; Tiago Antao; Jeffrey T. Chang; Brad A. Chapman; Cymon J. Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J. L. De Hoon

2009-01-01

188

Feeding Habits of the Diamond Python, Morelia s. spilota: Ambush Predation by a Boid Snake  

Microsoft Academic Search

Diamond pythons (Morelia s. spilota) are large (to 3 m) snakes of temperate-zone coastal eastern Australia. Foraging behavior was studied by observation of telemetered snakes, and diets deter- mined by dissection of museum specimens and collection of fecal samples from wild-caught snakes. Five adult snakes monitored in the field by radiotelemetry were found to be ambush foragers. In summer, telemetered

VID J. SLIP; RICHARD SHINE

189

Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity  

Microsoft Academic Search

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test

Lesley H. Rawlings; Stephen C. Donnellan

2003-01-01

190

Prototyping of a remote monitoring system for a medical Personal Area Network using Python  

Microsoft Academic Search

This paper presents a prototype developed in Python of a pervasive mobile health system aimed at monitoring a patient in indoor and outdoor environments continuously. The system is based on a Bluetooth PAN (Personal Area Network), worn by the patient, whose master node, a smartphone, collects information about patient's location and health status and detects emergency situations. These data are

M. J. Moro?n; J. R. Luque; A. Go?mez-Jaime; E. Casilari; A. Di?az-Estrella

2009-01-01

191

Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data  

PubMed Central

Summary In this paper, we introduce pebl, a Python library and application for learning Bayesian network structure from data and prior knowledge that provides features unmatched by alternative software packages: the ability to use interventional data, flexible specification of structural priors, modeling with hidden variables and exploitation of parallel processing.

Shah, Abhik; Woolf, Peter

2009-01-01

192

Digestive physiology of the Burmese python: broad regulation of integrated performance.  

PubMed

As an apparent adaptation to predictably long episodes of fasting, the sit-and-wait foraging Burmese python experiences unprecedented regulation of gastrointestinal and cardiovascular performance with feeding and fasting. The ingestion of a meal signals the quiescent gut tissues to start secreting digestive acid and enzymes, to upregulate intestinal brush-border enzymes and nutrient transporters, and to grow. An integrated phenomenon, digestion is also characterized by increases in the mass, and presumably the function, of the heart, pancreas, liver and kidneys. Once digestion is complete, the python's stomach and small intestine rapidly downregulate performance. Much of the modulation of intestinal function can be explained by the 5-fold increase in microvillus length and apical surface area with feeding, and the subsequent shortening of the microvilli after digestion has finished. Digestion for the Burmese python is a relatively expensive endeavor, evident by the as much as a 44-fold increase in metabolic rate and equivalent in cost to as much as 37% of the meal's energy. Their large metabolic response is supported by substantial increases in ventilation and cardiac output and the apparent catabolism of glucose and lipids. Unmatched in the magnitude of its numerous physiological responses to feeding, the Burmese python is a very attractive model for examining the capacities and regulatory mechanisms of physiological performance. PMID:19043049

Secor, Stephen M

2008-12-01

193

Large snakes in a mosaic rural landscape: The ecology of carpet pythons Morelia spilota (serpentes: Pythonidae) in coastal eastern Australia  

Microsoft Academic Search

How can large pythons coexist with human beings in highly modified habitats throughout the eastern coastal region of Australia, when the same species has undergone rapid declines in other parts of the country? To investigate this question, we surgically implanted miniature temperature-sensitive radiotransmitters into 19 adult carpet pythons Morelia spilota (body lengths 1·3–2·8 m; 1·4–7·0 kg) from two study sites

R. Shine; M. Fitzgerald

1996-01-01

194

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

PubMed

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. PMID:22162867

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

2012-01-01

195

GMES: A Python package for solving Maxwell's equations using the FDTD method  

NASA Astrophysics Data System (ADS)

This paper describes GMES, a free Python package for solving Maxwell's equations using the finite-difference time-domain (FDTD) method. The design of GMES follows the object-oriented programming (OOP) approach and adopts a unique design strategy where the voxels in the computational domain are grouped and then updated according to its material type. This piecewise updating scheme ensures that GMES can adopt OOP without losing its simple structure and time-stepping speed. The users can easily add various material types, sources, and boundary conditions into their code using the Python programming language. The key design features, along with the supported material types, excitation sources, boundary conditions and parallel calculations employed in GMES are also described in detail.

Chun, Kyungwon; Kim, Huioon; Kim, Hyounggyu; Jung, Kil Su; Chung, Youngjoo

2013-04-01

196

QuTiP 2: A Python framework for the dynamics of open quantum systems  

NASA Astrophysics Data System (ADS)

We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch–Redfield and Floquet–Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version.

Johansson, J. R.; Nation, P. D.; Nori, Franco

2013-04-01

197

Two-dimensional echocardiographic anatomy of the snake heart (Python molurus bivittatus).  

PubMed

Two-dimensional echocardiography was performed on Burmese pythons (Python molurus bivittatus) to determine an optimal echocardiographic imaging technique for snakes and to describe the echocardiographic anatomy of the snake heart. Five snakes immobilized with tiletamine/zolazepam and maintained on isoflurane in oxygen were imaged in dorsal recumbency. The portion of the snake's body containing the heart was submerged in warm water to reduce the artifact created by air trapped between and under the scales. Imaging in sagittal planes demonstrated the caudal vena cava, sinus venous valve, right atrium, various portions of the ventricle, horizontal septum, the left aortic arch, and pulmonary artery. Transverse imaging depicted the spatial relationship of the left and right aortic arches and pulmonary artery and the horizontal septum. Basic knowledge of cardiac blood flow in the reptile was necessary to understand the echocardiographic anatomy. PMID:10023997

Snyder, P S; Shaw, N G; Heard, D J

198

Rain, rats and pythons: Climate-driven population dynamics of predators and prey in tropical Australia  

Microsoft Academic Search

All natural populations fluctuate in abundance and age structure through time; understanding why they do so is a critical step towards their effective management and conservation. However, the long-term data sets needed for such an understanding are rarely available, especially for tropical organisms. A 17-year capture- mark-recapture study yielded detailed information on the demography of water pythons (Liasis fuscus) and

THOMAS MADSEN; BEATA UJVARI; RICHARD SHINE; MATS OLSSON

2006-01-01

199

An Object-Oriented Python Implementation of an Intermediate-Level Atmospheric Model  

NASA Astrophysics Data System (ADS)

The Neelin-Zeng Quasi-equilibrium Tropical Circulation Model (QTCM1) is a Fortran-based intermediate-level atmospheric model that includes simplified treatments of several physical processes, including a GCM-like convective scheme and a land-surface scheme with representations of different surface types, evaporation, and soil moisture. This model has been used in studies of the Madden-Julian oscillation, ENSO, and vegetation-atmosphere interaction effects on climate. Through the assumption of convective quasi-equilibrium in the troposphere, the QTCM1 is able to include full nonlinearity, resolve baroclinic disturbances, and generate a reasonable climatology, all at low computational cost. One year of simulation on a PC at 5.625 × 3.75 degree longitude-latitude resolution takes under three minutes of wall-clock time. The Python package qtcm implements the QTCM1 in a mixed-language environment that retains the speed of compiled Fortran while providing the benefits of Python's object-oriented framework and robust suite of utilities and datatypes. We describe key programming constructs used to create this modeling environment: the decomposition of model runs into Python objects, providing methods so visualization tools are attached to model runs, and the use of Python's mutable datatypes (lists and dictionaries) to implement the "run list" entity, which enables total runtime control of subroutine execution order and content. The result is an interactive modeling environment where the traditional sequence of "hypothesis ? modeling ? visualization and analysis" is opened up and made nonlinear and flexible. In this environment, science tasks such as parameter-space exploration and testing alternative parameterizations can be easily automated, without the need for multiple versions of the model code interacting with a bevy of makefiles and shell scripts. The environment also simplifies interfacing of the atmospheric model to other models (e.g., hydrologic models, statistical models) and analysis tools. The tools developed for this package can be adapted to create similar environments for hydrologic models.

Lin, J. W.

2008-12-01

200

Python scripting libraries for subsurface fluid and heat flow simulations with TOUGH2 and SHEMAT  

NASA Astrophysics Data System (ADS)

Numerical simulations of subsurface fluid and heat flow are commonly controlled manually via input files or from graphical user interfaces (GUIs). Manual editing of input files is often tedious and error-prone, while GUIs typically limit the full capability of the simulator. Neither approach lends itself to automation, which is desirable for more complex simulations.We propose an alternative approach based on the use of scripting. To this end we have developed Python libraries for scripting subsurface simulations using the SHEMAT and TOUGH2 simulators. For many problems the entire modeling process including grid generation, model setup, execution, post-processing and analysis of results can be carried out from a single Python script.Through example problems we demonstrate some of the potential power of the scripting approach, which does not only make model setup simpler and less error-prone, but also facilitates more complex simulations involving, for example, multiple model runs with varying parameters (e.g. permeabilities, heat inputs, and the level of grid refinement). It is also possible to apply the developed methods for extending the functionality of graphical user interfaces.Basing our approach on the Python language makes it simple to take advantage of other libraries available for scientific computation, with sophisticated analysis of results often a matter of a single function call. We envisage many other possible applications of the approach, including linking with geological modeling software, running stochastic ensembles of models and hybrid modeling using multiple interacting simulators.

Florian Wellmann, J.; Croucher, Adrian; Regenauer-Lieb, Klaus

2012-06-01

201

A Python Analytical Pipeline to Identify Prohormone Precursors and Predict Prohormone Cleavage Sites  

PubMed Central

Neuropeptides and hormones are signaling molecules that support cell–cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of an bioinformatic analytical pipeline to identify precursors from genomic data and to predict cleavage as these precursors are en route to the final bioactive peptides. We identified 75 precursors in the rhesus genome, predicted cleavage sites using support vector machines and compared the rhesus predictions to putative assignments based on homology to human sequences. The correct classification rate of cleavage using the support vector machines was over 97% for both human and rhesus data sets. The functionality of Python has been important to develop and maintain NeuroPred (http://neuroproteomics.scs.uiuc.edu/neuropred.html), a user-centered web application for the neuroscience community that provides cleavage site prediction from a wide range of models, precision and accuracy statistics, post-translational modifications, and the molecular mass of potential peptides. The combined results illustrate the suitability of the Python language to implement an all-inclusive bioinformatics approach to predict neuropeptides that encompasses a large number of interdependent steps, from scanning genomes for precursor genes to identification of potential bioactive neuropeptides.

Southey, Bruce R.; Sweedler, Jonathan V.; Rodriguez-Zas, Sandra L.

2008-01-01

202

Structural flexibility of the intestine of Burmese python in response to feeding.  

PubMed

The small intestine of Burmese pythons, Python molurus bivittatus, undergoes a remarkable size increase shortly after feeding. We studied the dynamics, reversibility and repeatability of organ size changes using noninvasive imaging techniques. We employed light and electron microscopy, flow cytometry and immunohistology to study the cytological mechanisms that drive the size changes of the small intestine. Within 2 days of feeding, the size of the small intestine increased to up to three times the fasting value. The size changes were fully reversible and could be elicited repeatedly by feeding. These enormous size changes were possible because the mucosal epithelium of the small intestine is a transitional epithelium that allows for considerable size changes without cell proliferation. Histological evidence suggested that a fluid pressure-pump system (lymphatic, blood pressure) was the driving force that inflated the intestinal villi. The rates of cell proliferation were not elevated immediately after feeding but peaked 1 week later when small intestine size was already declining. In contrast to the current paradigm, we suggest that the small intestine is not part of the previously proposed 'pay-before-pumping' model. Instead, the size of the python's small intestine may be upregulated without major metabolic investment. It can occur even if the individual is energetically exhausted. An evolutionary perspective of the transitional epithelium mechanism suggests superior functionality compared with the pay-before-pumping model because it allows for long periods of fasting and depletion of energy reserves, while still enabling the snake to digest prey and absorb nutrients. PMID:11136618

Starck, J M; Beese, K

2001-01-01

203

R.N. Reed and G.H. Rodda (eds): Giant constrictors: biological and management profiles and an establishment risk assessment for nine large species of pythons, anacondas, and the boa constrictor  

Microsoft Academic Search

Giant Constrictors estimates ecological risks associated with colonization of the United States by the world’s four largest snakes (green anaconda, Indian or Burmese python, northern African python, and reticulated python) plus four very similar species (the southern African python, yellow anaconda, DeSchaunsee’s anaconda, and Beni anaconda) and the boa constrictor. Possible economic costs are also detailed but not quantified. This

Daniel Simberloff

2010-01-01

204

Molecular evolution of peptide tyrosine–tyrosine: primary structure of PYY from the lampreys Geotria australis and Lampetra fluviatilis, bichir, python and desert tortoise  

Microsoft Academic Search

Peptide tyrosine–tyrosine (PYY) has been isolated from the intestines of two species of reptile, the desert tortoise Gopherus agassizii (Testudines) and the Burmese python Python molurus (Squamata), from the primitive Actinopterygian fish, the bichir Polypterus senegalis (Polypteriformes) and from two agnathans, the Southern-hemisphere lamprey Geotria australis (Geotriidae) and the holarctic lamprey Lampetra fluviatilis (Petromyzontidae). The primary structure of bichir PYY

Yuqi Wang; Per F Nielsen; John H Youson; Ian C Potter; Valentine A Lance; J. Michael Conlon

1999-01-01

205

Tools for managing invasions: acceptance of non-toxic baits by juvenile Nile monitor lizards and Burmese pythons under laboratory conditions  

Microsoft Academic Search

Nile monitor lizards (Varanus niloticus) and Burmese pythons (Python molurus bivittatus) are large, invasive, predatory reptiles, which are now well established in south Florida. Acetaminophen was recently shown to be lethal to both animals and therefore has potential for inclusion in an integrated pest management effort to control these species. However, acceptable bait matrices for both species are still needed

Peter J. Savarie; Richard M. Engeman; Richard E. Mauldin; Tom Mathies; Kenneth L. Tope

2011-01-01

206

TelluSim: A Python Plug-in Based Computational Framework for Spatially Distributed Environmental and Earth Sciences Modelling  

NASA Astrophysics Data System (ADS)

TelluSim is a python-based computational framework for integrating and manipulating modules written in a variety of computer languages. TelluSim consists of a main program that dynamically, at run time, assembles a series of modules. These modules can be written in any language that can be accessed by Python. Currently we have modules in Fortran and Python, with C to be supported soon. New modules are incorporated as plug-ins like done for a browser or Photoshop, simply by copying the module binary into a plug-in directory. TelluSim automatically generates a GUI for parameter and state I/O, and automatically creates the intermodule communication mechanisms needed for the computations. A decision to use Python was arrived at after detailed trials using other languages including C, Tcl/Tk and Fortran. An important aspect of the design of TelluSim was to minimise the overhead in interfacing the modules with TelluSim, and minimise any requirement for recoding of existing software, so eliminating a major disadvantage of more complex frameworks (e.g. JAMS, openMI). Several significant Fortran codes developed by the author have been incorporated as part of the design process and as proof of concept. In particular the SIBERIA landform evolution code (a high performance F90 code, including parallel capability) has been broken up into a series of TelluSim modules, so that the SIBERIA now consists of a Python script of 20 lines. These 20 lines assemble and run the underlying modules (about 50,000 lines of Fortran code). The presentation will discuss in more detail the design of TelluSim, and our experiences of the advantages and disadvantages of using Python relative to other approaches.

Willgoose, G. R.

2008-12-01

207

Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models  

PubMed Central

Background Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are not known and the possible effects of global warming on the potential expansion of the species are also unclear. Methodology/Principal Findings Here we show that a predicted continental expansion is unlikely based on the ecology of the organism and the climate of the U.S. Our ecological niche models, which include variables representing climatic extremes as well as averages, indicate that the only suitable habitat in the U.S. for Burmese pythons presently occurs in southern Florida and in extreme southern Texas. Models based on the current distribution of the snake predict suitable habitat in essentially the only region in which the snakes are found in the U.S. Future climate models based on global warming forecasts actually indicate a significant contraction in suitable habitat for Burmese pythons in the U.S. as well as in their native range. Conclusions/Significance The Burmese python is strongly limited to the small area of suitable environmental conditions in the United States it currently inhabits due to the ecological niche preferences of the snake. The ability of the Burmese python to expand further into the U.S. is severely limited by ecological constraints. Global warming is predicted to significantly reduce the area of suitable habitat worldwide, underscoring the potential negative effects of climate change for many species.

Pyron, R. Alexander; Burbrink, Frank T.; Guiher, Timothy J.

2008-01-01

208

SMMP v. 3.0—Simulating proteins and protein interactions in Python and Fortran  

NASA Astrophysics Data System (ADS)

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more. Catalogue identifier:ADOJ_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.html Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language used:FORTRAN, Python No. of lines in distributed program, including test data, etc.:52?105 No. of bytes in distributed program, including test data, etc.:599?150 Distribution format:tar.gz Computer:Platform independent Operating system:OS independent RAM:2 Mbytes Classification:3 Does the new version supersede the previous version?:Yes Nature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins. Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles. Reasons for new version:API changes and increased functionality. Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings. Restrictions:The consumed CPU time increases with the size of protein molecule. Running time:Depends on the size of the simulated molecule.

Meinke, Jan H.; Mohanty, Sandipan; Eisenmenger, Frank; Hansmann, Ulrich H. E.

2008-03-01

209

Parental behavior in pythons is responsive to both the hydric and thermal dynamics of the nest.  

PubMed

Parental behavior contributes to the success of a diverse array of taxa, and female-only nest attendance is particularly widespread. Python egg-brooding behavior is an intriguing example of female-only nest attendance because it significantly influences several critical developmental variables, namely embryonic predation, hydration, respiration and temperature. During brooding, females predominately adopt a tightly coiled posture that reduces the exchange of heat, water vapor, O(2) and CO(2) between the nest and clutch environment, which benefits egg water balance at the cost of respiration. To determine the plasticity of this important behavior, we manipulated nest temperature and humidity while monitoring nest-clutch thermal, hydric and respiratory relationships to test the hypothesis that female Children's pythons (Antaresia childreni) modify their egg-brooding behavior due to an interaction between environmental thermal and hydric conditions. During moderate and high nest humidity treatments (23 and 32 g m(-3) H(2)O, respectively), females spent more time coiling tightly when the nest was cooling than when it was warming, which benefited clutch temperature. However, brooding females in low-humidity nest environments (13 g m(-3) H(2)O) showed a high frequency of tight coiling even when the nest was warming; thus, nest temperature and humidity had an interactive effect on egg-brooding behavior in support of our hypothesis. Our results also suggest that certain egg-brooding behaviors (i.e. postural adjustments) are more energetically costly to females than other behaviors (i.e. tight coiling). In sum, we provide empirical support for the adaptive plasticity of python egg-brooding behavior, which offers insight into the general significance of female-only nest attendance in animals. PMID:20435820

Stahlschmidt, Zachary; Denardo, Dale F

2010-05-01

210

Pyff - A Pythonic Framework for Feedback Applications and Stimulus Presentation in Neuroscience  

PubMed Central

This paper introduces Pyff, the Pythonic feedback framework for feedback applications and stimulus presentation. Pyff provides a platform-independent framework that allows users to develop and run neuroscientific experiments in the programming language Python. Existing solutions have mostly been implemented in C++, which makes for a rather tedious programming task for non-computer-scientists, or in Matlab, which is not well suited for more advanced visual or auditory applications. Pyff was designed to make experimental paradigms (i.e., feedback and stimulus applications) easily programmable. It includes base classes for various types of common feedbacks and stimuli as well as useful libraries for external hardware such as eyetrackers. Pyff is also equipped with a steadily growing set of ready-to-use feedbacks and stimuli. It can be used as a standalone application, for instance providing stimulus presentation in psychophysics experiments, or within a closed loop such as in biofeedback or brain–computer interfacing experiments. Pyff communicates with other systems via a standardized communication protocol and is therefore suitable to be used with any system that may be adapted to send its data in the specified format. Having such a general, open-source framework will help foster a fruitful exchange of experimental paradigms between research groups. In particular, it will decrease the need of reprogramming standard paradigms, ease the reproducibility of published results, and naturally entail some standardization of stimulus presentation.

Venthur, Bastian; Scholler, Simon; Williamson, John; Dahne, Sven; Treder, Matthias S.; Kramarek, Maria T.; Muller, Klaus-Robert; Blankertz, Benjamin

2010-01-01

211

Automatic Parallelization of Numerical Python Applications using the Global Arrays Toolkit  

SciTech Connect

Global Arrays is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate distributed dense arrays. The NumPy module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. NumPy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, NumPy is inherently serial. Using a combination of Global Arrays and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Serial NumPy applications can become parallel, scalable GAiN applications with only minor source code changes. Scalability studies of several different GAiN applications will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Daily, Jeffrey A.; Lewis, Robert R.

2011-11-30

212

Trichinella papuae and Trichinella zimbabwensis induce infection in experimentally infected varans, caimans, pythons and turtles.  

PubMed

The discovery of Trichinella zimbabwensis in farm crocodiles of Zimbabwe has opened up a new frontier in the epidemiology of the Trichinella genus. The objective of the present study was to investigate the infectivity of encapsulated species (T. spiralis, T. nativa, T. britovi, T. murrelli and T. nelsoni) and non-encapsulated species (T. pseudospiralis, T. papuae and T. zimbabwensis) in caimans (Caiman crocodilus), varans (Varanus exanthematicus), pythons (Python molurus bivittatus) and turtles (Pelomedusa subrufa) raised at their natural temperature range (26-32 degrees C). Mice and chickens were used as controls. At 6 days post-infection (p.i.), adult worms were detected in the small intestine of reptiles infected with T. papuae and T. zimbabwensis, of chickens infected with T. pseudospiralis and of mice infected with all encapsulated and non-encapsulated species. At 60 days p.i., T. papuae and T. zimbabwensis adult worms were collected from the intestine of varans and caimans and larvae from muscles of the four reptile species, T. pseudospiralis larvae from muscles of chickens, and larvae of all Trichinella species from mouse muscles. The highest reproductive capacity index of both T. papuae and T. zimbabwensis was observed in varans. The results show that T. papuae and T. zimbabwensis are able to complete their entire life-cycle in both poikilothermic and homoiothermic animals. PMID:15074882

Pozio, E; Marucci, G; Casulli, A; Sacchi, L; Mukaratirwa, S; Foggin, C M; La Rosa, G

2004-03-01

213

PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data  

PubMed Central

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine-learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

Hanke, Michael; Halchenko, Yaroslav O.; Sederberg, Per B.; Hanson, Stephen Jose; Haxby, James V.; Pollmann, Stefan

2009-01-01

214

Effects of temperature on the metabolic response to feeding in Python molurus.  

PubMed

As ectothermic vertebrates, reptiles undergo diurnal and seasonal changes in body temperature, which affect many biological functions. In conjunction with a general review regarding the effects of temperature on digestion in reptiles, we describe the effects of various temperatures (20-35 degrees C) on the metabolic response to digestion in the Burmese python (Python molurus). The snakes were fed mice amounting to 20% of their body weight and gas exchange (oxygen uptake and CO(2) production) were measured until digestion had ended and gas exchange returned to fasting levels. Elevated temperature was associated with a faster and larger metabolic increase after ingestion, and the time required to return to fasting levels was markedly longer at low temperature. The factorial increase between fasting oxygen consumption (VO(2)) and maximal VO(2) during digestion was, however, similar at all temperatures studied. Furthermore, the integrated SDA response was not affected by temperature suggesting the costs associated with digestion are temperature-independent. Other studies on reptiles show that digestive efficiency is only marginally affected by temperature and we conclude that selection of higher body temperatures during digestion (postprandial thermophilic response) primarily reduces the time required for digestion. PMID:12443910

Wang, Tobias; Zaar, Morten; Arvedsen, Sine; Vedel-Smith, Christina; Overgaard, Johannes

2002-11-01

215

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

PubMed

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. PMID:21045117

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

2010-11-02

216

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

PubMed Central

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.

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

2011-01-01

217

SpacePy - a Python-based library of tools for the space sciences  

SciTech Connect

Space science deals with the bodies within the solar system and the interplanetary medium; the primary focus is on atmospheres and above - at Earth the short timescale variation in the the geomagnetic field, the Van Allen radiation belts and the deposition of energy into the upper atmosphere are key areas of investigation. SpacePy is a package for Python, targeted at the space sciences, that aims to make basic data analysis, modeling and visualization easier. It builds on the capabilities of the well-known NumPy and MatPlotLib packages. Publication quality output direct from analyses is emphasized. The SpacePy project seeks to promote accurate and open research standards by providing an open environment for code development. In the space physics community there has long been a significant reliance on proprietary languages that restrict free transfer of data and reproducibility of results. By providing a comprehensive, open-source library of widely used analysis and visualization tools in a free, modern and intuitive language, we hope that this reliance will be diminished. SpacePy includes implementations of widely used empirical models, statistical techniques used frequently in space science (e.g. superposed epoch analysis), and interfaces to advanced tools such as electron drift shell calculations for radiation belt studies. SpacePy also provides analysis and visualization tools for components of the Space Weather Modeling Framework - currently this only includes the BATS-R-US 3-D magnetohydrodynamic model and the RAM ring current model - including streamline tracing in vector fields. Further development is currently underway. External libraries, which include well-known magnetic field models, high-precision time conversions and coordinate transformations are wrapped for access from Python using SWIG and f2py. The rest of the tools have been implemented directly in Python. The provision of open-source tools to perform common tasks will provide openness in the analysis methods employed in scientific studies and will give access to advanced tools to all space scientists regardless of affiliation or circumstance.

Morley, Steven K [Los Alamos National Laboratory; Welling, Daniel T [Los Alamos National Laboratory; Koller, Josef [Los Alamos National Laboratory; Larsen, Brian A [Los Alamos National Laboratory; Henderson, Michael G [Los Alamos National Laboratory

2010-01-01

218

Wrapping Python around MODFLOW/MT3DMS based groundwater models  

NASA Astrophysics Data System (ADS)

Numerical models that simulate groundwater flow and solute transport require a great amount of input data that is often organized into different files. A large proportion of the input data consists of spatially-distributed model parameters. The model output consists of a variety data such as heads, fluxes and concentrations. Typically all files have different formats. Consequently, preparing input and managing output is a complex and error-prone task. Proprietary software tools are available that facilitate the preparation of input files and analysis of model outcomes. The use of such software may be limited if it does not support all the features of the groundwater model or when the costs of such tools are prohibitive. Therefore a Python library was developed that contains routines to generate input files and process output files of MODFLOW/MT3DMS based models. The library is freely available and has an open structure so that the routines can be customized and linked into other scripts and libraries. The current set of functions supports the generation of input files for MODFLOW and MT3DMS, including the capability to read spatially-distributed input parameters (e.g. hydraulic conductivity) from PNG files. Both ASCII and binary output files can be read efficiently allowing for visualization of, for example, solute concentration patterns in contour plots with superimposed flow vectors using matplotlib. Series of contour plots are then easily saved as an animation. The subroutines can also be used within scripts to calculate derived quantities such as the mass of a solute within a particular region of the model domain. Using Python as a wrapper around groundwater models provides an efficient and flexible way of processing input and output data, which is not constrained by limitations of third-party products.

Post, V.

2008-12-01

219

PySP : modeling and solving stochastic mixed-integer programs in Python.  

SciTech Connect

Although stochastic programming is a powerful tool for modeling decision-making under uncertainty, various impediments have historically prevented its widespread use. One key factor involves the ability of non-specialists to easily express stochastic programming problems as extensions of deterministic models, which are often formulated first. A second key factor relates to the difficulty of solving stochastic programming models, particularly the general mixed-integer, multi-stage case. Intricate, configurable, and parallel decomposition strategies are frequently required to achieve tractable run-times. We simultaneously address both of these factors in our PySP software package, which is part of the COIN-OR Coopr open-source Python project for optimization. To formulate a stochastic program in PySP, the user specifies both the deterministic base model and the scenario tree with associated uncertain parameters in the Pyomo open-source algebraic modeling language. Given these two models, PySP provides two paths for solution of the corresponding stochastic program. The first alternative involves writing the extensive form and invoking a standard deterministic (mixed-integer) solver. For more complex stochastic programs, we provide an implementation of Rockafellar and Wets Progressive Hedging algorithm. Our particular focus is on the use of Progressive Hedging as an effective heuristic for approximating general multi-stage, mixed-integer stochastic programs. By leveraging the combination of a high-level programming language (Python) and the embedding of the base deterministic model in that language (Pyomo), we are able to provide completely generic and highly configurable solver implementations. PySP has been used by a number of research groups, including our own, to rapidly prototype and solve difficult stochastic programming problems.

Woodruff, David L. (University of California, Davis); Watson, Jean-Paul

2010-08-01

220

Effect of nest temperature on egg-brooding dynamics in Children's pythons.  

PubMed

Parental care meets several critical needs of developing offspring. In particular, egg brooding in pythons is an exceptional model for examining environmental influences on specific parental behaviors because brooding behaviors are dynamic yet simple and modulate embryonic temperature, respiration, and water balance. We used captive Children's pythons (Antaresia childreni) to assess their facultative endothermic capability, the influence on egg-brooding behaviors of the gradient between the nest temperature (T(nest)) and clutch temperature (T(clutch)), and the effect of these behaviors on the developmental micro-environment. We monitored maternal egg-brooding behavior, rates of brooding unit (i.e., female and associated clutch) respiratory gas exchange, T(nest), T(clutch), and intra-clutch oxygen tension (PO(2)clutch) during acute changes among four incubation temperature conditions: constant preferred temperature (31.5 degrees C); 'cooling' (T(nest)T(clutch)). We demonstrated that A. childreni are not facultatively endothermic because brooding unit temperature coefficient (Q(10)) for V(O2) and V(CO2) was similar to other ectothermic boid snakes (1.9-5.7) and T(clutch) conformed to T(nest) at the constant, cool temperature treatment. Females coiled tightly around eggs more often during cooling than during warming. Further, the amount of time that females spent tightly coiled during warming significantly affected the T(nest)-T(clutch) gradient. Together these results indicate that, although female A. childreni are not facultatively endothermic, they are capable of assessing the T(nest)-T(clutch) gradient and making behavioral adjustments to enhance the thermal micro-environment of their developing offspring. PMID:19538977

Stahlschmidt, Zachary R; Denardo, Dale F

2009-06-16

221

Raman spectroscopic studies of the skins of the Sahara sand viper, the carpet python and the American black rat snake  

NASA Astrophysics Data System (ADS)

Vibrational Raman spectra of the skins of the snakes Cerastes vipera (Sahara sand viper) and Morelia argus (carpet python) have been recorded for the first time using visible and IR laser excitation. Full vibrational assignments are proposed and comparisons made with vibrational Raman spectra of the snake Elaphe obsoleta (American black rat snake); such studies may be important in correlating the permeabilities of human and snake skins to drugs and contaminants.

Edwards, H. G. M.; Farwell, D. W.; Williams, A. C.; Barry, B. W.

1993-07-01

222

Increased blood oxygen affinity during digestion in the snake Python molurus.  

PubMed

Many snakes exhibit large increases in metabolic rate during digestion that place extensive demands on efficient oxygen transport. In the present study, we describe blood oxygen affinity following three weeks of fasting and 48 h after feeding in the Burmese python (Python molurus). We also report simultaneous measurements of arterial blood gases and haematological parameters. Arterial blood was obtained from chronically implanted catheters, and blood oxygen-dissociation curves were constructed from oxygen content measurements at known oxygen partial pressure (P(O(2))) values at 2% and 5% CO(2). Arterial pH remained constant at approximately 7.6 after feeding, but digestion was associated with an approximately 6 mmol l(-1) increase in [HCO(3)(-)], while CO(2) partial pressure (P(CO(2))) increased from 2.21+/-0.13 kPa in fasted animals to 2.89+/-0.17 kPa at 48 h after feeding. Blood oxygen affinity in vivo was predicted on the basis of pH in vivo and the blood oxygen-dissociation curves obtained in vitro. The blood oxygen affinity in vivo increased during digestion, with P(50) values decreasing from 4.58+/-0.11 kPa to 3.53+/-0.24 kPa. This increase was associated with a significant decrease in the red blood cell [NTP]/[Hb(4)] ratio (relationship between the concentrations of organic phosphates and total haemoglobin) and a significant decrease in mean cellular haemoglobin content, which is indicative of swelling of the red blood cells. Our data for blood oxygen affinity and arterial oxygen levels, together with previously published values of oxygen uptake and blood flows, allow for a quantitative evaluation of oxygen transport during digestion. This analysis shows that a large part of the increased metabolism during digestion is supported by an increased venous extraction, while arterial P(O(2)) (Pa(O(2))) and haemoglobin saturation do not vary with digestive status. Thus, we predict that venous P(O(2)) (Pv(O(2))) is reduced from a fasting value of 5.2 kPa to 1.6 kPa during digestion. PMID:12324542

Overgaard, Johannes; Wang, Tobias

2002-11-01

223

The Integrated Plasma Simulator: A Flexible Python Framework for Coupled Multiphysics Simulation  

SciTech Connect

High-fidelity coupled multiphysics simulations are an increasingly important aspect of computational science. In many domains, however, there has been very limited experience with simulations of this sort, therefore research in coupled multiphysics often requires computational frameworks with significant flexibility to respond to the changing directions of the physics and mathematics. This paper presents the Integrated Plasma Simulator (IPS), a framework designed for loosely coupled simulations of fusion plasmas. The IPS provides users with a simple component architecture into which a wide range of existing plasma physics codes can be inserted as components. Simulations can take advantage of multiple levels of parallelism supported in the IPS, and can be controlled by a high-level ``driver'' component, or by other coordination mechanisms, such as an asynchronous event service. We describe the requirements and design of the framework, and how they were implemented in the Python language. We also illustrate the flexibility of the framework by providing examples of different types of simulations that utilize various features of the IPS.

Foley, Samantha S [ORNL; Elwasif, Wael R [ORNL; Bernholdt, David E [ORNL

2011-11-01

224

Analysis and Visualization of Multi-Scale Astrophysical Simulations using Python and NumPy  

SciTech Connect

The study the origins of cosmic structure requires large-scale computer simulations beginning with well-constrained, observationally-determined, initial conditions. We use Adaptive Mesh Refinement to conduct multi-resolution simulations spanning twelve orders of magnitude in spatial dimensions and over twenty orders of magnitude in density. These simulations must be analyzed and visualized in a manner that is fast, accurate, and reproducible. I present 'yt,' a cross-platform analysis toolkit written in Python. 'yt' consists of a data-management layer for transporting and tracking simulation outputs, a plotting layer, a parallel analysis layer for handling mesh-based and particle-based data, as well as several interfaces. I demonstrate how the origins of cosmic structure--from the scale of clusters of galaxies down to the formation of individual stars--can be analyzed and visualized using a NumPy-based toolkit. Additionally, I discuss efforts to port this analysis code to other adaptive mesh refinement data formats, enabling direct comparison of data between research groups using different methods to simulate the same objects.

Turk, M.; /KIPAC, Menlo Park

2008-09-30

225

Quantity or quality? Determinants of maternal reproductive success in tropical pythons (Liasis fuscus)  

PubMed Central

A female's reproductive output (size and number of offspring) may say little about her reproductive success; the 'quality' of her progeny and the time that they are produced may be more important in this respect. We marked and released 1224 hatchling water pythons (Liasis fuscus) from 116 clutches of laboratory-incubated eggs, in a study site in tropical Australia. Clutches varied widely in the number of eggs, mean offspring sizes, the proportion of eggs that hatched, and recapture rates of offspring. Clutch size was not significantly correlated with the number of recaptured hatchlings in either year, nor was mean offspring size related to recapture probability. Instead, offspring recapture rates varied as a function of the time of hatching. Recapture rates were higher for hatchlings released in a year with high prey availability than in a year with few prey. In addition, recapture rates were higher for earlier-hatching clutches in the year with few prey. The other significant effect on recapture rates involved offspring viability: some clutches had a much higher proportion of surviving offspring than did others, and recapture rates were higher from clutches with higher hatching success (i.e. proportion of eggs hatching). Hence, the usual measures of reproductive output (clutch size and offspring size) offer only a poor index of a female's reproductive success in this system.

Madsen, T.; Shine, R.

1998-01-01

226

Magnetic resonance imaging volumetry for noninvasive measures of phenotypic flexibility during digestion in Burmese pythons.  

PubMed

Pythons are renowned for the profound phenotypical flexibility of their visceral organs in response to ingestion of large meals following prolonged fasting. Traditionally, the phenotypic changes are studied by determining organ mass of snakes killed at different times during digestion. Here we evaluate the use of magnetic resonance imaging (MRI) for in vivo measurements of the visceral organs in fasting and digesting snakes. Twelve snakes were MRI scanned immediately before the organs were removed and weighed to provide direct comparison of the two methods. Both methods provided similar estimates for the mass of liver, gallbladder, and pancreas, whereas MRI overestimated the size of the heart and small intestine, probably because blood and digesta contributed to the volume determined by MRI. The correlations were used to derive wet organ mass from MRI-based volumes to evaluate the mass development through repeated MRI scans of five digesting snakes. MRI was performed at fasting and 24, 48, 72, 132, and 500 h after eating a meal corresponding to 25% of body mass. This observation period revealed a reversible volume upregulation of the visceral organs, supporting the view that successive MRI facilitates in vivo investigations of structural changes accompanied by digestion. PMID:23303329

Hansen, Kasper; Pedersen, Pil Birkefeldt Møller; Pedersen, Michael; Wang, Tobias

2012-12-18

227

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

PubMed Central

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.

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

2008-01-01

228

Application of MATLAB and Python optimizers to two case studies involving groundwater flow and contaminant transport modeling  

NASA Astrophysics Data System (ADS)

One approach for utilizing geoscience models for management or policy analysis is via a simulation-based optimization framework—where an underlying model is linked with an optimization search algorithm. In this regard, MATLAB and Python are high-level programming languages that implement numerous optimization routines, including gradient-based, heuristic, and direct-search optimizers. The ever-expanding number of available algorithms makes it challenging for practitioners to identify optimizers that deliver good performance when applied to problems of interest. Thus, the primary contribution of this paper is to present a series of numerical experiments that investigated the performance of various MATLAB and Python optimizers. The experiments considered two simulation-based optimization case studies involving groundwater flow and contaminant transport. One case study examined the design of a pump-and-treat system for groundwater remediation, while the other considered least-squares calibration of a model of strontium (Sr) transport. Using these case studies, the performance of 12 different MATLAB and Python optimizers was compared. Overall, the Hooke-Jeeves direct search algorithm yielded the best performance in terms of identifying least-cost and best-fit solutions to the design and calibration problems, respectively. The IFFCO (implicit filtering for constrained optimization) direct search algorithm and the dynamically dimensioned search (DDS) heuristic algorithm also consistently yielded good performance and were up to 80% more efficient than Hooke-Jeeves when applied to the pump-and-treat problem. These results provide empirical evidence that, relative to gradient- and population-based alternatives, direct search algorithms and heuristic variants, such as DDS, are good choices for application to simulation-based optimization problems involving groundwater management.

Matott, L. Shawn; Leung, Kenny; Sim, Junyoung

2011-11-01

229

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

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.

Reed, Robert N.; Rodda, Gordon H.

2009-01-01

230

Annotated checklist of the recent and extinct pythons (Serpentes, Pythonidae), with notes on nomenclature, taxonomy, and distribution  

PubMed Central

Abstract McDiarmid et al. (1999) published the first part of their planned taxonomic catalog of the snakes of the world. Since then, several new python taxa have been described in both the scientific literature and non-peer-reviewed publications. This checklist evaluates the nomenclatural status of the names and discusses the taxonomic status of the new taxa, and aims to continue the work of McDiarmid et al. (1999) for the family Pythonidae, covering the period 1999 to 2010. Numerous new taxa are listed, and where appropriate recent synonymies are included and annotations are made. A checklist and a taxonomic identification key of valid taxa are provided.

Schleip, Wulf D.; O'Shea, Mark

2010-01-01

231

CCMR: Creating Elemental Arrays in the Python Numeric Module and Band Gaps of High Temperature Superconductor Crystals  

NSDL National Science Digital Library

Numeric allows one to enter many different types of data in an array, ranging from integers and floating points to Python objects. Unfortunately, other arrays could not be assigned as data elements of an array. This project was to modify the C code for Numeric so that it would gain this functionality. The problem with the original code was that if one was given an array a of dimension 2x3, and a new array b was created: b = array([[a,a],[a,a

Friesen, Michael

2005-08-17

232

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python  

PubMed Central

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.

Gorgolewski, Krzysztof; Burns, Christopher D.; Madison, Cindee; Clark, Dav; Halchenko, Yaroslav O.; Waskom, Michael L.; Ghosh, Satrajit S.

2011-01-01

233

The Social Tunnel Versus the Python: A New Way to Understand the Impact of Baby Booms and Baby Busts on a Society.  

ERIC Educational Resources Information Center

Maintains that the "python analogy," often used to help students understand the negative societal impact of unusually small or large age cohorts, is better replaced by the social tunnel analogy, which is diagramed and illustrated with reference to the educational problems experienced in the United States as a result of the World War II baby boom.…

McFalls, Joseph A.; And Others

1986-01-01

234

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

Microsoft Academic Search

Summary Burmese Pythons may eat Ivory-billed W oodpeckers. As surprising as that statement may seem, it's listed as a genuine possibility in Table 4.2 on page 69 of this report. There is no better illustration of the extraordinary degree of bias and unfounded speculation that comprises the bulk of this report. W e make the following observations to summarize this

Robert N. Reed; Gordon H. Rodda; David G. Barker; Tracy M. Barker

2010-01-01

235

A Python Plug-in Based Computational Framework for Spatially Distributed Environmental and Earth Sciences Modelling  

NASA Astrophysics Data System (ADS)

One of the pioneering landform evolution models, SIBERIA, while developed in the 1980’s is still widely used in the science community and is a key component of engineering software used to assess the long-term stability of man-made landforms such as rehabilitated mine sites and nuclear waste repositories. While SIBERIA is very reliable, computationally fast and well tested (both its underlying science and the computer code) the range of emerging applications have challenged the ability of the author to maintain and extend the underlying computer code. Moreover, the architecture of the SIBERIA code is not well suited to collaborative extension of its capabilities without often triggering forking of the code base. This paper describes a new modelling framework designed to supersede SIBERIA (as well as other earth sciences codes by the author) called TelluSim. The design is such that it is potentially more than simply a new landform evolution model, but TelluSim is a more general dynamical system modelling framework using time evolving GIS data as its spatial discretisation. TelluSim is designed as an open modular framework facilitating open-sourcing of the code, while addressing compromises made in the original design of SIBERIA in the 1980’s. An important aspect of the design of TelluSim was to minimise the overhead in interfacing the modules with TelluSim, and minimise any requirement for recoding of existing software, so eliminating a major disadvantage of more complex frameworks. The presentation will discuss in more detail the reasoning behind the design of TelluSim, and experiences of the advantages and disadvantages of using Python relative to other approaches (e.g. Matlab, R). The paper will discuss examples of how TelluSim has facilitated the incorporation and testing of new algorithms, and environmental processes, and the support for novel science and data testing methodologies. It will also discuss plans to link TelluSim with other open source geoscience modelling frameworks such as CSDMS.

Willgoose, G. R.

2009-12-01

236

Zachary D. Barker: Final DHS HS-STEM Report  

SciTech Connect

Working at Lawrence Livermore National Laboratory (LLNL) this summer has provided a very unique and special experience for me. I feel that the research opportunities given to me have allowed me to significantly benefit my research group, the laboratory, the Department of Homeland Security, and the Department of Energy. The researchers in the Single Particle Aerosol Mass Spectrometry (SPAMS) group were very welcoming and clearly wanted me to get the most out of my time in Livermore. I feel that my research partner, Veena Venkatachalam of MIT, and I have been extremely productive in meeting our research goals throughout this summer, and have learned much about working in research at a national laboratory such as Lawrence Livermore. I have learned much about the technical aspects of research while working at LLNL, however I have also gained important experience and insight into how research groups at national laboratories function. I believe that this internship has given me valuable knowledge and experience which will certainly help my transition to graduate study and a career in engineering. My work with Veena Venkatachalam in the SPAMS group this summer has focused on two major projects. Initially, we were tasked with an analysis of data collected by the group this past spring in a large public environment. The SPAMS instrument was deployed for over two months, collecting information on many of the ambient air particles circulating through the area. Our analysis of the particle data collected during this deployment concerned several aspects, including finding groups, or clusters, of particles that seemed to appear more during certain times of day, analyzing the mass spectral data of clusters and comparing them with mass spectral data of known substances, and comparing the real-time detection capability of the SPAMS instrument with that of a commercially available biological detection instrument. This analysis was performed in support of a group report to the Department of Homeland Security on the results of the deployment. The analysis of the deployment data revealed some interesting applications of the SPAMS instrument to homeland security situations. Using software developed in-house by SPAMS group member Dr. Paul Steele, Veena and I were able to cluster a subset of data over a certain timeframe (ranging from a single hour to an entire week). The software used makes clusters based on the mass spectral characteristics of the each particle in the data set, as well as other parameters. By looking more closely at the characteristics of individual clusters, including the mass spectra, conclusions could be made about what these particles are. This was achieved partially through examination and discussion of the mass spectral data with the members of the SPAMS group, as well as through comparison with known mass spectra collected from substances tested in the laboratory. In many cases, broad conclusions could be drawn about the identity of a cluster of particles.

Barker, Z D

2008-08-14

237

Zachary D. Barker: Final DHS HS-STEM Report  

Microsoft Academic Search

Working at Lawrence Livermore National Laboratory (LLNL) this summer has provided a very unique and special experience for me. I feel that the research opportunities given to me have allowed me to significantly benefit my research group, the laboratory, the Department of Homeland Security, and the Department of Energy. The researchers in the Single Particle Aerosol Mass Spectrometry (SPAMS) group

2008-01-01

238

Python-based finite element code used as a universal and modular tool for electronic structure calculation  

NASA Astrophysics Data System (ADS)

Ab-initio calculations of electronic states within the density-functional framework has been performed by means of the open source finite element package SfePy (Simple Finite Elements in Python, http://sfepy.org). We describe a new robust ab-initio real-space code based on (i) density functional theory, (ii) finite element method and (iii) environment-reflecting pseudopotentials. This approach brings a new quality to solving Kohn-Sham equations, calculating electronic states, total energy, Hellmann-Feynman forces and material properties particularly for non-crystalline, non-periodic structures. The main asset of the above approach is an efficient combination of excellent convergence control of standard, universal basis used in industrially proved finite-element method, high precision of ab-initio environment-reflecting pseudopotentials, and applicability not restricted to electrically neutral periodic environment. We present also numerical examples illustrating the outputs of the method.

Cimrman, Robert; Tu?ma, Miroslav; Novák, Matyáš; ?ertík, Ond?ej; Plešek, Ji?í; Vacká?, Ji?í

2013-10-01

239

NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers.  

PubMed

To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings. PMID:23678341

Clos, Lawrence J; Jofre, M Fransisca; Ellinger, James J; Westler, William M; Markley, John L

2013-01-01

240

Application of python-based Abaqus preprocess and postprocess technique in analysis of gearbox vibration and noise reduction  

NASA Astrophysics Data System (ADS)

To reduce vibration and noise, a damping layer and constraint layer are usually pasted on the inner surface of a gearbox thin shell, and their thicknesses are the main parameters in the vibration and noise reduction design. The normal acceleration of the point on the gearbox surface is the main index that can reflect the vibration and noise of that point, and the normal accelerations of different points can reflect the degree of the vibration and noise of the whole structure. The K-S function is adopted to process many points' normal accelerations as the comprehensive index of the vibration characteristics of the whole structure, and the vibration acceleration level is adopted to measure the degree of the vibration and noise. Secondary development of the Abaqus preprocess and postprocess on the basis of the Python scripting programming automatically modifies the model parameters, submits the job, and restarts the analysis totally, which avoids the tedious work of returning to the Abaqus/CAE for modifying and resubmitting and improves the speed of the preprocess and postprocess and the computational efficiency.

Yi, Guilian; Sui, Yunkang; Du, Jiazheng

2011-06-01

241

Influence of temperature on the corticosterone stress-response: An experiment in the Children's python (Antaresia childreni).  

PubMed

To cope with environmental challenges, organisms have to adjust their behaviours and their physiology to the environmental conditions they face (i.e. allostasis). In vertebrates, such adjustments are often mediated through the secretion of glucocorticoids (GCs) that are well-known to activate and/or inhibit specific physiological and behavioural traits. In ectothermic species, most processes are temperature-dependent and according to previous studies, low external temperatures should be associated with low GC concentrations (both baseline and stress-induced concentrations). In this study, we experimentally tested this hypothesis by investigating the short term influence of temperature on the GC stress response in a squamate reptile, the Children's python (Antaresia childreni). Snakes were maintained in contrasting conditions (warm and cold groups), and their corticosterone (CORT) stress response was measured (baseline and stress-induced CORT concentrations), within 48h of treatment. Contrary to our prediction, baseline and stress-induced CORT concentrations were higher in the cold versus the warm treatment. In addition, we found a strong negative relationship between CORT concentrations (baseline and stress-induced) and temperature within the cold treatment. Although it remains unclear how cold temperatures can mechanistically result in increased CORT concentrations, we suggest that, at suboptimal temperature, high CORT concentrations may help the organism to maintain an alert state. PMID:23948369

Dupoué, Andréaz; Brischoux, François; Lourdais, Olivier; Angelier, Frédéric

2013-08-12

242

Molecular evolution of peptide tyrosine--tyrosine: primary structure of PYY from the lampreys Geotria australis and Lampetra fluviatilis, bichir, python and desert tortoise.  

PubMed

Peptide tyrosine-tyrosine (PYY) has been isolated from the intestines of two species of reptile, the desert tortoise Gopherus agassizii (Testudines) and the Burmese python Python molurus (Squamata), from the primitive Actinopterygian fish, the bichir Polypterus senegalis (Polypteriformes) and from two agnathans, the Southern-hemisphere lamprey Geotria australis (Geotriidae) and the holarctic lamprey Lampetra fluviatilis (Petromyzontidae). The primary structure of bichir PYY is identical to the proposed ancestral sequence of gnathostome PYY (YPPKPENPGE10/DAPPEELAKY20/YSALR HYINL30/ITRQRY). Tortoise and python PYY differ by six and seven residues, respectively, from the ancestral sequence consistent with the traditional view that the Testudines represent an earlier divergence from the primitive reptilian stock than the Squamates. The current views of agnathan phylogeny favor the hypothesis that the Southern-hemisphere lampreys and the holarctic lampreys arose from a common ancestral stock but their divergence is of a relatively ancient (pre-Tertiary) origin. The Geotria PYY-related peptide shows only two amino acid substitutions (Pro10-->Gln and Leu22-->Ser) compared with PYY from the holarctic lamprey Petromyzon marinus. This result was unexpected as Petromyzon PYY differs from Lampetra PYY deduced from the nucleotide sequence of a cDNA (Söderberg et al. J. Neurosci. Res. 1994;37:633-640) by 10 residues. However, a re-examination of an extract of Lampetra intestine revealed the presence of a PYY that differed in primary structure from Petromyzon PYY by only one amino acid residue (Pro10-->Ser). This result suggests that the structure of PYY has been strongly conserved during the evolution of Agnatha and that at least two genes encoding PYY-related peptides are expressed in Lampetra tissues. PMID:10100922

Wang, Y; Nielsen, P F; Youson, J H; Potter, I C; Lance, V A; Conlon, J M

1999-02-01

243

The contribution of gastric digestion and ingestion of amino acids on the postprandial rise in oxygen consumption, heart rate and growth of visceral organs in pythons.  

PubMed

To investigate the contribution of gastric and intestinal processes to the postprandial rise in metabolism in pythons (Python regius), we measured oxygen consumption after ligation of the pyloric sphincter to prevent the chyme from entering the intestine. Pyloric blockade reduced the postprandial rise in metabolism during the first 18h after ingestion of mice amounting to 18% of the snake's body mass by 60%. In another series of the experiments, we showed that infusion of amino acids directly into the stomach or the intestine elicited similar metabolic responses. This indicates a lower gastric contribution to the SDA response than previously reported. To include an assessment of the gastric contribution to the postprandial cardiovascular response, we also measured blood and heart rate. While heart rate increased during digestion in snakes with pyloric blockade, there was no rise in the double-blocked heart rates compared to fasting controls. Thus, the non-adrenergic-non-cholinergic factor that stimulates heart rate during digestion does not stem from the stomach. Finally, there was no growth of the visceral organs in response to digestion when chyme was prevented from reaching the intestine. PMID:23384684

Enok, Sanne; Simonsen, Lasse Stærdal; Wang, Tobias

2013-02-04

244

The Effects of Fasting Duration on the Metabolic Response to Feeding in [ITAL]Python molurus[\\/ITAL]: An Evaluation of the Energetic Costs Associated with Gastrointestinal Growth and Upregulation  

Microsoft Academic Search

The oxygen uptake of Python molurus increases enormously following feeding, and the elevated metabolism coincides with rapid growth of the gastrointestinal organs. There are opposing views regarding the energetic costs of the gastrointestinal hy- pertrophy, and this study concerns the metabolic response to feeding after fasting periods of different duration. Since mass and function of the gastrointestinal organs remain elevated

Johannes Overgaard; Johnnie B. Andersen; Tobias Wang

2002-01-01

245

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples  

PubMed Central

Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/.

Boitard, Simon; Kofler, Robert; Francoise, Pierre; Robelin, David; Schlotterer, Christian; Futschik, Andreas

2013-01-01

246

Python Microgravity Accelerometer System.  

National Technical Information Service (NTIS)

Scientists performing experiments in the unique microgravity environment of space frequently require an accurate and useful view of the acceleration at their experiment. Payload Systems has developed a Microgravity Accelerometer System for use in the Spac...

V. Nijhawan A. P. Arrott

1988-01-01

247

Data for giant constrictors - Biological management profiles and an establishment risk assessment for nine large species of pythons, anacondas, and the boa constrictor  

USGS Publications Warehouse

Giant Constrictors' Climate Space The giant constrictors' climate space data set represents the information needed to recreate the climate space and climate matching analyses in Reed and Rodda (2009). A detailed methodology and results are included in that report. The data include locations for nine species of large constrictors including Python molurus, Broghammerus reticulatus, P. sebae, P. natalensis, Boa constrictor, Eunectes notaeus, E. deschauenseei, E. beniensis, and E. murinus. The locations are from published sources. Climate data are included for monthly precipitation and average monthly temperature along with the species locations. The individual spreadsheets of location data match the figures in the Reed and Rodda (2009) report, illustrating areas of the mainland United States that match the climate envelope of the native range. The precipitation and temperature data at each location were used to determine the climate space for each species. Graphs of climate space formed the basis for the algorithms in the data set, and more details can be found in Reed and Rodda (2009). These algorithms were used in ArcGIS to generate maps of areas in the United States that matched the climate space of locations of the snakes in their native range. We discovered a rounding error in ArcGIS in the implementation of the algorithms, which has been corrected here. Therefore the shapefiles are slightly different than those appearing in the risk assessment figures illustrating areas of the United States that match the climate envelope of the species in their native ranges. However, the suitable localities are not different at the scale of intended use for these maps, although there are more noticeable differences between areas classified as 'too cold' and 'too hot'.

Jarnevich, C. S.; Rodda, G. H.; Reed, R. N.

2011-01-01

248

Design by Contract for Python  

Microsoft Academic Search

The idea of design by contract (DBC), realized in the statically typed object-oriented programming language Eiffel, can be viewed as a systematic approach to specifying and implementing object-oriented software systems. We believe that a statically typed programming language is not suitable in the analysis and design phase of a prototyping-oriented software life cycle. For this purpose, dynamically typed interpreted programming

Reinhold Plösch

1997-01-01

249

Compiling Little Languages in Python  

Microsoft Academic Search

"Little languages" such as configuration files orHTML documents are commonplace in computing.This paper divides the work of implementing a littlelanguage into four parts, and presents a frameworkwhich can be used to easily conquer the implementationof each. The pieces of the framework havethe unusual property that they may be extendedthrough normal object-oriented means, allowing featuresto be added to a little language

John Aycock

1998-01-01

250

PYM - A Macro Preprocessor Based on Python  

Microsoft Academic Search

In a number of tasks the need for a macro preprocessor arises. Most macro preprocessors, are either syntactically tied to the language they support (e.g., cpp, the C preprocessor, or the lisp macro facility), or they are limited in their functionality (cpp), or may even have an arcane syntax (e.g. m4, chakotay). We propose a macro preprocessor - PYM -

Robert F. Tobler

2001-01-01

251

Gist: A scientific graphics package for Python.  

National Technical Information Service (NTIS)

Gist 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 Metafile...

L. E. Busby

1996-01-01

252

GaPP: Gaussian Processes in Python  

NASA Astrophysics Data System (ADS)

The algorithm Gaussian processes can reconstruct a function from a sample of data without assuming a parameterization of the function. The GaPP code can be used on any dataset to reconstruct a function. It handles individual error bars on the data and can be used to determine the derivatives of the reconstructed function. The data sample can consist of observations of the function and of its first derivative.

Seikel, Marina; Clarkson, Chris; Smith, Mathew

2013-03-01

253

VisIt Python Interface Manual.  

National Technical Information Service (NTIS)

VisIt is a distributed, parallel, visualization tool for visualizing data defined on two and three-dimensional structured and unstructured meshes. VisIts distributed architecture allows it to leverage both the compute power of a large parallel computer an...

B. J. Whitlock

2005-01-01

254

Medieval Romances: "Perceval" to "Monty Python."  

ERIC Educational Resources Information Center

|A selection of romances from medieval literature can be used successfully in undergraduate literature classes to trace the appearance and relevance of medieval themes, motifs, and characters in works of modern poetry, fiction, and film. New scholarly editions, historiographies, translations, and modernizations give both teachers and students more…

Jehle, Dorothy M.

255

Intracardiac flow separation in an in situ perfused heart from Burmese python Python molurus  

Microsoft Academic Search

The heart of non-crocodilian reptiles has two separate atria that receive blood from the systemic and pulmonary circulations. The ventricle is not fully divided, but is compartmentalised into two chambers (cavum dorsale and cavum pulmonale) by a muscular ridge that runs from the apex to the base of the ventricle. The muscular ridge is small in turtles, but is well

Tobias Wang; Jordi Altimiras; Michael Axelsson

2002-01-01

256

Clutch size manipulation, hatching success and offspring phenotype in the ball python ( Python regius )  

Microsoft Academic Search

In a diverse array of avian and mammalian species, experimental manipulations of clutch size have tested the hypothesis that natural selection should adjust numbers of neonates produced so as to maximize the number of via- ble offspring at the end of the period of parental care. Reptiles have not been studied in this respect, probably because they rarely display parental

FABIEN AUBRET; XAVIER BONNET; RICHARD SHINE; STEPHANIE MAUMELAT

2003-01-01

257

Zachary-Fort Lauderdale pipeline construction and conversion project: final supplement to final environmental impact statement. Docket No. CP74-192  

SciTech Connect

This Final Supplement to the Final Environmental Impact Statement (Final Supplement) evaluates the economic, engineering, and environmental aspects of newly developed alternatives to an abandonment/conversion project proposed by Florida Gas Transmission Company (Florida Gas). It also updates the staff's previous FEIS and studies revisions to the original proposal. Wherever possible, the staff has adopted portions of its previous FEIS in lieu of reprinting portions of that analysis which require no change. 60 references, 8 figures, 35 tables.

None

1980-05-01

258

The Astropy Project: A Community Python Library for Astrophysics  

NASA Astrophysics Data System (ADS)

I introduce and describe progress on Astropy, a large, community effort to provide common astronomy/astrophysics utilities and promote reuse of software. It is based on a model of a collaborative open-source core package (currently under heavy development) and independent but affiliated packages contributed by individuals and organizations. I describe some of the features in the current core package, the organizational structure of the community, and the direction the project is headed in the near future.

Tollerud, E. J.; Greenfield, P. E.; Robitaille, T. P.; Astropy Developers

2013-10-01

259

Pablo Python Looks at Animals. [Multimedia Educational Kit].  

ERIC Educational Resources Information Center

|Teachers and students can view the world of animals together through an exploration of how-and-why questions about animals in this curriculum unit. The problem-solving and critical thinking skills of students are improved through interactive activities involving oral and written communication, mathematics, creative arts, music, dance, and…

Sullivan, Rick; Green, David

260

Respiratory consequences of feeding in the snake Python molorus  

Microsoft Academic Search

Snakes can ingest large meals and exhibit marked increases in metabolic rate during digestion. Because postprandial oxygen consumption in some snakes may surpass that attained during exercise, studies of digestion offers an alternative avenue to understand the cardio-respiratory responses to elevated metabolic rate in reptiles. The effects of feeding on metabolic rate, arterial oxygen levels, and arterial acid–base status in

Johannes Overgaard; Morten Busk; James W Hicks; Frank B Jensen; Tobias Wang

1999-01-01

261

Python: A Programming Language For Software Integration And Development  

Microsoft Academic Search

mational analysis, quantum mechanics, distance geometry, docking methods, ab-initio methods)is large and growing rapidly. Moreover, these programs come in many flavors and variations, using differentforce fields, search techniques, algorithmic details (e.g., continuous space vs. discrete, Cartesian vs.torsional). Each variation presents its own characteristic set of advantages and limitations. These programsalso tend to evolve rapidly and are usually not written as

M. F. Sanner

1999-01-01

262

The Monty Python method for generating random variables  

Microsoft Academic Search

We suggest an interesting and fast method for generating normal, exponential, t, von Mises, and certain other important random variables used in Monte Carlo studies. The right half of a symmetric density is cut into pieces, then, using simple area-preserving transformations, reassembled into a rectangle from which the x-coordinate—or a linear function of the x-coordinate—of a random point provides the

George Marsaglia; Wai Wan Tsang

1998-01-01

263

Pablo Python Looks at Animals. [Multimedia Educational Kit].  

ERIC Educational Resources Information Center

Teachers and students can view the world of animals together through an exploration of how-and-why questions about animals in this curriculum unit. The problem-solving and critical thinking skills of students are improved through interactive activities involving oral and written communication, mathematics, creative arts, music, dance, and creative…

Sullivan, Rick; Green, David

264

Why Complicate Things? Introducing Programming in High School Using Python  

Microsoft Academic Search

Abstract: Deciding what to teach novices about programmingand what programming language to use is a commontopic for debate. Should an industry relevantprogramming language be taught, or should a languagedesigned for teaching novices be used? Typically,these questions are raised at university level,but in this paper we address them from a high schoolperspective.

Linda Grandell; Mia Peltomki; Ralph-johan Back; Tapio Salakoski

265

Burmese python at SRS6, Shark River Slough  

Microsoft Academic Search

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514.\\u000aThis image is made available for non-commercial or educational use only.

Jessica Schedlbauer

2011-01-01

266

ANTP Protocol Suite Software Implementation Architecture in Python.  

National Technical Information Service (NTIS)

Due to the highly-dynamic nature of airborne telemetry networks, we have developed the ANTP protocol suite consisting of AeroTP, AeroRP, and AeroNP. Having verified these protocols through simulation and analysis, the next step towards deployment of the A...

D. Zhang E. K. Cetinkaya J. P. Sterbenz M. Alenazi S. A. Gogi

2011-01-01

267

Multi-Scale Investigation of Surface Topography of Ball Python ( Python regius ) Shed Skin in Comparison to Human Skin  

Microsoft Academic Search

A major concern in designing tribosystems is to minimize friction, save energy, and to reduce wear. Conventional philosophy\\u000a for design centers on mechanical and material considerations. In particular, designers pay more attention to material properties\\u000a and material choices based on mechanical properties rather than the design and shape of the contacting surfaces and the relation\\u000a of that surface to the

H. A. Abdel-Aal; M. El Mansori; S. Mezghani

2010-01-01

268

77 FR 3329 - Injurious Wildlife Species; Listing Three Python Species and One Anaconda Species as Injurious...  

Federal Register 2010, 2011, 2012, 2013

...Nuisance Species Task Force was created under the Nonindigenous...extensive review of the literature of the species, and while this information was used by the risk assessment...species, the extensive literature review was also used...

2012-01-23

269

A comparison of spent fuel assembly control instruments: The Cadarache PYTHON and the Los Alamos Fork  

SciTech Connect

Devices to monitor spent fuel assemblies while stored under water with nondestructive assay methods, have been developed in France and in the United States. Both devices are designed to verify operator's declared values of exposures and cooling-time but the applications and thus the designs of the systems differ. A study, whose results are presented in this paper, has been conducted to compare the features and the performances of the two instruments. 4 refs., 9 figs.

Bignan, G.; Capsie, J.; Romeyer-Dherbey, J. (CEA Centre d'Etudes Nucleaires de Cadarache, 13 - Saint-Paul-lez-Durance (France). Direction des Reacteurs Nucleaires); Rinard, P. (Los Alamos National Lab., NM (United States))

1991-01-01

270

Establishing a Novel Modeling Tool: A Python-Based Interface for a Neuromorphic Hardware System  

PubMed Central

Neuromorphic hardware systems provide new possibilities for the neuroscience modeling community. Due to the intrinsic parallelism of the micro-electronic emulation of neural computation, such models are highly scalable without a loss of speed. However, the communities of software simulator users and neuromorphic engineering in neuroscience are rather disjoint. We present a software concept that provides the possibility to establish such hardware devices as valuable modeling tools. It is based on the integration of the hardware interface into a simulator-independent language which allows for unified experiment descriptions that can be run on various simulation platforms without modification, implying experiment portability and a huge simplification of the quantitative comparison of hardware and simulator results. We introduce an accelerated neuromorphic hardware device and describe the implementation of the proposed concept for this system. An example setup and results acquired by utilizing both the hardware system and a software simulator are demonstrated.

Bruderle, Daniel; Muller, Eric; Davison, Andrew; Muller, Eilif; Schemmel, Johannes; Meier, Karlheinz

2008-01-01

271

Python scripting libraries for subsurface fluid and heat flow simulations with TOUGH2 and SHEMAT  

Microsoft Academic Search

Numerical simulations of subsurface fluid and heat flow are commonly controlled manually via input files or from graphical user interfaces (GUIs). Manual editing of input files is often tedious and error-prone, while GUIs typically limit the full capability of the simulator. Neither approach lends itself to automation, which is desirable for more complex simulations.We propose an alternative approach based on

J. Florian Wellmann; Adrian Croucher; Klaus Regenauer-Lieb

272

PHENIX: a comprehensive Python-based system for macromolecular structure solution  

PubMed Central

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How­ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

Adams, Paul D.; Afonine, Pavel V.; Bunkoczi, Gabor; Chen, Vincent B.; Davis, Ian W.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Kapral, Gary J.; Grosse-Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

2010-01-01

273

From Monty Python to Total Recall: A Feature Film Activity for the Cognitive Psychology Course.  

ERIC Educational Resources Information Center

Describes a college psychology course activity designed to help students define the parameters of cognitive psychology. Students selected a feature film and a journal article that represented some aspect of cognitive psychology. They then wrote a paper discussing the theoretical and empirical connections between the sources and the topic. (MJP)

Conner, David B.

1996-01-01

274

Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS  

Microsoft Academic Search

One of the challenges in biocomputing is to enable the efficient use of a wide variety of fast-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking, molec- ular surfaces, and the derivation of phenomenological potentials. In this paper we present an

Michel F. Sanner; Bruce S. Duncan; C. J. Carrillo; Arthur J. Olson

1999-01-01

275

pyGlobus: a Python interface to the Globus ToolkitTM  

Microsoft Academic Search

Developing high-performance problem solving environments\\/applications that allow scientiststo easily harness the power of the emerging national-scale "Grid" infrastructure is currently adifficult task. Although many of the necessary low-level services, e.g. security, resource discovery,remote access to compute\\/data resource, etc., are available, it can be a challenge to rapidly integratethem into a new application.To address this difficulty we have begun the development

Keith R. Jackson

2002-01-01

276

Representation-based just-in-time specialization and the psyco prototype for python  

Microsoft Academic Search

A powerful application of specialization is to remove interpretative overhead: a language can be implemented with an interpreter, whose performance is then improved by specializing it for a given program source. This approach is only moderately successful with very high level languages, where the operation of each single step can be highly dependent on run-time data and context. In the

Armin Rigo

2004-01-01

277

Pyro: A python-based versatile programming environment for teaching robotics  

Microsoft Academic Search

In this article we describe a programming framework called Pyro, which provides a set of abstractions that allows students to write platform-independent robot programs. This project is unique because of its focus on the pedagogical implications of teaching mobile robotics via a top-down approach. We describe the background of the project, its novel abstractions, its library of objects, and the

Douglas S. Blank; Deepak Kumar; Lisa Meeden; Holly A. Yanco

2003-01-01

278

Tabizi Pythons and Clendro Hawks: Using Imaginary Animals to Achieve Real Knowledge about Ecosystems  

ERIC Educational Resources Information Center

The author describes how he used to teach a unit on food webs and ecosystems using actual food webs as models. However, the models used by the author tend to be either too simplistic or too complicated for his students. A few years ago, he solved these problems by making up his own food web, complete with invented plants and animals. The model has…

Rockow, Michael

2007-01-01

279

Tabizi Pythons and Clendro Hawks: Using Imaginary Animals to Achieve Real Knowledge about Ecosystems  

NSDL National Science Digital Library

In the engaging unit described here, imaginary organisms are used to teach a variety of topics related to ecosystems--food chains and energy flow, food webs, limiting factors, carrying capacity, and the effects of natural and human-made events on ecosystems. By inventing organisms, the teacher is able to control the level of complexity, and the number of organisms can be modified to meet each student's level. Because the organisms are figments of the imagination, the assignment is not complicated by students' prior knowledge. Once the unit is finished, the class can discuss the ecosystem and how it is similar to and different from real ecosystems.

Rockow, Michael

2007-01-01

280

A standard python environment for software applications at the Robert C. Byrd Green Bank Telescope (GBT)  

NASA Astrophysics Data System (ADS)

Since 2003, the monitor and control software systems for the Robert C. Byrd Green Bank Telescope (GBT) have been substantially redesigned to make the telescope easier to use. The result is the release of the Astronomer's Integrated Desktop (Astrid), an observation management platform used to create and submit scheduling blocks, monitor their progress on the telescope, and provide a real time, quick look data display. Using Astrid, the astronomer launches one application and has access to all of the software, documentation, and feedback facilities that are required to conduct an interactive observing session. These systems together provide a common look and feel for GBT software applications, enable offline observation preparation, and facilitate dynamic scheduling and remote observing.

Radziwill, Nicole M.; Shelton, Amy L.

2006-07-01

281

Optimization of springback in L-bending process using a coupled Abaqus\\/Python algorithm  

Microsoft Academic Search

Sheet metal L-bending processes are widely used for mass production. The design of L-bending processes is connected with time-consuming\\u000a and costly experiments. Therefore, the finite element simulation of the process could be a helpful tool for the designer and\\u000a quality assurance of the products. In L-bending process, springback is an important phenomenon, and its accurate prediction\\u000a is important to control

Faiez Gassara; Ridha Hambli; Tarak Bouraoui; Foued El Halouani; Damien Soulat

2009-01-01

282

75 FR 11808 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...  

Federal Register 2010, 2011, 2012, 2013

...is most likely the world's longest snake...rabbits, tree shrews, porcupines, and many species...any snake in the world. In their native...as the snake gets older and larger. The...heaviest snakes in the world, ranging up to 200...that was 5 years old in 1976 and...

2010-03-12

283

Pyro: A Python-Based Versatile Programming Environment for Teaching Robotics  

ERIC Educational Resources Information Center

|In this article we describe a programming framework called Pyro, which provides a set of abstractions that allows students to write platform-independent robot programs. This project is unique because of its focus on the pedagogical implications of teaching mobile robotics via a top-down approach. We describe the background of the project, its…

Blank, Douglas; Kumar, Deepak; Meeden, Lisa; Yanco, Holly

2004-01-01

284

Creative Generation of Multiple Perspectives: Application to the Problem of Burmese Pythons in the Everglades  

Microsoft Academic Search

Many IS\\/DSS development methods advocate the inclusion of multiple perspectives during systems design activities to deal with problems more holistically. Yet, few techniques exist for generating these perspectives. This paper proposes a method for creative generation of multiple perspectives to aid designing systems for dealing with wicked problems involving multiple stakeholders. We illustrate the technique by applying it to the

Lars P. Linden; James F. Courtney

2009-01-01

285

Phenix - a comprehensive python-based system for macromolecular structure solution  

SciTech Connect

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

2009-01-01

286

Maternal brooding in the children’s python (Antaresia childreni) promotes egg water balance  

Microsoft Academic Search

Parental care provides considerable benefits to offspring and is widespread among animals, yet it is relatively uncommon among\\u000a squamate reptiles (e.g., lizards and snakes). However, all pythonine snakes show extended maternal egg brooding with some\\u000a species being facultatively endothermic. While facultative endothermy provides thermal benefits, the presence of brooding\\u000a in non-endothermic species suggests other potential benefits of brooding. In this

Olivier Lourdais; Ty C. M. Hoffman; Dale F. DeNardo

2007-01-01

287

Predation on sun bears by reticulated python in East kalimantan, Indonesian Borneo  

Microsoft Academic Search

The Malayan sun bear is the largest member of the order Carnivora on the island of Borneo. Few records exist of predation on this species beside humans, whereas accurate recordings of natural predation events can teach us about the ecology of the prey species. Here I report on an attempted and a successful predation of Malayan sun bears by a

Gabriella M. Fredriksson

2005-01-01

288

Exploratory trial to determine the efficacy of the PYthon and the PYthon Magnum slow-release insecticide ear tags for the control of midges (Culicoides spp.), attacking sheep and cattle and flies attacking cattle.  

PubMed

This study investigated the prophylactic action of the chemical combination zeta-cypermethrin and piperonyl butoxide, administered by means of slow-release insecticide-impregnated ear tags, against biting midges (Culicoides spp) attacking sheep and against midges, horn flies (Haematobia irritant), stable flies (Stomoxys calcitrans), and houseflies (Musca domestica) attacking cattle. Treated sheep and cattle were protected 100 percent against blood-feeding midges for two months and there was a clear reduction in the number of midges collected from treated animals. Three days after the ear tags were attached to cattle, the number of horn flies on the cattle was reduced to practically zero and remained at a low level until the end of the trial (day 85). There was also a strong reduction in the numbers of stable flies and houseflies counted. PMID:22930983

Goosen, H; de Vries, P J T; Fletcher, M G

2012-08-01

289

Outline Agenda for AMR Workshop  

Center for Drug Evaluation (CDER)

Text Version... Speakers: Howard Gebel Ron Kerman Andrea Zachary Nancy Reinsmoen Michael Amos (NIST) Annette Ragosta (CBER) Kevin Maher (CDRH) 12 ... More results from www.fda.gov/downloads/drugs/newsevents

290

An empirical comparison of C, C++, Java, Perl, Python, Rexx, and Tcl for a search\\/string-processing program  

Microsoft Academic Search

implementations of the same set of requirements, created by 74 different programmers in vari- ous languages, are compared for several properties, such as run time, memory consumption, source text length, comment density, program structure, reliability, and the amount of effort required for writing them. The results indicate that, for the given programming problem, \\

Lutz Prechelt

2000-01-01

291

Variation in mating systems and sexual size dimorphism between populations of the Australian python Morelia spilota (Serpentes: Pythonidae)  

Microsoft Academic Search

Although adaptationist hypotheses predict a functional relationship between mating systems and sexual size dimorphism, such predictions are difficult to test because of the high degree of phylogenetic conservatism in both of these traits. Taxa that show intraspecific variation in mating systems hence offer valuable opportunities for more direct tests of evolutionary-ecological hypotheses. Based on a collation of published and unpublished

R. Shine; M. Fitzgerald

1995-01-01

292

Are scripting languages any good? A validation of Perl, Python, Rexx, and Tcl against C, C++, and Java  

Microsoft Academic Search

Abstract Four scripting languages,are introduced shortly and their theoretical and purported characteristics are discussed and related to three more,conventional programming,languages. Then the comparison,is extended to an objective empirical one using 80 implementations of the same set of requirements, created by 74 different programmers. The limitations of the empirical data are laid out and discussed and then the 80 implementations are

Lutz Prechelt

2003-01-01

293

Application of python-based Abaqus preprocess and postprocess technique in analysis of gearbox vibration and noise reduction  

Microsoft Academic Search

To reduce vibration and noise, a damping layer and constraint layer are usually pasted on the inner surface of a gearbox thin\\u000a shell, and their thicknesses are the main parameters in the vibration and noise reduction design. The normal acceleration\\u000a of the point on the gearbox surface is the main index that can reflect the vibration and noise of that

Guilian Yi; Yunkang Sui; Jiazheng Du

2011-01-01

294

Rafael Travieso (left) and Kyle Tuntland (right) with a Burmese python at SRS6, Shark River Slough  

Microsoft Academic Search

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514.\\u000aThis image is made available for non-commercial or educational use only.

Kyle Tuntland

2011-01-01

295

Endoscopic examination of snakes by access through an air sac  

Microsoft Academic Search

Sixteen boa constrictors (Boa constrictor), three royal pythons (Python regius) and 15 Burmese pythons (Python molurus bivittatus) were examined endoscopically by access through the air sac. The snakes were immobilised in a ventral position using a half-open anaesthetic system with assisted ventilation and a mixture of isoflurane and oxygen. The rigid endoscope was introduced percutaneously and the internal structure of

V. Jekl; Z. Knotek

2006-01-01

296

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

National Technical Information Service (NTIS)

This document addresses primarily the biological impacts associated with potential colonization of the United States by any of the nine giant constrictors, and it tabulates the biological information germane to potential economic and social impacts. What ...

G. H. Rodda R. N. Reed

2009-01-01

297

Web Applications With Django  

Microsoft Academic Search

\\u000a Django is a modern Python web framework that redefined web development in the Python world. A fullstack approach, pragmatic\\u000a design, and superb documentation are some of the reasons for its success.

Josh Juneau; Jim Baker; Victor Ng; Leo Soto; Frank Wierzbicki

298

Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (85th, Miami, Florida, August 5-8, 2002). Commission on the Status of Women Division.  

ERIC Educational Resources Information Center

|The Commission on the Status of Women Division of the proceedings contains the following 6 papers: "Relationship Content in Four Men's and Women's Magazines" (Alexis Zachary and Bryan Denham); "Mind the Gender Gap: Gender Differences in Motivation to Contribute Online Content" (Cindy Royal); "Peering through the Glass Ceiling of the Boys' Club:…

2002

299

77 FR 23666 - Information Collection; Submission for OMB Review, Comment Request  

Federal Register 2010, 2011, 2012, 2013

...Zachary Jackson, at (202) 606-6948 or email to zjackson@cns.gov. Individuals who use a telecommunications device for the deaf (TTY-TDD) may call 1-800-833-3722 between 8 a.m. and 8 p.m. Eastern Time, Monday through Friday....

2012-04-20

300

"Creating Unity from Diversity: Finding Our Commonalities, Respecting Our Differences." Presenter Abstracts of the Annual National Conference of the National Multicultural Institute (9th, Washington, D.C., May 19-22, 1994).  

ERIC Educational Resources Information Center

|This is primarily a collection of abstracts for training workshops for professionals in the field of multicultural education. The abstracts are: (1) "An Exploration of the Unspoken: A Group Relations Approach to Multicultural Dialogue" (Zachary G. Green); (2) "Exploring Our Cultural Assumptions" (Daniel Rivera); (3) "Challenging Homophobia:…

National Multicultural Inst., Washington, DC.

301

Cancer Research Now: Adolescent and Young Adult Cancers  

MedlinePLUS Videos and Cool Tools

... Conversation with Matthew Zachary: The Young Adult Cancer Movement HIGHLIGHTS Breast Cancer Cells Found by Immunochemistry in Sentinel Nodes Not Associated with Survival Radiation Plus Short-Term Hormone Therapy Improves Survival of Men with Early-Stage Prostate Cancer In Hodgkin Lymphoma ...

302

Making Colonial Subjects: Education in the Age of Empire  

ERIC Educational Resources Information Center

|This article explores two attempts to envisage a new global world, one created by the West, and to create new colonial subjects. One of these attempts was in Sierra Leone in the 1790s, the other in India in the 1830s. The two case studies are seen through the lens of a father and son, Zachary and Thomas Babington Macaulay, each a representative…

Hall, Catherine

2008-01-01

303

"Creating Unity from Diversity: Finding Our Commonalities, Respecting Our Differences." Presenter Abstracts of the Annual National Conference of the National Multicultural Institute (9th, Washington, D.C., May 19-22, 1994).  

ERIC Educational Resources Information Center

This is primarily a collection of abstracts for training workshops for professionals in the field of multicultural education. The abstracts are: (1) "An Exploration of the Unspoken: A Group Relations Approach to Multicultural Dialogue" (Zachary G. Green); (2) "Exploring Our Cultural Assumptions" (Daniel Rivera); (3) "Challenging Homophobia:…

National Multicultural Inst., Washington, DC.

304

Do ‘liberal market economies’ really innovate more radically than ‘coordinated market economies’?  

Microsoft Academic Search

In Varieties of Capitalism; The Institutional Foundations of Comparative Advantage, Peter A. Hall and David Soskice (H&S) argue that technological specialization patterns are largely determined by the prevailing “variety of capitalism”. They hypothesize that “liberal market economies” (LMEs) specialize in radical innovation, while “coordinated market economies” (CMEs) focus more on incremental innovation. Mark Zachary Taylor [Taylor, M.Z., 2004. Empirical evidence

Dirk Akkermans; Carolina Castaldi; Bart Los

2009-01-01

305

Dryden: A Collection of Critical Essays. Twentieth Century Views Series.  

ERIC Educational Resources Information Center

|One of a series of works aimed at presenting contemporary critical opinion on major authors, this collection includes essays by Bernard Schilling, T. S. Eliot, Louis I. Bredvold, James M. Osborn, Reuben A. Brower, Edwin Morgan, Earl Wasserman, R. J. Kaufmann, Moody E. Prior, Earl W. Miner, Edward N. Hooker, E. M. W. Tillyard, John Hollander,…

Schilling, Bernard N., Ed.

306

Considerations in the transfer of software engineering technology  

Microsoft Academic Search

The development of new and increasingly efficient techniques of software engineering seems to be impressive to everyone except the professional software developers. In a recent summary of a panel discussing software engineering problems to be faced during the 1980's, Wasserman notes: Not surprisingly, the panel concluded that the problems of the '80's look very much like the problems of the

Michael J. Mcgill

1980-01-01

307

Effects of Stimulus Duration and Choice Delay on Visual Categorization in Pigeons  

ERIC Educational Resources Information Center

We [Lazareva, O. F., Freiburger, K. L., & Wasserman, E. A. (2004). "Pigeons concurrently categorize photographs at both basic and superordinate levels." "Psychonomic Bulletin and Review," 11, 1111-1117] previously trained four pigeons to classify color photographs into their basic-level categories (cars, chairs, flowers, or people) or into their…

Lazareva, Olga F.; Wasserman, Edward A.

2009-01-01

308

Photometric Measurements of 343 Ostara and Other Asteroids at Hobbs Observatory  

NASA Astrophysics Data System (ADS)

We observed 343 Ostara on 2008 October 4 and obtained R and V standard magnitudes. The period was found to be significantly greater than the previously reported value of 6.42 hours. Measurements of 2660 Wasserman and (17010) 199 CQ72 made on 2008 March 25 are also reported.

Ford, Lyle; Stecher, George; Lorenzen, Kayla; Cook, Cole

2009-07-01

309

STOCHASTIC A POSTERIORI BLOCKMODELS: CONSTRUCTION AND ASSESShiENT  

Microsoft Academic Search

In 1983, Holland, Laskey, and Leinhardt, using the ideas of Holland and Leinhardt, and Fienberg and Wasserman, introduced the notion of a stochastic blockmodel. The mathematics for stochastic a priori blockmodels, in which exogenous actor attribute data are used to partition actors independently of any statistical analysis of the available relational data, have been refined by several researchers and the

Stanley WASSERMAN; Carolyn ANDERSON

1987-01-01

310

Critical analysis of the “anaerobic threshold” during exercise at constant workloads  

Microsoft Academic Search

Summary  The method described by Wasserman for anaerobic threshold (AT) determination, based on the recording of ventilatory parameters, was supported by the simultaneous appearance of hyperlactacidemia and hyperventilation during a standardized incremental work test. Our study aimed at testing the AT in another profile of exercise, viz., during exercises at constant workloads.A homogenous population of 66 healthy subjects performed on a

A. Scheen; J. Juchmes; A. Cession-Fossion

1981-01-01

311

Research article The application of social network theory to animal behaviour  

Microsoft Academic Search

Social network analysis (SNA) is a mathematical technique for analysing social relationships and the patterns and implications of these relationships (Wasserman S, Faust K (1994) Social Network Analysis: Methods and Applications. Cambridge: Cambridge University Press). It has only recently been discovered by behavioural biologists as a useful tool in the study of animal behaviour (Wey T, Blumstein DT, Shen W

Amelia Coleing

312

Pupil Dilation and Object Permanence in Infants  

ERIC Educational Resources Information Center

|This paper examines the relative merits of looking time and pupil diameter measures in the study of early cognitive abilities of infants. Ten-month-old infants took part in a modified version of the classic drawbridge experiment used to study object permanence (Baillargeon, Spelke, & Wasserman, 1985). The study involved a factorial design where…

Sirois, Sylvain; Jackson, Iain R.

2012-01-01

313

Developing operational algorithms using linear and non-linear squares estimation in Python for the identification of Culex pipiens and Culex restuans in a mosquito abatement district (Cook County, Illinois, USA).  

PubMed

In this research, community level spatial models were developed for determining mosquito abundance and environmental factors that could aid in the risk prediction of West Nile virus (WNv) outbreaks. Adult Culex pipiens and Culex restuan mosquitoes and multiple habitat covariates were collected from nine sites within Cook County, Illinois, USA, to provide spatio-temporal information on the abundance of WNv vectors from 2002 to 2005. Regression analyses of the sampled covariates revealed that the adult Culex population was positively associated with temperature throughout the sampling frame. The model output also indicated that precipitation was negatively associated to mosquito abundance in 2002, 2003 and 2005 (P <0.05), but positively associated in 2004 (P <0.05). A land use land cover classification, based on QuickBird visible and near infra-red data, acquired at 0.61 m resolution, was used to investigate possible associations between geographical features and the abundance of sampled Culex oviposition surveillance sites. A maximum likelihood unsupervised classification in ArcInfo 9.2(R) revealed that the highest overall mosquito abundance was found in sites having a low-to-moderate range of built environment (40%) and high forest composition. A set of propagation equations were then designed to model the calibration uncertainties, which revealed that normalized difference vegetation index (NDVI), and two NDVI variants, were informative markers for the sampled mosquito data. Spatial dependence of the covariates of Cx. restuans and Cx. pipiens oviposition sites were indexed using semivariograms, which suggested that all main effects of the explanatory variables were statistically significant in the model. Additionally, a multispectral classification and digital elevation model-based geographical information system method were able to evaluate stream flow direction and accumulation for identification of terrain covariates associated with the sampled habitat data. These results demonstrate that remotely sensed operational indices can be used to identify parameters associated with field-sampled Cx. pipiens and Cx. restuans aquatic habitats. PMID:19440960

Jacob, Benjamin J; Gu, Weidong; Caamano, Erik X; Novak, Robert J

2009-05-01

314

Developing operational algorithms using linear and non-linear squares estimation in Python® for the identification of Culex pipiens and Culex restuans in a mosquito abatement district (Cook County, Illinois, USA)  

Microsoft Academic Search

In this research, community level spatial models were developed for determining mosquito abundance and envi- ronmental factors that could aid in the risk prediction of West Nile virus (WNv) outbreaks. Adult Culex pipiens and Culex restuan mosquitoes and multiple habitat covariates were collected from nine sites within Cook County, Illinois, USA, to provide spatio-temporal information on the abundance of WNv

Benjamin G. Jacob; Weidong Gu; Erik X. Caamano; Robert J. Novak

315

Factors Mediating Alcohol Craving and Relapse: Stress, Compulsivity, and Genetics  

PubMed Central

This article represents the proceedings of a symposium at the 2004 annual meeting of the International Society for Biomedical Research on Alcoholism in Heidelberg, Germany. The symposium was organized by Zachary A. Rodd and Giancarlo Colombo. The presentations were (1) Pharmacological reversal of cycled withdrawal-sensitized or stress-sensitized withdrawal anxiety and enhanced ethanol drinking, by Darin J. Knapp and George R. Breese, (2) Alcohol craving and relapse in rats genetically selected for high alcohol preference, by Zachary A. Rodd and Richard L. Bell, (3) Exposure to stress increases dopaminergic burst firing in awake rats, by Kristin Anstrom and Donald J. Woodward, (4) Involvement of cannabinoid CB1 and GABAB receptors in the control of relapse-like drinking in alcohol-preferring Sardinian alcohol-preferring rats by Giancarlo Colombo and Salvatore Serra, and (5) Stress-induced ethanol drinking in CB1?/?, POMC, and PENK knockout mice, by Idiko Racz and Andreas Zimmer.

Rodd, Zachary A.; Anstrom, Kristin K; Knapp, Darin J.; Racz, Ildiko; Zimmer, Andreas; Serra, Salvatore; Bell, Richard L.; Woodward, Donald J.; Breese, George R.; Colombo, Giancarlo

2010-01-01

316

Partition Density Functional Theory  

NASA Astrophysics Data System (ADS)

Partition Density Functional Theory (PDFT) is a formally exact method for obtaining molecular properties from self-consistent calculations on isolated fragments [1,2]. For a given choice of fragmentation, PDFT outputs the (in principle exact) molecular energy and density, as well as fragment densities that sum to the correct molecular density. I describe our progress understanding the behavior of the fragment energies as a function of fragment occupations, derivative discontinuities, practical implementation, and applications of PDFT to small molecules. I also discuss implications for ground-state Density Functional Theory, such as the promise of PDFT to circumvent the delocalization error of approximate density functionals. [4pt] [1] M.H. Cohen and A. Wasserman, J. Phys. Chem. A, 111, 2229(2007).[0pt] [2] P. Elliott, K. Burke, M.H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010).

Wasserman, Adam

2012-02-01

317

Summary of “Toward a Global Media Ethics: Theoretical Perspectives”  

Microsoft Academic Search

This is a summary of “Toward a Global Media Ethics: Theoretical Perspectives,” which appeared in Ecquid Novi: African Journalism Studies, 29(2), 2008, 135–172. The article was written by Clifford G. Christians, University of Illinois at Urbana-Champaign; Shakuntala Rao, State University of New York-Plattsburgh; Stephen J. A. Ward, University of Wisconsin-Madison; and Herman Wasserman, University of Sheffield. It was the result

Stephen J. A. Ward

2010-01-01

318

Referral Web: combining social networks and collaborative filtering  

Microsoft Academic Search

This paper appears in the Communications of the ACM,vol. 40 no. 3, March, 1997.Numerous studies have shown that one of the most the most effective channelsfor dissemination of information and expertise within an organization is itsinformal network of collaborators, colleagues, and friends (Granovetter 1973;Kraut 1990; Wasserman and Galaskiewicz 1994). Indeed, the social network1is as least as important as the official

Henry A. Kautz; Bart Selman; Mehul A. Shah

1997-01-01

319

A Hensel lifting to replace factorization in list-decoding of algebraic-geometric and Reed-Solomon codes  

Microsoft Academic Search

This correspondence presents an algorithmic improvement to Sudan's list-decoding algorithm for Reed-Solomon codes and its gener- alization to algebraic-geometric codes from Shokrollahi and Wasserman. Instead of completely factoring the interpolation polynomial over the func- tion field of the curve, we compute sufficiently many coefficients of a Hensel development to reconstruct the functions that correspond to codewords. We prove that these

Daniel Augot; Lancelot Pecquet

2000-01-01

320

Visual Basic VPython Interface: Charged Particle in a Magnetic Field  

Microsoft Academic Search

A simple Visual Basic (VB) to VPython interface is described and illustrated with the example of a charged particle in a magnetic field. This interface allows data to be passed to Python through a text file read by Python. The first component of the interface is a user-friendly data entry screen designed in VB, in which the user can input

Chandra Prayaga

2006-01-01

321

VPython  

NSDL National Science Digital Library

VPython is a 3D programming language developed at Carnegie Mellon University that is useful for presenting visualizations of physical phenomena. VPython is free and open-source. It includes: the Python programming language, an enhanced version of the Idle interactive development environment, and "Visual", a Python module that offers real-time 3D output, and is easily usable by novice programmers.

Scherer, David

2003-10-10

322

Effects of digestive status on the reptilian gut  

Microsoft Academic Search

Reptiles, including the Burmese python, Python molurus bivittatus, that feed at infrequent intervals show a prominent increase in gastrointestinal mass, metabolism and brush border transport rates after feeding. Current knowledge and theories around these phenomena, as well as studies on the innervation of the reptilian gut, are summarised in this review. Little is known about the putative changes in the

Anna Holmberg; Joanna Kaim; Anette Persson; Jörgen Jensen; Tobias Wang; Susanne Holmgren

2002-01-01

323

VPython  

NSDL National Science Digital Library

Python (from www.vpython.org) Python is a powerful object-oriented programming language initiated by Guido van Rossum in 1990. See the essay by van Rossum on "Programming for Everybody," www.python.org/cp4e. It is easy to start writing simple programs in Python, and even using classes and objects involves a relatively gentle learning curve. Python is cross-platform (Windows, Mac, Linux). It is open source (and therefore free) and supported by a sizable developer community. Python is a general-purpose programming language with significant numerical capabilities, though a common use of Python is managing servers, administering systems, etc. See the extensive web site, www.python.org. A good textbook is Learning Python by Mark Lutz and David Ascher, O'Reilly 1999. Realtime 3D Graphics: Visual Python itself does not provide graphics output. The Tk graphics library can be used to create 2D graphics, but it is difficult to use. In the spring of 2000, while a sophomore in computer science at Carnegie Mellon University, David Scherer created a 3D graphics module for Python, called "Visual," that is exceptionally easy to use. A program can create 3D objects (such as spheres, curves, etc.) and position them in 3D space. Visual, running in a separate thread, automatically updates a 3D scene many times per second, to reflect the current positions of the objects. The programmer does not need to deal with display management, but can focus on the computational aspects of the program. The user can navigate in the 3D scene by using the mouse to zoom and rotate while the program is running. Visual supports full vector algebra. Use in Classrooms Students in introductory physics courses have been using VPython to do computer modeling. VPython lets students focus on the physics computations without having to write explicit graphics statements yet obtain 3D visualization. Students can do true vector computations, which improves their understanding of the utility of vectors and vector notation. Platforms Supported The Python language itself is cross-platform. The Visual module, and the Idle integrated development environment, work with Python on Windows and Unix/Linux/MacOSX. Published Articles A journal article about VPython has been published: Scherer, D., Dubois, P., & Sherwood, B. (2000). VPython: 3D Interactive Scientific Graphics for Students, Computing in Science and Engineering, Sept./Oct. 2000, 82-88.

324

Component Technology for Laser Plasma Simulation  

SciTech Connect

This paper will discuss the application of high performance component software technology developed for a complex physics simulation development effort. The primary tool used to build software components is called Babel and is used to create language-independent libraries for high performance computers. Components were constructed from legacy code and wrapped with a thin Python layer to enable run-time scripting. Low-level components in Fortran, C++, and Python were composed directly as Babel components and invoked interactively from a parallel Python script.

Bosl, W J; Smith, S G; Dahlgren, T; Epperley, T; Kohn, S; Kumfert, G

2002-06-17

325

Analysis of thermal expansivity of iron (Fe) metal at ultra high temperature and pressure  

NASA Astrophysics Data System (ADS)

In the present investigation we have explained the thermal and compression properties of HCP iron (Fe) at high pressure with variable temperature (isobars) and at high temperature with variable pressure (isotherm). The usual Tait equation of state is modified by incorporating the effect of thermal pressure. The calculated values of pressure for different isotherms and isochors and thermal expansivity (et al.) as a function of both temperature and pressure have been compared with those values obtained by Isaak et al and Wasserman et al.

Kandpal, Deepika; Gupta, B. R. K.

2007-01-01

326

Phase Field Method: Spinodal Decomposition Computer Laboratory  

NSDL National Science Digital Library

In this lab, spinodal decomposition is numerically implemented in FiPy. A simple example python script (spinodal.py) summarizes the concepts. This lab is intended to complement the "Phase Field Method: An Introduction" lecture

Garcã­a, R. E.

2008-08-25

327

OSP with Jython Web Start application - step-by-step guide  

NSDL National Science Digital Library

A description of how to build Java Web Start applications using the OSP library. Integrates the OpenSourcePhysics .jar library files and the Python classes generated by Jython during compiling time with jythonc.

2008-11-13

328

On Bodily Autonomy  

Microsoft Academic Search

\\u000a There is a scene in Monty Python’s film Life of Brian in which, in the midst of a discussion amongst a group of revolutionaries enjoying the spectacles at the colosseum, a man\\u000a from the Judean Liberation Front expresses a strong desire to have a baby. He is told gently that this is an unrealistic desire,\\u000a but his failure to respond

Catriona Mackenzie

329

Data Reduction Software for the VLT Integral Field Spectrometer SPIFFI  

NASA Astrophysics Data System (ADS)

A data reduction software package is developed to reduce data of the near-IR integral field spectrometer SPIFFI built at MPE. The basic data reduction routines are coded in ANSI C. The high level scripting language Python is used to connect the C-routines allowing fast prototyping. Several Python scripts are written to produce the needed calibration data and to generate the final result, a wavelength calibrated data cube with the instrumental signatures removed.

Schreiber, J.; Thatte, N.; Eisenhauer, F.; Tecza, M.; Abuter, R.; Horrobin, M.

2004-07-01

330

Managing large SNP datasets with SNPpy.  

PubMed

Using relational databases to manage SNP datasets is a very useful technique that has significant advantages over alternative methods, including the ability to leverage the power of relational databases to perform data validation, and the use of the powerful SQL query language to export data. SNPpy is a Python program which uses the PostgreSQL database and the SQLAlchemy Python library to automate SNP data management. This chapter shows how to use SNPpy to store and manage large datasets. PMID:23756888

Mitha, Faheem

2013-01-01

331

Euthanasia attitude; A comparison of two scales  

PubMed Central

The main purposes of the present study were to see how the term “euthanasia” influences people’s support for or opposition to euthanasia; and to see how euthanasia attitude relates to religious orientation and personality factors. In this study two different euthanasia attitude scales were compared. 197 students were selected to fill out either the Euthanasia Attitude Scale (EAS) or Wasserman’s Attitude Towards Euthanasia scale (ATE scale). The former scale includes the term “euthanasia”, the latter does not. All participants filled out 50 items of International Personality Item Pool, 16 items of the the HEXACO openness, and 14 items of Religious Orientation Scale-Revised. Results indicated that even though the two groups were not different in terms of gender, age, education, religiosity and personality, mean score on the ATE scale was significantly higher than that of the EAS. Euthanasia attitude was negatively correlated with religiosity and conscientiousness and it was positively correlated with psychoticism and openness. It can be concluded that analyzing the attitude towards euthanasia with the use of EAS rather than the ATE scale results in lower levels of opposition against euthanasia. This study raises the question of whether euthanasia attitude scales should contain definitions and concepts of euthanasia or they should describe cases of it.

Aghababaei, Naser; Farahani, Hojjatollah; Hatami, Javad

2011-01-01

332

Humans deploy diverse strategies in learning same-different discrimination tasks.  

PubMed

Prior research suggests that variability discrimination is basic to same-different conceptualization (Young and Wasserman, 2001). In that research, people were trained with 16-item arrays; this training might have encouraged people to use perceptual variability to solve the task. Here, two groups of participants were trained with either 2- or 16-item Same and Different arrays (Groups 2 and 16, respectively). Participants had to learn which of two arbitrary responses was correct for the arrays without being told about the "sameness" or "differentness" of the stimuli. Surprisingly, 52% of participants in Group 2 did not learn the discrimination compared to only 21% of participants in Group 16; also, learners in Group 16 reached higher accuracy levels sooner and their choice responding was faster than learners in Group 2. A large disparity in the variability (measured by entropy) between the Same and Different arrays evidently helped participants to learn the same-different task. As well, in Group 16, we found the same two patterns of performance-Categorical and Continuous-as in prior research (Castro et al., 2006; Young and Wasserman, 2001). In Group 2, we again found the Categorical cluster, but we lost the genuine Continuous cluster and we observed a novel strategy: some participants developed a highly inclusive notion of "sameness" that applied to any array containing at least two identical icons. These findings indicate that individuals may deploy a multiplicity of possible strategies when learning a seemingly simple same-different discrimination. PMID:23073499

Castro, Leyre; Wasserman, Edward A

2012-10-13

333

Decreased aerobic capacity 4 years after aortic valve replacement in male patients operated upon for chronic aortic regurgitation  

PubMed Central

Exercise testing is underutilized in patients with valve disease. We have previously found a low physical work capacity in patients with aortic regurgitation 6 months after aortic valve replacement (AVR). The aim of this study was to evaluate aerobic capacity in patients 4 years after AVR, to study how their peak oxygen uptake (peakVO2) had changed postoperatively over a longer period of time. Twenty-one patients (all men, 52 ± 13 years) who had previously undergone cardiopulmonary exercise testing (CPET) pre- and 6 months postoperatively underwent maximal exercise testing 49 ± 15 months postoperatively using an electrically braked bicycle ergometer. Breathing gases were analysed and the patients' physical fitness levels categorized according to Åstrand's and Wasserman's classifications. Mean peakVO2 was 22·8 ± 5·1 ml × kg?1 × min?1 at the 49-month follow-up, which was lower than at the 6-month follow-up (25·6 ± 5·8 ml × kg?1 × min?1, P = 0·001). All but one patient presented with a physical fitness level below average using Åstrand's classification, while 13 patients had a low physical capacity according to Wasserman's classification. A significant decrease in peakVO2 was observed from six to 49 months postoperatively, and the decrease was larger than expected from the increased age of the patients. CPET could be helpful in timing aortic valve surgery and for the evaluation of need of physical activity as part of a rehabilitation programme.

Hedman, Kristofer; Tamas, Eva; Nylander, Eva

2012-01-01

334

The morphology, crystallography, and chemistry of phases in as-cast nickel-aluminum bronze  

NASA Astrophysics Data System (ADS)

The morphology, crystallography, and composition of the phases present in as-cast nickel-aluminum bronze of nominal composition copper-10 wt pct aluminum-5 wt pct nickel-5 wt pct iron have been investigated using optical, electron optical, and microprobe analysis techniques. The as-cast microstructure consists of copper-rich ?, martensitic ?, and ?-phases based on Fe3Al and NiAl. The ?z precipitates have a dendritic morphology and are cored; the composition ranges from iron-rich solid solution to Fe3Al. The ?II and ?iv precipitates have, respectively, a dendritic and an equiaxed/dendritic morphology, and are based on Fe3Al, while ?III is a eutectoidal decomposition product of lamellar or globular morphology based on NiAl. The ?I, ?II, and ?III precipitates have the Kurdjumov-Sachs orientation relationship with ? matrix. Small ?IV precipitates exhibit the Nishiyama-Wasserman orientation relationship with the ? matrix, while large ?iv precipitates have an orientation relationship which lies between Kurdjumov-Sachs and Nishiyama-Wasserman.

Hasan, F.; Jahanafrooz, A.; Lorimer, G. W.; Ridley, N.

1982-08-01

335

PyNEST: A Convenient Interface to the NEST Simulator  

PubMed Central

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.

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

2008-01-01

336

The PCMDI Climate Data Analysis Tool (CDAT) - an open system approach to model diagnosis infrastructure  

NASA Astrophysics Data System (ADS)

The Climate Data Analysis Tool (CDAT) is software infrastructure that uses the object-oriented python scripting language to link separate software subsystems and thus form an integrated environment for solving model diagnosis problems. The power of the system comes from python and the software subsystems. Python provides a general purpose and full-featured scripting language with a variety of user interfaces including command line interaction, stand-alone scripts (applications) and GUIs. The CDAT subsystems, implemented as python modules, provide access and management of gridded data; large-array numerical operations; and visualization. We characterize CDAT as "open system" because the software subsystems are independent and the object-oriented nature of python allows CDAT to be "delay bound" or that the actual tool is built at run time, i.e., is not fixed. Thus, CDAT is easily extended and represents a different approach to the technical problem of model diagnosis. In this paper, we compare and contrast the CDAT approach with more traditional tools built from system-level software (e.g., C and X windows), such as GrADS and ferret, and show how CDAT complements and offers an alternative interface to data accessible by these popular tools.

Fiorino, M.

2001-05-01

337

A multilingual programming model for coupled systems.  

SciTech Connect

Multiphysics and multiscale simulation systems share a common software requirement-infrastructure to implement data exchanges between their constituent parts-often called the coupling problem. On distributed-memory parallel platforms, the coupling problem is complicated by the need to describe, transfer, and transform distributed data, known as the parallel coupling problem. Parallel coupling is emerging as a new grand challenge in computational science as scientists attempt to build multiscale and multiphysics systems on parallel platforms. An additional coupling problem in these systems is language interoperability between their constituent codes. We have created a multilingual parallel coupling programming model based on a successful open-source parallel coupling library, the Model Coupling Toolkit (MCT). This programming model's capabilities reach beyond MCT's native Fortran implementation to include bindings for the C++ and Python programming languages. We describe the method used to generate the interlanguage bindings. This approach enables an object-based programming model for implementing parallel couplings in non-Fortran coupled systems and in systems with language heterogeneity. We describe the C++ and Python versions of the MCT programming model and provide short examples. We report preliminary performance results for the MCT interpolation benchmark. We describe a major Python application that uses the MCT Python bindings, a Python implementation of the control and coupling infrastructure for the community climate system model. We conclude with a discussion of the significance of this work to productivity computing in multidisciplinary computational science.

Ong, E. T.; Larson, J. W.; Norris, B.; Tobis, M.; Steder, M.; Jacob, R. L.; Mathematics and Computer Science; Univ. of Wisconsin; Univ. of Chicago; The Australian National Univ.

2008-01-01

338

First reports of ectoparasites collected from wild-caught exotic reptiles in Florida.  

PubMed

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. PMID:21337954

Corn, Joseph L; Mertins, James W; Hanson, Britta; Snow, Skip

2011-01-01

339

Hunter-gatherers and other primates as prey, predators, and competitors of snakes.  

PubMed

Relationships between primates and snakes are of widespread interest from anthropological, psychological, and evolutionary perspectives, but surprisingly, little is known about the dangers that serpents have posed to people with prehistoric lifestyles and nonhuman primates. Here, we report ethnographic observations of 120 Philippine Agta Negritos when they were still preliterate hunter-gatherers, among whom 26% of adult males had survived predation attempts by reticulated pythons. Six fatal attacks occurred between 1934 and 1973. Agta ate pythons as well as deer, wild pigs, and monkeys, which are also eaten by pythons, and therefore, the two species were reciprocally prey, predators, and potential competitors. Natural history data document snake predation on tree shrews and 26 species of nonhuman primates as well as many species of primates approaching, mobbing, killing, and sometimes eating snakes. These findings, interpreted within the context of snake and primate phylogenies, corroborate the hypothesis that complex ecological interactions have long characterized our shared evolutionary history. PMID:22160702

Headland, Thomas N; Greene, Harry W

2011-12-12

340

Bayesian Methods in Sherpa  

NASA Astrophysics Data System (ADS)

Bayesian Framework for modeling the high energy astrophysics data has been implemented in Sherpa, a modeling and fitting application in CIAO. Sherpa is written in Python and the latest version can be installed and used with Python 2.7. We describe the concept of models with priors, the MCMC options for exploring the posterior probability distributions, and available algorithms for hypothesis testing and model selection. The methods correctly account for the Poisson nature of high energy astrophysics data from space-based X-ray and gamma-ray missions such as Chandra or Fermi. In most situations the modeling has to account for instrumental effects characterized by a probability of detecting photons of a given energy at a particular detector channel, or a particular location on the detector. We provide variety of examples based on the high energy data with ready to use recipes. Some future directions and potential linking with other Python packages will also be presented.

Siemiginowska, Aneta; Aldcroft, T. L.; Kashyap, V.; Chandra X-ray Center CIAO Team

2013-04-01

341

VOLTTRON: An Agent Execution Platform for the Electric Power System  

SciTech Connect

Volttron is an agent execution platform that is engineered for use in the electric power system. Volttron provides resource guarantees for agents and the platform including memory and processor utilization; authentication and authorization services; directory services for agent and resource location; and agent mobility. Unlike most other agent platforms, Volttron does not depend on a single agent authoring language. Instead, we chose to design and implement Volttron as a platform service and framework that is decoupled from the agent execution environment. A prototype implementation of Volttron has been written in Python (using Python v2.7.2) and we have executed agents written in Python and Java and as shell scripts. The intended use of Volttron is in the power distribution system for managing distributed generation, demand-response, and plug-in electric vehicles.

Akyol, Bora A.; Haack, Jereme N.; Ciraci, Selim; Carpenter, Brandon J.; Vlachopoulou, Maria; Tews, Cody W.

2012-06-05

342

Introducing the Ginga FITS Viewer and Toolkit  

NASA Astrophysics Data System (ADS)

We introduce Ginga, a new open-source FITS viewer and toolkit based on Python astronomical packages such as pyfits, numpy, scipy, matplotlib, and pywcs. For developers, we present a set of Python classes for viewing FITS files under the modern Gtk and Qt widget sets and a more full-featured viewer that has a plugin architecture. We further describe how plugins can be written to extend the viewer with many different capabilities. The software may be of interest to software developers who are looking for a solution for integrating FITS visualization into their Python programs and end users interested in a new and different FITS viewer that is not based on Tcl/Tk widget technology. The software has been released under a BSD license.

Jeschke, E.; Inagaki, T.; Kackley, R.

2013-10-01

343

Jane Austen and Addison's disease: an unconvincing diagnosis.  

PubMed

Jane Austen's letters describe a two-year deterioration into bed-ridden exhaustion, with unusual colouring, bilious attacks and rheumatic pains. In 1964, Zachary Cope postulated tubercular Addison's to explain her symptoms and her relatively pain-free illness. Literary scholars later countered this posthumous diagnosis on grounds that are not well substantiated, while medical authors supported his conclusion. Important symptoms reported by contemporary Addison's patients-mental confusion, generalised pain and suffering, weight loss and anorexia-are absent from Jane Austen's letters. Thus, by listening to the patient's perspective, we can conclude it is unlikely that Addison's disease caused Jane Austen's demise. Disseminated bovine tuberculosis would offer a coherent explanation for her symptoms, so that Cope's original suggestion of infective tuberculosis as the cause of her illness may have been correct. PMID:23674705

White, K G

2009-12-01

344

The CARMA Data Reduction Pipeline  

NASA Astrophysics Data System (ADS)

The Combined Array for Millimeter-wave Astronomy (CARMA) data reduction pipeline (CADRE) has been developed to give investigators a first look at a fully reduced set of their data. It runs automatically on all data produced by the telescope as they arrive in the data archive. CADRE is written in Python and uses Python wrappers for MIRIAD subroutines for direct access to the data. It applies passband, gain and flux calibration to the data sets and produces a set of continuum and spectral line maps in both MIRIAD and FITS format. CADRE has been in production for a year and this poster will discuss the current capabilities and planned improvements.

Friedel, D. N.

2013-10-01

345

CADRE: CArma Data REduction pipeline  

NASA Astrophysics Data System (ADS)

CADRE, the Combined Array for Millimeter-wave Astronomy (CARMA) data reduction pipeline, gives investigators a first look at a fully reduced set of their data. It runs automatically on all data produced by the telescope as they arrive in the data archive. The pipeline is written in python and uses python wrappers for MIRIAD subroutines for direct access to the data. It applies passband, gain and flux calibration to the data sets and produces a set of continuum and spectral line maps in both MIRIAD and FITS format.

Friedel, Douglas

2013-03-01

346

CosmoHammer: Cosmological parameter estimation with the MCMC Hammer  

NASA Astrophysics Data System (ADS)

CosmoHammer is a Python framework for the estimation of cosmological parameters. The software embeds the Python package emcee by Foreman-Mackey et al. (2012) and gives the user the possibility to plug in modules for the computation of any desired likelihood. The major goal of the software is to reduce the complexity when one wants to extend or replace the existing computation by modules which fit the user's needs as well as to provide the possibility to easily use large scale computing environments. CosmoHammer can efficiently distribute the MCMC sampling over thousands of cores on modern cloud computing infrastructure.

Akeret, Joël; Seehars, Sebastian; Amara, Adam; Refregier, Alexandre; Csillaghy, André

2013-03-01

347

CASA: Common Astronomy Software Applications  

NASA Astrophysics Data System (ADS)

CASA, the Common Astronomy Software Applications package, is being developed with the primary goal of supporting the data post-processing needs of the next generation of radio astronomical telescopes such as ALMA and EVLA. The package can process both interferometric and single dish data. The CASA infrastructure consists of a set of C++ tools bundled together under an iPython interface as a set of data reduction tasks. This structure provides flexibility to process the data via task interface or as a python script. In addition to the data reduction tasks, many post-processing tools are available for even more flexibility and special purpose reduction needs.

International Consortium Of Scientists

2011-07-01

348

Final Report for "User Friendly Steering and Diagnostics for Modleing Heavy Ion Fusion Accelerators"  

SciTech Connect

The goal accomplished in thisproject was to improve the Synergia code by improving the integration of the Impact space charge algorithms into Synergia and improving the graphical user interface for analyzing results. We accomplished five tasks along these lines: (i) a refactoring of the Impact space charge algorithm to make it more accessible by other codes, (ii) development of the Forthon interface between Impact and Python, (iii) implementation of a Python-MPI interface to allow parallel space charge calculation, (iv) a new user-friendly interface for analyzing Synergia results, and (v) a toolkit for doing parallel analysis of Synergia results.

Peter Stoltz, Douglas R Dechow, Scott Kruger, Brian Granger

2007-10-15

349

EZ: A Tool For Automatic Redshift Measurement  

NASA Astrophysics Data System (ADS)

EZ (Easy-Z) estimates redshifts for extragalactic objects. It compares the observed spectrum with a set of (user given) spectral templates to find out the best value for the redshift. To accomplish this task, it uses a highly configurable set of algorithms. EZ is easily extendible with new algorithms. It is implemented as a set of C programs and a number of python classes. It can be used as a standalone program, or the python classes can be directly imported by other applications.

Fumana, Marco; Garilli, Bianca

2012-10-01

350

A transmission electron microscopic study of the Bethany iron meteorite  

NASA Astrophysics Data System (ADS)

The Bethany iron meteorite, which is a part of the Gibeon shower, is a fine octahedrite with zoned plessite fields of various sizes. The optically irresolvable microstructural details inside the plessitic fields have been studied by transmission electron microscopy, and the crystallographic relationships between the primary kamacite (alpha) and the parent taenite (gamma), and between the alpha and gamma particles in the coarse plessite, have been examined using electron diffraction. In the case of primary kamacite, the orientation-relationship with gamma was close to the Nishiyama-Wasserman relationship, whereas, for the plessitic alpha, the orientation-relationship with gamma was close to Kurdjumov-Sachs. It was also found that the (111)-gamma and (110)-alpha planes were not strictly parallel. Additionally, measurements of the composition profile through the zoned plessite have been made using STEM microanalysis technique, and related to microstructure.

Hasan, F.; Axon, H. J.

1985-02-01

351

Aedeagal divergence in sympatric populations of two sibling species of cactophilic Drosophila (Diptera: Drosophilidae): evidence of character displacement?  

PubMed

Aedeagal morphology of two sibling cactophilic species, Drosophila buzzatii Patterson & Wheeler and Drosophila koepferae Fontdevila & Wasserman, was analyzed in nine allopatric and three sympatric locations throughout South America. Morphological differences were detected for both aedeagus size and shape between sympatric and allopatric populations of D. buzzatii, despite the significant variability within both groups. Populations of D. buzzatii sympatric with D. koepferae displayed smaller aedeagus than the allopatric ones as well as more differentiated aedeagus shape. The shape differences were non-allometric and mainly consisted in a change of curvature of the dorsal margin of the aedeagus being more pronounced in males from populations sympatric with D. koepferae. It is concluded that aedeagal morphology presented some degree of character displacement in both size and shape in populations of D. buzzatii in sympatry with D. koepferae. These results might suggest the existence of mechanisms of interspecific recognition and hybridization prevention between these species that include the morphology of the male genitalia. PMID:23950045

Soto, I M

2012-05-04

352

Quantum oscillations in non-Fermi-liquid metals  

NASA Astrophysics Data System (ADS)

The temperature dependence of de Haas van Alphen (dHvA) and other quantum oscillations is governed in a Fermi liquid by the Lifshitz-Kosevich (LK) equationootnotetextsee e.g. D. Shoenberg, Magnetic Oscillations in Metals, CUP 1984. Several authors ootnotetexte.g. A. Wasserman and M. Springford, Adv. Phys.45 (1996) 471, and references therein. have extended the LK theory to non-Fermi-liquid metals, but these treatments tend to be very technical. We will give a simple interpretation of the non-Fermi-liquid effects that arise in these theories, and will briefly discuss the possible observation of non-Fermi-liquid temperature dependence in dHvA oscillations in CeCoIn5.

Julian, Stephen; Flouquet, Jacques

2005-03-01

353

IASP task force on euthanasia and assisted suicide.  

PubMed

The first meeting of the IASP Task Force on Euthanasia and Assisted Suicide took place in Venice on June 7, 1995. Several interested observers were present. It was decided that at the public IASP meeting the following day each speaker should address, briefly, the current legal situation and the pressure for change, as well as give a personal statement. David Clark spoke for North America, Bob Goldney for Australia, Michael Kelleher for Britain and Ireland, Jerzy Wasserman for Scandinavia, and Hans Wedler for the German-speaking world. Their views are published in this article. Ad Kerkhof requested that the Dutch television film "Death on Request" be discussed. The committee was of the opinion that clear definitions were essential. In their view, these should take into account the differences between active and passive euthanasia, as well as between professionally assisted and lay-assisted suicide. PMID:8720516

Kelleher, M; Clark, D; Goldney, B; Kerkhof, A; Wasserman, J; Wedler, H

1995-01-01

354

Retelling Arthurian Legend for an Ironic Age  

ERIC Educational Resources Information Center

|The author of this article, who writes a series of Arthurian books, states that Arthurian retellings for children often fall into one of two extreme categories: (1) they are prim, romantic, reverential tales with soft-focus illustrations and soft-headed heroes; or (2) they are overt spoofs of the literature, a la Mark Twain and Monty Python. He…

Morris, Gerald

2005-01-01

355

2010 ESRI Education User Conference Proceedings  

NSDL National Science Digital Library

This webpage presents the proceedings from ESRI's 2010 education conference. Documents cover using ArcGIS, ArcMap, teaching with Web GIS, using Python in ArcGIS and more. The documents are available to download in zip and pdf file formats.

2012-10-16

356

Frameworks for Geoscience Data Analysis and Visualization  

NASA Astrophysics Data System (ADS)

We present a suite of tools developed at NCAR for analyzing and visualizing geoscientific data. NCL, a self- contained scripting language, provides robust file input and output for a number of commonly used scientific formats, including NetCDF, HDF, and GRIB, and most recently GRIB 2. It provides hundreds of analysis functions and has easily accessed 2D visualization capabilities that many consider to be world class. Its diverse and rapidly growing user base is spread among more than 70 countries around the world. Recently, in order to reach a wider scientific community, we have developed new Python interfaces to NCL's capabilities. PyNGL and PyNIO are Python modules that provide access to essentially the same visualization and data I/O functionality as NCL. The programming style is remarkably similar, allowing users to easily move between the NCL and Python languages. The online documentation has step-by-step tutorials for getting up to speed with PyNGL and PyNIO. There are also hundreds of examples showing how to ingest, analyze and visualize many varieties of data. This year we are releasing the complete suite of tools as OSI-compliant open source. The tools are under continuous development with active community input. Our current projects are porting the analysis functions to the Python environment and adding support for the NetCDF 4 and HDF 5 file formats.

Brown, D. I.; Haley, M.; Clare, F.; Grubin, R.; Shea, D.

2007-05-01

357

Design of a Modular and Low-Latency Virtual-Environment Platform for Applications in Motor Adaptation Research, Neurological Disorders, and Neurorehabilitation  

Microsoft Academic Search

We have developed a modular virtual environment platform for movement research and rehabilitation. The system uses several networked computers running Linux to share computation. An electromagnetic tracker is the primary position tracker and both a head-mounted display and stereo goggles are used for visual display. System software is written in a combination of C++, JAVA, and Python and makes considerable

Daniel J. Myall; Michael R. MacAskill; Paul R. Davidson; Tim J. Anderson; Richard D. Jones

2008-01-01

358

The international trade in reptiles (Reptilia)—The cause of the transfer of exotic ticks (Acari: Ixodida) to Poland  

Microsoft Academic Search

The problem of the unnatural transfer of exotic ticks (Acari: Ixodida) on reptiles (Reptilia) imported to Poland is presented. In the period from 2003 to 2007, 382 specimens of reptiles belonging to the following genera were investigated: Testudo, Iguana, Varanus, Gongylophis, Python, Spalerosophis, Psammophis. The reptiles most infested with ticks are imported to Poland from Ghana in Africa, and are

Magdalena Nowak

2010-01-01

359

Sydewynder: rapid prototyping for mobile mixed-reality games  

Microsoft Academic Search

Sydewynder is an open-source SMS receiver and sender application written in Python for the Nokia S60 phones. It can automate the responses of messages and can be used as a mobile application server in areas where setting up a traditional server may be difficult or illegal. It also is very useful for prototyping mobile applications, such as games, without the

Michael J. Edwards; Joana Kelly; Michael Thibodeau

2008-01-01

360

A Mutation in the Mitochondrial Fission Gene Dnm1l Leads to Cardiomyopathy  

PubMed Central

Mutations in a number of genes have been linked to inherited dilated cardiomyopathy (DCM). However, such mutations account for only a small proportion of the clinical cases emphasising the need for alternative discovery approaches to uncovering novel pathogenic mutations in hitherto unidentified pathways. Accordingly, as part of a large-scale N-ethyl-N-nitrosourea mutagenesis screen, we identified a mouse mutant, Python, which develops DCM. We demonstrate that the Python phenotype is attributable to a dominant fully penetrant mutation in the dynamin-1-like (Dnm1l) gene, which has been shown to be critical for mitochondrial fission. The C452F mutation is in a highly conserved region of the M domain of Dnm1l that alters protein interactions in a yeast two-hybrid system, suggesting that the mutation might alter intramolecular interactions within the Dnm1l monomer. Heterozygous Python fibroblasts exhibit abnormal mitochondria and peroxisomes. Homozygosity for the mutation results in the death of embryos midway though gestation. Heterozygous Python hearts show reduced levels of mitochondria enzyme complexes and suffer from cardiac ATP depletion. The resulting energy deficiency may contribute to cardiomyopathy. This is the first demonstration that a defect in a gene involved in mitochondrial remodelling can result in cardiomyopathy, showing that the function of this gene is needed for the maintenance of normal cellular function in a relatively tissue-specific manner. This disease model attests to the importance of mitochondrial remodelling in the heart; similar defects might underlie human heart muscle disease.

Ashrafian, Houman; Docherty, Louise; Leo, Vincenzo; Towlson, Christopher; Neilan, Monica; Steeples, Violetta; Lygate, Craig A.; Hough, Tertius; Townsend, Stuart; Williams, Debbie; Wells, Sara; Norris, Dominic; Glyn-Jones, Sarah; Land, John; Barbaric, Ivana; Lalanne, Zuzanne; Denny, Paul; Szumska, Dorota; Bhattacharya, Shoumo; Griffin, Julian L.; Hargreaves, Iain; Fernandez-Fuentes, Narcis; Cheeseman, Michael; Watkins, Hugh; Dear, T. Neil

2010-01-01

361

Verification Technologies, third quarter 1992.  

National Technical Information Service (NTIS)

Tag and seal development has targeted primarily the on-site inspections of arms-control treaty-limited items. This issue provides a summary of overall projects and results. The following are covered: reflective particle tags, python seal, Star fiber-optic...

C. Talaber G. Staehle S. Stull

1992-01-01

362

EJS Programming by Example  

NSDL National Science Digital Library

Chapter 2 of Open Source tools for Computational Physics: An introduction to EJS and Python. After brief instructions on setting up EJS, this chapter demonstrates how to do basic computer programming using EJS. All of the most basic, fundamental aspects of programming are covered: variables, mathematical operations, loops, if-statements, using and creating methods (a.k.a., subroutines), etc.

Engelhardt, Larry

2011-11-25

363

What about a Simple Language? Analyzing the Difficulties in Learning to Program  

ERIC Educational Resources Information Center

In this paper, we present the results from a two-part study. We analyze 60 programs written by novice programmers aged 16-19 after their first programming course, in either Java or Python. The aim is to find difficulties independent of the language used, and such originating from the language. Second, we analyze the transition from a "simple"…

Mannila, Linda; Peltomaki, Mia; Salakoski, Tapio

2006-01-01

364

Verification and Validation using DAKOTA via the DakTools scripts  

SciTech Connect

Several of the intermediate capabilities which are being developed by the AX V&V program may be helpful in other ways. This paper describes a new PYTHON interface to one such tool, DAKOTA (a parallel optimizing controller from Sandia National Laboratory) and the subsequent simpler set of operations required to run and analyze sets of calculations using any LCC computational platform.

Brandon, S; Tipton, P

2004-12-10

365

Nobody expects the Spanish Inquistion  

NSDL National Science Digital Library

Is any one really ready for the Spanish Inquisition? Assign studnets to participate in reading the play, The Spanish Inquisition by Monty Python. While readiang the play, display the following pictures at appropiate times. Nobody expects the Spanish Inquistion Confess!!! Get the Cushions!!!! Get the comfy Chair! Now you'll confess! Confess women, CONFESS!!! Nobody expects the Spanish Inquisition!!! ...

Hirschi, Mrs.

2005-04-08

366

Alice: a rapid prototyping system for building virtual environments  

Microsoft Academic Search

Alice is a rapid prototyping system used to create three dimensional graphics simulations like those seen in virtual reality applications. Alice uses an interpreted language called Python to implement the semantics of user actions. This interactive development environment allows users to explore many more design options than is possible in a compiled language environment. The current state of 3D user

Matthew Conway; Randy Pausch; Rich Gossweiler; Tommy Burnette

1994-01-01

367

ACORNS-ADI: Algorithms for Calibration, Optimized Registration and Nulling the Star in Angular Differential Imaging  

NASA Astrophysics Data System (ADS)

ACORNS-ADI, written in python, is a parallelized software package which reduces high-contrast imaging data. Originally written for imaging data from Subaru/HiCIAO, it requires minimal modification to reduce data from other instruments. It is efficient, open-source, and includes several optional features which may improve performance.

Brandt, Tim

2013-03-01

368

Galactus: Modeling and fitting of galaxies from neutral hydrogen (HI) cubes  

NASA Astrophysics Data System (ADS)

Galactus, written in python, is an astronomical software tool for the modeling and fitting of galaxies from neutral hydrogen (HI) cubes. Galactus uses a uniform medium to generate a cube. Galactus can perform the full-radiative transfer for the HI, so can model self-absorption in the galaxy.

Peters, S. P. C.

2013-03-01

369

Retelling Arthurian Legend for an Ironic Age  

ERIC Educational Resources Information Center

The author of this article, who writes a series of Arthurian books, states that Arthurian retellings for children often fall into one of two extreme categories: (1) they are prim, romantic, reverential tales with soft-focus illustrations and soft-headed heroes; or (2) they are overt spoofs of the literature, a la Mark Twain and Monty Python. He…

Morris, Gerald

2005-01-01

370

Improving the Extension Facilities in C+  

SciTech Connect

CXX is a facility for extending Python using C++. Recently, the authors have substantially revised and improved the way in which you create extension objects and extension modules in C++. The method is now much more natural and has much less overhead, both in the code generated and in the effort needed to create the objects and extensions.

Dubois, P F; Scott, B A

1999-09-24

371

XAssist: A System for the Automation of X-ray Astrophysics Analysis  

Microsoft Academic Search

XAssist is a NASA AISR-funded project for the automation of X-ray astrophysics. It is capable of data reprocessing, source detection, and preliminary spatial, temporal and spectral analysis for each source with sufficient counts. The bulk of the system is written in Python, which in turn drives underlying software (CIAO for Chandra data, etc.). Future work will include a GUI (mainly

A. Ptak

2004-01-01

372

Enhancing student interest by extending graphics applications (abstract only)  

Microsoft Academic Search

Computer science teachers strive for new examples and problems to interest millenials. The Media Computation approach has proven successful in attracting students in contexts from community colleges to R1 universities - students are clearly excited by writing programs that make images. In this workshop, we show how to go a step further and have write scripts and plug-ins in Python

Samuel A. Rebelsky

2012-01-01

373

LOCALIZA: una herramienta SIG para resolver problemas de localización óptima  

Microsoft Academic Search

LOCALIZA software is a tool that increases GIS applications possibilities to analyze and solve optimal facility location problems. This system, that it is being migrated from Delphi to Python, allows to evaluate how existing facility supply covers the demand. On the other hand, it includes the resolution of an elevated number of classic location-allocation models and, in some cases, includes

J. Bosque Sendra; F. Palm; M. Gómez

374

Practical Application of the Computational Science Environment (CSE).  

National Technical Information Service (NTIS)

The Computational Science Environment (CSE) is a collection of open source software tools and utilities that encompass a large number of state-of- the-art application program interfaces (APIs) (i.e., Qt, Python, and SciPy). The CSE software development sy...

C. Spear E. Mark J. Martin J. Vines K. Kirk

2011-01-01

375

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta  

PubMed Central

Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. Availability: PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site. Contact: pyrosetta@graylab.jhu.edu

Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

2010-01-01

376

Dynamically Typed Languages  

Microsoft Academic Search

Dynamically typed languages such as Python and Ruby have experienced a rapid grown in popularity in recent times. However, there is much confusion as to what makes these languages interesting relative to statically typed languages, and little knowledge of their rich history. In this chapter I explore the general topic of dynamically typed languages, how they differ from statically typed

Laurence Tratt

2009-01-01

377

Parametric geometry representation to support aircraft design  

Microsoft Academic Search

Knowledge Based Engineering (KBE) plays an important role in automation and optimization of the aircraft design process. But the lack of real KBE tools limits the promise of Knowledge Based Engineering. To address this deficiency, we propose using the Python programming language to develop viable KBE application tools for aircraft design. Selecting geometric parameterization algorithms is fundamental to automation and

Marcos Elgueta Soulat

2012-01-01

378

An Empirical Comparison of Seven Programming Languages  

Microsoft Academic Search

Often heated, debates regarding different programming languages' effectiveness remain inconclusive because of scarce data and a lack of direct comparisons. The author addresses that challenge, comparatively analyzing 80 implementations of the phone-code program in seven different languages (C, C++, Java, Perl, Python, Rexx and Tcl). Further, for each language, the author analyzes several separate implementations by different programmers. The comparison

Lutz Prechelt

2000-01-01

379

Work in progress - the synergistic integration of an entering students program with an engaging introductory course in programming  

Microsoft Academic Search

We report on the synergistic integration of a required entering students' program with an introductory course in programming. The course is evenly divided among Python-based algorithmic-centric media programming modules and content specified for ESP students at the University of Texas at El Paso (UTEP). UTEP is an urban university serving a largely Hispanic student population principally drawn from the sister

Eric Freudenthal; Mary K. Roy; Ann Gates

2009-01-01

380

Using AI for Olympic Equestrian Event Preparation  

Microsoft Academic Search

This paper describes our experience in using modern Web 2.0 architecture, lightweight Python frameworks, and rapid prototyping to create an AI rostering and workforce management system to help prepare for the 2008 Beijing Olympic Equestrian Events, which will be held in Hong Kong. As part of the 2008 Olympics preparation, a scaled down \\

Andy Hon Wai Chun

2008-01-01

381

The design and implementation of the Redland RDF application framework  

Microsoft Academic Search

Resource description framework (RDF) is a general description technology that can be applied to many application domains. Redland is a flexible and efficient RDF system that complements this power and provides high-level interfaces allowing instances of the model to be stored, queried and manipulated in C, Perl, Python, Tcl, Java and other languages. It is implemented using an object-based API,

David Beckett

2002-01-01

382

Developmental basis of limblessness and axial patterning in snakes  

Microsoft Academic Search

The evolution of snakes involved major changes in vertebrate body plan organization, but the developmental basis of those changes is unknown. The python axial skeleton consists of hundreds of similar vertebrae, forelimbs are absent and hindlimbs are severely reduced. Combined limb loss and trunk elongation is found in many vertebrate taxa, suggesting that these changes may be linked by a

Martin J.. Cohn; Cheryll Tickle

1999-01-01

383

Endoscopic examination of snakes by access through an air sac.  

PubMed

Sixteen boa constrictors (Boa constrictor), three royal pythons (Python regius) and 15 Burmese pythons (Python molurus bivittatus) were examined endoscopically by access through the air sac. The snakes were immobilised in a ventral position using a half-open anaesthetic system with assisted ventilation and a mixture of isoflurane and oxygen. The rigid endoscope was introduced percutaneously and the internal structure of the lungs and the air sac, and the shape, size and external surface of the liver were visible in the cranial direction. In the smaller snakes the bifurcation and caudal part of the trachea could be viewed, provided the endoscope was positioned in a retrograde orientation. The caudal orientation of the endoscope made it possible to view the gall bladder and the size, shape and surface of the spleen. In some cases, the pancreas and the surface of the stomach and colon could be monitored. Endoscopy through the air sac also made it possible to check the major veins in the coelom. The snakes were monitored for at least 30 days after the intervention and no changes in their respiratory function or general health were observed. PMID:16565339

Jekl, V; Knotek, Z

2006-03-25

384

Cooking and grinding reduces the cost of meat digestion.  

PubMed

The cooking of food is hypothesized to have played a major role in human evolution partly by providing an increase in net energy gain. For meat, cooking compromises the structural integrity of the tissue by gelatinizing the collagen. Hence, cooked meat should take less effort to digest compared to raw meat. Likewise, less energy would be expended digesting ground meat compared to intact meat. We tested these hypotheses by assessing how the cooking and/or grinding of meat influences the energy expended on its digestion, absorption, and assimilation (i.e., specific dynamic action, SDA) using the Burmese python, Python molurus. Pythons were fed one of four experimental diets each weighing 25% of the snake's body mass: intact raw beef, intact cooked beef, ground raw beef, and ground cooked beef. We measured oxygen consumption rates of snakes prior to and up to 14 days following feeding and calculated SDA from the extra oxygen consumed above standard metabolic rate. Postprandial peak in oxygen consumption, the scope of peak rates, and SDA varied significantly among meal treatments. Pythons digesting raw or intact meals exhibited significantly larger postprandial metabolic responses than snakes digesting the cooked ground meals. We found cooking to decrease SDA by 12.7%, grinding to decrease SDA by 12.4%, and the combination of the two (cooking and grinding) to have an additive effect, decreasing SDA by 23.4%. These results support the hypothesis that the consumption of cooked meat provides an energetic benefit over the consumption of raw meat. PMID:17827047

Boback, Scott M; Cox, Christian L; Ott, Brian D; Carmody, Rachel; Wrangham, Richard W; Secor, Stephen M

2007-08-16

385

CHIANTI-AN ATOMIC DATABASE FOR EMISSION LINES. XII. VERSION 7 OF THE DATABASE  

SciTech Connect

The CHIANTI spectral code consists of an atomic database and a suite of computer programs to calculate the optically thin spectrum of astrophysical objects and carry out spectroscopic plasma diagnostics. The database includes atomic energy levels, wavelengths, radiative transition probabilities, collision excitation rate coefficients, and ionization and recombination rate coefficients, as well as data to calculate free-free, free-bound, and two-photon continuum emission. Version 7 has been released, which includes several new ions, significant updates to existing ions, as well as Chianti-Py, the implementation of CHIANTI software in the Python programming language. All data and programs are freely available at http://www.chiantidatabase.org, while the Python interface to CHIANTI can be found at http://chiantipy.sourceforge.net.

Landi, E. [Department of Atmospheric, Oceanic and Space Sciences, University of Michigan, Ann Arbor, MI 48109 (United States); Del Zanna, G.; Mason, H. E. [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom); Young, P. R. [College of Science, George Mason University, 4400 University Drive, Fairfax, VA, 22030 (United States); Dere, K. P. [School of Physics, Astronomy and Computational Sciences, MS 6A2, George Mason University, 4400 University Drive, Fairfax, VA 22030 (United States)

2012-01-10

386

STATUS OF THE ORBIT CODE: RECENT DEVELOPMENTS AND PLANS  

SciTech Connect

We report on recent enhancements to the physics modules of the ORBIT Code and on progress toward a new implementation of ORBIT using python. We have developed the capability to track particles through general three dimensional electromagnetic field configurations. This facility has proved essential in modeling beam transport through the complicated magnetic field regions of the SNS injection chicane and injection dump line, where beam losses are high. We have also enhanced the acceleration module to provide more flexibility for synchrotron calculations and we have developed alternative multiple Coulomb and Rutherford scattering models for the stripper foil and collimation routines. Finally, progress continues on the migration of the ORBIT physics models to a python user environment. We present the status of this work.

Holmes, Jeffrey A [ORNL; Cousineau, Sarah M [ORNL; Shishlo, Andrei P [ORNL

2008-01-01

387

Differential Photometry with OSCAAR: Open Source Differential Photometry Code for Amateur Astronomical Research  

NASA Astrophysics Data System (ADS)

We present a cross-platform, open-source differential photometry package written in Python, called OSCAAR (Open Source differential photometry Code for Amateur Astronomical Research). The code is intended for use by undergraduate students or small observatories, or to be used as a scaffolding to be built upon and refined by more advanced users. OSCAAR can be controlled with a graphical user interface for those unfamiliar with Python. OSCAAR makes extensive use of existing astronomical software packages, and the implementation of classes and methods within OSCAAR is designed to be highly modular and interchangeable. The aim of OSCAAR is to provide a free, practical differential photometry toolkit with which users can easily create light curves, and also to encourage the users to work with the source code and refine it for their own purposes.

Morris, Brett M.; Katz, H.; OSCAAR Team

2013-06-01

388

Plasma concentrations of chloramphenicol in snakes.  

PubMed

Plasma chloramphenicol concentrations after a subcutaneous injection were studied in 87 snakes of 16 different species. The biological half-life of chloramphenicol varied from 3.3 hours in the indigo snake (Drymarchon corais couperi) to 22.1 hours in the midland water snake (Nerodia sipedon). A single dosage of 50 mg of chloramphenicol/kg of body weight produced plasma concentrations greater than 5 micrograms/ml for nearly 72 hours in 2 species of water snakes (Nerodia erythrogaster, Nerodia sipedon), for 24 hours in the Burmese python (Python molurus bivittatus), and for less than 12 hours in the gray rat snake, Indigo snake, and eastern king snake (Elaphe obsoleta spiloides, Drymarchon coraise couperi, and Lampropeltis getulus getulus). A dosage of 50 mg/kg administered to water snakes every 72 hours for 18 days maintained a minimum plasma concentration of chloramphenicol between 2 and 5 micrograms/ml. PMID:4083608

Clark, C H; Rogers, E D; Milton, J L

1985-12-01

389

PAL: A Positional Astronomy Library  

NASA Astrophysics Data System (ADS)

PAL is a new positional astronomy library written in C that attempts to retain the SLALIB API but is distributed with an open source GPL license. The library depends on the IAU SOFA library wherever a SOFA routine exists and uses the most recent nutation and precession models. Currently about 100 of the 200 SLALIB routines are available. Interfaces are also available from Perl and Python. PAL is freely available via github.

Jenness, T.; Berry, D. S.

2013-10-01

390

The CMIP5 Model Documentation Questionnaire: Development of a Metadata Retrieval System for the METAFOR Common Information Model  

NASA Astrophysics Data System (ADS)

The EU METAFOR Project (http://metaforclimate.eu) has created a web-based model documentation questionnaire to collect metadata from the modelling groups that are running simulations in support of the Coupled Model Intercomparison Project - 5 (CMIP5). The CMIP5 model documentation questionnaire will retrieve information about the details of the models used, how the simulations were carried out, how the simulations conformed to the CMIP5 experiment requirements and details of the hardware used to perform the simulations. The metadata collected by the CMIP5 questionnaire will allow CMIP5 data to be compared in a scientifically meaningful way. This paper describes the life-cycle of the CMIP5 questionnaire development which starts with relatively unstructured input from domain specialists and ends with formal XML documents that comply with the METAFOR Common Information Model (CIM). Each development step is associated with a specific tool. (1) Mind maps are used to capture information requirements from domain experts and build a controlled vocabulary, (2) a python parser processes the XML files generated by the mind maps, (3) Django (python) is used to generate the dynamic structure and content of the web based questionnaire from processed xml and the METAFOR CIM, (4) Python parsers ensure that information entered into the CMIP5 questionnaire is output as CIM compliant xml, (5) CIM compliant output allows automatic information capture tools to harvest questionnaire content into databases such as the Earth System Grid (ESG) metadata catalogue. This paper will focus on how Django (python) and XML input files are used to generate the structure and content of the CMIP5 questionnaire. It will also address how the choice of development tools listed above provided a framework that enabled working scientists (who we would never ordinarily get to interact with UML and XML) to be part the iterative development process and ensure that the CMIP5 model documentation questionnaire reflects what scientists want to know about the models. Keywords: metadata, CMIP5, automatic information capture, tool development

Pascoe, Charlotte; Lawrence, Bryan; Moine, Marie-Pierre; Ford, Rupert; Devine, Gerry

2010-05-01

391

Secure Programming for Linux and Unix HOWTO  

Microsoft Academic Search

This paper provides a set of design and implementation guidelines for writing secure programs for Linux andUnix systems. Such programs include application programs used as viewers of remote data, web applications(including CGI scripts), network servers, and setuid\\/setgid programs. Specific guidelines for C, C++, Java,Perl, Python, TCL, and Ada95 are included.This document is Copyright (C) 1999-2000 David A. Wheeler. Permission is

David A. Wheeler

2000-01-01

392

Grid-Enabling a Problem Solving Environment: Implementation and Everyday Use  

Microsoft Academic Search

We describe a simple, yet powerful API for accessing and using Grid resources from within Jylab, a novel, extensible scientific\\u000a computing workbench consisting of a suite of open-source Java libraries scriptable through a Jython interpreter. The API provides\\u000a a Java-based, Python-scriptable interactive environment and aims to simplify Grid application development and use. We demonstrate\\u000a the utilization of the API in

Konstantinos Georgiou; Giorgios Kollias; Efstratios Gallopoulos

2007-01-01

393

A next-generation open-source toolkit for FITS file image viewing  

NASA Astrophysics Data System (ADS)

The astronomical community has a long tradition of sharing and collaborating on FITS file tools, including viewers. Several excellent viewers such as DS9 and Skycat have been successfully reused again and again. Yet this "first generation" of viewers predate the emergence of a new class of powerful object-oriented scripting languages such as Python, which has quickly become a very popular language for astronomical (and general scientific) use. Integration and extension of these viewers by Python is cumbersome. Furthermore, these viewers are also built on older widget toolkits such as Tcl/Tk, which are becoming increasingly difficult to support and extend as time passes. Suburu Telescope's second-generation observation control system (Gen2) is built on a a foundation of Python-based technologies and leverages several important astronomically useful packages such as numpy and pyfits. We have written a new flexible core widget for viewing FITS files which is available in versions for both the modern Gtk and Qt-based desktops. The widget offers seamless integration with pyfits and numpy arrays of FITS data. A full-featured viewer based on this widget has been developed, and supports a plug-in architecture in which new features can be added by scripting simple Python modules. In this paper we will describe and demonstrate the capabilities of the new widget and viewer and discuss the architecture of the software which allows new features and widgets to easily developed by subclassing a powerful abstract base class. The software will be released as open-source.

Jeschke, Eric; Inagaki, Takeshi; Kackley, Russell

2012-09-01

394

wradlib - An Open Source Library for Weather Radar Data Processing  

NASA Astrophysics Data System (ADS)

Weather radar data is potentially useful in meteorology, hydrology, disaster prevention and mitigation. Its ability to provide information on precipitation with high spatial and temporal resolution over large areas makes it an invaluable tool for short term weather forecasting or flash flood forecasting. The indirect method of measuring the precipitation field, however, leads to a significant number of data artifacts, which usually must be removed or dealt with before the data can be used with acceptable quality. Data processing requires e.g. the transformation of measurements from polar to cartesian coordinates and from reflectivity to rainfall intensity, the composition of data from several radar sites in a common grid, clutter identification and removal, attenuation and VPR corrections, gauge adjustment and visualization. The complexity of these processing steps is a major obstacle for many potential users in science and practice. Adequate tools are available either only at significant costs with no access to the uncerlying source code, or they are incomplete, insufficiently documented and intransparent. The wradlib project has been initiated in order to lower the barrier for potential users of weather radar data in the geosciences and to provide a common platform for research on new algorithms. wradlib is an open source library for the full range of weather radar related processing algorithms, which is well documented and easy to use. The main parts of the library are currently implemented in the python programming language. Python is well known both for its ease of use as well as its ability to integrate code written in other programming languages like Fortran or C/C++. The well established Numpy and Scipy packages are used to provide decent performance for pure Python implementations of algorithms. We welcome contributions written in any computer language and will try to make them accessible from Python. We would like to present the current state of this library together with a few showcase examples.

Heistermann, M.; Pfaff, Th.; Jacobi, S.

2012-04-01

395

Verfication Technologies, third quarter 1992  

SciTech Connect

Tag and seal development has targeted primarily the on-site inspections of arms-control treaty-limited items. This issue provides a summary of overall projects and results. The following are covered: reflective particle tags, python seal, Star fiber-optic seal, ultrasonic intrinsic tagging, buddy tags, electronic identification devices, holographic correlation system, microvideography of intrinsic or applied features, plastic casting fingerprints, tamper tapes (overview), and shrink-wrap seals.

Staehle, G.; Stull, S.; Talaber, C. [eds.] [Lawrence Livermore National Lab., CA (United States)

1992-12-31

396

Verfication Technologies, third quarter 1992  

Microsoft Academic Search

Tag and seal development has targeted primarily the on-site inspections of arms-control treaty-limited items. This issue provides a summary of overall projects and results. The following are covered: reflective particle tags, python seal, Star fiber-optic seal, ultrasonic intrinsic tagging, buddy tags, electronic identification devices, holographic correlation system, microvideography of intrinsic or applied features, plastic casting fingerprints, tamper tapes (overview), and

G. Staehle; S. Stull; C. Talaber

1992-01-01

397

Verfication Technologies, third quarter 1992  

SciTech Connect

Tag and seal development has targeted primarily the on-site inspections of arms-control treaty-limited items. This issue provides a summary of overall projects and results. The following are covered: reflective particle tags, python seal, Star fiber-optic seal, ultrasonic intrinsic tagging, buddy tags, electronic identification devices, holographic correlation system, microvideography of intrinsic or applied features, plastic casting fingerprints, tamper tapes (overview), and shrink-wrap seals.

Staehle, G.; Stull, S.; Talaber, C. (eds.) (Lawrence Livermore National Lab., CA (United States))

1992-01-01

398

Development and Application of a Predictive Computational Tool for Short-Pulse, High-Intensity Target Interactions  

SciTech Connect

The widely differing spatial, temporal, and density scales needed to accurately model the fast ignition process and other short-pulse laser-plasma interactions leads to a computationally challenging project that is difficult to solve using a single code. This report summarizes the work performed on a three year LDRD to couple together three independent codes using PYTHON to build a new integrated computational tool. An example calculation using this new model is described.

Town, R J; Chung, H; Langdon, A B; Lasinski, B F; Lund, S M; McCandless, B C; Still, C H; Tabak, M

2007-01-26

399

Automatically generating Feynman rules for improved lattice field theories  

SciTech Connect

Deriving the Feynman rules for lattice perturbation theory from actions and operators is complicated, especially when improvement terms are present. This physically important task is, however, suitable for automation. We describe a flexible algorithm for generating Feynman rules for a wide range of lattice field theories including gluons, relativistic fermions and heavy quarks. We also present an efficient implementation of this in a freely available, multi-platform programming language (PYTHON), optimised to deal with a wide class of lattice field theories.

Hart, A. [School of Physics, University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ (United Kingdom)]. E-mail: a.hart@ed.ac.uk; Hippel, G.M. von [DAMTP, CMS, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom) and Department of Physics, University of Regina, Regina, SK, Canada S4S 0A2 (Canada); Horgan, R.R. [DAMTP, CMS, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom); Storoni, L.C. [DAMTP, CMS, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom)

2005-10-10

400

Using the Computer as a Black Box  

NSDL National Science Digital Library

Chapter 1 of Open Source tools for Computational Physics: An introduction to EJS and Python. This chapter introduces the use of the computer as a âblack boxâ (i.e., without programming) for solving a variety of physics and engineering problems, making use of the General Purpose Math Visualizer Package. Using this package, the reader is asked to create and analyze plots and animations, numerically differentiate and integrate functions of relevance to physical problems, and numerically solve systems of coupled linear algebraic equations.

Engelhardt, Larry

2011-07-19

401

TPZ: Trees for Photo-Z  

NASA Astrophysics Data System (ADS)

TPZ, a parallel code written in python, produces robust and accurate photometric redshift PDFs by using prediction tree and random forests. The code also produces ancillary information about the sample used, such as prior unbiased errors estimations (giving an estimation of performance) and a ranking of importance of variables as well as a map of performance indicating where extra training data is needed to improve overall performance. It is designed to be easy to use and a tutorial is available.

Carrasco Kind, Matias; Brunner, Robert

2013-04-01

402

ReSP: A Nonintrusive Transaction-Level Reflective MPSoC Simulation Platform for Design Space Exploration  

Microsoft Academic Search

This paper presents reflective simulation platform (ReSP), a transaction-level multiprocessor simulation platform based on the integration of SystemC and Python. ReSP exploits the concept of reflection, enabling the integration of SystemC components without source-code modifications and providing full observability of their internal state. ReSP offers fine-grained simulation control and supports the evaluation of different hardware\\/software configurations of a given application,

Giovanni Beltrame; Luca Fossati; Donatella Sciuto

2009-01-01

403

Project 5: A Virtual Tea Party  

Microsoft Academic Search

\\u000a In this project, you do some serious network programming. You’ll write a chat server—a program that lets several people connect\\u000a via the Internet and chat with each other in real time. There are many ways to create such a beast in Python. A simple and\\u000a natural approach might be to use the Twisted framework (discussed in Chapter 14), for example,

Magnus Lie Hetland

404

How to distinguish between the vacuum cleaner and flippase mechanisms of the lmrA multi-drug transporter in Lactococcus lactis.  

PubMed

A numerical model of the LmrA multi-drug transport system of Lactococcus lactis is used to explore the possibility of distinguishing experimentally between two putative transport mechanisms, i.e., the vacuum-cleaner and the flippase mechanisms. This comparative model also serves as an example of numerical simulation with the scripting language Python and its scientific add-on Scipy. PMID:12241038

Hofmeyr, J H S; Rohwer, J M; Snoep, J L; Westerhoff, H V; Konings, W N

2002-01-01

405

An Automatic Image Reduction Pipeline for the Advanced Camera for Surveys  

Microsoft Academic Search

We have written an automatic image processing pipeline for the Advanced\\u000aCamera for Surveys (ACS) Guaranteed Time Observation (GTO) program. The\\u000apipeline, known as Apsis, supports the different cameras available on the ACS\\u000ainstrument and is written in Python with a flexible object-oriented design that\\u000asimplifies the incorporation of new pipeline modules. The processing steps\\u000ainclude empirical determination of image

John P. Blakeslee; Kenneth R. Anderson; G. R. Meurer; N. Ben ´ itez; D. Magee

2002-01-01

406

Topological Analysis and Measurements of an Online Chinese Student Social Network  

Microsoft Academic Search

Online social network attracts more researchers now. In this paper, we topologically analyze an online Chinese student social\\u000a network–Xiaonei.com. We use Python language to crawl two datasets of Xiaonei in January and February, 2008. The degree distribution\\u000a and small world phenomena are testified. We also use a social network analysis tool to analyze these two datasets from the\\u000a viewpoint of

Duoyong Sun; Jiang Wu; Shenghua Zheng; Bin Hu; Kathleen M. Carley

2009-01-01

407

EggLib: processing, analysis and simulation tools for population genetics and genomics  

PubMed Central

Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.

2012-01-01

408

An active registry for bioinformatics web services  

PubMed Central

Summary: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks. Availability and implementation: Web site implemented with PHP, Python, MySQL and Apache, with all major browsers supported. (www.embraceregistry.net) Contact: steve.pettifer@manchester.ac.uk

Pettifer, S.; Thorne, D.; McDermott, P.; Attwood, T.; Baran, J.; Bryne, J. C.; Hupponen, T.; Mowbray, D.; Vriend, G.

2009-01-01

409

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server  

Microsoft Academic Search

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base

J. C. Reyes; F. L. Vernon; R. L. Newman; J. H. Steidl

2010-01-01

410

Django on Google App Engine  

Microsoft Academic Search

\\u000a In mid-2008, Google finally opened up Google App Engine for use by the public. Google App Engine is a cloud infrastructure\\u000a onto which developers can deploy Java-or Python-based web applications. This is an exciting prospect; Google has finally created\\u000a a cloud into which we can deploy web sites. Much like Amazon’s own Elastic Cloud Compute service, it’s an option that

Jim McGaw

411

An object-oriented approach for modeling and simulation of crack growth in cyclically loaded structures  

Microsoft Academic Search

We present an object-oriented modeling frame for simulating crack propagation due to cyclic loadings. Central to the approach is that the crack propagates when a user-defined propagation criterion is fulfilled, i.e., the crack propagation rate is not prescribed but predicted. The approach utilizes the commercial finite element software package ABAQUS and its associated Python based scripting interface. The crack propagation

D. Cojocaru; A. M. Karlsson

2008-01-01

412

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.  

PubMed

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample--a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable. PMID:22348032

Castoe, Todd A; Poole, Alexander W; de Koning, A P Jason; Jones, Kenneth L; Tomback, Diana F; Oyler-McCance, Sara J; Fike, Jennifer A; Lance, Stacey L; Streicher, Jeffrey W; Smith, Eric N; Pollock, David D

2012-02-14

413

Challenges in Identifying Sites Climatically Matched to the Native Ranges of Animal Invaders  

PubMed Central

Background Species distribution models are often used to characterize a species' native range climate, so as to identify sites elsewhere in the world that may be climatically similar and therefore at risk of invasion by the species. This endeavor provoked intense public controversy over recent attempts to model areas at risk of invasion by the Indian Python (Python molurus). We evaluated a number of MaxEnt models on this species to assess MaxEnt's utility for vertebrate climate matching. Methodology/Principal Findings Overall, we found MaxEnt models to be very sensitive to modeling choices and selection of input localities and background regions. As used, MaxEnt invoked minimal protections against data dredging, multi-collinearity of explanatory axes, and overfitting. As used, MaxEnt endeavored to identify a single ideal climate, whereas different climatic considerations may determine range boundaries in different parts of the native range. MaxEnt was extremely sensitive to both the choice of background locations for the python, and to selection of presence points: inclusion of just four erroneous localities was responsible for Pyron et al.'s conclusion that no additional portions of the U.S. mainland were at risk of python invasion. When used with default settings, MaxEnt overfit the realized climate space, identifying models with about 60 parameters, about five times the number of parameters justifiable when optimized on the basis of Akaike's Information Criterion. Conclusions/Significance When used with default settings, MaxEnt may not be an appropriate vehicle for identifying all sites at risk of colonization. Model instability and dearth of protections against overfitting, multi-collinearity, and data dredging may combine with a failure to distinguish fundamental from realized climate envelopes to produce models of limited utility. A priori identification of biologically realistic model structure, combined with computational protections against these statistical problems, may produce more robust models of invasion risk.

Rodda, Gordon H.; Jarnevich, Catherine S.; Reed, Robert N.

2011-01-01

414

Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing.  

PubMed

We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and the Burmese python (Python molurus bivittatus). These two genomes are both relatively small (?1.4 Gb) but have surprisingly extensive differences in the abundance and expansion histories of their repeat elements. In the python, the readily identifiable repeat element content is low (21%), similar to bird genomes, whereas that of the copperhead is higher (45%), similar to mammalian genomes. The copperhead's greater repeat content arises from the recent expansion of many different microsatellites and transposable element (TE) families, and the copperhead had 23-fold greater levels of TE-related transcripts than the python. This suggests the possibility that greater TE activity in the copperhead is ongoing. Expansion of CR1 LINEs in the copperhead genome has resulted in TE-mediated microsatellite expansion ("microsatellite seeding") at a scale several orders of magnitude greater than previously observed in vertebrates. Snakes also appear to be prone to horizontal transfer of TEs, particularly in the copperhead lineage. The reason that the copperhead has such a small genome in the face of so much recent expansion of repeat elements remains an open question, although selective pressure related to extreme metabolic performance is an obvious candidate. TE activity can affect gene regulation as well as rates of recombination and gene duplication, and it is therefore possible that TE activity played a role in the evolution of major adaptations in snakes; some evidence suggests this may include the evolution of venom repertoires. PMID:21572095

Castoe, Todd A; Hall, Kathryn T; Guibotsy Mboulas, Marcel L; Gu, Wanjun; de Koning, A P Jason; Fox, Samuel E; Poole, Alexander W; Vemulapalli, Vijetha; Daza, Juan M; Mockler, Todd; Smith, Eric N; Feschotte, Cédric; Pollock, David D

2011-05-13

415

Altered visual experience and acute visual deprivation affect predatory targeting by infrared-imaging Boid snakes.  

PubMed

Boid and Crotaline snakes use both their eyes and infrared-imaging facial pit organs to target homeothermic prey. These snakes can target in complete darkness, but the eyes can also effectively direct predatory strikes. We investigated the behavioral correlates of boid snakes' simultaneous use of two imaging systems by testing whether congenital unilateral visual deprivation affects targeting performance. Normally sighted Burmese pythons exhibited average targeting angle of zero (on the midline axis of the head), but three unilaterally anophthalmic Burmese pythons targeted preferentially on the sighted side. A unilaterally anophthalmic amethystine python also targeted on the sighted side, and a unilaterally anophthalmic Brazilian rainbow boa tended to target on the sighted side, though its mean targeting angle was not significantly different from zero. When unilaterally anophthalmic Burmese pythons were temporarily blinded, mean strike angle changed to that of normally sighted snakes. These results show that while infrared-imaging snakes can shift between visual and infrared information under acute experimental conditions, loss of part of the visual field during development results in abnormal predatory targeting behavior. In contrast, normally sighted snakes subjected to temporary unilateral blinding do not target preferentially on the sighted side. Therefore, while loss of part of the visual field may be compensated for by infrared input in normal snakes, partial absence of visual input during development may alter central organization of visual information. Conversely, absence of half the visual field during development does not alter targeting performance based upon infrared input alone, suggesting that organization of the central infrared map does not depend upon normal organization of visual input. PMID:11701137

Grace, M S; Woodward, O M

2001-11-23

416

Ancient scientific basis of the "great serpent" from historical evidence.  

PubMed

Zoological data and a growing mythology contributed to ancient Western knowledge about large serpents. Yet little modern attention has been paid to the sources, transmission, and receipt in the early Middle Ages of the ancients' information concerning "dragons" and "sea serpents." Real animals--primarily pythons and whales--lie behind the ancient stories. Other animals, conflations of different animals, simple misunderstandings, and willful exaggerations are found to account for the fanciful embellishments, but primitive myths played no significant role in this process during classical times. The expedition of Alexander the Great into India (327-325 B.C.) and the Bagradas River incident in North Africa (256 B.C.) had enormous repercussions on the development of serpent lore. Credible evidence is found for the presence of ancient populations of pythons living along the North African coast west of Egypt and along the coast of the Arabian Sea between the Indus River and the Strait of Hormuz--places where they no longer exist today. The maximum sizes of ancient pythons may have been greater than those of today's specimens. PMID:15490966

Stothers, Richard B

2004-06-01

417

The nightly build and test system for LCG AA and LHCb software  

NASA Astrophysics Data System (ADS)

The core software stack both from the LCG Application Area and LHCb consists of more than 25 C++/Fortran/Python projects built for about 20 different configurations on Linux, Windows and MacOSX. To these projects, one can also add about 70 external software packages (Boost, Python, Qt, CLHEP, ...) which also have to be built for the same configurations. It order to reduce the time of the development cycle and assure the quality, a framework has been developed for the daily (in fact nightly) build and test of the software. Performing the build and the tests on several configurations and platforms increases the efficiency of the unit and integration tests. Main features: - flexible and fine grained setup (full, partial build) through a web interface; - possibility to build several "slots" with different configurations; - precise and highly granular reports on a web server; - support for CMT projects (but not only) with their cross-dependencies; - scalable client-server architecture for the control machine and its build machines; - copy of the results in a common place to allow early view of the software stack. The nightly build framework is written in Python for portability and it is easily extensible to accommodate new build procedures.

Kruzelecki, Karol; Roiser, Stefan; Degaudenzi, Hubert

2010-04-01

418

A first prototype of PyACTS  

SciTech Connect

The ACTS Collection is a set of software tools that help developers or programmers write high performance parallel codes for their scientific applications. PyACTS is a Python-based interface to some of the tools in the ACTS Collection. The main purpose of developing PyACTS is to provide a uniform easy-to-use external interface to existing ACTS tools,and support ACTS users to rapidly prototype their codes with the tools. In particular, for users who are new to ACTS, they will find PyACTS helpful to test and try the functionality available in the collection. Further, this training will allow users to acquire the necessary experience to develop their own applications. In the current development phase of PyACTS, part of the ScaLAPACK subroutines are being made available. This report illustrates how we develop the idea of wrapping the ACTS Collection with a high level scripting language, like Python, and a status of the development of the Python front-end interface and future plans.

Kang, Ning; Drummond, Leroy A.

2003-08-31

419

Detection of pathogens in Boidae and Pythonidae with and without respiratory disease.  

PubMed

Respiratory diseases in boid snakes are common in captivity, but little information is available on their aetiology. This study was carried out to determine the occurrence of lung associated pathogens in boid snakes with and without respiratory signs and/or pneumonia. In total, 80 boid snakes of the families Boidae (n = 30) and Pythonidae (n = 50) from 48 private and zoo collections were included in this survey. Husbandry conditions were evaluated using a detailed questionnaire. All snakes were examined clinically and grouped into snakes with or without respiratory signs. Tracheal wash samples from all snakes were examined bacteriologically as well as virologically. All snakes were euthanased, and a complete pathological examination was performed. Respiratory signs and pneumonia were detected more often in pythons than in boas. An acute catarrhal pneumonia was diagnosed more often in snakes without respiratory signs than in snakes with respiratory signs, which revealed fibrinous and fibrous pneumonia. Poor husbandry conditions are an important trigger for the development of respiratory signs and pneumonia. Different bacterial pathogens were isolated in almost all snakes with pneumonia, with Salmonella species being the most common. Ferlavirus (formerly known as ophidian paramyxovirus)-RNA was detected only in pythons. Inclusion body disease was rarely seen in pythons but often in boas. Adenovirus and Mycoplasma were other pathogens that were diagnosed in single snakes with pneumonia. In living boid snakes with respiratory signs, tracheal wash samples were found to be a useful diagnostic tool for the detection of viral and bacterial pathogens. PMID:23322542

Schmidt, V; Marschang, R E; Abbas, M D; Ball, I; Szabo, I; Helmuth, R; Plenz, B; Spergser, J; Pees, M

2013-01-15

420

A pipeline for comprehensive and automated processing of electron diffraction data in IPLT.  

PubMed

Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library and Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs. PMID:23500887

Schenk, Andreas D; Philippsen, Ansgar; Engel, Andreas; Walz, Thomas

2013-03-14

421

Technical Integration of Hippocampus, Basal Ganglia and Physical Models for Spatial Navigation  

PubMed Central

Computational neuroscience is increasingly moving beyond modeling individual neurons or neural systems to consider the integration of multiple models, often constructed by different research groups. We report on our preliminary technical integration of recent hippocampal formation, basal ganglia and physical environment models, together with visualisation tools, as a case study in the use of Python across the modelling tool-chain. We do not present new modeling results here. The architecture incorporates leaky-integrator and rate-coded neurons, a 3D environment with collision detection and tactile sensors, 3D graphics and 2D plots. We found Python to be a flexible platform, offering a significant reduction in development time, without a corresponding significant increase in execution time. We illustrate this by implementing a part of the model in various alternative languages and coding styles, and comparing their execution times. For very large-scale system integration, communication with other languages and parallel execution may be required, which we demonstrate using the BRAHMS framework's Python bindings.

Fox, Charles; Humphries, Mark; Mitchinson, Ben; Kiss, Tamas; Somogyvari, Zoltan; Prescott, Tony

2008-01-01

422

A pipeline for comprehensive and automated processing of electron diffraction data in IPLT  

PubMed Central

Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library & Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs.

Schenk, Andreas D.; Philippsen, Ansgar; Engel, Andreas; Walz, Thomas

2013-01-01

423

Exploring network structure, dynamics, and function using networkx  

SciTech Connect

NetworkX is a Python language package for exploration and analysis of networks and network algorithms. The core package provides data structures for representing many types of networks, or graphs, including simple graphs, directed graphs, and graphs with parallel edges and self loops. The nodes in NetworkX graphs can be any (hashable) Python object and edges can contain arbitrary data; this flexibility mades NetworkX ideal for representing networks found in many different scientific fields. In addition to the basic data structures many graph algorithms are implemented for calculating network properties and structure measures: shortest paths, betweenness centrality, clustering, and degree distribution and many more. NetworkX can read and write various graph formats for eash exchange with existing data, and provides generators for many classic graphs and popular graph models, such as the Erdoes-Renyi, Small World, and Barabasi-Albert models, are included. The ease-of-use and flexibility of the Python programming language together with connection to the SciPy tools make NetworkX a powerful tool for scientific computations. We discuss some of our recent work studying synchronization of coupled oscillators to demonstrate how NetworkX enables research in the field of computational networks.

Hagberg, Aric [Los Alamos National Laboratory; Swart, Pieter [Los Alamos National Laboratory; S Chult, Daniel [COLGATE UNIV

2008-01-01

424

Near-Infrared Neuroimaging with NinPy  

PubMed Central

There has been substantial recent growth in the use of non-invasive optical brain imaging in studies of human brain function in health and disease. Near-infrared neuroimaging (NIN) is one of the most promising of these techniques and, although NIN hardware continues to evolve at a rapid pace, software tools supporting optical data acquisition, image processing, statistical modeling, and visualization remain less refined. Python, a modular and computationally efficient development language, can support functional neuroimaging studies of diverse design and implementation. In particular, Python's easily readable syntax and modular architecture allow swift prototyping followed by efficient transition to stable production systems. As an introduction to our ongoing efforts to develop Python software tools for structural and functional neuroimaging, we discuss: (i) the role of non-invasive diffuse optical imaging in measuring brain function, (ii) the key computational requirements to support NIN experiments, (iii) our collection of software tools to support NIN, called NinPy, and (iv) future extensions of these tools that will allow integration of optical with other structural and functional neuroimaging data sources. Source code for the software discussed here will be made available at www.nmr.mgh.harvard.edu/Neural_SystemsGroup/software.html.

Strangman, Gary E.; Zhang, Quan; Zeffiro, Thomas

2009-01-01

425

Oviduct adenocarcinoma in some species of captive snakes.  

PubMed

This article reports 5 cases of oviduct adenocarcinoma in adult captive snakes from Smithsonian's National Zoological Park. This neoplasm was found in 1 of each of the following species: emerald tree boa (Corallus caninus), Amazonian tree boa (Corallus enydris enydris), Burmese rock python (Python molurus bivittatus), Northern pine snake (Pituophis melanoleucus melanoleucus), and corn snake (Elaphe guttata). Grossly, tan to red firm masses were found within oviducts in 3 cases. In an additional 2 cases, the primary tumor was detected only histologically. Microscopically, neoplasms were papillary, and often extended transmurally. The neoplastic cells were polygonal and organized in acini or cords, with often abundant fibrovascular stroma. Hemorrhages and necrosis were present in all cases. Inflammation, myxomatous material, desmoplasia, and bacteria were often observed. Histologic evidence of metastasis was present in all cases. Solid metastases were seen in all animals except the Northern pine snake and involved several organs including the liver, lung, and heart. Emboli of neoplastic cells were observed in all animals but the Burmese rock python and corn snake. PMID:18725476

Pereira, M E; Viner, T C

2008-09-01

426

Evidence of IgY subclass diversification in snakes: evolutionary implications.  

PubMed

Mammalian IgG and IgE are thought to have evolved from IgY of nonmammalian tetrapods; however, no diversification of IgY subclasses has been reported in reptiles or birds, which are phylogenetically close to mammals. To our knowledge, we report the first evidence of the presence of multiple IgY-encoding (?) genes in snakes. Two ? genes were identified in the snake Elaphe taeniura, and three ? genes were identified in the Burmese python (Python molurus bivittatus). Although four of the ? genes displayed a conventional four-H chain C region exon structure, one of the ? genes in the Burmese python lacked the H chain C region 2 exon, thus exhibiting a structure similar to that of the mammalian ? genes. We developed mouse mAbs specific for the IgY1 and IgY2 of E. taeniura and showed that both were expressed in serum; each had two isoforms: one full-length and one truncated at the C terminus. The truncation was not caused by alternative splicing or transcriptional termination. We also identified the ? and ? genes, but no ? gene, in both snakes. This study provides valuable clues for our understanding of Ig gene evolution in tetrapods. PMID:22933626

Wang, Tao; Sun, Yi; Shao, Wenwei; Cheng, Gang; Li, Lingxiao; Cao, Zubing; Yang, Zhi; Zou, Huiying; Zhang, Wei; Han, Binyue; Hu, Yang; Ren, Liming; Hu, Xiaoxiang; Guo, Ying; Fei, Jing; Hammarström, Lennart; Li, Ning; Zhao, Yaofeng

2012-08-29

427

Jane Austen's lifelong health problems and final illness: New evidence points to a fatal Hodgkin's disease and excludes the widely accepted Addison's.  

PubMed

Jane Austen is typically described as having excellent health until the age of 40 and the onset of a mysterious and fatal illness, initially identified by Sir Zachary Cope in 1964 as Addison's disease. Her biographers, deceived both by Cassandra Austen's destruction of letters containing medical detail, and the cheerful high spirits of the existing letters, have seriously underestimated the extent to which illness affected Austen's life. A medical history reveals that she was particularly susceptible to infection, and suffered unusually severe infective illnesses, as well as a chronic conjunctivitis that impeded her ability to write. There is evidence that Austen was already suffering from an immune deficiency and fatal lymphoma in January 1813, when her second and most popular novel, Pride and Prejudice, was published. Four more novels would follow, written or revised in the shadow of her increasing illness and debility. Whilst it is impossible now to conclusively establish the cause of her death, the existing medical evidence tends to exclude Addison's disease, and suggests there is a high possibility that Jane Austen's fatal illness was Hodgkin's disease, a form of lymphoma. PMID:23674643

Upfal, A

2005-06-01

428

Intersite coupling effects in a Kondo lattice near an antiferromagnetic instability  

NASA Astrophysics Data System (ADS)

Critcal fluctuations due to the proximity to a magnetic instability are believed to be the origin of a variety of non-Fermi-liquid behavior and unconventional superconductivity observed in heavy fermion systems. Near the quantum critical points, prominent effect of intersite coupling in Kondo lattice systems may appear. With this in mind, we studied the La dilution effects in CeCoIn_5, a heavy fermion superconductor located near an antiferromangetic instability [1,2]. The scaling laws found for the magnetic susceptibility and the specific heat reveal two well-separated energy scales, corresponding to the single impurity Kondo temperature TK and an intersite spin-liquid temperature T. The Ce-dilute alloy has the expected Fermi liquid ground state, while the specific heat and resistivity in the dense Kondo regime exhibit non-Fermi-liquid behavior, which scales with T^*. These observations indicate that the screening of the magnetic moments in the lattice involves antiferromagnetic intersite correlations with a larger energy scale in comparison with the Kondo impurity case. This work was supported by NSF DMR-9527035. [1] C. Petrovic ´it et al., J.Phys.: Condens. Matter ´bf 13, L337 (2001). [2] S. Nakatsuji ´it et al., Phys. Rev. Lett. 89, 106402 (2002) ^´ast Work done in collaboration with Zachary Fisk, Sunmog Yeo, Luis Balicas, Pedro Schlottmann, Pagliuso G. Pagliuso, Nelson O. Moreno, John L. Sarrao, and Joe D. Thompson

Nakatsuji, Satoru

2003-03-01

429

Extended three-dimensional impedance map methods for identifying ultrasonic scattering sites  

PubMed Central

The frequency-dependent ultrasound backscatter from tissues contains information about the microstructure that can be quantified. In many cases, the anatomic microstructure details responsible for ultrasonic scattering remain unidentified. However, their identification would lead to potentially improved methodologies for characterizing tissue and diagnosing disease from ultrasonic backscatter measurements. Recently, three-dimensional (3D) acoustic models of tissue microstructure, termed 3D impedance maps (3DZMs), were introduced to help to identify scattering sources [J. Mamou, M. L. Oelze, W. D. O’Brien, Jr., and J. F. Zachary, “Identifying ultrasonic scattering sites from 3D impedance maps,” J. Acoust. Soc. Am. 117, 413–423 (2005)]. In the current study, new 3DZM methodologies are used to model and identify scattering structures. New processing procedures (e.g., registration, interpolations) are presented that allow more accurate 3DZMs to be constructed from histology. New strategies are proposed to construct scattering models [i.e., form factor (FF)] from 3DZMs. These new methods are tested on simulated 3DZMs, and then used to evaluate 3DZMs from three different rodent tumor models. Simulation results demonstrate the ability of the extended strategies to accurately predict FFs and estimate scatterer properties. Using the 3DZM methods, distinct FFs and scatterer properties were obtained for each tumor examined.

Mamou, Jonathan; Oelze, Michael L.; O'Brien, William D.; Zachary, James F.

2011-01-01

430

Comparison of Predicted Exercise Capacity Equations and the Effect of Actual versus Ideal Body Weight among Subjects Undergoing Cardiopulmonary Exercise Testing  

PubMed Central

Background. Oxygen uptake at maximal exercise (VO2 max) is considered the best available index for assessment of exercise capacity. The purpose of this study is to determine if the use of actual versus ideal body weight in standard regression equations for predicted VO2 max results in differences in predicted VO2 max. Methods. This is a retrospective chart review of patients who were predominantly in active military duty with complaints of dyspnea or exercise tolerance and who underwent cardiopulmonary exercise testing (CPET) from 2007 to 2009. Results. A total of 230 subjects completed CPET on a bicycle ergometer with a male predominance (62%) and an average age of 37?±?15 years. There was significant discordance between the measured VO2 max and predicted VO2 max when measured by the Hansen and Wasserman reference equations (P < 0.001). Specifically, there was less overestimation when predicted VO2 max was based on ideal body weight as opposed to actual body weight. Conclusion. Our retrospective analysis confirmed the wide variations in predicted versus measured VO2 max based on varying prediction equations and showed the potential advantage of using ideal body weight as opposed to actual body weight in order to further standardize reference norms.

Ahmadian, H. Reza; Sclafani, Joseph J.; Emmons, Ethan E.; Morris, Michael J.; Leclerc, Kenneth M.; Slim, Ahmad M.

2013-01-01

431

Comparison of Predicted Exercise Capacity Equations and the Effect of Actual versus Ideal Body Weight among Subjects Undergoing Cardiopulmonary Exercise Testing.  

PubMed

Background. Oxygen uptake at maximal exercise (VO2 max) is considered the best available index for assessment of exercise capacity. The purpose of this study is to determine if the use of actual versus ideal body weight in standard regression equations for predicted VO2 max results in differences in predicted VO2 max. Methods. This is a retrospective chart review of patients who were predominantly in active military duty with complaints of dyspnea or exercise tolerance and who underwent cardiopulmonary exercise testing (CPET) from 2007 to 2009. Results. A total of 230 subjects completed CPET on a bicycle ergometer with a male predominance (62%) and an average age of 37?±?15 years. There was significant discordance between the measured VO2 max and predicted VO2 max when measured by the Hansen and Wasserman reference equations (P < 0.001). Specifically, there was less overestimation when predicted VO2 max was based on ideal body weight as opposed to actual body weight. Conclusion. Our retrospective analysis confirmed the wide variations in predicted versus measured VO2 max based on varying prediction equations and showed the potential advantage of using ideal body weight as opposed to actual body weight in order to further standardize reference norms. PMID:23653881

Ahmadian, H Reza; Sclafani, Joseph J; Emmons, Ethan E; Morris, Michael J; Leclerc, Kenneth M; Slim, Ahmad M

2013-04-03

432

Color Superconductivity in Compact Stars  

NASA Astrophysics Data System (ADS)

After a brief review of the phenomena expected in cold dense quark matter, color superconductivity and color-flavor locking, we sketch some implications of recent developments in our understanding of cold dense quark matter for the physics of compact stars. We give a more detailed summary of our recent work on crystalline color superconductivity and the consequent realization that (some) pulsar glitches may originate in quark matter.We acknowledge helpful discussions with P. Bedaque, J. Berges, D. Blaschke, I. Bombaci, G. Carter, D. Chakrabarty, J. Madsen, C. Nayak, M. Prakash, D. Psaltis, S. Reddy, M. Ruderman, S.-J. Rey, T. Schäfer, A. Sedrakian, E. Shuryak, E. Shuster, D. Son, M. Stephanov, I. Wasserman, F. Weber and F. Wilczek. KR thanks the organizers of the ECT Workshop on Neutron Star Interiors for providing a stimulating environment within which many of the helpful discussions acknowledged above took place. This work is supported in part by the DOE under cooperative research agreement #DF-FC02-94ER40818. The work of JB was supported in part by an NDSEG Fellowship; that of KR was supported in part by a DOE OJI Award and by the A. P. Sloan Foundation.

Alford, Mark; Bowers, Jeffrey A.; Rajagopal, Krishna

433

Fabrication and Characterization of Naturally Selected Epitaxial Fe-{111} Y2Ti2O7 Mesoscopic Interfaces: Some Potential Implications to Nano-Oxide Dispersion-Strengthened Steels  

NASA Astrophysics Data System (ADS)

The smallest features of ?2 to 3 nm in nanostructured ferritic alloys (NFA), a variant of oxide dispersion-strengthened steels, include the Y2Ti2O7 complex oxide cubic pyrochlore phase. The interface between the bcc Fe-Cr ferrite matrix and the fcc nanometer-scale Y2Ti2O7 plays a critical role in the stability, strength, and damage tolerance of NFA. To complement other characterization studies of the actual nanofeatures (NF) themselves, mesoscopic interfaces were created by electron beam deposition of a thin Fe layer on a 5 deg miscut {111} Y2Ti2O7 bulk single crystal surface. While the mesoscopic interfaces may differ from those of the embedded NF, the former facilitate characterization of controlled interfaces, such as interactions with point defects and helium. The Fe-Y2Ti2O7 interfaces were studied using scanning electron microscopy, including electron backscatter diffraction, atomic force microscopy, X-ray diffraction, and transmission electron microscopy (TEM). The polycrystalline Fe layer has two general orientation relationships (OR) that are close to (a) the Nishiyama-Wasserman (NW) OR and and (b) and . High-resolution TEM shows that the NW interface is near-atomically flat, while the {100}Fe grains are an artifact associated with a thin oxide layer. However, the fact that there is still a Fe-Y2Ti2O7 OR is significant. No OR is observed in the presence of a thicker oxide layer.

Stan, Tiberiu; Wu, Yuan; Odette, George R.; Sickafus, Kurt E.; Dabkowska, Hannah A.; Gaulin, Bruce D.

2013-10-01

434

The Relative Surface Roughness of the two Sides of Iapetus  

NASA Astrophysics Data System (ADS)

We apply Cassini ISS (Imaging Science Subsystem) data from the January 1st, 2005 flyby of Iapetus to a surface roughness model originally developed by Buratti and Veverka (1985). Since macroscopic features of topography alter the scattering properties of a planetary surface (Schoenberg, 1925; Hameen-Antilla et al., 1965; Hapke, 1966, 1984; Veverka and Wasserman, 1972; Lumme and Bowell, 1981; Buratti et al., 1985), this model uses the observed scattering behavior to provide a depth to radius factor q quantifying the size of craters on the surface. Relative surface roughness of the low albedo (leading) hemisphere and high albedo (trailing) hemisphere can then be determined by comparing the value for the two hemispheres, and any differences observed will provide an estimate of the depth of the dark material. Our preliminary findings show marked differences in macroscopic roughness between the high and low albedo hemispheres, indicating that the surface on the dark side is much smoother than the bright. Our results further suggest that the dark material is substantial enough to cause significant infilling of the craters on the dark side. Funded by the NASA Space Grant.

Lee, J.; Buratti, B.; Mosher, J.

2007-12-01

435

Pluto-Charon: a test of the astrometric approach for finding asteroid satellites  

NASA Astrophysics Data System (ADS)

The astrometric method to find asteroid satellites is based on the search for the reflex effect on the primary object due to the orbital motion of a possible satellite (Monet & Monet 1998, Kikwaya et al. 2002). As reported by Kikwaya et al. (2003), the astrometric signature of a satellite of 146 Lucina may reach several mas. Spectral analysis might then detect the signal under good conditions of signal/noise ratio, with high quality astrometric measurements and large coverage by different sites of observation. However, the astrometric method cannot be applied to any binary system of asteroids. It depends strongly on the mass ratio of the two bodies and the distance between them (Kikwaya et al. 2002). Pluto-Charon provides a good test of this method. Previous works based on direct imaging of Charon show that its period is 6.357 days and the mass ratio is 0.122 (Wasserman et al. 2000), putting this system into the range that can be observed by our method. Using archived photographic observations (1914-1995) and CCD observations from US Naval Observatory, Flagstaff station (1995-1998), Bordeaux observatory (1996-1997) and Mc Donald Observatory (1997), we are analyzing the position of Pluto to see if its wobble effect due to Charon (amplitude around 95 mas) can be detected and if the orbital period of Charon can be recovered through a spectral analysis. If successful, this will reinforce the ability of our astrometric method to find asteroid satellites.

Kikwaya, J.-B.; Thuillot, W.; Berthier, J.

2003-05-01

436

Chemoenzymatic synthesis of alpha-hydroxy-beta-methyl-gamma-hydroxy esters: role of the keto-enol equilibrium to control the stereoselective hydrogenation in a key step.  

PubMed

Alpha-hydroxy-beta-methyl-gamma-hydroxy esters not only are found in many natural products and potent drugs but also are useful intermediates in organic synthesis due to their highly functionalized skeleton that can be further manipulated and applied in the synthesis of many compounds with remarkable biological activities. This work was based on a chemoenzymatic approach to obtain these molecules with three contiguous stereogenic centers in a highly enantio- and diastereoselective way. Two distinct linear routes were proposed in which the key steps in both routes consisted of initial stereocontrolled ketoester bioreduction followed by unsaturated carbonyl bioreduction or reduction with Pd-C. Other key reactions in the synthesis include a Wasserman protocol for chain homologation and a Mannich-type olefination with maintenance of enantiomeric excess for all intermediates during the sequence. Whereas route A gave exclusively the skeleton with 3R,4R,5S configuration (99% ee and 11.5% global yield after 7 steps), route B gave the skeleton with 3R,4R,5S and 3R,4S,5R configurations (dr 1:12, 98% ee and 20% global yield after 5 steps). PMID:20143825

Milagre, Cíntia D F; Milagre, Humberto M S; Moran, Paulo J S; Rodrigues, J Augusto R

2010-03-01

437

Progress report for FACETS (Framework Application for Core-Edge Transport Simulations): C.S. SAP  

SciTech Connect

The mission of the Computer Science Scientific Application Partnership (C.S. SAP) at LLNL is to develop and apply leading-edge scientific component technology to FACETS software. Contributions from LLNL's fusion energy program staff towards the underlying physics modules are described in a separate report. FACETS uses component technology to combine selectively multiple physics and solver software modules written in different languages by different institutions together in an tightly-integrated, parallel computing framework for Tokamak reactor modeling. In the past fiscal year, the C.S. SAP has focused on two primary tasks: applying Babel to connect UEDGE into the FACETS framework through UEDGE's existing Python interface and developing a next generation componentization strategy for UEDGE which avoids the use of Python. The FACETS project uses Babel to solve its language interoperability challenges. Specific accomplishments for the year include: (1) Refined SIDL interfaces for UEDGE to meet satisfy the standard interfaces required by FACETS for all physics modules. This required consensus building between framework and UEDGE developers. (2) Wrote prototype C++ driver for UEDGE to demonstrate how UEDGE can be called from C++ using Babel. (3) Supported the FACETS project by adding new features to Babel such as release number tagging, porting to new machines, and adding new configuration options. Babel modifications were delivered to FACETS by testing and publishing development snapshots in the projects software repository. (4) Assisted Tech-X Corporation in testing and debugging of a high level build system for the complete FACETS tool chain--the complete list of third-party software libraries that FACETS depends on directly or indirectly (e.g., MPI, HDF5, PACT, etc.). (5) Designed and implemented a new approach to wrapping UEDGE as a FACETS component without requiring Python. To get simulation results as soon as possible, our initial connection from the FACETS framework to UEDGE uses a Forthon-generated Python layer that sits on top of the UEDGE Fortran code. To run on leadership class machines that do not support shared libraries such as Franklin (NERSCS) and Jaguar (ORNL), FACETS requires a more direct connection to the UEDGE Fortran that eliminates the Python layer. We designed and developed an extension for Forthon to provide a direct connection from C++ to the UEDGE Fortran using Babel. This also required added annotations to the Forthon '.v' input files to indicate how function parameters are used.

Epperly, T W

2008-10-01

438

[Transfer of exotic ticks (Acari: ixodida) on reptiles (Reptilia) imported to Poland].  

PubMed

In the of period 2003-2007, a total of 382 specimens of reptiles belonging to the following genera were investigated: Testudo, Iguana, Varanus, Gongylophis, Python, Spalerosophis, Psammophis. The material for the present study was a collection of reptiles owned by the "Animals" Ltd from Swietoch?owice (Upper Silesia, Poland), specialising in import of exotic animals to Poland, as well as the reptile collections of private breeders. The reptiles that turned out to be the most heavily infected with ticks were the commonly bred terrarium reptiles: Varanus exanthematicus and Python regius and they were imported to Poland from Ghana, Africa. Exotic reptiles are also imported from Southern Europe, Asia and Central America. The presently reported study helped to confirm the fact of transfer of exotic ticks on reptiles to Poland. A total of 2104 tick specimens, representing all stages of development (males, females, nymphs, larvae), were collected. They represented species of the genera Amblyomma and Hyalomma. The following species were found: Amblyomma exornatum Koch, 1844, Amblyomma flavomaculatum (Lucas, 1846), Amblyomma latum Koch, 1844, Amblyomma nuttalli Dönitz, 1909, Amblyomma quadricavum Schulze, 1941, Amblyomma transversale (Lucas, 1844), Amblyomma varanense (Supino, 1897), Amblyomma spp. Koch, 1844, Hyalomma aegyptium (Linnaeus, 1758). All the species of ticks of genus Ambylomma revealed have been discovered in Poland for the first time. The overall prevalence of infection was 77.6%. The highest prevalence value (81.2%) was observed on pythons (Python regius) and (78.7%) on monitor lizards (Varanus exanthematicus). The highest number of ticks was collected from Python regius and Varanus exanthematicus. The mean infection intensity for V. exanthematicus was 7.6 ticks per host, while for P. regius the intensity reached 4.7 ticks. The most abundant tick transferred to Poland on a host was an African tick, Amblyomma latum. Fifty eight specimens of monitor lizards (V. salvator and V. exanthematicus) and 92 specimens pythons (P. regius) were examined, with detailed descriptions of where the parasite was feeding on the body of the host. Among the 434 specimens of ticks collected from the monitor lizards, the majority were attached on the host's legs (40.5%), on the trunk (29.3%), on the head (20.3%), with fewest on the tail (9.9%). Also, 430 specimens of ticks were collected from the bodies of pythons. They mostly parasitized along the whole length of the back (54.4%) and on the stomach side of the trunk (29.8%), less frequently in the area of the cloaca (5.6%), around the eyes (3.7%), in the nostril openings (0.9%) and on the remainder of the head (5.6%). On the hosts, ticks were found at different development stages, but adult development stages dominated. The most frequent were males (999 specimens), then adult females (552 specimens), nymphs (508 specimens) and larvae (45 specimens). During the research, 13 cases of anomalies of morphological structure were confirmed for ticks Amblyomma flavomaculatum, Amblyomma latum and Hyalomma aegyptium. Asymmetries and deformations of the general body shape were observed, as were anomalies concerning structures on the surface of the body and anomalies of the legs. For the first time in Poland, epidemiological tests were carried out in the direction of the infection of exotic ticks gathered from reptiles with micro-organisms which pose a threat for the health of people and animals. For this purpose, molecular techniques - polymerase chain reaction (PCR) and DNA sequencing were used. The isolates from 345 ticks, were examined for the presence of DNA of Anaplasma phagocytophilum, which is the etiological factor in human granulocytic anaplasmosis, and Rickettsia spp. from the spotted fever group, causing human rickettsiosis. This study confirmed the presence of Anaplasma phagocytophilum in two ticks of Amblyomma flavomaculatum (constituting 0.6% of all the ticks investigated) feeding on Varanus exanthematicus. None of the tick specimens, however, contained Rickettsia spp. DNA

2009-01-01

439

Towards a new Mercator Observatory Control System  

NASA Astrophysics Data System (ADS)

A new control system is currently being developed for the 1.2-meter Mercator Telescope at the Roque de Los Muchachos Observatory (La Palma, Spain). Formerly based on transputers, the new Mercator Observatory Control System (MOCS) consists of a small network of Linux computers complemented by a central industrial controller and an industrial real-time data communication network. Python is chosen as the high-level language to develop flexible yet powerful supervisory control and data acquisition (SCADA) software for the Linux computers. Specialized applications such as detector control, auto-guiding and middleware management are also integrated in the same Python software package. The industrial controller, on the other hand, is connected to the majority of the field devices and is targeted to run various control loops, some of which are real-time critical. Independently of the Linux distributed control system (DCS), this controller makes sure that high priority tasks such as the telescope motion, mirror support and hydrostatic bearing control are carried out in a reliable and safe way. A comparison is made between different controller technologies including a LabVIEW embedded system, a PROFINET Programmable Logic Controller (PLC) and motion controller, and an EtherCAT embedded PC (soft-PLC). As the latter is chosen as the primary platform for the lower level control, a substantial part of the software is being ported to the IEC 61131-3 standard programming languages. Additionally, obsolete hardware is gradually being replaced by standard industrial alternatives with fast EtherCAT communication. The use of Python as a scripting language allows a smooth migration to the final MOCS: finished parts of the new control system can readily be commissioned to replace the corresponding transputer units of the old control system with minimal downtime. In this contribution, we give an overview of the systems design, implementation details and the current status of the project.

Pessemier, W.; Raskin, G.; Prins, S.; Saey, P.; Merges, F.; Padilla, J. P.; van Winckel, H.; Waelkens, C.

2010-07-01

440

Parasitisation and localisation of ticks (Acari: Ixodida) on exotic reptiles imported into Poland.  

PubMed

As a result of examinations, the following species of ticks have been found parasitising on Python regius brought from Africa to Poland: Amblyomma latum, Amblyomma transversale, Amblyomma spp., on Varanus exanthematicus: Amblyomma exornatum, Amblyomma flavomaculatum, Amblyomma latum, Amblyomma nuttalli, Amblyomma spp., on Varanus salvator brought from Indonesia to Poland: Amblyomma varanensis. There were 58 specimens of monitor lizard (V. salvator and V. exanthematicus) and 92 specimens of python (P. regius) examined, with the selected locations of parasitisation by the ticks on the host`s body described in detail. Among the 434 specimens of tick collected from the monitor lizards, the majority parasitised the host`s limbs (40.5%), on the trunk (29.3%), the head (20.3%), and least on the tail (9.9%). There were 430 tick specimens collected from the bodies of the pythons. They chiefly parasitised the whole length of the back (54.4%) and on the abdominal side of the trunk (29.8%), less numerously in the neighbourhood of the cloaca (5.6%), around the eyes (3.7%), in the nasal openings (0.9%) and the remaining parts of the head (5.6%). Examination of the ticks` location on the reptiles` bodies enabled us to discover the specific parasitisation locations of ticks along the entire length of the host`s body. Knowledge of the ticks` location on the bodies of specific reptile species, particularly at a time when the import of exotic animals is growing all over the world, will help in drawing up methods of fighting the parasites, and may give valuable clues to veterinary services and private breeders. PMID:21186765

Nowak, Magdalena

2010-12-01

441

APIRP: The Automated Photometric Data Reduction Package  

NASA Astrophysics Data System (ADS)

For decades the Image Reduction and Analysis Facility (IRAF) has been the standard for processing CCD-based image datasets. During that time, technology has advanced and the astronomical record greatly expanded. However, the discovery process is often bogged down by the time consuming procedures of image reduction. To keep up with demand and shorten reduction steps programmers have developed a series of command languages (CL) for IRAF and most recently, within only the past five years, the Python-based language, Pyraf. Python is a robust and powerful language that combines syntactical simplicity with versatile and dynamic file management, database access and software development capabilities, to name just a few features. Pyraf, by extension, incorporates all of the qualities of IRAF CL, with all of the power and flexibility provided by Python. Pyraf scripts may be written to automate file processing at the same time that reduction tasks are called from IRAF. Thus, the potential to write fully automated reduction procedures is here; tightening the gaps of scientific advancement. We have created such a tool for CCD Photometry. Our Automated Photometric Image Reduction Package (APIRP) uses a range of graphical user interfaces (GUI's) to form an interactive yet non-overbearing user environment. A combination of built-in file management and procedural variability makes APIRP a perfect choice for both amateur and professional astronomers. Due to the programs design, it can be run from anywhere on your computer and users can specify exactly what steps of reduction they wish to execute. Thus, setup is easy with no need for cumbersome documentation and tasks may be preformed piecewise or in blocks, depending on the users needs.

Hebert, Ian; Ziffer, J.; Walker, M.

2009-09-01

442

Pseudo-Real-Time Signal Visualization during Pulsar Observations on the Green Bank Telescope  

NASA Astrophysics Data System (ADS)

Pseudo-Real-Time Signal Visualization during Pulsar Observations on the Green Bank Telescope J. Kelly (Rockbridge County Public Schools & NRAO), K. O'Neil (NRAO) When using the Robert C. Byrd Green Bank Telescope (GBT) for pulsar observations, observers need to be able to insure the data reaching the observer is of the highest quality possible. To do this, telescope users need to be able to monitor, in real time, the raw signal intensity of data as it flows in from the GBT. In the summer of 2004 at NRAO-Greenbank, my Research Experience For Teachers project was spent developing this utility. For portability and compatibility, the computer language python was used to build the visualization utility. The major hurdle in developing the python modules was in reading and manipulating the tremendous quantity of unprocessed data acquired during an observation. (The spigot data rate is set to be 25 Mb/s.) The data stream is intercepted by a "spigot" card, buffered and then stored on a hard drive as a series of binary files. The python modules attempt to read, parse and organize these binary files to ultimately produce a simple intensity versus time plot of the data stream. The modules developed run as a loop to update the plot several times per minute. Integrating the knowledge and experience of this research in the classroom involves an introductory unit on radio astronomy and astrophysics. Additionally, students will have the opportunity to analyze data collected from the Crab Nebula Pulsar and experience backend processes such as data folding. These activities will be described. This work was funded by the National Science Foundation RET program.

Kelly, C. J.; O'Neil, K.

2004-12-01

443

Solving spatial inverse problems using the probability perturbation method: An S-GEMS implementation  

NASA Astrophysics Data System (ADS)

The probability perturbation method (PPM) is introduced as a flexible and efficient sampling technique for generating inverse solutions under a given prior geological constraint (prior model). In this paper, we present a methodology for producing software code that runs PPM within a public domain geostatistical software called the Stanford Geostatistical Earth Modeling Software (S-GEMS). The challenge in creating such code lies in the great diversity of forward models as well as prior models that can be handled by the PPM. Therefore, our software solution must be highly flexible and extensible such that it can be tailored to the various applications at hand. Our implementation has two main objectives: (1) to create an integrated working environment which provides users easy access to functionalities of the PPM through a general user interface as well as visualize results; (2) allow the users to plug-in their application specific code into the PPM algorithm workflow. We provide a two-part solution. The first part, which is hard-coded in S-GEMS as a plug-in module, runs the Dekker-Brent optimization algorithm to control the parameter perturbation needed for the inversion. It generates the PPM user interface and allows visualization of the spatial domain of interest using S-GEMS graphics capability. The second part is coded in object-oriented Python scripts and is used to control the PPM execution in S-GEMS. Users can program their particular needs in scripts and load them into S-GEMS as part of the PPM workflow. The same mechanism can be used to extend the capabilities of PPM itself by implementing new PPM variants in Python and making them a part of the base class hierarchy. Case studies are used to demonstrate the flexibility of our code. This approach requires the user to adapt only a small amount of python code, without modifying, or re-compiling the core S-GEMS code.

Li, Ting; Caers, Jef

2008-09-01

444

An enterprise software architecture for the Green Bank Telescope (GBT)  

NASA Astrophysics Data System (ADS)

The enterprise architecture presents a view of how software utilities and applications are related to one another under unifying rules and principles of development. By constructing an enterprise architecture, an organization will be able to manage the components of its systems within a solid conceptual framework. This largely prevents duplication of effort, focuses the organization on its core technical competencies, and ultimately makes software more maintainable. In the beginning of 2003, several prominent challenges faced software development at the GBT. The telescope was not easily configurable, and observing often presented a challenge, particularly to new users. High priority projects required new experimental developments on short time scales. Migration paths were required for applications which had proven difficult to maintain. In order to solve these challenges, an enterprise architecture was created, consisting of five layers: 1) the telescope control system, and the raw data produced during an observation, 2) Low-level Application Programming Interfaces (APIs) in C++, for managing interactions with the telescope control system and its data, 3) High-Level APIs in Python, which can be used by astronomers or software developers to create custom applications, 4) Application Components in Python, which can be either standalone applications or plug-in modules to applications, and 5) Application Management Systems in Python, which package application components for use by a particular user group (astronomers, engineers or operators) in terms of resource configurations. This presentation describes how these layers combine to make the GBT easier to use, while concurrently making the software easier to develop and maintain.

Radziwill, Nicole M.; Mello, Melinda; Sessoms, Eric; Shelton, Amy

2004-09-01

445

Seasonal Pulses of Marburg Virus Circulation in Juvenile Rousettus aegyptiacus Bats Coincide with Periods of Increased Risk of Human Infection  

PubMed Central

Marburg virus (family Filoviridae) causes sporadic outbreaks of severe hemorrhagic disease in sub-Saharan Africa. Bats have been implicated as likely natural reservoir hosts based most recently on an investigation of cases among miners infected in 2007 at the Kitaka mine, Uganda, which contained a large population of Marburg virus-infected Rousettus aegyptiacus fruit bats. Described here is an ecologic investigation of Python Cave, Uganda, where an American and a Dutch tourist acquired Marburg virus infection in December 2007 and July 2008. More than 40,000 R. aegyptiacus were found in the cave and were the sole bat species present. Between August 2008 and November 2009, 1,622 bats were captured and tested for Marburg virus. Q-RT-PCR analysis of bat liver/spleen tissues indicated ?2.5% of the bats were actively infected, seven of which yielded Marburg virus isolates. Moreover, Q-RT-PCR-positive lung, kidney, colon and reproductive tissues were found, consistent with potential for oral, urine, fecal or sexual transmission. The combined data for R. aegyptiacus tested from Python Cave and Kitaka mine indicate low level horizontal transmission throughout the year. However, Q-RT-PCR data show distinct pulses of virus infection in older juvenile bats (?six months of age) that temporarily coincide with the peak twice-yearly birthing seasons. Retrospective analysis of historical human infections suspected to have been the result of discrete spillover events directly from nature found 83% (54/65) events occurred during these seasonal pulses in virus circulation, perhaps demonstrating periods of increased risk of human infection. The discovery of two tags at Python Cave from bats marked at Kitaka mine, together with the close genetic linkages evident between viruses detected in geographically distant locations, are consistent with R. aegyptiacus bats existing as a large meta-population with associated virus circulation over broad geographic ranges. These findings provide a basis for developing Marburg hemorrhagic fever risk reduction strategies.

Amman, Brian R.; Carroll, Serena A.; Reed, Zachary D.; Sealy, Tara K.; Balinandi, Stephen; Swanepoel, Robert; Kemp, Alan; Erickson, Bobbie Rae; Comer, James A.; Campbell, Shelley; Cannon, Deborah L.; Khristova, Marina L.; Atimnedi, Patrick; Paddock, Christopher D.; Kent Crockett, Rebekah J.; Flietstra, Timothy D.; Warfield, Kelly L.; Unfer, Robert; Katongole-Mbidde, Edward; Downing, Robert; Tappero, Jordan W.; Zaki, Sherif R.; Rollin, Pierre E.; Ksiazek, Thomas G.; Nichol, Stuart T.; Towner, Jonathan S.

2012-01-01

446

Structural flexibility of the small intestine and liver of garter snakes in response to feeding and fasting.  

PubMed

Garter snakes Thamnophis sirtalis parietalis feed frequently but also tolerate extended periods of fasting when food is unavailable. We studied the dynamics, reversibility and repeatability of size changes of the small intestine and liver using ultrasonography. We employed light and transmission electron microscopy and flow cytometry to study the tissue mechanism that drives this flexibility. We compared garter snakes that fed every other day, snakes that fed once a week and fasting snakes. In all feeding trials, the size of the small intestine and the liver increased rapidly after feeding. Constantly feeding snakes maintained an elevated level of organ size, while snakes that were fed only once a week showed a marked up- and downregulation of organ size. Histology revealed the mucosal epithelium to be a transitional epithelium that can change cell configuration considerably to accommodate organ size changes. Upregulation of small intestine and liver size was always associated with the incorporation of lipid droplets into enterocytes and hepatocytes. Cell proliferation was not involved in upregulation of organ size. In contrast, cell proliferation increased during downregulation of organ size, indicating that cells worn out during digestion were replaced. The dynamics of flexibility and the functional features of the tissue were the same as described for the Burmese python Python molurus bivittatus. We suggest that garter snakes employ the same energetically cheap mechanism of organ size regulation as pythons, which allows for rapid, repeated and reversible size changes with no cell proliferation involved. Comparative evidence suggests that the transitional mucosal epithelium is an ancestral character of snakes and that feeding ecology is not directly related to the cytological features of the mucosal epithelium. PMID:11976350

Starck, J Matthias; Beese, Kathleen

2002-05-01

447

Climate Data Analysis Tools - (CDAT)  

NASA Astrophysics Data System (ADS)

Climate Data Analysis Tools (CDAT) is a software infrastructure that uses an object-oriented scripting language to link together separate software subsystems and packages thus forming an integrated environment for solving model diagnosis problems. The power of the system comes from Python and its ability to seamlessly interconnect software. Python provides a general purpose and full-featured scripting language with a variety of user interfaces including command-line interaction, stand-alone scripts (applications) and graphical user interfaces (GUI). The CDAT subsystems, implemented as modules, provide access to and management of gridded data (Climate Data Management System or CDMS); large-array numerical operations (Numerical Python); and visualization (Visualization and Control System or VCS). One of the most difficult challenges facing climate researchers today is the cataloging and analysis of massive amounts of multi-dimensional global atmospheric and oceanic model data. To reduce the labor intensive and time-consuming process of data management, retrieval, and analysis, PCMDI and other DOE sites have come together to develop intelligent filing system and data management software for the linking of storage devices located throughout the United States and the international climate research community. This effort, headed by PCMDI, NCAR, and ANL will allow users anywhere to remotely access this distributed multi-petabyte archive and perform analysis. PCMDI's CDAT is an innovative system that supports exploration and visualization of climate scientific datasets. As an "open system", the software sub-systems (i.e., modules) are independent and freely available to the global climate community. CDAT is easily extended to include new modules and as a result of its flexibility, PCMDI has integrated other popular software components, such as: the popular Live Access Server (LAS) and the Distributed Oceanographic Data System (DODS). Together with ANL's Globus middleware software, CDAT's focus is to allow climate researchers the ability to access and analyze multi-dimensional distributed climate datasets.

Doutriaux, C.; Jennifer, A.; Drach, R.; Dubois, P.; Williams, D.

2003-12-01

448

A Data Management Framework for Real-Time Water Quality Monitoring  

NASA Astrophysics Data System (ADS)

CSU East Bay operates two in-situ, near-real-time water quality monitoring stations in San Francisco Bay as a member of the Center for Integrative Coastal Ocean Observation, Research, and Education (CICORE) and the Central and Northern California Ocean Observing System (CeNCOOS). We have been operating stations at Dumbarton Pier and San Leandro Marina for the past two years. At each station, a sonde measures seven water quality parameters every six minutes. During the first year of operation, we retrieved data from the sondes every few weeks by visiting the sites and uploading data to a handheld logger. Last year we implemented a telemetry system utilizing a cellular CDMA modem to transfer data from the field to our data center on an hourly basis. Data from each station are initially stored in monthly files in native format. We import data from these files into a SQL database every hour. SQL is handled by Django, an open source web framework. Django provides a user- friendly web user interface (UI) to administer the data. We utilized parts of the Django UI for our database web- front, which allows users to access our database via the World Wide Web and perform basic queries. We also serve our data to other aggregating sites, including the central CICORE website and NOAA's National Data Buoy Center (NDBC). Since Django is written in Python, it allows us to integrate other Python modules into our software, such as the Matplot library for scientific graphics. We store our code in a Subversion repository, which keeps track of software revisions. Code is tested using Python's unittest and doctest modules within Django's testing facility, which warns us when our code modifications cause other parts of the software to break. During the past two years of data acquisition, we have incrementally updated our data model to accommodate changes in physical hardware, including equipment moves, instrument replacements, and sensor upgrades that affected data format.

Mulyono, E.; Yang, D.; Craig, M.

2007-12-01

449

Quantum Criticality and Superconductivity in ?-YbAlB4  

NASA Astrophysics Data System (ADS)

Heavy fermion systems have provided a number of prototypical compounds to study unconventional superconductivity and non-Fermi-liquid (NFL) states. A long standing issue in the research of heavy fermion superconductivity in 4f intermetallics is the dramatically different behavior between the electron like Ce (4f^1) and hole like Yb (4f^13) compounds. While superconductivity has been found in a number of Ce based heavy fermion compounds, no superconductivity has been reported for the corresponding Yb systems. In this talk, I present our recent finding of the superconductivity in the new heavy fermion system ?-YbAlB4 [1-3]. The superconducting transition temperature is 80 mK, and above it, the system exhibits pronounced NFL behavior in the transport and thermodynamic properties [2,3]. Furthermore, the magnetic field dependence of the NFL behavior indicates that the system is a rare example of a pure metal that displays quantum criticality at ambient pressure and under zero magnetic field. Using our latest results, we discuss the detailed properties of superconductivity and quantum criticality. This is the work performed in collaboration with K. Kuga, Y. Matsumoto, T. Tomita, Y. Machida, T. Tayama, T. Sakakibara, Y. Karaki, H. Ishimoto, S. Yonezawa, Y. Maeno, E. Pearson, G. G. Lonzarich, L.Balicas, H. Lee, and Z. Fisk. [4pt] [1] Robin T. Macaluso, Satoru Nakatsuji, Kentaro Kuga, Evan Lyle Thomas, Yo Machida, Yoshiteru Maeno, Zachary Fisk, and Julia Y. Chan, Chem. Mater. 19 1918 (2007). [0pt] [2] S. Nakatsuji, K.Kuga, Y. Machida, T. Tayama, T. Sakakibara, Y. Karaki, H. Ishimoto, S. Yonezawa, Y. Maeno, E. Pearson, G. G. Lonzarich, L.Balicas, H. Lee, and Z. Fisk, Nature Phys 4, 603-607 (2008). [0pt] [3] K. Kuga, Y. Karaki, Y. Matsumoto, Y. Machida, and S. Nakatsuji, Phys. Rev. Lett. 101, 137004 (2008).

Nakatsuji, Satoru

2009-03-01

450

William R. Maples, forensic historian: four men, four centuries, four countries.  

PubMed

Prior to 1984, William R. Maples, Ph.D. worked primarily with Medical Examiners in the State of Florida in investigation of and testimony in criminal cases. In 1984 the Republic of Peru requested him to identify skeletal remains thought to be those of Francisco Pizarro, conqueror of Peru and the Incas in the early 16th Century. Dr. Maples made a positive identification of those remains as Pizarro, resulting in their substitution in a glass-sided coffin in the Cathedral of Lima, where other remains had been displayed as those of Pizarro for a hundred years. In addition, it was proved that the remains removed could not have been those of Pizarro. In 1988, Dr. Maples examined the skeletal remains of Joseph Merrick ("The Elephant Man") at Royal London Hospital, Whitechapel, and made photographic studies of them for comparison with death casts of limbs and skull to ascertain depth of tissue by video-superimposition. In 1991, Dr. Maples, headed a team which removed President Zachary Taylor (1779-1842) from his tomb in Louisville, Kentucky. The purpose was to determine if he had been poisoned, as had been proposed by some at the time. Test results showed that he had not been. In 1992, Dr. Maples and a team of forensic specialists went by invitation to Ekaterinburg, Russia to study skeletal remains which the Russians had tentatively identified as the Russian Royal Family, and entourage, murdered in 1918. The American team identified them as Tsar Nicholas II, his wife, three of his children, his physician, and three of his servants. William Ross Maples died in Gainesville, Florida, 27 February 1997. PMID:10432600

Goza, W M

1999-07-01

451

Managing the ADS Citation Database  

NASA Astrophysics Data System (ADS)

The NASA Astrophysics Data System (ADS) has become the standard tool for searching the literature in the astronomy and astrophysics community. Within the ADS we are now consolidating the article reference catalog. Reference sources come in a variety of data formats. OCR'ed scanned articles (HTML, LaTeX, XML...) from a large number of different publications. We present in this paper new developments allowing the automation of the reference digester through a set of highly configurable, object-oriented, Python/XML applications and tools. We expect the use of these tools to ease the burden of incorporating new publications to the reference databases.

Rey-Bakaikoa, V.; Accomazzi, A.; Eichhorn, G.; Grant, C. S.

452

Mayavi2: 3D Scientific Data Visualization and Plotting  

NASA Astrophysics Data System (ADS)

Mayavi is an open-source, general-purpose, 3D scientific visualization package. It seeks to provide easy and interactive tools for data visualization that fit with the scientific user's workflow. Mayavi provides several entry points: a full-blown interactive application; a Python library with both a MATLAB-like interface focused on easy scripting and a feature-rich object hierarchy; widgets associated with these objects for assembling in a domain-specific application, and plugins that work with a general purpose application-building framework.

Ramachandran, Prabhu; Varoquaux, Gail

2012-05-01

453

VPython applications for Teaching Physics  

NASA Astrophysics Data System (ADS)

VPython, a real-time 3D graphics module for the Python programming language, provides a simple but powerful programming environment for physics educators and students. On the website listed below, we provide a small but growing collection of interactive visualizations and simulations (along with their VPython source code) that we have written for teaching physics. In the poster, we will demonstrate our examples in wave interference, kinematics, electromagnetism, relativity, tensor visualization, and nonlinear dynamics. (http://physics.syr.edu/ salgado/software/vpython/ also features a list of the growing community of VPython websites.)

Salgado, Roberto B.

2006-12-01

454

Spectrum and photon statistics of an optomechanical cavity QED system  

NASA Astrophysics Data System (ADS)

Work to date in cavity optomechanics has primarily focused on the coupling between the cavity field and the mechanical oscillator. We investigate a weakly driven, damped optomechanical cavity containing a two-level atom with an oscillating end mirror or an intracavity dielectric membrane. We carry out numerical simulations of the system using the framework of quantum trajectories implemented with the Quantum Toolbox in Python (QuTiP). We calculate the cavity probe spectrum and second-order field-field and atom-field correlations, finding they are modified by the coupling between the cavity field and the mechanical oscillator.

Jacobs, Andrew; Clemens, James

2012-06-01

455

Molecule Viewers and Editors  

NSDL National Science Digital Library

This metasite is an excellent resource for chemical researchers and educators. It provides links to three free software programs: JchemPaint, Jmol, and OpenChem. JchemPaint, developed at the Max Planck Institute of Chemical Ecology, is a Java program for drawing 2-D chemical structures. Jmol, primarily authored by J. Daniel Gezelter of Notre Dame University, is a Java/Swing program for viewing molecular visualization and measurement. OpenChem, a large collaborative effort, is a Python-based program for investigating nanotechnology, machines and molecular structures. All three of the programs are still under construction, but each page contains helpful troubleshooting information and discussion lists.

2007-06-01

456

Molecule Viewers and Editors  

NSDL National Science Digital Library

This metasite is an excellent resource for chemical researchers and educators. It provides links to three free software programs: JchemPaint, Jmol, and OpenChem. JchemPaint, developed at the Max Planck Institute of Chemical Ecology, is a Java program for drawing 2-D chemical structures. Jmol, primarily authored by J. Daniel Gezelter of Notre Dame University, is a Java/Swing program for viewing molecular visualization and measurement. OpenChem, a large collaborative effort, is a Python-based program for investigating nanotechnology, machines and molecular structures.